Search results for the GEO ID: GSE6751  |
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|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM155448 | GPL570 |
|
Patient 08, time point 1
|
Patient 08 PBMC, collected at time point 1
|
Time: one week prior to commencement of periodontal therapy
Tissue: Peripheral blood monocytes
Phenotype: severe periodontitis
|
Patients were recruited among the ones seeking treatment at the clinic for post-doctoral Periodontics, Columbia University College of Dental Medicine. To be eligible for enrollment, patients had to be diagnosed with severe periodontitis, with radiographic evidence of bone loss extending to greater or equal to 30% of the tooth length at several teeth. Additional inclusion criteria required: age greater or equal to 18 years; presence of greater or equal to 2 teeth/quadrant with a pocket depth of greater or equal to 6 mm and concomitant attachment loss of greater or equal to 3 mm; a minimum of 20 teeth present; no prior periodontal therapy; no systemic conditions or genetic disorders that entail the diagnosis of periodontitis as a manifestation of systemic diseases; no use of systemic antibiotics or regular use of anti-inflammatory drugs for the preceding 6-month period; no diabetes mellitus; no current use of tobacco products or of nicotine replacement medication; not currently pregnant. A total of 15 subjects, 7 male and 8 female, were enrolled. All participants were informed about the scope and procedures of the study and informed consent was obtained.
|
| Sample_geo_accession | GSM155448
| | Sample_status | Public on Dec 31 2007
| | Sample_submission_date | Jan 16 2007
| | Sample_last_update_date | Jan 16 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Fifty ml of blood were obtained by venipucture and collected in Vacutainer cell preparation tubes (Beckton-Dickinson, NJ, USA) with sodium heparin, and were used to harvest peripheral blood mononuclear cells (PBMCs). A 1:1 dilution with PBS was made and the diluted blood sample was centrifuged at 1,000 g in Ficoll tubes (Sigma Accuspin, St. Louis, MO). After washing and counting of the cells in a phase hemacytometer (Hauser Scientific, Horsham, PA), PBMCs were re-suspended in 80 microlitres of MACS buffer (PBS pH 7.2, 0.5% BSA and 2 mM EDTA) and incubated on ice with 20 microlitres of CD14 microbeads (Miltenyi Biotec, Auburn CA) per 107 total cells for 15 minutes. After washings, the cell suspension was applied to a MACS LS separation column (Miltenyi Biotec) placed in the magnetic field of a MACS separator (Miltenyi Biotec). Thereafter, the column was removed from the separator and CD14 positive cells were collected by washings in MACS buffer.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | CD14 positive cells were vigorously pipetted in Trizol (Invitrogen Life Technologies, Carlsbad, CA, USA). After incubation with chloroform and centrifugation at 12,000 g, RNA in the upper aqueous phase was precipitated by mixing with isopropyl alcohol, further centrifugation and washing in 75% ethanol. Further purification of the extracted RNA was achieved by the use of the RNeasy total RNA isolation kit (Qiagen, Valencia, CA, USA) according to the manufacturer.s instructions. The purified RNA was quantified spectrophotometrically. One hundred nanograms of total RNA were amplified and reverse transcribed using the GeneChip expression 3.-amplification two-cycle cDNA synthesis kit (Affymetrix, Santa Clara, CA, USA) and the MEGAscript T7 transcription kit (Ambion, Austin, TX, USA) according to the manufacturers. instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Synthesis of biotin-labeled cRNA and subsequent fragmentation were performed by the use of the IVT labeling kit (Affymetrix, Santa Clara, CA, USA). The cRNA yield was determined spectrophotometrically at 260 nm. Fragmented cRNA was stored at -80C until hybridization.
| | Sample_hyb_protocol | According to the manufacturer's instructions.
| | Sample_scan_protocol | According to the manufacturer's instructions.
| | Sample_data_processing | All CEL files in the series were processed using RMA in R using justRMA with default parameters.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Paul,,Pavlidis
| | Sample_contact_email | paul@chibi.ubc.ca
| | Sample_contact_department | Centre for High-Throughput Biology / Psychiatry
| | Sample_contact_institute | University of British Columbia
| | Sample_contact_address | 177 Michael Smith Laboratories 2185 East Mall
| | Sample_contact_city | Vancouver
| | Sample_contact_state | British Columbia
| | Sample_contact_zip/postal_code | V6T 1Z4
| | Sample_contact_country | Canada
| | Sample_contact_web_link | http://www.chibi.ubc.ca/faculty/pavlidis
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM155nnn/GSM155448/suppl/GSM155448.CEL.gz
| | Sample_series_id | GSE6751
| | Sample_data_row_count | 54675
| | |
|
GSM155449 | GPL570 |
|
Patient 08, time point 2
|
Patient 08 PBMC, collected at time point 2
|
Time: at commencement of periodontal therapy
Tissue: Peripheral blood monocytes
Phenotype: severe periodontitis
|
Patients were recruited among the ones seeking treatment at the clinic for post-doctoral Periodontics, Columbia University College of Dental Medicine. To be eligible for enrollment, patients had to be diagnosed with severe periodontitis, with radiographic evidence of bone loss extending to greater or equal to 30% of the tooth length at several teeth. Additional inclusion criteria required: age greater or equal to 18 years; presence of greater or equal to 2 teeth/quadrant with a pocket depth of greater or equal to 6 mm and concomitant attachment loss of greater or equal to 3 mm; a minimum of 20 teeth present; no prior periodontal therapy; no systemic conditions or genetic disorders that entail the diagnosis of periodontitis as a manifestation of systemic diseases; no use of systemic antibiotics or regular use of anti-inflammatory drugs for the preceding 6-month period; no diabetes mellitus; no current use of tobacco products or of nicotine replacement medication; not currently pregnant. A total of 15 subjects, 7 male and 8 female, were enrolled. All participants were informed about the scope and procedures of the study and informed consent was obtained.
|
| Sample_geo_accession | GSM155449
| | Sample_status | Public on Dec 31 2007
| | Sample_submission_date | Jan 16 2007
| | Sample_last_update_date | Jan 16 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Fifty ml of blood were obtained by venipucture and collected in Vacutainer cell preparation tubes (Beckton-Dickinson, NJ, USA) with sodium heparin, and were used to harvest peripheral blood mononuclear cells (PBMCs). A 1:1 dilution with PBS was made and the diluted blood sample was centrifuged at 1,000 g in Ficoll tubes (Sigma Accuspin, St. Louis, MO). After washing and counting of the cells in a phase hemacytometer (Hauser Scientific, Horsham, PA), PBMCs were re-suspended in 80 microlitres of MACS buffer (PBS pH 7.2, 0.5% BSA and 2 mM EDTA) and incubated on ice with 20 microlitres of CD14 microbeads (Miltenyi Biotec, Auburn CA) per 107 total cells for 15 minutes. After washings, the cell suspension was applied to a MACS LS separation column (Miltenyi Biotec) placed in the magnetic field of a MACS separator (Miltenyi Biotec). Thereafter, the column was removed from the separator and CD14 positive cells were collected by washings in MACS buffer.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | CD14 positive cells were vigorously pipetted in Trizol (Invitrogen Life Technologies, Carlsbad, CA, USA). After incubation with chloroform and centrifugation at 12,000 g, RNA in the upper aqueous phase was precipitated by mixing with isopropyl alcohol, further centrifugation and washing in 75% ethanol. Further purification of the extracted RNA was achieved by the use of the RNeasy total RNA isolation kit (Qiagen, Valencia, CA, USA) according to the manufacturer.s instructions. The purified RNA was quantified spectrophotometrically. One hundred nanograms of total RNA were amplified and reverse transcribed using the GeneChip expression 3.-amplification two-cycle cDNA synthesis kit (Affymetrix, Santa Clara, CA, USA) and the MEGAscript T7 transcription kit (Ambion, Austin, TX, USA) according to the manufacturers. instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Synthesis of biotin-labeled cRNA and subsequent fragmentation were performed by the use of the IVT labeling kit (Affymetrix, Santa Clara, CA, USA). The cRNA yield was determined spectrophotometrically at 260 nm. Fragmented cRNA was stored at -80C until hybridization.
| | Sample_hyb_protocol | According to the manufacturer's instructions.
| | Sample_scan_protocol | According to the manufacturer's instructions.
| | Sample_data_processing | All CEL files in the series were processed using RMA in R using justRMA with default parameters.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Paul,,Pavlidis
| | Sample_contact_email | paul@chibi.ubc.ca
| | Sample_contact_department | Centre for High-Throughput Biology / Psychiatry
| | Sample_contact_institute | University of British Columbia
| | Sample_contact_address | 177 Michael Smith Laboratories 2185 East Mall
| | Sample_contact_city | Vancouver
| | Sample_contact_state | British Columbia
| | Sample_contact_zip/postal_code | V6T 1Z4
| | Sample_contact_country | Canada
| | Sample_contact_web_link | http://www.chibi.ubc.ca/faculty/pavlidis
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM155nnn/GSM155449/suppl/GSM155449.CEL.gz
| | Sample_series_id | GSE6751
| | Sample_data_row_count | 54675
| | |
|
GSM155450 | GPL570 |
|
Patient 08, time point 3
|
Patient 08 PBMC, collected at time point 3
|
Time: six weeks after commencement of periodontal therapy (after treatment end)
Tissue: Peripheral blood monocytes
Phenotype: severe periodontitis
|
Patients were recruited among the ones seeking treatment at the clinic for post-doctoral Periodontics, Columbia University College of Dental Medicine. To be eligible for enrollment, patients had to be diagnosed with severe periodontitis, with radiographic evidence of bone loss extending to greater or equal to 30% of the tooth length at several teeth. Additional inclusion criteria required: age greater or equal to 18 years; presence of greater or equal to 2 teeth/quadrant with a pocket depth of greater or equal to 6 mm and concomitant attachment loss of greater or equal to 3 mm; a minimum of 20 teeth present; no prior periodontal therapy; no systemic conditions or genetic disorders that entail the diagnosis of periodontitis as a manifestation of systemic diseases; no use of systemic antibiotics or regular use of anti-inflammatory drugs for the preceding 6-month period; no diabetes mellitus; no current use of tobacco products or of nicotine replacement medication; not currently pregnant. A total of 15 subjects, 7 male and 8 female, were enrolled. All participants were informed about the scope and procedures of the study and informed consent was obtained.
|
| Sample_geo_accession | GSM155450
| | Sample_status | Public on Dec 31 2007
| | Sample_submission_date | Jan 16 2007
| | Sample_last_update_date | Jan 16 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Fifty ml of blood were obtained by venipucture and collected in Vacutainer cell preparation tubes (Beckton-Dickinson, NJ, USA) with sodium heparin, and were used to harvest peripheral blood mononuclear cells (PBMCs). A 1:1 dilution with PBS was made and the diluted blood sample was centrifuged at 1,000 g in Ficoll tubes (Sigma Accuspin, St. Louis, MO). After washing and counting of the cells in a phase hemacytometer (Hauser Scientific, Horsham, PA), PBMCs were re-suspended in 80 microlitres of MACS buffer (PBS pH 7.2, 0.5% BSA and 2 mM EDTA) and incubated on ice with 20 microlitres of CD14 microbeads (Miltenyi Biotec, Auburn CA) per 107 total cells for 15 minutes. After washings, the cell suspension was applied to a MACS LS separation column (Miltenyi Biotec) placed in the magnetic field of a MACS separator (Miltenyi Biotec). Thereafter, the column was removed from the separator and CD14 positive cells were collected by washings in MACS buffer.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | CD14 positive cells were vigorously pipetted in Trizol (Invitrogen Life Technologies, Carlsbad, CA, USA). After incubation with chloroform and centrifugation at 12,000 g, RNA in the upper aqueous phase was precipitated by mixing with isopropyl alcohol, further centrifugation and washing in 75% ethanol. Further purification of the extracted RNA was achieved by the use of the RNeasy total RNA isolation kit (Qiagen, Valencia, CA, USA) according to the manufacturer.s instructions. The purified RNA was quantified spectrophotometrically. One hundred nanograms of total RNA were amplified and reverse transcribed using the GeneChip expression 3.-amplification two-cycle cDNA synthesis kit (Affymetrix, Santa Clara, CA, USA) and the MEGAscript T7 transcription kit (Ambion, Austin, TX, USA) according to the manufacturers. instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Synthesis of biotin-labeled cRNA and subsequent fragmentation were performed by the use of the IVT labeling kit (Affymetrix, Santa Clara, CA, USA). The cRNA yield was determined spectrophotometrically at 260 nm. Fragmented cRNA was stored at -80C until hybridization.
| | Sample_hyb_protocol | According to the manufacturer's instructions.
| | Sample_scan_protocol | According to the manufacturer's instructions.
| | Sample_data_processing | All CEL files in the series were processed using RMA in R using justRMA with default parameters.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Paul,,Pavlidis
| | Sample_contact_email | paul@chibi.ubc.ca
| | Sample_contact_department | Centre for High-Throughput Biology / Psychiatry
| | Sample_contact_institute | University of British Columbia
| | Sample_contact_address | 177 Michael Smith Laboratories 2185 East Mall
| | Sample_contact_city | Vancouver
| | Sample_contact_state | British Columbia
| | Sample_contact_zip/postal_code | V6T 1Z4
| | Sample_contact_country | Canada
| | Sample_contact_web_link | http://www.chibi.ubc.ca/faculty/pavlidis
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM155nnn/GSM155450/suppl/GSM155450.CEL.gz
| | Sample_series_id | GSE6751
| | Sample_data_row_count | 54675
| | |
|
GSM155451 | GPL570 |
|
Patient 08, time point 4
|
Patient 08 PBMC, collected at time point 4
|
Time: ten weeks after prior to commencement of periodontal therapy (four weeks after treatment end)
Tissue: Peripheral blood monocytes
Phenotype: severe periodontitis
|
Patients were recruited among the ones seeking treatment at the clinic for post-doctoral Periodontics, Columbia University College of Dental Medicine. To be eligible for enrollment, patients had to be diagnosed with severe periodontitis, with radiographic evidence of bone loss extending to greater or equal to 30% of the tooth length at several teeth. Additional inclusion criteria required: age greater or equal to 18 years; presence of greater or equal to 2 teeth/quadrant with a pocket depth of greater or equal to 6 mm and concomitant attachment loss of greater or equal to 3 mm; a minimum of 20 teeth present; no prior periodontal therapy; no systemic conditions or genetic disorders that entail the diagnosis of periodontitis as a manifestation of systemic diseases; no use of systemic antibiotics or regular use of anti-inflammatory drugs for the preceding 6-month period; no diabetes mellitus; no current use of tobacco products or of nicotine replacement medication; not currently pregnant. A total of 15 subjects, 7 male and 8 female, were enrolled. All participants were informed about the scope and procedures of the study and informed consent was obtained.
|
| Sample_geo_accession | GSM155451
| | Sample_status | Public on Dec 31 2007
| | Sample_submission_date | Jan 16 2007
| | Sample_last_update_date | Jan 16 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Fifty ml of blood were obtained by venipucture and collected in Vacutainer cell preparation tubes (Beckton-Dickinson, NJ, USA) with sodium heparin, and were used to harvest peripheral blood mononuclear cells (PBMCs). A 1:1 dilution with PBS was made and the diluted blood sample was centrifuged at 1,000 g in Ficoll tubes (Sigma Accuspin, St. Louis, MO). After washing and counting of the cells in a phase hemacytometer (Hauser Scientific, Horsham, PA), PBMCs were re-suspended in 80 microlitres of MACS buffer (PBS pH 7.2, 0.5% BSA and 2 mM EDTA) and incubated on ice with 20 microlitres of CD14 microbeads (Miltenyi Biotec, Auburn CA) per 107 total cells for 15 minutes. After washings, the cell suspension was applied to a MACS LS separation column (Miltenyi Biotec) placed in the magnetic field of a MACS separator (Miltenyi Biotec). Thereafter, the column was removed from the separator and CD14 positive cells were collected by washings in MACS buffer.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | CD14 positive cells were vigorously pipetted in Trizol (Invitrogen Life Technologies, Carlsbad, CA, USA). After incubation with chloroform and centrifugation at 12,000 g, RNA in the upper aqueous phase was precipitated by mixing with isopropyl alcohol, further centrifugation and washing in 75% ethanol. Further purification of the extracted RNA was achieved by the use of the RNeasy total RNA isolation kit (Qiagen, Valencia, CA, USA) according to the manufacturer.s instructions. The purified RNA was quantified spectrophotometrically. One hundred nanograms of total RNA were amplified and reverse transcribed using the GeneChip expression 3.-amplification two-cycle cDNA synthesis kit (Affymetrix, Santa Clara, CA, USA) and the MEGAscript T7 transcription kit (Ambion, Austin, TX, USA) according to the manufacturers. instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Synthesis of biotin-labeled cRNA and subsequent fragmentation were performed by the use of the IVT labeling kit (Affymetrix, Santa Clara, CA, USA). The cRNA yield was determined spectrophotometrically at 260 nm. Fragmented cRNA was stored at -80C until hybridization.
| | Sample_hyb_protocol | According to the manufacturer's instructions.
| | Sample_scan_protocol | According to the manufacturer's instructions.
| | Sample_data_processing | All CEL files in the series were processed using RMA in R using justRMA with default parameters.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Paul,,Pavlidis
| | Sample_contact_email | paul@chibi.ubc.ca
| | Sample_contact_department | Centre for High-Throughput Biology / Psychiatry
| | Sample_contact_institute | University of British Columbia
| | Sample_contact_address | 177 Michael Smith Laboratories 2185 East Mall
| | Sample_contact_city | Vancouver
| | Sample_contact_state | British Columbia
| | Sample_contact_zip/postal_code | V6T 1Z4
| | Sample_contact_country | Canada
| | Sample_contact_web_link | http://www.chibi.ubc.ca/faculty/pavlidis
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM155nnn/GSM155451/suppl/GSM155451.CEL.gz
| | Sample_series_id | GSE6751
| | Sample_data_row_count | 54675
| | |
|
GSM155452 | GPL570 |
|
Patient 11, time point 1
|
Patient 11 PBMC, collected at time point 1
|
Time: one week prior to commencement of periodontal therapy
Tissue: Peripheral blood monocytes
Phenotype: severe periodontitis
|
Patients were recruited among the ones seeking treatment at the clinic for post-doctoral Periodontics, Columbia University College of Dental Medicine. To be eligible for enrollment, patients had to be diagnosed with severe periodontitis, with radiographic evidence of bone loss extending to greater or equal to 30% of the tooth length at several teeth. Additional inclusion criteria required: age greater or equal to 18 years; presence of greater or equal to 2 teeth/quadrant with a pocket depth of greater or equal to 6 mm and concomitant attachment loss of greater or equal to 3 mm; a minimum of 20 teeth present; no prior periodontal therapy; no systemic conditions or genetic disorders that entail the diagnosis of periodontitis as a manifestation of systemic diseases; no use of systemic antibiotics or regular use of anti-inflammatory drugs for the preceding 6-month period; no diabetes mellitus; no current use of tobacco products or of nicotine replacement medication; not currently pregnant. A total of 15 subjects, 7 male and 8 female, were enrolled. All participants were informed about the scope and procedures of the study and informed consent was obtained.
|
| Sample_geo_accession | GSM155452
| | Sample_status | Public on Dec 31 2007
| | Sample_submission_date | Jan 16 2007
| | Sample_last_update_date | Jan 16 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Fifty ml of blood were obtained by venipucture and collected in Vacutainer cell preparation tubes (Beckton-Dickinson, NJ, USA) with sodium heparin, and were used to harvest peripheral blood mononuclear cells (PBMCs). A 1:1 dilution with PBS was made and the diluted blood sample was centrifuged at 1,000 g in Ficoll tubes (Sigma Accuspin, St. Louis, MO). After washing and counting of the cells in a phase hemacytometer (Hauser Scientific, Horsham, PA), PBMCs were re-suspended in 80 microlitres of MACS buffer (PBS pH 7.2, 0.5% BSA and 2 mM EDTA) and incubated on ice with 20 microlitres of CD14 microbeads (Miltenyi Biotec, Auburn CA) per 107 total cells for 15 minutes. After washings, the cell suspension was applied to a MACS LS separation column (Miltenyi Biotec) placed in the magnetic field of a MACS separator (Miltenyi Biotec). Thereafter, the column was removed from the separator and CD14 positive cells were collected by washings in MACS buffer.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | CD14 positive cells were vigorously pipetted in Trizol (Invitrogen Life Technologies, Carlsbad, CA, USA). After incubation with chloroform and centrifugation at 12,000 g, RNA in the upper aqueous phase was precipitated by mixing with isopropyl alcohol, further centrifugation and washing in 75% ethanol. Further purification of the extracted RNA was achieved by the use of the RNeasy total RNA isolation kit (Qiagen, Valencia, CA, USA) according to the manufacturer.s instructions. The purified RNA was quantified spectrophotometrically. One hundred nanograms of total RNA were amplified and reverse transcribed using the GeneChip expression 3.-amplification two-cycle cDNA synthesis kit (Affymetrix, Santa Clara, CA, USA) and the MEGAscript T7 transcription kit (Ambion, Austin, TX, USA) according to the manufacturers. instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Synthesis of biotin-labeled cRNA and subsequent fragmentation were performed by the use of the IVT labeling kit (Affymetrix, Santa Clara, CA, USA). The cRNA yield was determined spectrophotometrically at 260 nm. Fragmented cRNA was stored at -80C until hybridization.
| | Sample_hyb_protocol | According to the manufacturer's instructions.
| | Sample_scan_protocol | According to the manufacturer's instructions.
| | Sample_data_processing | All CEL files in the series were processed using RMA in R using justRMA with default parameters.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Paul,,Pavlidis
| | Sample_contact_email | paul@chibi.ubc.ca
| | Sample_contact_department | Centre for High-Throughput Biology / Psychiatry
| | Sample_contact_institute | University of British Columbia
| | Sample_contact_address | 177 Michael Smith Laboratories 2185 East Mall
| | Sample_contact_city | Vancouver
| | Sample_contact_state | British Columbia
| | Sample_contact_zip/postal_code | V6T 1Z4
| | Sample_contact_country | Canada
| | Sample_contact_web_link | http://www.chibi.ubc.ca/faculty/pavlidis
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM155nnn/GSM155452/suppl/GSM155452.CEL.gz
| | Sample_series_id | GSE6751
| | Sample_data_row_count | 54675
| | |
|
GSM155453 | GPL570 |
|
Patient 11, time point 3
|
Patient 11 PBMC, collected at time point 3
|
Time: six weeks after commencement of periodontal therapy (after treatment end)
Tissue: Peripheral blood monocytes
Phenotype: severe periodontitis
|
Patients were recruited among the ones seeking treatment at the clinic for post-doctoral Periodontics, Columbia University College of Dental Medicine. To be eligible for enrollment, patients had to be diagnosed with severe periodontitis, with radiographic evidence of bone loss extending to greater or equal to 30% of the tooth length at several teeth. Additional inclusion criteria required: age greater or equal to 18 years; presence of greater or equal to 2 teeth/quadrant with a pocket depth of greater or equal to 6 mm and concomitant attachment loss of greater or equal to 3 mm; a minimum of 20 teeth present; no prior periodontal therapy; no systemic conditions or genetic disorders that entail the diagnosis of periodontitis as a manifestation of systemic diseases; no use of systemic antibiotics or regular use of anti-inflammatory drugs for the preceding 6-month period; no diabetes mellitus; no current use of tobacco products or of nicotine replacement medication; not currently pregnant. A total of 15 subjects, 7 male and 8 female, were enrolled. All participants were informed about the scope and procedures of the study and informed consent was obtained.
|
| Sample_geo_accession | GSM155453
| | Sample_status | Public on Dec 31 2007
| | Sample_submission_date | Jan 16 2007
| | Sample_last_update_date | Jan 16 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Fifty ml of blood were obtained by venipucture and collected in Vacutainer cell preparation tubes (Beckton-Dickinson, NJ, USA) with sodium heparin, and were used to harvest peripheral blood mononuclear cells (PBMCs). A 1:1 dilution with PBS was made and the diluted blood sample was centrifuged at 1,000 g in Ficoll tubes (Sigma Accuspin, St. Louis, MO). After washing and counting of the cells in a phase hemacytometer (Hauser Scientific, Horsham, PA), PBMCs were re-suspended in 80 microlitres of MACS buffer (PBS pH 7.2, 0.5% BSA and 2 mM EDTA) and incubated on ice with 20 microlitres of CD14 microbeads (Miltenyi Biotec, Auburn CA) per 107 total cells for 15 minutes. After washings, the cell suspension was applied to a MACS LS separation column (Miltenyi Biotec) placed in the magnetic field of a MACS separator (Miltenyi Biotec). Thereafter, the column was removed from the separator and CD14 positive cells were collected by washings in MACS buffer.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | CD14 positive cells were vigorously pipetted in Trizol (Invitrogen Life Technologies, Carlsbad, CA, USA). After incubation with chloroform and centrifugation at 12,000 g, RNA in the upper aqueous phase was precipitated by mixing with isopropyl alcohol, further centrifugation and washing in 75% ethanol. Further purification of the extracted RNA was achieved by the use of the RNeasy total RNA isolation kit (Qiagen, Valencia, CA, USA) according to the manufacturer.s instructions. The purified RNA was quantified spectrophotometrically. One hundred nanograms of total RNA were amplified and reverse transcribed using the GeneChip expression 3.-amplification two-cycle cDNA synthesis kit (Affymetrix, Santa Clara, CA, USA) and the MEGAscript T7 transcription kit (Ambion, Austin, TX, USA) according to the manufacturers. instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Synthesis of biotin-labeled cRNA and subsequent fragmentation were performed by the use of the IVT labeling kit (Affymetrix, Santa Clara, CA, USA). The cRNA yield was determined spectrophotometrically at 260 nm. Fragmented cRNA was stored at -80C until hybridization.
| | Sample_hyb_protocol | According to the manufacturer's instructions.
| | Sample_scan_protocol | According to the manufacturer's instructions.
| | Sample_data_processing | All CEL files in the series were processed using RMA in R using justRMA with default parameters.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Paul,,Pavlidis
| | Sample_contact_email | paul@chibi.ubc.ca
| | Sample_contact_department | Centre for High-Throughput Biology / Psychiatry
| | Sample_contact_institute | University of British Columbia
| | Sample_contact_address | 177 Michael Smith Laboratories 2185 East Mall
| | Sample_contact_city | Vancouver
| | Sample_contact_state | British Columbia
| | Sample_contact_zip/postal_code | V6T 1Z4
| | Sample_contact_country | Canada
| | Sample_contact_web_link | http://www.chibi.ubc.ca/faculty/pavlidis
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM155nnn/GSM155453/suppl/GSM155453.CEL.gz
| | Sample_series_id | GSE6751
| | Sample_data_row_count | 54675
| | |
|
GSM155454 | GPL570 |
|
Patient 11, time point 4
|
Patient 11 PBMC, collected at time point 4
|
Time: ten weeks after prior to commencement of periodontal therapy (four weeks after treatment end)
Tissue: Peripheral blood monocytes
Phenotype: severe periodontitis
|
Patients were recruited among the ones seeking treatment at the clinic for post-doctoral Periodontics, Columbia University College of Dental Medicine. To be eligible for enrollment, patients had to be diagnosed with severe periodontitis, with radiographic evidence of bone loss extending to greater or equal to 30% of the tooth length at several teeth. Additional inclusion criteria required: age greater or equal to 18 years; presence of greater or equal to 2 teeth/quadrant with a pocket depth of greater or equal to 6 mm and concomitant attachment loss of greater or equal to 3 mm; a minimum of 20 teeth present; no prior periodontal therapy; no systemic conditions or genetic disorders that entail the diagnosis of periodontitis as a manifestation of systemic diseases; no use of systemic antibiotics or regular use of anti-inflammatory drugs for the preceding 6-month period; no diabetes mellitus; no current use of tobacco products or of nicotine replacement medication; not currently pregnant. A total of 15 subjects, 7 male and 8 female, were enrolled. All participants were informed about the scope and procedures of the study and informed consent was obtained.
|
| Sample_geo_accession | GSM155454
| | Sample_status | Public on Dec 31 2007
| | Sample_submission_date | Jan 16 2007
| | Sample_last_update_date | Jan 16 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Fifty ml of blood were obtained by venipucture and collected in Vacutainer cell preparation tubes (Beckton-Dickinson, NJ, USA) with sodium heparin, and were used to harvest peripheral blood mononuclear cells (PBMCs). A 1:1 dilution with PBS was made and the diluted blood sample was centrifuged at 1,000 g in Ficoll tubes (Sigma Accuspin, St. Louis, MO). After washing and counting of the cells in a phase hemacytometer (Hauser Scientific, Horsham, PA), PBMCs were re-suspended in 80 microlitres of MACS buffer (PBS pH 7.2, 0.5% BSA and 2 mM EDTA) and incubated on ice with 20 microlitres of CD14 microbeads (Miltenyi Biotec, Auburn CA) per 107 total cells for 15 minutes. After washings, the cell suspension was applied to a MACS LS separation column (Miltenyi Biotec) placed in the magnetic field of a MACS separator (Miltenyi Biotec). Thereafter, the column was removed from the separator and CD14 positive cells were collected by washings in MACS buffer.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | CD14 positive cells were vigorously pipetted in Trizol (Invitrogen Life Technologies, Carlsbad, CA, USA). After incubation with chloroform and centrifugation at 12,000 g, RNA in the upper aqueous phase was precipitated by mixing with isopropyl alcohol, further centrifugation and washing in 75% ethanol. Further purification of the extracted RNA was achieved by the use of the RNeasy total RNA isolation kit (Qiagen, Valencia, CA, USA) according to the manufacturer.s instructions. The purified RNA was quantified spectrophotometrically. One hundred nanograms of total RNA were amplified and reverse transcribed using the GeneChip expression 3.-amplification two-cycle cDNA synthesis kit (Affymetrix, Santa Clara, CA, USA) and the MEGAscript T7 transcription kit (Ambion, Austin, TX, USA) according to the manufacturers. instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Synthesis of biotin-labeled cRNA and subsequent fragmentation were performed by the use of the IVT labeling kit (Affymetrix, Santa Clara, CA, USA). The cRNA yield was determined spectrophotometrically at 260 nm. Fragmented cRNA was stored at -80C until hybridization.
| | Sample_hyb_protocol | According to the manufacturer's instructions.
| | Sample_scan_protocol | According to the manufacturer's instructions.
| | Sample_data_processing | All CEL files in the series were processed using RMA in R using justRMA with default parameters.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Paul,,Pavlidis
| | Sample_contact_email | paul@chibi.ubc.ca
| | Sample_contact_department | Centre for High-Throughput Biology / Psychiatry
| | Sample_contact_institute | University of British Columbia
| | Sample_contact_address | 177 Michael Smith Laboratories 2185 East Mall
| | Sample_contact_city | Vancouver
| | Sample_contact_state | British Columbia
| | Sample_contact_zip/postal_code | V6T 1Z4
| | Sample_contact_country | Canada
| | Sample_contact_web_link | http://www.chibi.ubc.ca/faculty/pavlidis
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM155nnn/GSM155454/suppl/GSM155454.CEL.gz
| | Sample_series_id | GSE6751
| | Sample_data_row_count | 54675
| | |
|
GSM155455 | GPL570 |
|
Patient 17, time point 1
|
Patient 17 PBMC, collected at time point 1
|
Time: one week prior to commencement of periodontal therapy
Tissue: Peripheral blood monocytes
Phenotype: severe periodontitis
|
Patients were recruited among the ones seeking treatment at the clinic for post-doctoral Periodontics, Columbia University College of Dental Medicine. To be eligible for enrollment, patients had to be diagnosed with severe periodontitis, with radiographic evidence of bone loss extending to greater or equal to 30% of the tooth length at several teeth. Additional inclusion criteria required: age greater or equal to 18 years; presence of greater or equal to 2 teeth/quadrant with a pocket depth of greater or equal to 6 mm and concomitant attachment loss of greater or equal to 3 mm; a minimum of 20 teeth present; no prior periodontal therapy; no systemic conditions or genetic disorders that entail the diagnosis of periodontitis as a manifestation of systemic diseases; no use of systemic antibiotics or regular use of anti-inflammatory drugs for the preceding 6-month period; no diabetes mellitus; no current use of tobacco products or of nicotine replacement medication; not currently pregnant. A total of 15 subjects, 7 male and 8 female, were enrolled. All participants were informed about the scope and procedures of the study and informed consent was obtained.
|
| Sample_geo_accession | GSM155455
| | Sample_status | Public on Dec 31 2007
| | Sample_submission_date | Jan 16 2007
| | Sample_last_update_date | Jan 16 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Fifty ml of blood were obtained by venipucture and collected in Vacutainer cell preparation tubes (Beckton-Dickinson, NJ, USA) with sodium heparin, and were used to harvest peripheral blood mononuclear cells (PBMCs). A 1:1 dilution with PBS was made and the diluted blood sample was centrifuged at 1,000 g in Ficoll tubes (Sigma Accuspin, St. Louis, MO). After washing and counting of the cells in a phase hemacytometer (Hauser Scientific, Horsham, PA), PBMCs were re-suspended in 80 microlitres of MACS buffer (PBS pH 7.2, 0.5% BSA and 2 mM EDTA) and incubated on ice with 20 microlitres of CD14 microbeads (Miltenyi Biotec, Auburn CA) per 107 total cells for 15 minutes. After washings, the cell suspension was applied to a MACS LS separation column (Miltenyi Biotec) placed in the magnetic field of a MACS separator (Miltenyi Biotec). Thereafter, the column was removed from the separator and CD14 positive cells were collected by washings in MACS buffer.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | CD14 positive cells were vigorously pipetted in Trizol (Invitrogen Life Technologies, Carlsbad, CA, USA). After incubation with chloroform and centrifugation at 12,000 g, RNA in the upper aqueous phase was precipitated by mixing with isopropyl alcohol, further centrifugation and washing in 75% ethanol. Further purification of the extracted RNA was achieved by the use of the RNeasy total RNA isolation kit (Qiagen, Valencia, CA, USA) according to the manufacturer.s instructions. The purified RNA was quantified spectrophotometrically. One hundred nanograms of total RNA were amplified and reverse transcribed using the GeneChip expression 3.-amplification two-cycle cDNA synthesis kit (Affymetrix, Santa Clara, CA, USA) and the MEGAscript T7 transcription kit (Ambion, Austin, TX, USA) according to the manufacturers. instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Synthesis of biotin-labeled cRNA and subsequent fragmentation were performed by the use of the IVT labeling kit (Affymetrix, Santa Clara, CA, USA). The cRNA yield was determined spectrophotometrically at 260 nm. Fragmented cRNA was stored at -80C until hybridization.
| | Sample_hyb_protocol | According to the manufacturer's instructions.
| | Sample_scan_protocol | According to the manufacturer's instructions.
| | Sample_data_processing | All CEL files in the series were processed using RMA in R using justRMA with default parameters.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Paul,,Pavlidis
| | Sample_contact_email | paul@chibi.ubc.ca
| | Sample_contact_department | Centre for High-Throughput Biology / Psychiatry
| | Sample_contact_institute | University of British Columbia
| | Sample_contact_address | 177 Michael Smith Laboratories 2185 East Mall
| | Sample_contact_city | Vancouver
| | Sample_contact_state | British Columbia
| | Sample_contact_zip/postal_code | V6T 1Z4
| | Sample_contact_country | Canada
| | Sample_contact_web_link | http://www.chibi.ubc.ca/faculty/pavlidis
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM155nnn/GSM155455/suppl/GSM155455.CEL.gz
| | Sample_series_id | GSE6751
| | Sample_data_row_count | 54675
| | |
|
GSM155456 | GPL570 |
|
Patient 17, time point 2
|
Patient 17 PBMC, collected at time point 2
|
Time: at commencement of periodontal therapy
Tissue: Peripheral blood monocytes
Phenotype: severe periodontitis
|
Patients were recruited among the ones seeking treatment at the clinic for post-doctoral Periodontics, Columbia University College of Dental Medicine. To be eligible for enrollment, patients had to be diagnosed with severe periodontitis, with radiographic evidence of bone loss extending to greater or equal to 30% of the tooth length at several teeth. Additional inclusion criteria required: age greater or equal to 18 years; presence of greater or equal to 2 teeth/quadrant with a pocket depth of greater or equal to 6 mm and concomitant attachment loss of greater or equal to 3 mm; a minimum of 20 teeth present; no prior periodontal therapy; no systemic conditions or genetic disorders that entail the diagnosis of periodontitis as a manifestation of systemic diseases; no use of systemic antibiotics or regular use of anti-inflammatory drugs for the preceding 6-month period; no diabetes mellitus; no current use of tobacco products or of nicotine replacement medication; not currently pregnant. A total of 15 subjects, 7 male and 8 female, were enrolled. All participants were informed about the scope and procedures of the study and informed consent was obtained.
|
| Sample_geo_accession | GSM155456
| | Sample_status | Public on Dec 31 2007
| | Sample_submission_date | Jan 16 2007
| | Sample_last_update_date | Jan 16 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Fifty ml of blood were obtained by venipucture and collected in Vacutainer cell preparation tubes (Beckton-Dickinson, NJ, USA) with sodium heparin, and were used to harvest peripheral blood mononuclear cells (PBMCs). A 1:1 dilution with PBS was made and the diluted blood sample was centrifuged at 1,000 g in Ficoll tubes (Sigma Accuspin, St. Louis, MO). After washing and counting of the cells in a phase hemacytometer (Hauser Scientific, Horsham, PA), PBMCs were re-suspended in 80 microlitres of MACS buffer (PBS pH 7.2, 0.5% BSA and 2 mM EDTA) and incubated on ice with 20 microlitres of CD14 microbeads (Miltenyi Biotec, Auburn CA) per 107 total cells for 15 minutes. After washings, the cell suspension was applied to a MACS LS separation column (Miltenyi Biotec) placed in the magnetic field of a MACS separator (Miltenyi Biotec). Thereafter, the column was removed from the separator and CD14 positive cells were collected by washings in MACS buffer.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | CD14 positive cells were vigorously pipetted in Trizol (Invitrogen Life Technologies, Carlsbad, CA, USA). After incubation with chloroform and centrifugation at 12,000 g, RNA in the upper aqueous phase was precipitated by mixing with isopropyl alcohol, further centrifugation and washing in 75% ethanol. Further purification of the extracted RNA was achieved by the use of the RNeasy total RNA isolation kit (Qiagen, Valencia, CA, USA) according to the manufacturer.s instructions. The purified RNA was quantified spectrophotometrically. One hundred nanograms of total RNA were amplified and reverse transcribed using the GeneChip expression 3.-amplification two-cycle cDNA synthesis kit (Affymetrix, Santa Clara, CA, USA) and the MEGAscript T7 transcription kit (Ambion, Austin, TX, USA) according to the manufacturers. instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Synthesis of biotin-labeled cRNA and subsequent fragmentation were performed by the use of the IVT labeling kit (Affymetrix, Santa Clara, CA, USA). The cRNA yield was determined spectrophotometrically at 260 nm. Fragmented cRNA was stored at -80C until hybridization.
| | Sample_hyb_protocol | According to the manufacturer's instructions.
| | Sample_scan_protocol | According to the manufacturer's instructions.
| | Sample_data_processing | All CEL files in the series were processed using RMA in R using justRMA with default parameters.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Paul,,Pavlidis
| | Sample_contact_email | paul@chibi.ubc.ca
| | Sample_contact_department | Centre for High-Throughput Biology / Psychiatry
| | Sample_contact_institute | University of British Columbia
| | Sample_contact_address | 177 Michael Smith Laboratories 2185 East Mall
| | Sample_contact_city | Vancouver
| | Sample_contact_state | British Columbia
| | Sample_contact_zip/postal_code | V6T 1Z4
| | Sample_contact_country | Canada
| | Sample_contact_web_link | http://www.chibi.ubc.ca/faculty/pavlidis
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM155nnn/GSM155456/suppl/GSM155456.CEL.gz
| | Sample_series_id | GSE6751
| | Sample_data_row_count | 54675
| | |
|
GSM155457 | GPL570 |
|
Patient 17, time point 3
|
Patient 17 PBMC, collected at time point 3
|
Time: six weeks after commencement of periodontal therapy (after treatment end)
Tissue: Peripheral blood monocytes
Phenotype: severe periodontitis
|
Patients were recruited among the ones seeking treatment at the clinic for post-doctoral Periodontics, Columbia University College of Dental Medicine. To be eligible for enrollment, patients had to be diagnosed with severe periodontitis, with radiographic evidence of bone loss extending to greater or equal to 30% of the tooth length at several teeth. Additional inclusion criteria required: age greater or equal to 18 years; presence of greater or equal to 2 teeth/quadrant with a pocket depth of greater or equal to 6 mm and concomitant attachment loss of greater or equal to 3 mm; a minimum of 20 teeth present; no prior periodontal therapy; no systemic conditions or genetic disorders that entail the diagnosis of periodontitis as a manifestation of systemic diseases; no use of systemic antibiotics or regular use of anti-inflammatory drugs for the preceding 6-month period; no diabetes mellitus; no current use of tobacco products or of nicotine replacement medication; not currently pregnant. A total of 15 subjects, 7 male and 8 female, were enrolled. All participants were informed about the scope and procedures of the study and informed consent was obtained.
|
| Sample_geo_accession | GSM155457
| | Sample_status | Public on Dec 31 2007
| | Sample_submission_date | Jan 16 2007
| | Sample_last_update_date | Jan 16 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Fifty ml of blood were obtained by venipucture and collected in Vacutainer cell preparation tubes (Beckton-Dickinson, NJ, USA) with sodium heparin, and were used to harvest peripheral blood mononuclear cells (PBMCs). A 1:1 dilution with PBS was made and the diluted blood sample was centrifuged at 1,000 g in Ficoll tubes (Sigma Accuspin, St. Louis, MO). After washing and counting of the cells in a phase hemacytometer (Hauser Scientific, Horsham, PA), PBMCs were re-suspended in 80 microlitres of MACS buffer (PBS pH 7.2, 0.5% BSA and 2 mM EDTA) and incubated on ice with 20 microlitres of CD14 microbeads (Miltenyi Biotec, Auburn CA) per 107 total cells for 15 minutes. After washings, the cell suspension was applied to a MACS LS separation column (Miltenyi Biotec) placed in the magnetic field of a MACS separator (Miltenyi Biotec). Thereafter, the column was removed from the separator and CD14 positive cells were collected by washings in MACS buffer.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | CD14 positive cells were vigorously pipetted in Trizol (Invitrogen Life Technologies, Carlsbad, CA, USA). After incubation with chloroform and centrifugation at 12,000 g, RNA in the upper aqueous phase was precipitated by mixing with isopropyl alcohol, further centrifugation and washing in 75% ethanol. Further purification of the extracted RNA was achieved by the use of the RNeasy total RNA isolation kit (Qiagen, Valencia, CA, USA) according to the manufacturer.s instructions. The purified RNA was quantified spectrophotometrically. One hundred nanograms of total RNA were amplified and reverse transcribed using the GeneChip expression 3.-amplification two-cycle cDNA synthesis kit (Affymetrix, Santa Clara, CA, USA) and the MEGAscript T7 transcription kit (Ambion, Austin, TX, USA) according to the manufacturers. instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Synthesis of biotin-labeled cRNA and subsequent fragmentation were performed by the use of the IVT labeling kit (Affymetrix, Santa Clara, CA, USA). The cRNA yield was determined spectrophotometrically at 260 nm. Fragmented cRNA was stored at -80C until hybridization.
| | Sample_hyb_protocol | According to the manufacturer's instructions.
| | Sample_scan_protocol | According to the manufacturer's instructions.
| | Sample_data_processing | All CEL files in the series were processed using RMA in R using justRMA with default parameters.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Paul,,Pavlidis
| | Sample_contact_email | paul@chibi.ubc.ca
| | Sample_contact_department | Centre for High-Throughput Biology / Psychiatry
| | Sample_contact_institute | University of British Columbia
| | Sample_contact_address | 177 Michael Smith Laboratories 2185 East Mall
| | Sample_contact_city | Vancouver
| | Sample_contact_state | British Columbia
| | Sample_contact_zip/postal_code | V6T 1Z4
| | Sample_contact_country | Canada
| | Sample_contact_web_link | http://www.chibi.ubc.ca/faculty/pavlidis
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM155nnn/GSM155457/suppl/GSM155457.CEL.gz
| | Sample_series_id | GSE6751
| | Sample_data_row_count | 54675
| | |
|
GSM155458 | GPL570 |
|
Patient 17, time point 4
|
Patient 17 PBMC, collected at time point 4
|
Time: ten weeks after prior to commencement of periodontal therapy (four weeks after treatment end)
Tissue: Peripheral blood monocytes
Phenotype: severe periodontitis
|
Patients were recruited among the ones seeking treatment at the clinic for post-doctoral Periodontics, Columbia University College of Dental Medicine. To be eligible for enrollment, patients had to be diagnosed with severe periodontitis, with radiographic evidence of bone loss extending to greater or equal to 30% of the tooth length at several teeth. Additional inclusion criteria required: age greater or equal to 18 years; presence of greater or equal to 2 teeth/quadrant with a pocket depth of greater or equal to 6 mm and concomitant attachment loss of greater or equal to 3 mm; a minimum of 20 teeth present; no prior periodontal therapy; no systemic conditions or genetic disorders that entail the diagnosis of periodontitis as a manifestation of systemic diseases; no use of systemic antibiotics or regular use of anti-inflammatory drugs for the preceding 6-month period; no diabetes mellitus; no current use of tobacco products or of nicotine replacement medication; not currently pregnant. A total of 15 subjects, 7 male and 8 female, were enrolled. All participants were informed about the scope and procedures of the study and informed consent was obtained.
|
| Sample_geo_accession | GSM155458
| | Sample_status | Public on Dec 31 2007
| | Sample_submission_date | Jan 16 2007
| | Sample_last_update_date | Jan 16 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Fifty ml of blood were obtained by venipucture and collected in Vacutainer cell preparation tubes (Beckton-Dickinson, NJ, USA) with sodium heparin, and were used to harvest peripheral blood mononuclear cells (PBMCs). A 1:1 dilution with PBS was made and the diluted blood sample was centrifuged at 1,000 g in Ficoll tubes (Sigma Accuspin, St. Louis, MO). After washing and counting of the cells in a phase hemacytometer (Hauser Scientific, Horsham, PA), PBMCs were re-suspended in 80 microlitres of MACS buffer (PBS pH 7.2, 0.5% BSA and 2 mM EDTA) and incubated on ice with 20 microlitres of CD14 microbeads (Miltenyi Biotec, Auburn CA) per 107 total cells for 15 minutes. After washings, the cell suspension was applied to a MACS LS separation column (Miltenyi Biotec) placed in the magnetic field of a MACS separator (Miltenyi Biotec). Thereafter, the column was removed from the separator and CD14 positive cells were collected by washings in MACS buffer.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | CD14 positive cells were vigorously pipetted in Trizol (Invitrogen Life Technologies, Carlsbad, CA, USA). After incubation with chloroform and centrifugation at 12,000 g, RNA in the upper aqueous phase was precipitated by mixing with isopropyl alcohol, further centrifugation and washing in 75% ethanol. Further purification of the extracted RNA was achieved by the use of the RNeasy total RNA isolation kit (Qiagen, Valencia, CA, USA) according to the manufacturer.s instructions. The purified RNA was quantified spectrophotometrically. One hundred nanograms of total RNA were amplified and reverse transcribed using the GeneChip expression 3.-amplification two-cycle cDNA synthesis kit (Affymetrix, Santa Clara, CA, USA) and the MEGAscript T7 transcription kit (Ambion, Austin, TX, USA) according to the manufacturers. instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Synthesis of biotin-labeled cRNA and subsequent fragmentation were performed by the use of the IVT labeling kit (Affymetrix, Santa Clara, CA, USA). The cRNA yield was determined spectrophotometrically at 260 nm. Fragmented cRNA was stored at -80C until hybridization.
| | Sample_hyb_protocol | According to the manufacturer's instructions.
| | Sample_scan_protocol | According to the manufacturer's instructions.
| | Sample_data_processing | All CEL files in the series were processed using RMA in R using justRMA with default parameters.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Paul,,Pavlidis
| | Sample_contact_email | paul@chibi.ubc.ca
| | Sample_contact_department | Centre for High-Throughput Biology / Psychiatry
| | Sample_contact_institute | University of British Columbia
| | Sample_contact_address | 177 Michael Smith Laboratories 2185 East Mall
| | Sample_contact_city | Vancouver
| | Sample_contact_state | British Columbia
| | Sample_contact_zip/postal_code | V6T 1Z4
| | Sample_contact_country | Canada
| | Sample_contact_web_link | http://www.chibi.ubc.ca/faculty/pavlidis
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM155nnn/GSM155458/suppl/GSM155458.CEL.gz
| | Sample_series_id | GSE6751
| | Sample_data_row_count | 54675
| | |
|
GSM155459 | GPL570 |
|
Patient 23, time point 1
|
Patient 23 PBMC, collected at time point 1
|
Time: one week prior to commencement of periodontal therapy
Tissue: Peripheral blood monocytes
Phenotype: severe periodontitis
|
Patients were recruited among the ones seeking treatment at the clinic for post-doctoral Periodontics, Columbia University College of Dental Medicine. To be eligible for enrollment, patients had to be diagnosed with severe periodontitis, with radiographic evidence of bone loss extending to greater or equal to 30% of the tooth length at several teeth. Additional inclusion criteria required: age greater or equal to 18 years; presence of greater or equal to 2 teeth/quadrant with a pocket depth of greater or equal to 6 mm and concomitant attachment loss of greater or equal to 3 mm; a minimum of 20 teeth present; no prior periodontal therapy; no systemic conditions or genetic disorders that entail the diagnosis of periodontitis as a manifestation of systemic diseases; no use of systemic antibiotics or regular use of anti-inflammatory drugs for the preceding 6-month period; no diabetes mellitus; no current use of tobacco products or of nicotine replacement medication; not currently pregnant. A total of 15 subjects, 7 male and 8 female, were enrolled. All participants were informed about the scope and procedures of the study and informed consent was obtained.
|
| Sample_geo_accession | GSM155459
| | Sample_status | Public on Dec 31 2007
| | Sample_submission_date | Jan 16 2007
| | Sample_last_update_date | Jan 16 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Fifty ml of blood were obtained by venipucture and collected in Vacutainer cell preparation tubes (Beckton-Dickinson, NJ, USA) with sodium heparin, and were used to harvest peripheral blood mononuclear cells (PBMCs). A 1:1 dilution with PBS was made and the diluted blood sample was centrifuged at 1,000 g in Ficoll tubes (Sigma Accuspin, St. Louis, MO). After washing and counting of the cells in a phase hemacytometer (Hauser Scientific, Horsham, PA), PBMCs were re-suspended in 80 microlitres of MACS buffer (PBS pH 7.2, 0.5% BSA and 2 mM EDTA) and incubated on ice with 20 microlitres of CD14 microbeads (Miltenyi Biotec, Auburn CA) per 107 total cells for 15 minutes. After washings, the cell suspension was applied to a MACS LS separation column (Miltenyi Biotec) placed in the magnetic field of a MACS separator (Miltenyi Biotec). Thereafter, the column was removed from the separator and CD14 positive cells were collected by washings in MACS buffer.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | CD14 positive cells were vigorously pipetted in Trizol (Invitrogen Life Technologies, Carlsbad, CA, USA). After incubation with chloroform and centrifugation at 12,000 g, RNA in the upper aqueous phase was precipitated by mixing with isopropyl alcohol, further centrifugation and washing in 75% ethanol. Further purification of the extracted RNA was achieved by the use of the RNeasy total RNA isolation kit (Qiagen, Valencia, CA, USA) according to the manufacturer.s instructions. The purified RNA was quantified spectrophotometrically. One hundred nanograms of total RNA were amplified and reverse transcribed using the GeneChip expression 3.-amplification two-cycle cDNA synthesis kit (Affymetrix, Santa Clara, CA, USA) and the MEGAscript T7 transcription kit (Ambion, Austin, TX, USA) according to the manufacturers. instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Synthesis of biotin-labeled cRNA and subsequent fragmentation were performed by the use of the IVT labeling kit (Affymetrix, Santa Clara, CA, USA). The cRNA yield was determined spectrophotometrically at 260 nm. Fragmented cRNA was stored at -80C until hybridization.
| | Sample_hyb_protocol | According to the manufacturer's instructions.
| | Sample_scan_protocol | According to the manufacturer's instructions.
| | Sample_data_processing | All CEL files in the series were processed using RMA in R using justRMA with default parameters.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Paul,,Pavlidis
| | Sample_contact_email | paul@chibi.ubc.ca
| | Sample_contact_department | Centre for High-Throughput Biology / Psychiatry
| | Sample_contact_institute | University of British Columbia
| | Sample_contact_address | 177 Michael Smith Laboratories 2185 East Mall
| | Sample_contact_city | Vancouver
| | Sample_contact_state | British Columbia
| | Sample_contact_zip/postal_code | V6T 1Z4
| | Sample_contact_country | Canada
| | Sample_contact_web_link | http://www.chibi.ubc.ca/faculty/pavlidis
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM155nnn/GSM155459/suppl/GSM155459.CEL.gz
| | Sample_series_id | GSE6751
| | Sample_data_row_count | 54675
| | |
|
GSM155460 | GPL570 |
|
Patient 23, time point 2
|
Patient 23 PBMC, collected at time point 2
|
Time: at commencement of periodontal therapy
Tissue: Peripheral blood monocytes
Phenotype: severe periodontitis
|
Patients were recruited among the ones seeking treatment at the clinic for post-doctoral Periodontics, Columbia University College of Dental Medicine. To be eligible for enrollment, patients had to be diagnosed with severe periodontitis, with radiographic evidence of bone loss extending to greater or equal to 30% of the tooth length at several teeth. Additional inclusion criteria required: age greater or equal to 18 years; presence of greater or equal to 2 teeth/quadrant with a pocket depth of greater or equal to 6 mm and concomitant attachment loss of greater or equal to 3 mm; a minimum of 20 teeth present; no prior periodontal therapy; no systemic conditions or genetic disorders that entail the diagnosis of periodontitis as a manifestation of systemic diseases; no use of systemic antibiotics or regular use of anti-inflammatory drugs for the preceding 6-month period; no diabetes mellitus; no current use of tobacco products or of nicotine replacement medication; not currently pregnant. A total of 15 subjects, 7 male and 8 female, were enrolled. All participants were informed about the scope and procedures of the study and informed consent was obtained.
|
| Sample_geo_accession | GSM155460
| | Sample_status | Public on Dec 31 2007
| | Sample_submission_date | Jan 16 2007
| | Sample_last_update_date | Jan 16 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Fifty ml of blood were obtained by venipucture and collected in Vacutainer cell preparation tubes (Beckton-Dickinson, NJ, USA) with sodium heparin, and were used to harvest peripheral blood mononuclear cells (PBMCs). A 1:1 dilution with PBS was made and the diluted blood sample was centrifuged at 1,000 g in Ficoll tubes (Sigma Accuspin, St. Louis, MO). After washing and counting of the cells in a phase hemacytometer (Hauser Scientific, Horsham, PA), PBMCs were re-suspended in 80 microlitres of MACS buffer (PBS pH 7.2, 0.5% BSA and 2 mM EDTA) and incubated on ice with 20 microlitres of CD14 microbeads (Miltenyi Biotec, Auburn CA) per 107 total cells for 15 minutes. After washings, the cell suspension was applied to a MACS LS separation column (Miltenyi Biotec) placed in the magnetic field of a MACS separator (Miltenyi Biotec). Thereafter, the column was removed from the separator and CD14 positive cells were collected by washings in MACS buffer.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | CD14 positive cells were vigorously pipetted in Trizol (Invitrogen Life Technologies, Carlsbad, CA, USA). After incubation with chloroform and centrifugation at 12,000 g, RNA in the upper aqueous phase was precipitated by mixing with isopropyl alcohol, further centrifugation and washing in 75% ethanol. Further purification of the extracted RNA was achieved by the use of the RNeasy total RNA isolation kit (Qiagen, Valencia, CA, USA) according to the manufacturer.s instructions. The purified RNA was quantified spectrophotometrically. One hundred nanograms of total RNA were amplified and reverse transcribed using the GeneChip expression 3.-amplification two-cycle cDNA synthesis kit (Affymetrix, Santa Clara, CA, USA) and the MEGAscript T7 transcription kit (Ambion, Austin, TX, USA) according to the manufacturers. instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Synthesis of biotin-labeled cRNA and subsequent fragmentation were performed by the use of the IVT labeling kit (Affymetrix, Santa Clara, CA, USA). The cRNA yield was determined spectrophotometrically at 260 nm. Fragmented cRNA was stored at -80C until hybridization.
| | Sample_hyb_protocol | According to the manufacturer's instructions.
| | Sample_scan_protocol | According to the manufacturer's instructions.
| | Sample_data_processing | All CEL files in the series were processed using RMA in R using justRMA with default parameters.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Paul,,Pavlidis
| | Sample_contact_email | paul@chibi.ubc.ca
| | Sample_contact_department | Centre for High-Throughput Biology / Psychiatry
| | Sample_contact_institute | University of British Columbia
| | Sample_contact_address | 177 Michael Smith Laboratories 2185 East Mall
| | Sample_contact_city | Vancouver
| | Sample_contact_state | British Columbia
| | Sample_contact_zip/postal_code | V6T 1Z4
| | Sample_contact_country | Canada
| | Sample_contact_web_link | http://www.chibi.ubc.ca/faculty/pavlidis
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM155nnn/GSM155460/suppl/GSM155460.CEL.gz
| | Sample_series_id | GSE6751
| | Sample_data_row_count | 54675
| | |
|
GSM155461 | GPL570 |
|
Patient 23, time point 3
|
Patient 23 PBMC, collected at time point 3
|
Time: six weeks after commencement of periodontal therapy (after treatment end)
Tissue: Peripheral blood monocytes
Phenotype: severe periodontitis
|
Patients were recruited among the ones seeking treatment at the clinic for post-doctoral Periodontics, Columbia University College of Dental Medicine. To be eligible for enrollment, patients had to be diagnosed with severe periodontitis, with radiographic evidence of bone loss extending to greater or equal to 30% of the tooth length at several teeth. Additional inclusion criteria required: age greater or equal to 18 years; presence of greater or equal to 2 teeth/quadrant with a pocket depth of greater or equal to 6 mm and concomitant attachment loss of greater or equal to 3 mm; a minimum of 20 teeth present; no prior periodontal therapy; no systemic conditions or genetic disorders that entail the diagnosis of periodontitis as a manifestation of systemic diseases; no use of systemic antibiotics or regular use of anti-inflammatory drugs for the preceding 6-month period; no diabetes mellitus; no current use of tobacco products or of nicotine replacement medication; not currently pregnant. A total of 15 subjects, 7 male and 8 female, were enrolled. All participants were informed about the scope and procedures of the study and informed consent was obtained.
|
| Sample_geo_accession | GSM155461
| | Sample_status | Public on Dec 31 2007
| | Sample_submission_date | Jan 16 2007
| | Sample_last_update_date | Jan 16 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Fifty ml of blood were obtained by venipucture and collected in Vacutainer cell preparation tubes (Beckton-Dickinson, NJ, USA) with sodium heparin, and were used to harvest peripheral blood mononuclear cells (PBMCs). A 1:1 dilution with PBS was made and the diluted blood sample was centrifuged at 1,000 g in Ficoll tubes (Sigma Accuspin, St. Louis, MO). After washing and counting of the cells in a phase hemacytometer (Hauser Scientific, Horsham, PA), PBMCs were re-suspended in 80 microlitres of MACS buffer (PBS pH 7.2, 0.5% BSA and 2 mM EDTA) and incubated on ice with 20 microlitres of CD14 microbeads (Miltenyi Biotec, Auburn CA) per 107 total cells for 15 minutes. After washings, the cell suspension was applied to a MACS LS separation column (Miltenyi Biotec) placed in the magnetic field of a MACS separator (Miltenyi Biotec). Thereafter, the column was removed from the separator and CD14 positive cells were collected by washings in MACS buffer.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | CD14 positive cells were vigorously pipetted in Trizol (Invitrogen Life Technologies, Carlsbad, CA, USA). After incubation with chloroform and centrifugation at 12,000 g, RNA in the upper aqueous phase was precipitated by mixing with isopropyl alcohol, further centrifugation and washing in 75% ethanol. Further purification of the extracted RNA was achieved by the use of the RNeasy total RNA isolation kit (Qiagen, Valencia, CA, USA) according to the manufacturer.s instructions. The purified RNA was quantified spectrophotometrically. One hundred nanograms of total RNA were amplified and reverse transcribed using the GeneChip expression 3.-amplification two-cycle cDNA synthesis kit (Affymetrix, Santa Clara, CA, USA) and the MEGAscript T7 transcription kit (Ambion, Austin, TX, USA) according to the manufacturers. instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Synthesis of biotin-labeled cRNA and subsequent fragmentation were performed by the use of the IVT labeling kit (Affymetrix, Santa Clara, CA, USA). The cRNA yield was determined spectrophotometrically at 260 nm. Fragmented cRNA was stored at -80C until hybridization.
| | Sample_hyb_protocol | According to the manufacturer's instructions.
| | Sample_scan_protocol | According to the manufacturer's instructions.
| | Sample_data_processing | All CEL files in the series were processed using RMA in R using justRMA with default parameters.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Paul,,Pavlidis
| | Sample_contact_email | paul@chibi.ubc.ca
| | Sample_contact_department | Centre for High-Throughput Biology / Psychiatry
| | Sample_contact_institute | University of British Columbia
| | Sample_contact_address | 177 Michael Smith Laboratories 2185 East Mall
| | Sample_contact_city | Vancouver
| | Sample_contact_state | British Columbia
| | Sample_contact_zip/postal_code | V6T 1Z4
| | Sample_contact_country | Canada
| | Sample_contact_web_link | http://www.chibi.ubc.ca/faculty/pavlidis
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM155nnn/GSM155461/suppl/GSM155461.CEL.gz
| | Sample_series_id | GSE6751
| | Sample_data_row_count | 54675
| | |
|
GSM155462 | GPL570 |
|
Patient 23, time point 4
|
Patient 23 PBMC, collected at time point 4
|
Time: ten weeks after prior to commencement of periodontal therapy (four weeks after treatment end)
Tissue: Peripheral blood monocytes
Phenotype: severe periodontitis
|
Patients were recruited among the ones seeking treatment at the clinic for post-doctoral Periodontics, Columbia University College of Dental Medicine. To be eligible for enrollment, patients had to be diagnosed with severe periodontitis, with radiographic evidence of bone loss extending to greater or equal to 30% of the tooth length at several teeth. Additional inclusion criteria required: age greater or equal to 18 years; presence of greater or equal to 2 teeth/quadrant with a pocket depth of greater or equal to 6 mm and concomitant attachment loss of greater or equal to 3 mm; a minimum of 20 teeth present; no prior periodontal therapy; no systemic conditions or genetic disorders that entail the diagnosis of periodontitis as a manifestation of systemic diseases; no use of systemic antibiotics or regular use of anti-inflammatory drugs for the preceding 6-month period; no diabetes mellitus; no current use of tobacco products or of nicotine replacement medication; not currently pregnant. A total of 15 subjects, 7 male and 8 female, were enrolled. All participants were informed about the scope and procedures of the study and informed consent was obtained.
|
| Sample_geo_accession | GSM155462
| | Sample_status | Public on Dec 31 2007
| | Sample_submission_date | Jan 16 2007
| | Sample_last_update_date | Jan 16 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Fifty ml of blood were obtained by venipucture and collected in Vacutainer cell preparation tubes (Beckton-Dickinson, NJ, USA) with sodium heparin, and were used to harvest peripheral blood mononuclear cells (PBMCs). A 1:1 dilution with PBS was made and the diluted blood sample was centrifuged at 1,000 g in Ficoll tubes (Sigma Accuspin, St. Louis, MO). After washing and counting of the cells in a phase hemacytometer (Hauser Scientific, Horsham, PA), PBMCs were re-suspended in 80 microlitres of MACS buffer (PBS pH 7.2, 0.5% BSA and 2 mM EDTA) and incubated on ice with 20 microlitres of CD14 microbeads (Miltenyi Biotec, Auburn CA) per 107 total cells for 15 minutes. After washings, the cell suspension was applied to a MACS LS separation column (Miltenyi Biotec) placed in the magnetic field of a MACS separator (Miltenyi Biotec). Thereafter, the column was removed from the separator and CD14 positive cells were collected by washings in MACS buffer.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | CD14 positive cells were vigorously pipetted in Trizol (Invitrogen Life Technologies, Carlsbad, CA, USA). After incubation with chloroform and centrifugation at 12,000 g, RNA in the upper aqueous phase was precipitated by mixing with isopropyl alcohol, further centrifugation and washing in 75% ethanol. Further purification of the extracted RNA was achieved by the use of the RNeasy total RNA isolation kit (Qiagen, Valencia, CA, USA) according to the manufacturer.s instructions. The purified RNA was quantified spectrophotometrically. One hundred nanograms of total RNA were amplified and reverse transcribed using the GeneChip expression 3.-amplification two-cycle cDNA synthesis kit (Affymetrix, Santa Clara, CA, USA) and the MEGAscript T7 transcription kit (Ambion, Austin, TX, USA) according to the manufacturers. instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Synthesis of biotin-labeled cRNA and subsequent fragmentation were performed by the use of the IVT labeling kit (Affymetrix, Santa Clara, CA, USA). The cRNA yield was determined spectrophotometrically at 260 nm. Fragmented cRNA was stored at -80C until hybridization.
| | Sample_hyb_protocol | According to the manufacturer's instructions.
| | Sample_scan_protocol | According to the manufacturer's instructions.
| | Sample_data_processing | All CEL files in the series were processed using RMA in R using justRMA with default parameters.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Paul,,Pavlidis
| | Sample_contact_email | paul@chibi.ubc.ca
| | Sample_contact_department | Centre for High-Throughput Biology / Psychiatry
| | Sample_contact_institute | University of British Columbia
| | Sample_contact_address | 177 Michael Smith Laboratories 2185 East Mall
| | Sample_contact_city | Vancouver
| | Sample_contact_state | British Columbia
| | Sample_contact_zip/postal_code | V6T 1Z4
| | Sample_contact_country | Canada
| | Sample_contact_web_link | http://www.chibi.ubc.ca/faculty/pavlidis
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM155nnn/GSM155462/suppl/GSM155462.CEL.gz
| | Sample_series_id | GSE6751
| | Sample_data_row_count | 54675
| | |
|
GSM155463 | GPL570 |
|
Patient 26, time point 1
|
Patient 26 PBMC, collected at time point 1
|
Time: one week prior to commencement of periodontal therapy
Tissue: Peripheral blood monocytes
Phenotype: severe periodontitis
|
Patients were recruited among the ones seeking treatment at the clinic for post-doctoral Periodontics, Columbia University College of Dental Medicine. To be eligible for enrollment, patients had to be diagnosed with severe periodontitis, with radiographic evidence of bone loss extending to greater or equal to 30% of the tooth length at several teeth. Additional inclusion criteria required: age greater or equal to 18 years; presence of greater or equal to 2 teeth/quadrant with a pocket depth of greater or equal to 6 mm and concomitant attachment loss of greater or equal to 3 mm; a minimum of 20 teeth present; no prior periodontal therapy; no systemic conditions or genetic disorders that entail the diagnosis of periodontitis as a manifestation of systemic diseases; no use of systemic antibiotics or regular use of anti-inflammatory drugs for the preceding 6-month period; no diabetes mellitus; no current use of tobacco products or of nicotine replacement medication; not currently pregnant. A total of 15 subjects, 7 male and 8 female, were enrolled. All participants were informed about the scope and procedures of the study and informed consent was obtained.
|
| Sample_geo_accession | GSM155463
| | Sample_status | Public on Dec 31 2007
| | Sample_submission_date | Jan 16 2007
| | Sample_last_update_date | Jan 16 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Fifty ml of blood were obtained by venipucture and collected in Vacutainer cell preparation tubes (Beckton-Dickinson, NJ, USA) with sodium heparin, and were used to harvest peripheral blood mononuclear cells (PBMCs). A 1:1 dilution with PBS was made and the diluted blood sample was centrifuged at 1,000 g in Ficoll tubes (Sigma Accuspin, St. Louis, MO). After washing and counting of the cells in a phase hemacytometer (Hauser Scientific, Horsham, PA), PBMCs were re-suspended in 80 microlitres of MACS buffer (PBS pH 7.2, 0.5% BSA and 2 mM EDTA) and incubated on ice with 20 microlitres of CD14 microbeads (Miltenyi Biotec, Auburn CA) per 107 total cells for 15 minutes. After washings, the cell suspension was applied to a MACS LS separation column (Miltenyi Biotec) placed in the magnetic field of a MACS separator (Miltenyi Biotec). Thereafter, the column was removed from the separator and CD14 positive cells were collected by washings in MACS buffer.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | CD14 positive cells were vigorously pipetted in Trizol (Invitrogen Life Technologies, Carlsbad, CA, USA). After incubation with chloroform and centrifugation at 12,000 g, RNA in the upper aqueous phase was precipitated by mixing with isopropyl alcohol, further centrifugation and washing in 75% ethanol. Further purification of the extracted RNA was achieved by the use of the RNeasy total RNA isolation kit (Qiagen, Valencia, CA, USA) according to the manufacturer.s instructions. The purified RNA was quantified spectrophotometrically. One hundred nanograms of total RNA were amplified and reverse transcribed using the GeneChip expression 3.-amplification two-cycle cDNA synthesis kit (Affymetrix, Santa Clara, CA, USA) and the MEGAscript T7 transcription kit (Ambion, Austin, TX, USA) according to the manufacturers. instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Synthesis of biotin-labeled cRNA and subsequent fragmentation were performed by the use of the IVT labeling kit (Affymetrix, Santa Clara, CA, USA). The cRNA yield was determined spectrophotometrically at 260 nm. Fragmented cRNA was stored at -80C until hybridization.
| | Sample_hyb_protocol | According to the manufacturer's instructions.
| | Sample_scan_protocol | According to the manufacturer's instructions.
| | Sample_data_processing | All CEL files in the series were processed using RMA in R using justRMA with default parameters.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Paul,,Pavlidis
| | Sample_contact_email | paul@chibi.ubc.ca
| | Sample_contact_department | Centre for High-Throughput Biology / Psychiatry
| | Sample_contact_institute | University of British Columbia
| | Sample_contact_address | 177 Michael Smith Laboratories 2185 East Mall
| | Sample_contact_city | Vancouver
| | Sample_contact_state | British Columbia
| | Sample_contact_zip/postal_code | V6T 1Z4
| | Sample_contact_country | Canada
| | Sample_contact_web_link | http://www.chibi.ubc.ca/faculty/pavlidis
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM155nnn/GSM155463/suppl/GSM155463.CEL.gz
| | Sample_series_id | GSE6751
| | Sample_data_row_count | 54675
| | |
|
GSM155464 | GPL570 |
|
Patient 26, time point 2
|
Patient 26 PBMC, collected at time point 2
|
Time: at commencement of periodontal therapy
Tissue: Peripheral blood monocytes
Phenotype: severe periodontitis
|
Patients were recruited among the ones seeking treatment at the clinic for post-doctoral Periodontics, Columbia University College of Dental Medicine. To be eligible for enrollment, patients had to be diagnosed with severe periodontitis, with radiographic evidence of bone loss extending to greater or equal to 30% of the tooth length at several teeth. Additional inclusion criteria required: age greater or equal to 18 years; presence of greater or equal to 2 teeth/quadrant with a pocket depth of greater or equal to 6 mm and concomitant attachment loss of greater or equal to 3 mm; a minimum of 20 teeth present; no prior periodontal therapy; no systemic conditions or genetic disorders that entail the diagnosis of periodontitis as a manifestation of systemic diseases; no use of systemic antibiotics or regular use of anti-inflammatory drugs for the preceding 6-month period; no diabetes mellitus; no current use of tobacco products or of nicotine replacement medication; not currently pregnant. A total of 15 subjects, 7 male and 8 female, were enrolled. All participants were informed about the scope and procedures of the study and informed consent was obtained.
|
| Sample_geo_accession | GSM155464
| | Sample_status | Public on Dec 31 2007
| | Sample_submission_date | Jan 16 2007
| | Sample_last_update_date | Jan 16 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Fifty ml of blood were obtained by venipucture and collected in Vacutainer cell preparation tubes (Beckton-Dickinson, NJ, USA) with sodium heparin, and were used to harvest peripheral blood mononuclear cells (PBMCs). A 1:1 dilution with PBS was made and the diluted blood sample was centrifuged at 1,000 g in Ficoll tubes (Sigma Accuspin, St. Louis, MO). After washing and counting of the cells in a phase hemacytometer (Hauser Scientific, Horsham, PA), PBMCs were re-suspended in 80 microlitres of MACS buffer (PBS pH 7.2, 0.5% BSA and 2 mM EDTA) and incubated on ice with 20 microlitres of CD14 microbeads (Miltenyi Biotec, Auburn CA) per 107 total cells for 15 minutes. After washings, the cell suspension was applied to a MACS LS separation column (Miltenyi Biotec) placed in the magnetic field of a MACS separator (Miltenyi Biotec). Thereafter, the column was removed from the separator and CD14 positive cells were collected by washings in MACS buffer.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | CD14 positive cells were vigorously pipetted in Trizol (Invitrogen Life Technologies, Carlsbad, CA, USA). After incubation with chloroform and centrifugation at 12,000 g, RNA in the upper aqueous phase was precipitated by mixing with isopropyl alcohol, further centrifugation and washing in 75% ethanol. Further purification of the extracted RNA was achieved by the use of the RNeasy total RNA isolation kit (Qiagen, Valencia, CA, USA) according to the manufacturer.s instructions. The purified RNA was quantified spectrophotometrically. One hundred nanograms of total RNA were amplified and reverse transcribed using the GeneChip expression 3.-amplification two-cycle cDNA synthesis kit (Affymetrix, Santa Clara, CA, USA) and the MEGAscript T7 transcription kit (Ambion, Austin, TX, USA) according to the manufacturers. instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Synthesis of biotin-labeled cRNA and subsequent fragmentation were performed by the use of the IVT labeling kit (Affymetrix, Santa Clara, CA, USA). The cRNA yield was determined spectrophotometrically at 260 nm. Fragmented cRNA was stored at -80C until hybridization.
| | Sample_hyb_protocol | According to the manufacturer's instructions.
| | Sample_scan_protocol | According to the manufacturer's instructions.
| | Sample_data_processing | All CEL files in the series were processed using RMA in R using justRMA with default parameters.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Paul,,Pavlidis
| | Sample_contact_email | paul@chibi.ubc.ca
| | Sample_contact_department | Centre for High-Throughput Biology / Psychiatry
| | Sample_contact_institute | University of British Columbia
| | Sample_contact_address | 177 Michael Smith Laboratories 2185 East Mall
| | Sample_contact_city | Vancouver
| | Sample_contact_state | British Columbia
| | Sample_contact_zip/postal_code | V6T 1Z4
| | Sample_contact_country | Canada
| | Sample_contact_web_link | http://www.chibi.ubc.ca/faculty/pavlidis
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM155nnn/GSM155464/suppl/GSM155464.CEL.gz
| | Sample_series_id | GSE6751
| | Sample_data_row_count | 54675
| | |
|
GSM155465 | GPL570 |
|
Patient 26, time point 3
|
Patient 26 PBMC, collected at time point 3
|
Time: six weeks after commencement of periodontal therapy (after treatment end)
Tissue: Peripheral blood monocytes
Phenotype: severe periodontitis
|
Patients were recruited among the ones seeking treatment at the clinic for post-doctoral Periodontics, Columbia University College of Dental Medicine. To be eligible for enrollment, patients had to be diagnosed with severe periodontitis, with radiographic evidence of bone loss extending to greater or equal to 30% of the tooth length at several teeth. Additional inclusion criteria required: age greater or equal to 18 years; presence of greater or equal to 2 teeth/quadrant with a pocket depth of greater or equal to 6 mm and concomitant attachment loss of greater or equal to 3 mm; a minimum of 20 teeth present; no prior periodontal therapy; no systemic conditions or genetic disorders that entail the diagnosis of periodontitis as a manifestation of systemic diseases; no use of systemic antibiotics or regular use of anti-inflammatory drugs for the preceding 6-month period; no diabetes mellitus; no current use of tobacco products or of nicotine replacement medication; not currently pregnant. A total of 15 subjects, 7 male and 8 female, were enrolled. All participants were informed about the scope and procedures of the study and informed consent was obtained.
|
| Sample_geo_accession | GSM155465
| | Sample_status | Public on Dec 31 2007
| | Sample_submission_date | Jan 16 2007
| | Sample_last_update_date | Jan 16 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Fifty ml of blood were obtained by venipucture and collected in Vacutainer cell preparation tubes (Beckton-Dickinson, NJ, USA) with sodium heparin, and were used to harvest peripheral blood mononuclear cells (PBMCs). A 1:1 dilution with PBS was made and the diluted blood sample was centrifuged at 1,000 g in Ficoll tubes (Sigma Accuspin, St. Louis, MO). After washing and counting of the cells in a phase hemacytometer (Hauser Scientific, Horsham, PA), PBMCs were re-suspended in 80 microlitres of MACS buffer (PBS pH 7.2, 0.5% BSA and 2 mM EDTA) and incubated on ice with 20 microlitres of CD14 microbeads (Miltenyi Biotec, Auburn CA) per 107 total cells for 15 minutes. After washings, the cell suspension was applied to a MACS LS separation column (Miltenyi Biotec) placed in the magnetic field of a MACS separator (Miltenyi Biotec). Thereafter, the column was removed from the separator and CD14 positive cells were collected by washings in MACS buffer.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | CD14 positive cells were vigorously pipetted in Trizol (Invitrogen Life Technologies, Carlsbad, CA, USA). After incubation with chloroform and centrifugation at 12,000 g, RNA in the upper aqueous phase was precipitated by mixing with isopropyl alcohol, further centrifugation and washing in 75% ethanol. Further purification of the extracted RNA was achieved by the use of the RNeasy total RNA isolation kit (Qiagen, Valencia, CA, USA) according to the manufacturer.s instructions. The purified RNA was quantified spectrophotometrically. One hundred nanograms of total RNA were amplified and reverse transcribed using the GeneChip expression 3.-amplification two-cycle cDNA synthesis kit (Affymetrix, Santa Clara, CA, USA) and the MEGAscript T7 transcription kit (Ambion, Austin, TX, USA) according to the manufacturers. instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Synthesis of biotin-labeled cRNA and subsequent fragmentation were performed by the use of the IVT labeling kit (Affymetrix, Santa Clara, CA, USA). The cRNA yield was determined spectrophotometrically at 260 nm. Fragmented cRNA was stored at -80C until hybridization.
| | Sample_hyb_protocol | According to the manufacturer's instructions.
| | Sample_scan_protocol | According to the manufacturer's instructions.
| | Sample_data_processing | All CEL files in the series were processed using RMA in R using justRMA with default parameters.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Paul,,Pavlidis
| | Sample_contact_email | paul@chibi.ubc.ca
| | Sample_contact_department | Centre for High-Throughput Biology / Psychiatry
| | Sample_contact_institute | University of British Columbia
| | Sample_contact_address | 177 Michael Smith Laboratories 2185 East Mall
| | Sample_contact_city | Vancouver
| | Sample_contact_state | British Columbia
| | Sample_contact_zip/postal_code | V6T 1Z4
| | Sample_contact_country | Canada
| | Sample_contact_web_link | http://www.chibi.ubc.ca/faculty/pavlidis
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM155nnn/GSM155465/suppl/GSM155465.CEL.gz
| | Sample_series_id | GSE6751
| | Sample_data_row_count | 54675
| | |
|
GSM155466 | GPL570 |
|
Patient 26, time point 4
|
Patient 26 PBMC, collected at time point 4
|
Time: ten weeks after prior to commencement of periodontal therapy (four weeks after treatment end)
Tissue: Peripheral blood monocytes
Phenotype: severe periodontitis
|
Patients were recruited among the ones seeking treatment at the clinic for post-doctoral Periodontics, Columbia University College of Dental Medicine. To be eligible for enrollment, patients had to be diagnosed with severe periodontitis, with radiographic evidence of bone loss extending to greater or equal to 30% of the tooth length at several teeth. Additional inclusion criteria required: age greater or equal to 18 years; presence of greater or equal to 2 teeth/quadrant with a pocket depth of greater or equal to 6 mm and concomitant attachment loss of greater or equal to 3 mm; a minimum of 20 teeth present; no prior periodontal therapy; no systemic conditions or genetic disorders that entail the diagnosis of periodontitis as a manifestation of systemic diseases; no use of systemic antibiotics or regular use of anti-inflammatory drugs for the preceding 6-month period; no diabetes mellitus; no current use of tobacco products or of nicotine replacement medication; not currently pregnant. A total of 15 subjects, 7 male and 8 female, were enrolled. All participants were informed about the scope and procedures of the study and informed consent was obtained.
|
| Sample_geo_accession | GSM155466
| | Sample_status | Public on Dec 31 2007
| | Sample_submission_date | Jan 16 2007
| | Sample_last_update_date | Jan 16 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Fifty ml of blood were obtained by venipucture and collected in Vacutainer cell preparation tubes (Beckton-Dickinson, NJ, USA) with sodium heparin, and were used to harvest peripheral blood mononuclear cells (PBMCs). A 1:1 dilution with PBS was made and the diluted blood sample was centrifuged at 1,000 g in Ficoll tubes (Sigma Accuspin, St. Louis, MO). After washing and counting of the cells in a phase hemacytometer (Hauser Scientific, Horsham, PA), PBMCs were re-suspended in 80 microlitres of MACS buffer (PBS pH 7.2, 0.5% BSA and 2 mM EDTA) and incubated on ice with 20 microlitres of CD14 microbeads (Miltenyi Biotec, Auburn CA) per 107 total cells for 15 minutes. After washings, the cell suspension was applied to a MACS LS separation column (Miltenyi Biotec) placed in the magnetic field of a MACS separator (Miltenyi Biotec). Thereafter, the column was removed from the separator and CD14 positive cells were collected by washings in MACS buffer.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | CD14 positive cells were vigorously pipetted in Trizol (Invitrogen Life Technologies, Carlsbad, CA, USA). After incubation with chloroform and centrifugation at 12,000 g, RNA in the upper aqueous phase was precipitated by mixing with isopropyl alcohol, further centrifugation and washing in 75% ethanol. Further purification of the extracted RNA was achieved by the use of the RNeasy total RNA isolation kit (Qiagen, Valencia, CA, USA) according to the manufacturer.s instructions. The purified RNA was quantified spectrophotometrically. One hundred nanograms of total RNA were amplified and reverse transcribed using the GeneChip expression 3.-amplification two-cycle cDNA synthesis kit (Affymetrix, Santa Clara, CA, USA) and the MEGAscript T7 transcription kit (Ambion, Austin, TX, USA) according to the manufacturers. instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Synthesis of biotin-labeled cRNA and subsequent fragmentation were performed by the use of the IVT labeling kit (Affymetrix, Santa Clara, CA, USA). The cRNA yield was determined spectrophotometrically at 260 nm. Fragmented cRNA was stored at -80C until hybridization.
| | Sample_hyb_protocol | According to the manufacturer's instructions.
| | Sample_scan_protocol | According to the manufacturer's instructions.
| | Sample_data_processing | All CEL files in the series were processed using RMA in R using justRMA with default parameters.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Paul,,Pavlidis
| | Sample_contact_email | paul@chibi.ubc.ca
| | Sample_contact_department | Centre for High-Throughput Biology / Psychiatry
| | Sample_contact_institute | University of British Columbia
| | Sample_contact_address | 177 Michael Smith Laboratories 2185 East Mall
| | Sample_contact_city | Vancouver
| | Sample_contact_state | British Columbia
| | Sample_contact_zip/postal_code | V6T 1Z4
| | Sample_contact_country | Canada
| | Sample_contact_web_link | http://www.chibi.ubc.ca/faculty/pavlidis
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM155nnn/GSM155466/suppl/GSM155466.CEL.gz
| | Sample_series_id | GSE6751
| | Sample_data_row_count | 54675
| | |
|
GSM155467 | GPL570 |
|
Patient 29, time point 1
|
Patient 29 PBMC, collected at time point 1
|
Time: one week prior to commencement of periodontal therapy
Tissue: Peripheral blood monocytes
Phenotype: severe periodontitis
|
Patients were recruited among the ones seeking treatment at the clinic for post-doctoral Periodontics, Columbia University College of Dental Medicine. To be eligible for enrollment, patients had to be diagnosed with severe periodontitis, with radiographic evidence of bone loss extending to greater or equal to 30% of the tooth length at several teeth. Additional inclusion criteria required: age greater or equal to 18 years; presence of greater or equal to 2 teeth/quadrant with a pocket depth of greater or equal to 6 mm and concomitant attachment loss of greater or equal to 3 mm; a minimum of 20 teeth present; no prior periodontal therapy; no systemic conditions or genetic disorders that entail the diagnosis of periodontitis as a manifestation of systemic diseases; no use of systemic antibiotics or regular use of anti-inflammatory drugs for the preceding 6-month period; no diabetes mellitus; no current use of tobacco products or of nicotine replacement medication; not currently pregnant. A total of 15 subjects, 7 male and 8 female, were enrolled. All participants were informed about the scope and procedures of the study and informed consent was obtained.
|
| Sample_geo_accession | GSM155467
| | Sample_status | Public on Dec 31 2007
| | Sample_submission_date | Jan 16 2007
| | Sample_last_update_date | Jan 16 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Fifty ml of blood were obtained by venipucture and collected in Vacutainer cell preparation tubes (Beckton-Dickinson, NJ, USA) with sodium heparin, and were used to harvest peripheral blood mononuclear cells (PBMCs). A 1:1 dilution with PBS was made and the diluted blood sample was centrifuged at 1,000 g in Ficoll tubes (Sigma Accuspin, St. Louis, MO). After washing and counting of the cells in a phase hemacytometer (Hauser Scientific, Horsham, PA), PBMCs were re-suspended in 80 microlitres of MACS buffer (PBS pH 7.2, 0.5% BSA and 2 mM EDTA) and incubated on ice with 20 microlitres of CD14 microbeads (Miltenyi Biotec, Auburn CA) per 107 total cells for 15 minutes. After washings, the cell suspension was applied to a MACS LS separation column (Miltenyi Biotec) placed in the magnetic field of a MACS separator (Miltenyi Biotec). Thereafter, the column was removed from the separator and CD14 positive cells were collected by washings in MACS buffer.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | CD14 positive cells were vigorously pipetted in Trizol (Invitrogen Life Technologies, Carlsbad, CA, USA). After incubation with chloroform and centrifugation at 12,000 g, RNA in the upper aqueous phase was precipitated by mixing with isopropyl alcohol, further centrifugation and washing in 75% ethanol. Further purification of the extracted RNA was achieved by the use of the RNeasy total RNA isolation kit (Qiagen, Valencia, CA, USA) according to the manufacturer.s instructions. The purified RNA was quantified spectrophotometrically. One hundred nanograms of total RNA were amplified and reverse transcribed using the GeneChip expression 3.-amplification two-cycle cDNA synthesis kit (Affymetrix, Santa Clara, CA, USA) and the MEGAscript T7 transcription kit (Ambion, Austin, TX, USA) according to the manufacturers. instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Synthesis of biotin-labeled cRNA and subsequent fragmentation were performed by the use of the IVT labeling kit (Affymetrix, Santa Clara, CA, USA). The cRNA yield was determined spectrophotometrically at 260 nm. Fragmented cRNA was stored at -80C until hybridization.
| | Sample_hyb_protocol | According to the manufacturer's instructions.
| | Sample_scan_protocol | According to the manufacturer's instructions.
| | Sample_data_processing | All CEL files in the series were processed using RMA in R using justRMA with default parameters.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Paul,,Pavlidis
| | Sample_contact_email | paul@chibi.ubc.ca
| | Sample_contact_department | Centre for High-Throughput Biology / Psychiatry
| | Sample_contact_institute | University of British Columbia
| | Sample_contact_address | 177 Michael Smith Laboratories 2185 East Mall
| | Sample_contact_city | Vancouver
| | Sample_contact_state | British Columbia
| | Sample_contact_zip/postal_code | V6T 1Z4
| | Sample_contact_country | Canada
| | Sample_contact_web_link | http://www.chibi.ubc.ca/faculty/pavlidis
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM155nnn/GSM155467/suppl/GSM155467.CEL.gz
| | Sample_series_id | GSE6751
| | Sample_data_row_count | 54675
| | |
|
GSM155468 | GPL570 |
|
Patient 29, time point 2
|
Patient 29 PBMC, collected at time point 2
|
Time: at commencement of periodontal therapy
Tissue: Peripheral blood monocytes
Phenotype: severe periodontitis
|
Patients were recruited among the ones seeking treatment at the clinic for post-doctoral Periodontics, Columbia University College of Dental Medicine. To be eligible for enrollment, patients had to be diagnosed with severe periodontitis, with radiographic evidence of bone loss extending to greater or equal to 30% of the tooth length at several teeth. Additional inclusion criteria required: age greater or equal to 18 years; presence of greater or equal to 2 teeth/quadrant with a pocket depth of greater or equal to 6 mm and concomitant attachment loss of greater or equal to 3 mm; a minimum of 20 teeth present; no prior periodontal therapy; no systemic conditions or genetic disorders that entail the diagnosis of periodontitis as a manifestation of systemic diseases; no use of systemic antibiotics or regular use of anti-inflammatory drugs for the preceding 6-month period; no diabetes mellitus; no current use of tobacco products or of nicotine replacement medication; not currently pregnant. A total of 15 subjects, 7 male and 8 female, were enrolled. All participants were informed about the scope and procedures of the study and informed consent was obtained.
|
| Sample_geo_accession | GSM155468
| | Sample_status | Public on Dec 31 2007
| | Sample_submission_date | Jan 16 2007
| | Sample_last_update_date | Jan 16 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Fifty ml of blood were obtained by venipucture and collected in Vacutainer cell preparation tubes (Beckton-Dickinson, NJ, USA) with sodium heparin, and were used to harvest peripheral blood mononuclear cells (PBMCs). A 1:1 dilution with PBS was made and the diluted blood sample was centrifuged at 1,000 g in Ficoll tubes (Sigma Accuspin, St. Louis, MO). After washing and counting of the cells in a phase hemacytometer (Hauser Scientific, Horsham, PA), PBMCs were re-suspended in 80 microlitres of MACS buffer (PBS pH 7.2, 0.5% BSA and 2 mM EDTA) and incubated on ice with 20 microlitres of CD14 microbeads (Miltenyi Biotec, Auburn CA) per 107 total cells for 15 minutes. After washings, the cell suspension was applied to a MACS LS separation column (Miltenyi Biotec) placed in the magnetic field of a MACS separator (Miltenyi Biotec). Thereafter, the column was removed from the separator and CD14 positive cells were collected by washings in MACS buffer.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | CD14 positive cells were vigorously pipetted in Trizol (Invitrogen Life Technologies, Carlsbad, CA, USA). After incubation with chloroform and centrifugation at 12,000 g, RNA in the upper aqueous phase was precipitated by mixing with isopropyl alcohol, further centrifugation and washing in 75% ethanol. Further purification of the extracted RNA was achieved by the use of the RNeasy total RNA isolation kit (Qiagen, Valencia, CA, USA) according to the manufacturer.s instructions. The purified RNA was quantified spectrophotometrically. One hundred nanograms of total RNA were amplified and reverse transcribed using the GeneChip expression 3.-amplification two-cycle cDNA synthesis kit (Affymetrix, Santa Clara, CA, USA) and the MEGAscript T7 transcription kit (Ambion, Austin, TX, USA) according to the manufacturers. instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Synthesis of biotin-labeled cRNA and subsequent fragmentation were performed by the use of the IVT labeling kit (Affymetrix, Santa Clara, CA, USA). The cRNA yield was determined spectrophotometrically at 260 nm. Fragmented cRNA was stored at -80C until hybridization.
| | Sample_hyb_protocol | According to the manufacturer's instructions.
| | Sample_scan_protocol | According to the manufacturer's instructions.
| | Sample_data_processing | All CEL files in the series were processed using RMA in R using justRMA with default parameters.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Paul,,Pavlidis
| | Sample_contact_email | paul@chibi.ubc.ca
| | Sample_contact_department | Centre for High-Throughput Biology / Psychiatry
| | Sample_contact_institute | University of British Columbia
| | Sample_contact_address | 177 Michael Smith Laboratories 2185 East Mall
| | Sample_contact_city | Vancouver
| | Sample_contact_state | British Columbia
| | Sample_contact_zip/postal_code | V6T 1Z4
| | Sample_contact_country | Canada
| | Sample_contact_web_link | http://www.chibi.ubc.ca/faculty/pavlidis
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM155nnn/GSM155468/suppl/GSM155468.CEL.gz
| | Sample_series_id | GSE6751
| | Sample_data_row_count | 54675
| | |
|
GSM155469 | GPL570 |
|
Patient 29, time point 3
|
Patient 29 PBMC, collected at time point 3
|
Time: six weeks after commencement of periodontal therapy (after treatment end)
Tissue: Peripheral blood monocytes
Phenotype: severe periodontitis
|
Patients were recruited among the ones seeking treatment at the clinic for post-doctoral Periodontics, Columbia University College of Dental Medicine. To be eligible for enrollment, patients had to be diagnosed with severe periodontitis, with radiographic evidence of bone loss extending to greater or equal to 30% of the tooth length at several teeth. Additional inclusion criteria required: age greater or equal to 18 years; presence of greater or equal to 2 teeth/quadrant with a pocket depth of greater or equal to 6 mm and concomitant attachment loss of greater or equal to 3 mm; a minimum of 20 teeth present; no prior periodontal therapy; no systemic conditions or genetic disorders that entail the diagnosis of periodontitis as a manifestation of systemic diseases; no use of systemic antibiotics or regular use of anti-inflammatory drugs for the preceding 6-month period; no diabetes mellitus; no current use of tobacco products or of nicotine replacement medication; not currently pregnant. A total of 15 subjects, 7 male and 8 female, were enrolled. All participants were informed about the scope and procedures of the study and informed consent was obtained.
|
| Sample_geo_accession | GSM155469
| | Sample_status | Public on Dec 31 2007
| | Sample_submission_date | Jan 16 2007
| | Sample_last_update_date | Jan 16 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Fifty ml of blood were obtained by venipucture and collected in Vacutainer cell preparation tubes (Beckton-Dickinson, NJ, USA) with sodium heparin, and were used to harvest peripheral blood mononuclear cells (PBMCs). A 1:1 dilution with PBS was made and the diluted blood sample was centrifuged at 1,000 g in Ficoll tubes (Sigma Accuspin, St. Louis, MO). After washing and counting of the cells in a phase hemacytometer (Hauser Scientific, Horsham, PA), PBMCs were re-suspended in 80 microlitres of MACS buffer (PBS pH 7.2, 0.5% BSA and 2 mM EDTA) and incubated on ice with 20 microlitres of CD14 microbeads (Miltenyi Biotec, Auburn CA) per 107 total cells for 15 minutes. After washings, the cell suspension was applied to a MACS LS separation column (Miltenyi Biotec) placed in the magnetic field of a MACS separator (Miltenyi Biotec). Thereafter, the column was removed from the separator and CD14 positive cells were collected by washings in MACS buffer.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | CD14 positive cells were vigorously pipetted in Trizol (Invitrogen Life Technologies, Carlsbad, CA, USA). After incubation with chloroform and centrifugation at 12,000 g, RNA in the upper aqueous phase was precipitated by mixing with isopropyl alcohol, further centrifugation and washing in 75% ethanol. Further purification of the extracted RNA was achieved by the use of the RNeasy total RNA isolation kit (Qiagen, Valencia, CA, USA) according to the manufacturer.s instructions. The purified RNA was quantified spectrophotometrically. One hundred nanograms of total RNA were amplified and reverse transcribed using the GeneChip expression 3.-amplification two-cycle cDNA synthesis kit (Affymetrix, Santa Clara, CA, USA) and the MEGAscript T7 transcription kit (Ambion, Austin, TX, USA) according to the manufacturers. instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Synthesis of biotin-labeled cRNA and subsequent fragmentation were performed by the use of the IVT labeling kit (Affymetrix, Santa Clara, CA, USA). The cRNA yield was determined spectrophotometrically at 260 nm. Fragmented cRNA was stored at -80C until hybridization.
| | Sample_hyb_protocol | According to the manufacturer's instructions.
| | Sample_scan_protocol | According to the manufacturer's instructions.
| | Sample_data_processing | All CEL files in the series were processed using RMA in R using justRMA with default parameters.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Paul,,Pavlidis
| | Sample_contact_email | paul@chibi.ubc.ca
| | Sample_contact_department | Centre for High-Throughput Biology / Psychiatry
| | Sample_contact_institute | University of British Columbia
| | Sample_contact_address | 177 Michael Smith Laboratories 2185 East Mall
| | Sample_contact_city | Vancouver
| | Sample_contact_state | British Columbia
| | Sample_contact_zip/postal_code | V6T 1Z4
| | Sample_contact_country | Canada
| | Sample_contact_web_link | http://www.chibi.ubc.ca/faculty/pavlidis
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM155nnn/GSM155469/suppl/GSM155469.CEL.gz
| | Sample_series_id | GSE6751
| | Sample_data_row_count | 54675
| | |
|
GSM155470 | GPL570 |
|
Patient 29, time point 4
|
Patient 29 PBMC, collected at time point 4
|
Time: ten weeks after prior to commencement of periodontal therapy (four weeks after treatment end)
Tissue: Peripheral blood monocytes
Phenotype: severe periodontitis
|
Patients were recruited among the ones seeking treatment at the clinic for post-doctoral Periodontics, Columbia University College of Dental Medicine. To be eligible for enrollment, patients had to be diagnosed with severe periodontitis, with radiographic evidence of bone loss extending to greater or equal to 30% of the tooth length at several teeth. Additional inclusion criteria required: age greater or equal to 18 years; presence of greater or equal to 2 teeth/quadrant with a pocket depth of greater or equal to 6 mm and concomitant attachment loss of greater or equal to 3 mm; a minimum of 20 teeth present; no prior periodontal therapy; no systemic conditions or genetic disorders that entail the diagnosis of periodontitis as a manifestation of systemic diseases; no use of systemic antibiotics or regular use of anti-inflammatory drugs for the preceding 6-month period; no diabetes mellitus; no current use of tobacco products or of nicotine replacement medication; not currently pregnant. A total of 15 subjects, 7 male and 8 female, were enrolled. All participants were informed about the scope and procedures of the study and informed consent was obtained.
|
| Sample_geo_accession | GSM155470
| | Sample_status | Public on Dec 31 2007
| | Sample_submission_date | Jan 16 2007
| | Sample_last_update_date | Jan 16 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Fifty ml of blood were obtained by venipucture and collected in Vacutainer cell preparation tubes (Beckton-Dickinson, NJ, USA) with sodium heparin, and were used to harvest peripheral blood mononuclear cells (PBMCs). A 1:1 dilution with PBS was made and the diluted blood sample was centrifuged at 1,000 g in Ficoll tubes (Sigma Accuspin, St. Louis, MO). After washing and counting of the cells in a phase hemacytometer (Hauser Scientific, Horsham, PA), PBMCs were re-suspended in 80 microlitres of MACS buffer (PBS pH 7.2, 0.5% BSA and 2 mM EDTA) and incubated on ice with 20 microlitres of CD14 microbeads (Miltenyi Biotec, Auburn CA) per 107 total cells for 15 minutes. After washings, the cell suspension was applied to a MACS LS separation column (Miltenyi Biotec) placed in the magnetic field of a MACS separator (Miltenyi Biotec). Thereafter, the column was removed from the separator and CD14 positive cells were collected by washings in MACS buffer.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | CD14 positive cells were vigorously pipetted in Trizol (Invitrogen Life Technologies, Carlsbad, CA, USA). After incubation with chloroform and centrifugation at 12,000 g, RNA in the upper aqueous phase was precipitated by mixing with isopropyl alcohol, further centrifugation and washing in 75% ethanol. Further purification of the extracted RNA was achieved by the use of the RNeasy total RNA isolation kit (Qiagen, Valencia, CA, USA) according to the manufacturer.s instructions. The purified RNA was quantified spectrophotometrically. One hundred nanograms of total RNA were amplified and reverse transcribed using the GeneChip expression 3.-amplification two-cycle cDNA synthesis kit (Affymetrix, Santa Clara, CA, USA) and the MEGAscript T7 transcription kit (Ambion, Austin, TX, USA) according to the manufacturers. instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Synthesis of biotin-labeled cRNA and subsequent fragmentation were performed by the use of the IVT labeling kit (Affymetrix, Santa Clara, CA, USA). The cRNA yield was determined spectrophotometrically at 260 nm. Fragmented cRNA was stored at -80C until hybridization.
| | Sample_hyb_protocol | According to the manufacturer's instructions.
| | Sample_scan_protocol | According to the manufacturer's instructions.
| | Sample_data_processing | All CEL files in the series were processed using RMA in R using justRMA with default parameters.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Paul,,Pavlidis
| | Sample_contact_email | paul@chibi.ubc.ca
| | Sample_contact_department | Centre for High-Throughput Biology / Psychiatry
| | Sample_contact_institute | University of British Columbia
| | Sample_contact_address | 177 Michael Smith Laboratories 2185 East Mall
| | Sample_contact_city | Vancouver
| | Sample_contact_state | British Columbia
| | Sample_contact_zip/postal_code | V6T 1Z4
| | Sample_contact_country | Canada
| | Sample_contact_web_link | http://www.chibi.ubc.ca/faculty/pavlidis
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM155nnn/GSM155470/suppl/GSM155470.CEL.gz
| | Sample_series_id | GSE6751
| | Sample_data_row_count | 54675
| | |
|
GSM155471 | GPL570 |
|
Patient 32, time point 1
|
Patient 32 PBMC, collected at time point 1
|
Time: one week prior to commencement of periodontal therapy
Tissue: Peripheral blood monocytes
Phenotype: severe periodontitis
|
Patients were recruited among the ones seeking treatment at the clinic for post-doctoral Periodontics, Columbia University College of Dental Medicine. To be eligible for enrollment, patients had to be diagnosed with severe periodontitis, with radiographic evidence of bone loss extending to greater or equal to 30% of the tooth length at several teeth. Additional inclusion criteria required: age greater or equal to 18 years; presence of greater or equal to 2 teeth/quadrant with a pocket depth of greater or equal to 6 mm and concomitant attachment loss of greater or equal to 3 mm; a minimum of 20 teeth present; no prior periodontal therapy; no systemic conditions or genetic disorders that entail the diagnosis of periodontitis as a manifestation of systemic diseases; no use of systemic antibiotics or regular use of anti-inflammatory drugs for the preceding 6-month period; no diabetes mellitus; no current use of tobacco products or of nicotine replacement medication; not currently pregnant. A total of 15 subjects, 7 male and 8 female, were enrolled. All participants were informed about the scope and procedures of the study and informed consent was obtained.
|
| Sample_geo_accession | GSM155471
| | Sample_status | Public on Dec 31 2007
| | Sample_submission_date | Jan 16 2007
| | Sample_last_update_date | Jan 16 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Fifty ml of blood were obtained by venipucture and collected in Vacutainer cell preparation tubes (Beckton-Dickinson, NJ, USA) with sodium heparin, and were used to harvest peripheral blood mononuclear cells (PBMCs). A 1:1 dilution with PBS was made and the diluted blood sample was centrifuged at 1,000 g in Ficoll tubes (Sigma Accuspin, St. Louis, MO). After washing and counting of the cells in a phase hemacytometer (Hauser Scientific, Horsham, PA), PBMCs were re-suspended in 80 microlitres of MACS buffer (PBS pH 7.2, 0.5% BSA and 2 mM EDTA) and incubated on ice with 20 microlitres of CD14 microbeads (Miltenyi Biotec, Auburn CA) per 107 total cells for 15 minutes. After washings, the cell suspension was applied to a MACS LS separation column (Miltenyi Biotec) placed in the magnetic field of a MACS separator (Miltenyi Biotec). Thereafter, the column was removed from the separator and CD14 positive cells were collected by washings in MACS buffer.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | CD14 positive cells were vigorously pipetted in Trizol (Invitrogen Life Technologies, Carlsbad, CA, USA). After incubation with chloroform and centrifugation at 12,000 g, RNA in the upper aqueous phase was precipitated by mixing with isopropyl alcohol, further centrifugation and washing in 75% ethanol. Further purification of the extracted RNA was achieved by the use of the RNeasy total RNA isolation kit (Qiagen, Valencia, CA, USA) according to the manufacturer.s instructions. The purified RNA was quantified spectrophotometrically. One hundred nanograms of total RNA were amplified and reverse transcribed using the GeneChip expression 3.-amplification two-cycle cDNA synthesis kit (Affymetrix, Santa Clara, CA, USA) and the MEGAscript T7 transcription kit (Ambion, Austin, TX, USA) according to the manufacturers. instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Synthesis of biotin-labeled cRNA and subsequent fragmentation were performed by the use of the IVT labeling kit (Affymetrix, Santa Clara, CA, USA). The cRNA yield was determined spectrophotometrically at 260 nm. Fragmented cRNA was stored at -80C until hybridization.
| | Sample_hyb_protocol | According to the manufacturer's instructions.
| | Sample_scan_protocol | According to the manufacturer's instructions.
| | Sample_data_processing | All CEL files in the series were processed using RMA in R using justRMA with default parameters.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Paul,,Pavlidis
| | Sample_contact_email | paul@chibi.ubc.ca
| | Sample_contact_department | Centre for High-Throughput Biology / Psychiatry
| | Sample_contact_institute | University of British Columbia
| | Sample_contact_address | 177 Michael Smith Laboratories 2185 East Mall
| | Sample_contact_city | Vancouver
| | Sample_contact_state | British Columbia
| | Sample_contact_zip/postal_code | V6T 1Z4
| | Sample_contact_country | Canada
| | Sample_contact_web_link | http://www.chibi.ubc.ca/faculty/pavlidis
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM155nnn/GSM155471/suppl/GSM155471.CEL.gz
| | Sample_series_id | GSE6751
| | Sample_data_row_count | 54675
| | |
|
GSM155472 | GPL570 |
|
Patient 32, time point 2
|
Patient 32 PBMC, collected at time point 2
|
Time: at commencement of periodontal therapy
Tissue: Peripheral blood monocytes
Phenotype: severe periodontitis
|
Patients were recruited among the ones seeking treatment at the clinic for post-doctoral Periodontics, Columbia University College of Dental Medicine. To be eligible for enrollment, patients had to be diagnosed with severe periodontitis, with radiographic evidence of bone loss extending to greater or equal to 30% of the tooth length at several teeth. Additional inclusion criteria required: age greater or equal to 18 years; presence of greater or equal to 2 teeth/quadrant with a pocket depth of greater or equal to 6 mm and concomitant attachment loss of greater or equal to 3 mm; a minimum of 20 teeth present; no prior periodontal therapy; no systemic conditions or genetic disorders that entail the diagnosis of periodontitis as a manifestation of systemic diseases; no use of systemic antibiotics or regular use of anti-inflammatory drugs for the preceding 6-month period; no diabetes mellitus; no current use of tobacco products or of nicotine replacement medication; not currently pregnant. A total of 15 subjects, 7 male and 8 female, were enrolled. All participants were informed about the scope and procedures of the study and informed consent was obtained.
|
| Sample_geo_accession | GSM155472
| | Sample_status | Public on Dec 31 2007
| | Sample_submission_date | Jan 16 2007
| | Sample_last_update_date | Jan 16 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Fifty ml of blood were obtained by venipucture and collected in Vacutainer cell preparation tubes (Beckton-Dickinson, NJ, USA) with sodium heparin, and were used to harvest peripheral blood mononuclear cells (PBMCs). A 1:1 dilution with PBS was made and the diluted blood sample was centrifuged at 1,000 g in Ficoll tubes (Sigma Accuspin, St. Louis, MO). After washing and counting of the cells in a phase hemacytometer (Hauser Scientific, Horsham, PA), PBMCs were re-suspended in 80 microlitres of MACS buffer (PBS pH 7.2, 0.5% BSA and 2 mM EDTA) and incubated on ice with 20 microlitres of CD14 microbeads (Miltenyi Biotec, Auburn CA) per 107 total cells for 15 minutes. After washings, the cell suspension was applied to a MACS LS separation column (Miltenyi Biotec) placed in the magnetic field of a MACS separator (Miltenyi Biotec). Thereafter, the column was removed from the separator and CD14 positive cells were collected by washings in MACS buffer.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | CD14 positive cells were vigorously pipetted in Trizol (Invitrogen Life Technologies, Carlsbad, CA, USA). After incubation with chloroform and centrifugation at 12,000 g, RNA in the upper aqueous phase was precipitated by mixing with isopropyl alcohol, further centrifugation and washing in 75% ethanol. Further purification of the extracted RNA was achieved by the use of the RNeasy total RNA isolation kit (Qiagen, Valencia, CA, USA) according to the manufacturer.s instructions. The purified RNA was quantified spectrophotometrically. One hundred nanograms of total RNA were amplified and reverse transcribed using the GeneChip expression 3.-amplification two-cycle cDNA synthesis kit (Affymetrix, Santa Clara, CA, USA) and the MEGAscript T7 transcription kit (Ambion, Austin, TX, USA) according to the manufacturers. instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Synthesis of biotin-labeled cRNA and subsequent fragmentation were performed by the use of the IVT labeling kit (Affymetrix, Santa Clara, CA, USA). The cRNA yield was determined spectrophotometrically at 260 nm. Fragmented cRNA was stored at -80C until hybridization.
| | Sample_hyb_protocol | According to the manufacturer's instructions.
| | Sample_scan_protocol | According to the manufacturer's instructions.
| | Sample_data_processing | All CEL files in the series were processed using RMA in R using justRMA with default parameters.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Paul,,Pavlidis
| | Sample_contact_email | paul@chibi.ubc.ca
| | Sample_contact_department | Centre for High-Throughput Biology / Psychiatry
| | Sample_contact_institute | University of British Columbia
| | Sample_contact_address | 177 Michael Smith Laboratories 2185 East Mall
| | Sample_contact_city | Vancouver
| | Sample_contact_state | British Columbia
| | Sample_contact_zip/postal_code | V6T 1Z4
| | Sample_contact_country | Canada
| | Sample_contact_web_link | http://www.chibi.ubc.ca/faculty/pavlidis
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM155nnn/GSM155472/suppl/GSM155472.CEL.gz
| | Sample_series_id | GSE6751
| | Sample_data_row_count | 54675
| | |
|
GSM155473 | GPL570 |
|
Patient 32, time point 3
|
Patient 32 PBMC, collected at time point 3
|
Time: six weeks after commencement of periodontal therapy (after treatment end)
Tissue: Peripheral blood monocytes
Phenotype: severe periodontitis
|
Patients were recruited among the ones seeking treatment at the clinic for post-doctoral Periodontics, Columbia University College of Dental Medicine. To be eligible for enrollment, patients had to be diagnosed with severe periodontitis, with radiographic evidence of bone loss extending to greater or equal to 30% of the tooth length at several teeth. Additional inclusion criteria required: age greater or equal to 18 years; presence of greater or equal to 2 teeth/quadrant with a pocket depth of greater or equal to 6 mm and concomitant attachment loss of greater or equal to 3 mm; a minimum of 20 teeth present; no prior periodontal therapy; no systemic conditions or genetic disorders that entail the diagnosis of periodontitis as a manifestation of systemic diseases; no use of systemic antibiotics or regular use of anti-inflammatory drugs for the preceding 6-month period; no diabetes mellitus; no current use of tobacco products or of nicotine replacement medication; not currently pregnant. A total of 15 subjects, 7 male and 8 female, were enrolled. All participants were informed about the scope and procedures of the study and informed consent was obtained.
|
| Sample_geo_accession | GSM155473
| | Sample_status | Public on Dec 31 2007
| | Sample_submission_date | Jan 16 2007
| | Sample_last_update_date | Jan 16 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Fifty ml of blood were obtained by venipucture and collected in Vacutainer cell preparation tubes (Beckton-Dickinson, NJ, USA) with sodium heparin, and were used to harvest peripheral blood mononuclear cells (PBMCs). A 1:1 dilution with PBS was made and the diluted blood sample was centrifuged at 1,000 g in Ficoll tubes (Sigma Accuspin, St. Louis, MO). After washing and counting of the cells in a phase hemacytometer (Hauser Scientific, Horsham, PA), PBMCs were re-suspended in 80 microlitres of MACS buffer (PBS pH 7.2, 0.5% BSA and 2 mM EDTA) and incubated on ice with 20 microlitres of CD14 microbeads (Miltenyi Biotec, Auburn CA) per 107 total cells for 15 minutes. After washings, the cell suspension was applied to a MACS LS separation column (Miltenyi Biotec) placed in the magnetic field of a MACS separator (Miltenyi Biotec). Thereafter, the column was removed from the separator and CD14 positive cells were collected by washings in MACS buffer.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | CD14 positive cells were vigorously pipetted in Trizol (Invitrogen Life Technologies, Carlsbad, CA, USA). After incubation with chloroform and centrifugation at 12,000 g, RNA in the upper aqueous phase was precipitated by mixing with isopropyl alcohol, further centrifugation and washing in 75% ethanol. Further purification of the extracted RNA was achieved by the use of the RNeasy total RNA isolation kit (Qiagen, Valencia, CA, USA) according to the manufacturer.s instructions. The purified RNA was quantified spectrophotometrically. One hundred nanograms of total RNA were amplified and reverse transcribed using the GeneChip expression 3.-amplification two-cycle cDNA synthesis kit (Affymetrix, Santa Clara, CA, USA) and the MEGAscript T7 transcription kit (Ambion, Austin, TX, USA) according to the manufacturers. instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Synthesis of biotin-labeled cRNA and subsequent fragmentation were performed by the use of the IVT labeling kit (Affymetrix, Santa Clara, CA, USA). The cRNA yield was determined spectrophotometrically at 260 nm. Fragmented cRNA was stored at -80C until hybridization.
| | Sample_hyb_protocol | According to the manufacturer's instructions.
| | Sample_scan_protocol | According to the manufacturer's instructions.
| | Sample_data_processing | All CEL files in the series were processed using RMA in R using justRMA with default parameters.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Paul,,Pavlidis
| | Sample_contact_email | paul@chibi.ubc.ca
| | Sample_contact_department | Centre for High-Throughput Biology / Psychiatry
| | Sample_contact_institute | University of British Columbia
| | Sample_contact_address | 177 Michael Smith Laboratories 2185 East Mall
| | Sample_contact_city | Vancouver
| | Sample_contact_state | British Columbia
| | Sample_contact_zip/postal_code | V6T 1Z4
| | Sample_contact_country | Canada
| | Sample_contact_web_link | http://www.chibi.ubc.ca/faculty/pavlidis
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM155nnn/GSM155473/suppl/GSM155473.CEL.gz
| | Sample_series_id | GSE6751
| | Sample_data_row_count | 54675
| | |
|
GSM155474 | GPL570 |
|
Patient 32, time point 4
|
Patient 32 PBMC, collected at time point 4
|
Time: ten weeks after prior to commencement of periodontal therapy (four weeks after treatment end)
Tissue: Peripheral blood monocytes
Phenotype: severe periodontitis
|
Patients were recruited among the ones seeking treatment at the clinic for post-doctoral Periodontics, Columbia University College of Dental Medicine. To be eligible for enrollment, patients had to be diagnosed with severe periodontitis, with radiographic evidence of bone loss extending to greater or equal to 30% of the tooth length at several teeth. Additional inclusion criteria required: age greater or equal to 18 years; presence of greater or equal to 2 teeth/quadrant with a pocket depth of greater or equal to 6 mm and concomitant attachment loss of greater or equal to 3 mm; a minimum of 20 teeth present; no prior periodontal therapy; no systemic conditions or genetic disorders that entail the diagnosis of periodontitis as a manifestation of systemic diseases; no use of systemic antibiotics or regular use of anti-inflammatory drugs for the preceding 6-month period; no diabetes mellitus; no current use of tobacco products or of nicotine replacement medication; not currently pregnant. A total of 15 subjects, 7 male and 8 female, were enrolled. All participants were informed about the scope and procedures of the study and informed consent was obtained.
|
| Sample_geo_accession | GSM155474
| | Sample_status | Public on Dec 31 2007
| | Sample_submission_date | Jan 16 2007
| | Sample_last_update_date | Jan 16 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Fifty ml of blood were obtained by venipucture and collected in Vacutainer cell preparation tubes (Beckton-Dickinson, NJ, USA) with sodium heparin, and were used to harvest peripheral blood mononuclear cells (PBMCs). A 1:1 dilution with PBS was made and the diluted blood sample was centrifuged at 1,000 g in Ficoll tubes (Sigma Accuspin, St. Louis, MO). After washing and counting of the cells in a phase hemacytometer (Hauser Scientific, Horsham, PA), PBMCs were re-suspended in 80 microlitres of MACS buffer (PBS pH 7.2, 0.5% BSA and 2 mM EDTA) and incubated on ice with 20 microlitres of CD14 microbeads (Miltenyi Biotec, Auburn CA) per 107 total cells for 15 minutes. After washings, the cell suspension was applied to a MACS LS separation column (Miltenyi Biotec) placed in the magnetic field of a MACS separator (Miltenyi Biotec). Thereafter, the column was removed from the separator and CD14 positive cells were collected by washings in MACS buffer.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | CD14 positive cells were vigorously pipetted in Trizol (Invitrogen Life Technologies, Carlsbad, CA, USA). After incubation with chloroform and centrifugation at 12,000 g, RNA in the upper aqueous phase was precipitated by mixing with isopropyl alcohol, further centrifugation and washing in 75% ethanol. Further purification of the extracted RNA was achieved by the use of the RNeasy total RNA isolation kit (Qiagen, Valencia, CA, USA) according to the manufacturer.s instructions. The purified RNA was quantified spectrophotometrically. One hundred nanograms of total RNA were amplified and reverse transcribed using the GeneChip expression 3.-amplification two-cycle cDNA synthesis kit (Affymetrix, Santa Clara, CA, USA) and the MEGAscript T7 transcription kit (Ambion, Austin, TX, USA) according to the manufacturers. instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Synthesis of biotin-labeled cRNA and subsequent fragmentation were performed by the use of the IVT labeling kit (Affymetrix, Santa Clara, CA, USA). The cRNA yield was determined spectrophotometrically at 260 nm. Fragmented cRNA was stored at -80C until hybridization.
| | Sample_hyb_protocol | According to the manufacturer's instructions.
| | Sample_scan_protocol | According to the manufacturer's instructions.
| | Sample_data_processing | All CEL files in the series were processed using RMA in R using justRMA with default parameters.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Paul,,Pavlidis
| | Sample_contact_email | paul@chibi.ubc.ca
| | Sample_contact_department | Centre for High-Throughput Biology / Psychiatry
| | Sample_contact_institute | University of British Columbia
| | Sample_contact_address | 177 Michael Smith Laboratories 2185 East Mall
| | Sample_contact_city | Vancouver
| | Sample_contact_state | British Columbia
| | Sample_contact_zip/postal_code | V6T 1Z4
| | Sample_contact_country | Canada
| | Sample_contact_web_link | http://www.chibi.ubc.ca/faculty/pavlidis
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM155nnn/GSM155474/suppl/GSM155474.CEL.gz
| | Sample_series_id | GSE6751
| | Sample_data_row_count | 54675
| | |
|
GSM155475 | GPL570 |
|
Patient 35, time point 1
|
Patient 35 PBMC, collected at time point 1
|
Time: one week prior to commencement of periodontal therapy
Tissue: Peripheral blood monocytes
Phenotype: severe periodontitis
|
Patients were recruited among the ones seeking treatment at the clinic for post-doctoral Periodontics, Columbia University College of Dental Medicine. To be eligible for enrollment, patients had to be diagnosed with severe periodontitis, with radiographic evidence of bone loss extending to greater or equal to 30% of the tooth length at several teeth. Additional inclusion criteria required: age greater or equal to 18 years; presence of greater or equal to 2 teeth/quadrant with a pocket depth of greater or equal to 6 mm and concomitant attachment loss of greater or equal to 3 mm; a minimum of 20 teeth present; no prior periodontal therapy; no systemic conditions or genetic disorders that entail the diagnosis of periodontitis as a manifestation of systemic diseases; no use of systemic antibiotics or regular use of anti-inflammatory drugs for the preceding 6-month period; no diabetes mellitus; no current use of tobacco products or of nicotine replacement medication; not currently pregnant. A total of 15 subjects, 7 male and 8 female, were enrolled. All participants were informed about the scope and procedures of the study and informed consent was obtained.
|
| Sample_geo_accession | GSM155475
| | Sample_status | Public on Dec 31 2007
| | Sample_submission_date | Jan 16 2007
| | Sample_last_update_date | Jan 16 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Fifty ml of blood were obtained by venipucture and collected in Vacutainer cell preparation tubes (Beckton-Dickinson, NJ, USA) with sodium heparin, and were used to harvest peripheral blood mononuclear cells (PBMCs). A 1:1 dilution with PBS was made and the diluted blood sample was centrifuged at 1,000 g in Ficoll tubes (Sigma Accuspin, St. Louis, MO). After washing and counting of the cells in a phase hemacytometer (Hauser Scientific, Horsham, PA), PBMCs were re-suspended in 80 microlitres of MACS buffer (PBS pH 7.2, 0.5% BSA and 2 mM EDTA) and incubated on ice with 20 microlitres of CD14 microbeads (Miltenyi Biotec, Auburn CA) per 107 total cells for 15 minutes. After washings, the cell suspension was applied to a MACS LS separation column (Miltenyi Biotec) placed in the magnetic field of a MACS separator (Miltenyi Biotec). Thereafter, the column was removed from the separator and CD14 positive cells were collected by washings in MACS buffer.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | CD14 positive cells were vigorously pipetted in Trizol (Invitrogen Life Technologies, Carlsbad, CA, USA). After incubation with chloroform and centrifugation at 12,000 g, RNA in the upper aqueous phase was precipitated by mixing with isopropyl alcohol, further centrifugation and washing in 75% ethanol. Further purification of the extracted RNA was achieved by the use of the RNeasy total RNA isolation kit (Qiagen, Valencia, CA, USA) according to the manufacturer.s instructions. The purified RNA was quantified spectrophotometrically. One hundred nanograms of total RNA were amplified and reverse transcribed using the GeneChip expression 3.-amplification two-cycle cDNA synthesis kit (Affymetrix, Santa Clara, CA, USA) and the MEGAscript T7 transcription kit (Ambion, Austin, TX, USA) according to the manufacturers. instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Synthesis of biotin-labeled cRNA and subsequent fragmentation were performed by the use of the IVT labeling kit (Affymetrix, Santa Clara, CA, USA). The cRNA yield was determined spectrophotometrically at 260 nm. Fragmented cRNA was stored at -80C until hybridization.
| | Sample_hyb_protocol | According to the manufacturer's instructions.
| | Sample_scan_protocol | According to the manufacturer's instructions.
| | Sample_data_processing | All CEL files in the series were processed using RMA in R using justRMA with default parameters.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Paul,,Pavlidis
| | Sample_contact_email | paul@chibi.ubc.ca
| | Sample_contact_department | Centre for High-Throughput Biology / Psychiatry
| | Sample_contact_institute | University of British Columbia
| | Sample_contact_address | 177 Michael Smith Laboratories 2185 East Mall
| | Sample_contact_city | Vancouver
| | Sample_contact_state | British Columbia
| | Sample_contact_zip/postal_code | V6T 1Z4
| | Sample_contact_country | Canada
| | Sample_contact_web_link | http://www.chibi.ubc.ca/faculty/pavlidis
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM155nnn/GSM155475/suppl/GSM155475.CEL.gz
| | Sample_series_id | GSE6751
| | Sample_data_row_count | 54675
| | |
|
GSM155476 | GPL570 |
|
Patient 35, time point 2
|
Patient 35 PBMC, collected at time point 2
|
Time: at commencement of periodontal therapy
Tissue: Peripheral blood monocytes
Phenotype: severe periodontitis
|
Patients were recruited among the ones seeking treatment at the clinic for post-doctoral Periodontics, Columbia University College of Dental Medicine. To be eligible for enrollment, patients had to be diagnosed with severe periodontitis, with radiographic evidence of bone loss extending to greater or equal to 30% of the tooth length at several teeth. Additional inclusion criteria required: age greater or equal to 18 years; presence of greater or equal to 2 teeth/quadrant with a pocket depth of greater or equal to 6 mm and concomitant attachment loss of greater or equal to 3 mm; a minimum of 20 teeth present; no prior periodontal therapy; no systemic conditions or genetic disorders that entail the diagnosis of periodontitis as a manifestation of systemic diseases; no use of systemic antibiotics or regular use of anti-inflammatory drugs for the preceding 6-month period; no diabetes mellitus; no current use of tobacco products or of nicotine replacement medication; not currently pregnant. A total of 15 subjects, 7 male and 8 female, were enrolled. All participants were informed about the scope and procedures of the study and informed consent was obtained.
|
| Sample_geo_accession | GSM155476
| | Sample_status | Public on Dec 31 2007
| | Sample_submission_date | Jan 16 2007
| | Sample_last_update_date | Jan 16 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Fifty ml of blood were obtained by venipucture and collected in Vacutainer cell preparation tubes (Beckton-Dickinson, NJ, USA) with sodium heparin, and were used to harvest peripheral blood mononuclear cells (PBMCs). A 1:1 dilution with PBS was made and the diluted blood sample was centrifuged at 1,000 g in Ficoll tubes (Sigma Accuspin, St. Louis, MO). After washing and counting of the cells in a phase hemacytometer (Hauser Scientific, Horsham, PA), PBMCs were re-suspended in 80 microlitres of MACS buffer (PBS pH 7.2, 0.5% BSA and 2 mM EDTA) and incubated on ice with 20 microlitres of CD14 microbeads (Miltenyi Biotec, Auburn CA) per 107 total cells for 15 minutes. After washings, the cell suspension was applied to a MACS LS separation column (Miltenyi Biotec) placed in the magnetic field of a MACS separator (Miltenyi Biotec). Thereafter, the column was removed from the separator and CD14 positive cells were collected by washings in MACS buffer.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | CD14 positive cells were vigorously pipetted in Trizol (Invitrogen Life Technologies, Carlsbad, CA, USA). After incubation with chloroform and centrifugation at 12,000 g, RNA in the upper aqueous phase was precipitated by mixing with isopropyl alcohol, further centrifugation and washing in 75% ethanol. Further purification of the extracted RNA was achieved by the use of the RNeasy total RNA isolation kit (Qiagen, Valencia, CA, USA) according to the manufacturer.s instructions. The purified RNA was quantified spectrophotometrically. One hundred nanograms of total RNA were amplified and reverse transcribed using the GeneChip expression 3.-amplification two-cycle cDNA synthesis kit (Affymetrix, Santa Clara, CA, USA) and the MEGAscript T7 transcription kit (Ambion, Austin, TX, USA) according to the manufacturers. instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Synthesis of biotin-labeled cRNA and subsequent fragmentation were performed by the use of the IVT labeling kit (Affymetrix, Santa Clara, CA, USA). The cRNA yield was determined spectrophotometrically at 260 nm. Fragmented cRNA was stored at -80C until hybridization.
| | Sample_hyb_protocol | According to the manufacturer's instructions.
| | Sample_scan_protocol | According to the manufacturer's instructions.
| | Sample_data_processing | All CEL files in the series were processed using RMA in R using justRMA with default parameters.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Paul,,Pavlidis
| | Sample_contact_email | paul@chibi.ubc.ca
| | Sample_contact_department | Centre for High-Throughput Biology / Psychiatry
| | Sample_contact_institute | University of British Columbia
| | Sample_contact_address | 177 Michael Smith Laboratories 2185 East Mall
| | Sample_contact_city | Vancouver
| | Sample_contact_state | British Columbia
| | Sample_contact_zip/postal_code | V6T 1Z4
| | Sample_contact_country | Canada
| | Sample_contact_web_link | http://www.chibi.ubc.ca/faculty/pavlidis
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM155nnn/GSM155476/suppl/GSM155476.CEL.gz
| | Sample_series_id | GSE6751
| | Sample_data_row_count | 54675
| | |
|
GSM155477 | GPL570 |
|
Patient 35, time point 3
|
Patient 35 PBMC, collected at time point 3
|
Time: six weeks after commencement of periodontal therapy (after treatment end)
Tissue: Peripheral blood monocytes
Phenotype: severe periodontitis
|
Patients were recruited among the ones seeking treatment at the clinic for post-doctoral Periodontics, Columbia University College of Dental Medicine. To be eligible for enrollment, patients had to be diagnosed with severe periodontitis, with radiographic evidence of bone loss extending to greater or equal to 30% of the tooth length at several teeth. Additional inclusion criteria required: age greater or equal to 18 years; presence of greater or equal to 2 teeth/quadrant with a pocket depth of greater or equal to 6 mm and concomitant attachment loss of greater or equal to 3 mm; a minimum of 20 teeth present; no prior periodontal therapy; no systemic conditions or genetic disorders that entail the diagnosis of periodontitis as a manifestation of systemic diseases; no use of systemic antibiotics or regular use of anti-inflammatory drugs for the preceding 6-month period; no diabetes mellitus; no current use of tobacco products or of nicotine replacement medication; not currently pregnant. A total of 15 subjects, 7 male and 8 female, were enrolled. All participants were informed about the scope and procedures of the study and informed consent was obtained.
|
| Sample_geo_accession | GSM155477
| | Sample_status | Public on Dec 31 2007
| | Sample_submission_date | Jan 16 2007
| | Sample_last_update_date | Jan 16 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Fifty ml of blood were obtained by venipucture and collected in Vacutainer cell preparation tubes (Beckton-Dickinson, NJ, USA) with sodium heparin, and were used to harvest peripheral blood mononuclear cells (PBMCs). A 1:1 dilution with PBS was made and the diluted blood sample was centrifuged at 1,000 g in Ficoll tubes (Sigma Accuspin, St. Louis, MO). After washing and counting of the cells in a phase hemacytometer (Hauser Scientific, Horsham, PA), PBMCs were re-suspended in 80 microlitres of MACS buffer (PBS pH 7.2, 0.5% BSA and 2 mM EDTA) and incubated on ice with 20 microlitres of CD14 microbeads (Miltenyi Biotec, Auburn CA) per 107 total cells for 15 minutes. After washings, the cell suspension was applied to a MACS LS separation column (Miltenyi Biotec) placed in the magnetic field of a MACS separator (Miltenyi Biotec). Thereafter, the column was removed from the separator and CD14 positive cells were collected by washings in MACS buffer.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | CD14 positive cells were vigorously pipetted in Trizol (Invitrogen Life Technologies, Carlsbad, CA, USA). After incubation with chloroform and centrifugation at 12,000 g, RNA in the upper aqueous phase was precipitated by mixing with isopropyl alcohol, further centrifugation and washing in 75% ethanol. Further purification of the extracted RNA was achieved by the use of the RNeasy total RNA isolation kit (Qiagen, Valencia, CA, USA) according to the manufacturer.s instructions. The purified RNA was quantified spectrophotometrically. One hundred nanograms of total RNA were amplified and reverse transcribed using the GeneChip expression 3.-amplification two-cycle cDNA synthesis kit (Affymetrix, Santa Clara, CA, USA) and the MEGAscript T7 transcription kit (Ambion, Austin, TX, USA) according to the manufacturers. instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Synthesis of biotin-labeled cRNA and subsequent fragmentation were performed by the use of the IVT labeling kit (Affymetrix, Santa Clara, CA, USA). The cRNA yield was determined spectrophotometrically at 260 nm. Fragmented cRNA was stored at -80C until hybridization.
| | Sample_hyb_protocol | According to the manufacturer's instructions.
| | Sample_scan_protocol | According to the manufacturer's instructions.
| | Sample_data_processing | All CEL files in the series were processed using RMA in R using justRMA with default parameters.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Paul,,Pavlidis
| | Sample_contact_email | paul@chibi.ubc.ca
| | Sample_contact_department | Centre for High-Throughput Biology / Psychiatry
| | Sample_contact_institute | University of British Columbia
| | Sample_contact_address | 177 Michael Smith Laboratories 2185 East Mall
| | Sample_contact_city | Vancouver
| | Sample_contact_state | British Columbia
| | Sample_contact_zip/postal_code | V6T 1Z4
| | Sample_contact_country | Canada
| | Sample_contact_web_link | http://www.chibi.ubc.ca/faculty/pavlidis
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM155nnn/GSM155477/suppl/GSM155477.CEL.gz
| | Sample_series_id | GSE6751
| | Sample_data_row_count | 54675
| | |
|
GSM155478 | GPL570 |
|
Patient 35, time point 4
|
Patient 35 PBMC, collected at time point 4
|
Time: ten weeks after prior to commencement of periodontal therapy (four weeks after treatment end)
Tissue: Peripheral blood monocytes
Phenotype: severe periodontitis
|
Patients were recruited among the ones seeking treatment at the clinic for post-doctoral Periodontics, Columbia University College of Dental Medicine. To be eligible for enrollment, patients had to be diagnosed with severe periodontitis, with radiographic evidence of bone loss extending to greater or equal to 30% of the tooth length at several teeth. Additional inclusion criteria required: age greater or equal to 18 years; presence of greater or equal to 2 teeth/quadrant with a pocket depth of greater or equal to 6 mm and concomitant attachment loss of greater or equal to 3 mm; a minimum of 20 teeth present; no prior periodontal therapy; no systemic conditions or genetic disorders that entail the diagnosis of periodontitis as a manifestation of systemic diseases; no use of systemic antibiotics or regular use of anti-inflammatory drugs for the preceding 6-month period; no diabetes mellitus; no current use of tobacco products or of nicotine replacement medication; not currently pregnant. A total of 15 subjects, 7 male and 8 female, were enrolled. All participants were informed about the scope and procedures of the study and informed consent was obtained.
|
| Sample_geo_accession | GSM155478
| | Sample_status | Public on Dec 31 2007
| | Sample_submission_date | Jan 16 2007
| | Sample_last_update_date | Jan 16 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Fifty ml of blood were obtained by venipucture and collected in Vacutainer cell preparation tubes (Beckton-Dickinson, NJ, USA) with sodium heparin, and were used to harvest peripheral blood mononuclear cells (PBMCs). A 1:1 dilution with PBS was made and the diluted blood sample was centrifuged at 1,000 g in Ficoll tubes (Sigma Accuspin, St. Louis, MO). After washing and counting of the cells in a phase hemacytometer (Hauser Scientific, Horsham, PA), PBMCs were re-suspended in 80 microlitres of MACS buffer (PBS pH 7.2, 0.5% BSA and 2 mM EDTA) and incubated on ice with 20 microlitres of CD14 microbeads (Miltenyi Biotec, Auburn CA) per 107 total cells for 15 minutes. After washings, the cell suspension was applied to a MACS LS separation column (Miltenyi Biotec) placed in the magnetic field of a MACS separator (Miltenyi Biotec). Thereafter, the column was removed from the separator and CD14 positive cells were collected by washings in MACS buffer.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | CD14 positive cells were vigorously pipetted in Trizol (Invitrogen Life Technologies, Carlsbad, CA, USA). After incubation with chloroform and centrifugation at 12,000 g, RNA in the upper aqueous phase was precipitated by mixing with isopropyl alcohol, further centrifugation and washing in 75% ethanol. Further purification of the extracted RNA was achieved by the use of the RNeasy total RNA isolation kit (Qiagen, Valencia, CA, USA) according to the manufacturer.s instructions. The purified RNA was quantified spectrophotometrically. One hundred nanograms of total RNA were amplified and reverse transcribed using the GeneChip expression 3.-amplification two-cycle cDNA synthesis kit (Affymetrix, Santa Clara, CA, USA) and the MEGAscript T7 transcription kit (Ambion, Austin, TX, USA) according to the manufacturers. instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Synthesis of biotin-labeled cRNA and subsequent fragmentation were performed by the use of the IVT labeling kit (Affymetrix, Santa Clara, CA, USA). The cRNA yield was determined spectrophotometrically at 260 nm. Fragmented cRNA was stored at -80C until hybridization.
| | Sample_hyb_protocol | According to the manufacturer's instructions.
| | Sample_scan_protocol | According to the manufacturer's instructions.
| | Sample_data_processing | All CEL files in the series were processed using RMA in R using justRMA with default parameters.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Paul,,Pavlidis
| | Sample_contact_email | paul@chibi.ubc.ca
| | Sample_contact_department | Centre for High-Throughput Biology / Psychiatry
| | Sample_contact_institute | University of British Columbia
| | Sample_contact_address | 177 Michael Smith Laboratories 2185 East Mall
| | Sample_contact_city | Vancouver
| | Sample_contact_state | British Columbia
| | Sample_contact_zip/postal_code | V6T 1Z4
| | Sample_contact_country | Canada
| | Sample_contact_web_link | http://www.chibi.ubc.ca/faculty/pavlidis
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM155nnn/GSM155478/suppl/GSM155478.CEL.gz
| | Sample_series_id | GSE6751
| | Sample_data_row_count | 54675
| | |
|
GSM155479 | GPL570 |
|
Patient 36, time point 1
|
Patient 36 PBMC, collected at time point 1
|
Time: one week prior to commencement of periodontal therapy
Tissue: Peripheral blood monocytes
Phenotype: severe periodontitis
|
Patients were recruited among the ones seeking treatment at the clinic for post-doctoral Periodontics, Columbia University College of Dental Medicine. To be eligible for enrollment, patients had to be diagnosed with severe periodontitis, with radiographic evidence of bone loss extending to greater or equal to 30% of the tooth length at several teeth. Additional inclusion criteria required: age greater or equal to 18 years; presence of greater or equal to 2 teeth/quadrant with a pocket depth of greater or equal to 6 mm and concomitant attachment loss of greater or equal to 3 mm; a minimum of 20 teeth present; no prior periodontal therapy; no systemic conditions or genetic disorders that entail the diagnosis of periodontitis as a manifestation of systemic diseases; no use of systemic antibiotics or regular use of anti-inflammatory drugs for the preceding 6-month period; no diabetes mellitus; no current use of tobacco products or of nicotine replacement medication; not currently pregnant. A total of 15 subjects, 7 male and 8 female, were enrolled. All participants were informed about the scope and procedures of the study and informed consent was obtained.
|
| Sample_geo_accession | GSM155479
| | Sample_status | Public on Dec 31 2007
| | Sample_submission_date | Jan 16 2007
| | Sample_last_update_date | Jan 16 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Fifty ml of blood were obtained by venipucture and collected in Vacutainer cell preparation tubes (Beckton-Dickinson, NJ, USA) with sodium heparin, and were used to harvest peripheral blood mononuclear cells (PBMCs). A 1:1 dilution with PBS was made and the diluted blood sample was centrifuged at 1,000 g in Ficoll tubes (Sigma Accuspin, St. Louis, MO). After washing and counting of the cells in a phase hemacytometer (Hauser Scientific, Horsham, PA), PBMCs were re-suspended in 80 microlitres of MACS buffer (PBS pH 7.2, 0.5% BSA and 2 mM EDTA) and incubated on ice with 20 microlitres of CD14 microbeads (Miltenyi Biotec, Auburn CA) per 107 total cells for 15 minutes. After washings, the cell suspension was applied to a MACS LS separation column (Miltenyi Biotec) placed in the magnetic field of a MACS separator (Miltenyi Biotec). Thereafter, the column was removed from the separator and CD14 positive cells were collected by washings in MACS buffer.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | CD14 positive cells were vigorously pipetted in Trizol (Invitrogen Life Technologies, Carlsbad, CA, USA). After incubation with chloroform and centrifugation at 12,000 g, RNA in the upper aqueous phase was precipitated by mixing with isopropyl alcohol, further centrifugation and washing in 75% ethanol. Further purification of the extracted RNA was achieved by the use of the RNeasy total RNA isolation kit (Qiagen, Valencia, CA, USA) according to the manufacturer.s instructions. The purified RNA was quantified spectrophotometrically. One hundred nanograms of total RNA were amplified and reverse transcribed using the GeneChip expression 3.-amplification two-cycle cDNA synthesis kit (Affymetrix, Santa Clara, CA, USA) and the MEGAscript T7 transcription kit (Ambion, Austin, TX, USA) according to the manufacturers. instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Synthesis of biotin-labeled cRNA and subsequent fragmentation were performed by the use of the IVT labeling kit (Affymetrix, Santa Clara, CA, USA). The cRNA yield was determined spectrophotometrically at 260 nm. Fragmented cRNA was stored at -80C until hybridization.
| | Sample_hyb_protocol | According to the manufacturer's instructions.
| | Sample_scan_protocol | According to the manufacturer's instructions.
| | Sample_data_processing | All CEL files in the series were processed using RMA in R using justRMA with default parameters.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Paul,,Pavlidis
| | Sample_contact_email | paul@chibi.ubc.ca
| | Sample_contact_department | Centre for High-Throughput Biology / Psychiatry
| | Sample_contact_institute | University of British Columbia
| | Sample_contact_address | 177 Michael Smith Laboratories 2185 East Mall
| | Sample_contact_city | Vancouver
| | Sample_contact_state | British Columbia
| | Sample_contact_zip/postal_code | V6T 1Z4
| | Sample_contact_country | Canada
| | Sample_contact_web_link | http://www.chibi.ubc.ca/faculty/pavlidis
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM155nnn/GSM155479/suppl/GSM155479.CEL.gz
| | Sample_series_id | GSE6751
| | Sample_data_row_count | 54675
| | |
|
GSM155480 | GPL570 |
|
Patient 36, time point 2
|
Patient 36 PBMC, collected at time point 2
|
Time: at commencement of periodontal therapy
Tissue: Peripheral blood monocytes
Phenotype: severe periodontitis
|
Patients were recruited among the ones seeking treatment at the clinic for post-doctoral Periodontics, Columbia University College of Dental Medicine. To be eligible for enrollment, patients had to be diagnosed with severe periodontitis, with radiographic evidence of bone loss extending to greater or equal to 30% of the tooth length at several teeth. Additional inclusion criteria required: age greater or equal to 18 years; presence of greater or equal to 2 teeth/quadrant with a pocket depth of greater or equal to 6 mm and concomitant attachment loss of greater or equal to 3 mm; a minimum of 20 teeth present; no prior periodontal therapy; no systemic conditions or genetic disorders that entail the diagnosis of periodontitis as a manifestation of systemic diseases; no use of systemic antibiotics or regular use of anti-inflammatory drugs for the preceding 6-month period; no diabetes mellitus; no current use of tobacco products or of nicotine replacement medication; not currently pregnant. A total of 15 subjects, 7 male and 8 female, were enrolled. All participants were informed about the scope and procedures of the study and informed consent was obtained.
|
| Sample_geo_accession | GSM155480
| | Sample_status | Public on Dec 31 2007
| | Sample_submission_date | Jan 16 2007
| | Sample_last_update_date | Jan 16 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Fifty ml of blood were obtained by venipucture and collected in Vacutainer cell preparation tubes (Beckton-Dickinson, NJ, USA) with sodium heparin, and were used to harvest peripheral blood mononuclear cells (PBMCs). A 1:1 dilution with PBS was made and the diluted blood sample was centrifuged at 1,000 g in Ficoll tubes (Sigma Accuspin, St. Louis, MO). After washing and counting of the cells in a phase hemacytometer (Hauser Scientific, Horsham, PA), PBMCs were re-suspended in 80 microlitres of MACS buffer (PBS pH 7.2, 0.5% BSA and 2 mM EDTA) and incubated on ice with 20 microlitres of CD14 microbeads (Miltenyi Biotec, Auburn CA) per 107 total cells for 15 minutes. After washings, the cell suspension was applied to a MACS LS separation column (Miltenyi Biotec) placed in the magnetic field of a MACS separator (Miltenyi Biotec). Thereafter, the column was removed from the separator and CD14 positive cells were collected by washings in MACS buffer.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | CD14 positive cells were vigorously pipetted in Trizol (Invitrogen Life Technologies, Carlsbad, CA, USA). After incubation with chloroform and centrifugation at 12,000 g, RNA in the upper aqueous phase was precipitated by mixing with isopropyl alcohol, further centrifugation and washing in 75% ethanol. Further purification of the extracted RNA was achieved by the use of the RNeasy total RNA isolation kit (Qiagen, Valencia, CA, USA) according to the manufacturer.s instructions. The purified RNA was quantified spectrophotometrically. One hundred nanograms of total RNA were amplified and reverse transcribed using the GeneChip expression 3.-amplification two-cycle cDNA synthesis kit (Affymetrix, Santa Clara, CA, USA) and the MEGAscript T7 transcription kit (Ambion, Austin, TX, USA) according to the manufacturers. instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Synthesis of biotin-labeled cRNA and subsequent fragmentation were performed by the use of the IVT labeling kit (Affymetrix, Santa Clara, CA, USA). The cRNA yield was determined spectrophotometrically at 260 nm. Fragmented cRNA was stored at -80C until hybridization.
| | Sample_hyb_protocol | According to the manufacturer's instructions.
| | Sample_scan_protocol | According to the manufacturer's instructions.
| | Sample_data_processing | All CEL files in the series were processed using RMA in R using justRMA with default parameters.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Paul,,Pavlidis
| | Sample_contact_email | paul@chibi.ubc.ca
| | Sample_contact_department | Centre for High-Throughput Biology / Psychiatry
| | Sample_contact_institute | University of British Columbia
| | Sample_contact_address | 177 Michael Smith Laboratories 2185 East Mall
| | Sample_contact_city | Vancouver
| | Sample_contact_state | British Columbia
| | Sample_contact_zip/postal_code | V6T 1Z4
| | Sample_contact_country | Canada
| | Sample_contact_web_link | http://www.chibi.ubc.ca/faculty/pavlidis
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM155nnn/GSM155480/suppl/GSM155480.CEL.gz
| | Sample_series_id | GSE6751
| | Sample_data_row_count | 54675
| | |
|
GSM155481 | GPL570 |
|
Patient 36, time point 3
|
Patient 36 PBMC, collected at time point 3
|
Time: six weeks after commencement of periodontal therapy (after treatment end)
Tissue: Peripheral blood monocytes
Phenotype: severe periodontitis
|
Patients were recruited among the ones seeking treatment at the clinic for post-doctoral Periodontics, Columbia University College of Dental Medicine. To be eligible for enrollment, patients had to be diagnosed with severe periodontitis, with radiographic evidence of bone loss extending to greater or equal to 30% of the tooth length at several teeth. Additional inclusion criteria required: age greater or equal to 18 years; presence of greater or equal to 2 teeth/quadrant with a pocket depth of greater or equal to 6 mm and concomitant attachment loss of greater or equal to 3 mm; a minimum of 20 teeth present; no prior periodontal therapy; no systemic conditions or genetic disorders that entail the diagnosis of periodontitis as a manifestation of systemic diseases; no use of systemic antibiotics or regular use of anti-inflammatory drugs for the preceding 6-month period; no diabetes mellitus; no current use of tobacco products or of nicotine replacement medication; not currently pregnant. A total of 15 subjects, 7 male and 8 female, were enrolled. All participants were informed about the scope and procedures of the study and informed consent was obtained.
|
| Sample_geo_accession | GSM155481
| | Sample_status | Public on Dec 31 2007
| | Sample_submission_date | Jan 16 2007
| | Sample_last_update_date | Jan 16 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Fifty ml of blood were obtained by venipucture and collected in Vacutainer cell preparation tubes (Beckton-Dickinson, NJ, USA) with sodium heparin, and were used to harvest peripheral blood mononuclear cells (PBMCs). A 1:1 dilution with PBS was made and the diluted blood sample was centrifuged at 1,000 g in Ficoll tubes (Sigma Accuspin, St. Louis, MO). After washing and counting of the cells in a phase hemacytometer (Hauser Scientific, Horsham, PA), PBMCs were re-suspended in 80 microlitres of MACS buffer (PBS pH 7.2, 0.5% BSA and 2 mM EDTA) and incubated on ice with 20 microlitres of CD14 microbeads (Miltenyi Biotec, Auburn CA) per 107 total cells for 15 minutes. After washings, the cell suspension was applied to a MACS LS separation column (Miltenyi Biotec) placed in the magnetic field of a MACS separator (Miltenyi Biotec). Thereafter, the column was removed from the separator and CD14 positive cells were collected by washings in MACS buffer.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | CD14 positive cells were vigorously pipetted in Trizol (Invitrogen Life Technologies, Carlsbad, CA, USA). After incubation with chloroform and centrifugation at 12,000 g, RNA in the upper aqueous phase was precipitated by mixing with isopropyl alcohol, further centrifugation and washing in 75% ethanol. Further purification of the extracted RNA was achieved by the use of the RNeasy total RNA isolation kit (Qiagen, Valencia, CA, USA) according to the manufacturer.s instructions. The purified RNA was quantified spectrophotometrically. One hundred nanograms of total RNA were amplified and reverse transcribed using the GeneChip expression 3.-amplification two-cycle cDNA synthesis kit (Affymetrix, Santa Clara, CA, USA) and the MEGAscript T7 transcription kit (Ambion, Austin, TX, USA) according to the manufacturers. instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Synthesis of biotin-labeled cRNA and subsequent fragmentation were performed by the use of the IVT labeling kit (Affymetrix, Santa Clara, CA, USA). The cRNA yield was determined spectrophotometrically at 260 nm. Fragmented cRNA was stored at -80C until hybridization.
| | Sample_hyb_protocol | According to the manufacturer's instructions.
| | Sample_scan_protocol | According to the manufacturer's instructions.
| | Sample_data_processing | All CEL files in the series were processed using RMA in R using justRMA with default parameters.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Paul,,Pavlidis
| | Sample_contact_email | paul@chibi.ubc.ca
| | Sample_contact_department | Centre for High-Throughput Biology / Psychiatry
| | Sample_contact_institute | University of British Columbia
| | Sample_contact_address | 177 Michael Smith Laboratories 2185 East Mall
| | Sample_contact_city | Vancouver
| | Sample_contact_state | British Columbia
| | Sample_contact_zip/postal_code | V6T 1Z4
| | Sample_contact_country | Canada
| | Sample_contact_web_link | http://www.chibi.ubc.ca/faculty/pavlidis
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM155nnn/GSM155481/suppl/GSM155481.CEL.gz
| | Sample_series_id | GSE6751
| | Sample_data_row_count | 54675
| | |
|
GSM155482 | GPL570 |
|
Patient 36, time point 4
|
Patient 36 PBMC, collected at time point 4
|
Time: ten weeks after prior to commencement of periodontal therapy (four weeks after treatment end)
Tissue: Peripheral blood monocytes
Phenotype: severe periodontitis
|
Patients were recruited among the ones seeking treatment at the clinic for post-doctoral Periodontics, Columbia University College of Dental Medicine. To be eligible for enrollment, patients had to be diagnosed with severe periodontitis, with radiographic evidence of bone loss extending to greater or equal to 30% of the tooth length at several teeth. Additional inclusion criteria required: age greater or equal to 18 years; presence of greater or equal to 2 teeth/quadrant with a pocket depth of greater or equal to 6 mm and concomitant attachment loss of greater or equal to 3 mm; a minimum of 20 teeth present; no prior periodontal therapy; no systemic conditions or genetic disorders that entail the diagnosis of periodontitis as a manifestation of systemic diseases; no use of systemic antibiotics or regular use of anti-inflammatory drugs for the preceding 6-month period; no diabetes mellitus; no current use of tobacco products or of nicotine replacement medication; not currently pregnant. A total of 15 subjects, 7 male and 8 female, were enrolled. All participants were informed about the scope and procedures of the study and informed consent was obtained.
|
| Sample_geo_accession | GSM155482
| | Sample_status | Public on Dec 31 2007
| | Sample_submission_date | Jan 16 2007
| | Sample_last_update_date | Jan 16 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Fifty ml of blood were obtained by venipucture and collected in Vacutainer cell preparation tubes (Beckton-Dickinson, NJ, USA) with sodium heparin, and were used to harvest peripheral blood mononuclear cells (PBMCs). A 1:1 dilution with PBS was made and the diluted blood sample was centrifuged at 1,000 g in Ficoll tubes (Sigma Accuspin, St. Louis, MO). After washing and counting of the cells in a phase hemacytometer (Hauser Scientific, Horsham, PA), PBMCs were re-suspended in 80 microlitres of MACS buffer (PBS pH 7.2, 0.5% BSA and 2 mM EDTA) and incubated on ice with 20 microlitres of CD14 microbeads (Miltenyi Biotec, Auburn CA) per 107 total cells for 15 minutes. After washings, the cell suspension was applied to a MACS LS separation column (Miltenyi Biotec) placed in the magnetic field of a MACS separator (Miltenyi Biotec). Thereafter, the column was removed from the separator and CD14 positive cells were collected by washings in MACS buffer.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | CD14 positive cells were vigorously pipetted in Trizol (Invitrogen Life Technologies, Carlsbad, CA, USA). After incubation with chloroform and centrifugation at 12,000 g, RNA in the upper aqueous phase was precipitated by mixing with isopropyl alcohol, further centrifugation and washing in 75% ethanol. Further purification of the extracted RNA was achieved by the use of the RNeasy total RNA isolation kit (Qiagen, Valencia, CA, USA) according to the manufacturer.s instructions. The purified RNA was quantified spectrophotometrically. One hundred nanograms of total RNA were amplified and reverse transcribed using the GeneChip expression 3.-amplification two-cycle cDNA synthesis kit (Affymetrix, Santa Clara, CA, USA) and the MEGAscript T7 transcription kit (Ambion, Austin, TX, USA) according to the manufacturers. instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Synthesis of biotin-labeled cRNA and subsequent fragmentation were performed by the use of the IVT labeling kit (Affymetrix, Santa Clara, CA, USA). The cRNA yield was determined spectrophotometrically at 260 nm. Fragmented cRNA was stored at -80C until hybridization.
| | Sample_hyb_protocol | According to the manufacturer's instructions.
| | Sample_scan_protocol | According to the manufacturer's instructions.
| | Sample_data_processing | All CEL files in the series were processed using RMA in R using justRMA with default parameters.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Paul,,Pavlidis
| | Sample_contact_email | paul@chibi.ubc.ca
| | Sample_contact_department | Centre for High-Throughput Biology / Psychiatry
| | Sample_contact_institute | University of British Columbia
| | Sample_contact_address | 177 Michael Smith Laboratories 2185 East Mall
| | Sample_contact_city | Vancouver
| | Sample_contact_state | British Columbia
| | Sample_contact_zip/postal_code | V6T 1Z4
| | Sample_contact_country | Canada
| | Sample_contact_web_link | http://www.chibi.ubc.ca/faculty/pavlidis
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM155nnn/GSM155482/suppl/GSM155482.CEL.gz
| | Sample_series_id | GSE6751
| | Sample_data_row_count | 54675
| | |
|
GSM155483 | GPL570 |
|
Patient 38, time point 1
|
Patient 38 PBMC, collected at time point 1
|
Time: one week prior to commencement of periodontal therapy
Tissue: Peripheral blood monocytes
Phenotype: severe periodontitis
|
Patients were recruited among the ones seeking treatment at the clinic for post-doctoral Periodontics, Columbia University College of Dental Medicine. To be eligible for enrollment, patients had to be diagnosed with severe periodontitis, with radiographic evidence of bone loss extending to greater or equal to 30% of the tooth length at several teeth. Additional inclusion criteria required: age greater or equal to 18 years; presence of greater or equal to 2 teeth/quadrant with a pocket depth of greater or equal to 6 mm and concomitant attachment loss of greater or equal to 3 mm; a minimum of 20 teeth present; no prior periodontal therapy; no systemic conditions or genetic disorders that entail the diagnosis of periodontitis as a manifestation of systemic diseases; no use of systemic antibiotics or regular use of anti-inflammatory drugs for the preceding 6-month period; no diabetes mellitus; no current use of tobacco products or of nicotine replacement medication; not currently pregnant. A total of 15 subjects, 7 male and 8 female, were enrolled. All participants were informed about the scope and procedures of the study and informed consent was obtained.
|
| Sample_geo_accession | GSM155483
| | Sample_status | Public on Dec 31 2007
| | Sample_submission_date | Jan 16 2007
| | Sample_last_update_date | Jan 16 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Fifty ml of blood were obtained by venipucture and collected in Vacutainer cell preparation tubes (Beckton-Dickinson, NJ, USA) with sodium heparin, and were used to harvest peripheral blood mononuclear cells (PBMCs). A 1:1 dilution with PBS was made and the diluted blood sample was centrifuged at 1,000 g in Ficoll tubes (Sigma Accuspin, St. Louis, MO). After washing and counting of the cells in a phase hemacytometer (Hauser Scientific, Horsham, PA), PBMCs were re-suspended in 80 microlitres of MACS buffer (PBS pH 7.2, 0.5% BSA and 2 mM EDTA) and incubated on ice with 20 microlitres of CD14 microbeads (Miltenyi Biotec, Auburn CA) per 107 total cells for 15 minutes. After washings, the cell suspension was applied to a MACS LS separation column (Miltenyi Biotec) placed in the magnetic field of a MACS separator (Miltenyi Biotec). Thereafter, the column was removed from the separator and CD14 positive cells were collected by washings in MACS buffer.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | CD14 positive cells were vigorously pipetted in Trizol (Invitrogen Life Technologies, Carlsbad, CA, USA). After incubation with chloroform and centrifugation at 12,000 g, RNA in the upper aqueous phase was precipitated by mixing with isopropyl alcohol, further centrifugation and washing in 75% ethanol. Further purification of the extracted RNA was achieved by the use of the RNeasy total RNA isolation kit (Qiagen, Valencia, CA, USA) according to the manufacturer.s instructions. The purified RNA was quantified spectrophotometrically. One hundred nanograms of total RNA were amplified and reverse transcribed using the GeneChip expression 3.-amplification two-cycle cDNA synthesis kit (Affymetrix, Santa Clara, CA, USA) and the MEGAscript T7 transcription kit (Ambion, Austin, TX, USA) according to the manufacturers. instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Synthesis of biotin-labeled cRNA and subsequent fragmentation were performed by the use of the IVT labeling kit (Affymetrix, Santa Clara, CA, USA). The cRNA yield was determined spectrophotometrically at 260 nm. Fragmented cRNA was stored at -80C until hybridization.
| | Sample_hyb_protocol | According to the manufacturer's instructions.
| | Sample_scan_protocol | According to the manufacturer's instructions.
| | Sample_data_processing | All CEL files in the series were processed using RMA in R using justRMA with default parameters.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Paul,,Pavlidis
| | Sample_contact_email | paul@chibi.ubc.ca
| | Sample_contact_department | Centre for High-Throughput Biology / Psychiatry
| | Sample_contact_institute | University of British Columbia
| | Sample_contact_address | 177 Michael Smith Laboratories 2185 East Mall
| | Sample_contact_city | Vancouver
| | Sample_contact_state | British Columbia
| | Sample_contact_zip/postal_code | V6T 1Z4
| | Sample_contact_country | Canada
| | Sample_contact_web_link | http://www.chibi.ubc.ca/faculty/pavlidis
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM155nnn/GSM155483/suppl/GSM155483.CEL.gz
| | Sample_series_id | GSE6751
| | Sample_data_row_count | 54675
| | |
|
GSM155484 | GPL570 |
|
Patient 38, time point 2
|
Patient 38 PBMC, collected at time point 2
|
Time: at commencement of periodontal therapy
Tissue: Peripheral blood monocytes
Phenotype: severe periodontitis
|
Patients were recruited among the ones seeking treatment at the clinic for post-doctoral Periodontics, Columbia University College of Dental Medicine. To be eligible for enrollment, patients had to be diagnosed with severe periodontitis, with radiographic evidence of bone loss extending to greater or equal to 30% of the tooth length at several teeth. Additional inclusion criteria required: age greater or equal to 18 years; presence of greater or equal to 2 teeth/quadrant with a pocket depth of greater or equal to 6 mm and concomitant attachment loss of greater or equal to 3 mm; a minimum of 20 teeth present; no prior periodontal therapy; no systemic conditions or genetic disorders that entail the diagnosis of periodontitis as a manifestation of systemic diseases; no use of systemic antibiotics or regular use of anti-inflammatory drugs for the preceding 6-month period; no diabetes mellitus; no current use of tobacco products or of nicotine replacement medication; not currently pregnant. A total of 15 subjects, 7 male and 8 female, were enrolled. All participants were informed about the scope and procedures of the study and informed consent was obtained.
|
| Sample_geo_accession | GSM155484
| | Sample_status | Public on Dec 31 2007
| | Sample_submission_date | Jan 16 2007
| | Sample_last_update_date | Jan 16 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Fifty ml of blood were obtained by venipucture and collected in Vacutainer cell preparation tubes (Beckton-Dickinson, NJ, USA) with sodium heparin, and were used to harvest peripheral blood mononuclear cells (PBMCs). A 1:1 dilution with PBS was made and the diluted blood sample was centrifuged at 1,000 g in Ficoll tubes (Sigma Accuspin, St. Louis, MO). After washing and counting of the cells in a phase hemacytometer (Hauser Scientific, Horsham, PA), PBMCs were re-suspended in 80 microlitres of MACS buffer (PBS pH 7.2, 0.5% BSA and 2 mM EDTA) and incubated on ice with 20 microlitres of CD14 microbeads (Miltenyi Biotec, Auburn CA) per 107 total cells for 15 minutes. After washings, the cell suspension was applied to a MACS LS separation column (Miltenyi Biotec) placed in the magnetic field of a MACS separator (Miltenyi Biotec). Thereafter, the column was removed from the separator and CD14 positive cells were collected by washings in MACS buffer.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | CD14 positive cells were vigorously pipetted in Trizol (Invitrogen Life Technologies, Carlsbad, CA, USA). After incubation with chloroform and centrifugation at 12,000 g, RNA in the upper aqueous phase was precipitated by mixing with isopropyl alcohol, further centrifugation and washing in 75% ethanol. Further purification of the extracted RNA was achieved by the use of the RNeasy total RNA isolation kit (Qiagen, Valencia, CA, USA) according to the manufacturer.s instructions. The purified RNA was quantified spectrophotometrically. One hundred nanograms of total RNA were amplified and reverse transcribed using the GeneChip expression 3.-amplification two-cycle cDNA synthesis kit (Affymetrix, Santa Clara, CA, USA) and the MEGAscript T7 transcription kit (Ambion, Austin, TX, USA) according to the manufacturers. instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Synthesis of biotin-labeled cRNA and subsequent fragmentation were performed by the use of the IVT labeling kit (Affymetrix, Santa Clara, CA, USA). The cRNA yield was determined spectrophotometrically at 260 nm. Fragmented cRNA was stored at -80C until hybridization.
| | Sample_hyb_protocol | According to the manufacturer's instructions.
| | Sample_scan_protocol | According to the manufacturer's instructions.
| | Sample_data_processing | All CEL files in the series were processed using RMA in R using justRMA with default parameters.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Paul,,Pavlidis
| | Sample_contact_email | paul@chibi.ubc.ca
| | Sample_contact_department | Centre for High-Throughput Biology / Psychiatry
| | Sample_contact_institute | University of British Columbia
| | Sample_contact_address | 177 Michael Smith Laboratories 2185 East Mall
| | Sample_contact_city | Vancouver
| | Sample_contact_state | British Columbia
| | Sample_contact_zip/postal_code | V6T 1Z4
| | Sample_contact_country | Canada
| | Sample_contact_web_link | http://www.chibi.ubc.ca/faculty/pavlidis
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM155nnn/GSM155484/suppl/GSM155484.CEL.gz
| | Sample_series_id | GSE6751
| | Sample_data_row_count | 54675
| | |
|
GSM155485 | GPL570 |
|
Patient 38, time point 3
|
Patient 38 PBMC, collected at time point 3
|
Time: six weeks after commencement of periodontal therapy (after treatment end)
Tissue: Peripheral blood monocytes
Phenotype: severe periodontitis
|
Patients were recruited among the ones seeking treatment at the clinic for post-doctoral Periodontics, Columbia University College of Dental Medicine. To be eligible for enrollment, patients had to be diagnosed with severe periodontitis, with radiographic evidence of bone loss extending to greater or equal to 30% of the tooth length at several teeth. Additional inclusion criteria required: age greater or equal to 18 years; presence of greater or equal to 2 teeth/quadrant with a pocket depth of greater or equal to 6 mm and concomitant attachment loss of greater or equal to 3 mm; a minimum of 20 teeth present; no prior periodontal therapy; no systemic conditions or genetic disorders that entail the diagnosis of periodontitis as a manifestation of systemic diseases; no use of systemic antibiotics or regular use of anti-inflammatory drugs for the preceding 6-month period; no diabetes mellitus; no current use of tobacco products or of nicotine replacement medication; not currently pregnant. A total of 15 subjects, 7 male and 8 female, were enrolled. All participants were informed about the scope and procedures of the study and informed consent was obtained.
|
| Sample_geo_accession | GSM155485
| | Sample_status | Public on Dec 31 2007
| | Sample_submission_date | Jan 16 2007
| | Sample_last_update_date | Jan 16 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Fifty ml of blood were obtained by venipucture and collected in Vacutainer cell preparation tubes (Beckton-Dickinson, NJ, USA) with sodium heparin, and were used to harvest peripheral blood mononuclear cells (PBMCs). A 1:1 dilution with PBS was made and the diluted blood sample was centrifuged at 1,000 g in Ficoll tubes (Sigma Accuspin, St. Louis, MO). After washing and counting of the cells in a phase hemacytometer (Hauser Scientific, Horsham, PA), PBMCs were re-suspended in 80 microlitres of MACS buffer (PBS pH 7.2, 0.5% BSA and 2 mM EDTA) and incubated on ice with 20 microlitres of CD14 microbeads (Miltenyi Biotec, Auburn CA) per 107 total cells for 15 minutes. After washings, the cell suspension was applied to a MACS LS separation column (Miltenyi Biotec) placed in the magnetic field of a MACS separator (Miltenyi Biotec). Thereafter, the column was removed from the separator and CD14 positive cells were collected by washings in MACS buffer.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | CD14 positive cells were vigorously pipetted in Trizol (Invitrogen Life Technologies, Carlsbad, CA, USA). After incubation with chloroform and centrifugation at 12,000 g, RNA in the upper aqueous phase was precipitated by mixing with isopropyl alcohol, further centrifugation and washing in 75% ethanol. Further purification of the extracted RNA was achieved by the use of the RNeasy total RNA isolation kit (Qiagen, Valencia, CA, USA) according to the manufacturer.s instructions. The purified RNA was quantified spectrophotometrically. One hundred nanograms of total RNA were amplified and reverse transcribed using the GeneChip expression 3.-amplification two-cycle cDNA synthesis kit (Affymetrix, Santa Clara, CA, USA) and the MEGAscript T7 transcription kit (Ambion, Austin, TX, USA) according to the manufacturers. instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Synthesis of biotin-labeled cRNA and subsequent fragmentation were performed by the use of the IVT labeling kit (Affymetrix, Santa Clara, CA, USA). The cRNA yield was determined spectrophotometrically at 260 nm. Fragmented cRNA was stored at -80C until hybridization.
| | Sample_hyb_protocol | According to the manufacturer's instructions.
| | Sample_scan_protocol | According to the manufacturer's instructions.
| | Sample_data_processing | All CEL files in the series were processed using RMA in R using justRMA with default parameters.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Paul,,Pavlidis
| | Sample_contact_email | paul@chibi.ubc.ca
| | Sample_contact_department | Centre for High-Throughput Biology / Psychiatry
| | Sample_contact_institute | University of British Columbia
| | Sample_contact_address | 177 Michael Smith Laboratories 2185 East Mall
| | Sample_contact_city | Vancouver
| | Sample_contact_state | British Columbia
| | Sample_contact_zip/postal_code | V6T 1Z4
| | Sample_contact_country | Canada
| | Sample_contact_web_link | http://www.chibi.ubc.ca/faculty/pavlidis
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM155nnn/GSM155485/suppl/GSM155485.CEL.gz
| | Sample_series_id | GSE6751
| | Sample_data_row_count | 54675
| | |
|
GSM155486 | GPL570 |
|
Patient 38, time point 4
|
Patient 38 PBMC, collected at time point 4
|
Time: ten weeks after prior to commencement of periodontal therapy (four weeks after treatment end)
Tissue: Peripheral blood monocytes
Phenotype: severe periodontitis
|
Patients were recruited among the ones seeking treatment at the clinic for post-doctoral Periodontics, Columbia University College of Dental Medicine. To be eligible for enrollment, patients had to be diagnosed with severe periodontitis, with radiographic evidence of bone loss extending to greater or equal to 30% of the tooth length at several teeth. Additional inclusion criteria required: age greater or equal to 18 years; presence of greater or equal to 2 teeth/quadrant with a pocket depth of greater or equal to 6 mm and concomitant attachment loss of greater or equal to 3 mm; a minimum of 20 teeth present; no prior periodontal therapy; no systemic conditions or genetic disorders that entail the diagnosis of periodontitis as a manifestation of systemic diseases; no use of systemic antibiotics or regular use of anti-inflammatory drugs for the preceding 6-month period; no diabetes mellitus; no current use of tobacco products or of nicotine replacement medication; not currently pregnant. A total of 15 subjects, 7 male and 8 female, were enrolled. All participants were informed about the scope and procedures of the study and informed consent was obtained.
|
| Sample_geo_accession | GSM155486
| | Sample_status | Public on Dec 31 2007
| | Sample_submission_date | Jan 16 2007
| | Sample_last_update_date | Jan 16 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Fifty ml of blood were obtained by venipucture and collected in Vacutainer cell preparation tubes (Beckton-Dickinson, NJ, USA) with sodium heparin, and were used to harvest peripheral blood mononuclear cells (PBMCs). A 1:1 dilution with PBS was made and the diluted blood sample was centrifuged at 1,000 g in Ficoll tubes (Sigma Accuspin, St. Louis, MO). After washing and counting of the cells in a phase hemacytometer (Hauser Scientific, Horsham, PA), PBMCs were re-suspended in 80 microlitres of MACS buffer (PBS pH 7.2, 0.5% BSA and 2 mM EDTA) and incubated on ice with 20 microlitres of CD14 microbeads (Miltenyi Biotec, Auburn CA) per 107 total cells for 15 minutes. After washings, the cell suspension was applied to a MACS LS separation column (Miltenyi Biotec) placed in the magnetic field of a MACS separator (Miltenyi Biotec). Thereafter, the column was removed from the separator and CD14 positive cells were collected by washings in MACS buffer.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | CD14 positive cells were vigorously pipetted in Trizol (Invitrogen Life Technologies, Carlsbad, CA, USA). After incubation with chloroform and centrifugation at 12,000 g, RNA in the upper aqueous phase was precipitated by mixing with isopropyl alcohol, further centrifugation and washing in 75% ethanol. Further purification of the extracted RNA was achieved by the use of the RNeasy total RNA isolation kit (Qiagen, Valencia, CA, USA) according to the manufacturer.s instructions. The purified RNA was quantified spectrophotometrically. One hundred nanograms of total RNA were amplified and reverse transcribed using the GeneChip expression 3.-amplification two-cycle cDNA synthesis kit (Affymetrix, Santa Clara, CA, USA) and the MEGAscript T7 transcription kit (Ambion, Austin, TX, USA) according to the manufacturers. instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Synthesis of biotin-labeled cRNA and subsequent fragmentation were performed by the use of the IVT labeling kit (Affymetrix, Santa Clara, CA, USA). The cRNA yield was determined spectrophotometrically at 260 nm. Fragmented cRNA was stored at -80C until hybridization.
| | Sample_hyb_protocol | According to the manufacturer's instructions.
| | Sample_scan_protocol | According to the manufacturer's instructions.
| | Sample_data_processing | All CEL files in the series were processed using RMA in R using justRMA with default parameters.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Paul,,Pavlidis
| | Sample_contact_email | paul@chibi.ubc.ca
| | Sample_contact_department | Centre for High-Throughput Biology / Psychiatry
| | Sample_contact_institute | University of British Columbia
| | Sample_contact_address | 177 Michael Smith Laboratories 2185 East Mall
| | Sample_contact_city | Vancouver
| | Sample_contact_state | British Columbia
| | Sample_contact_zip/postal_code | V6T 1Z4
| | Sample_contact_country | Canada
| | Sample_contact_web_link | http://www.chibi.ubc.ca/faculty/pavlidis
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM155nnn/GSM155486/suppl/GSM155486.CEL.gz
| | Sample_series_id | GSE6751
| | Sample_data_row_count | 54675
| | |
|
GSM155487 | GPL570 |
|
Patient 40, time point 1
|
Patient 40 PBMC, collected at time point 1
|
Time: one week prior to commencement of periodontal therapy
Tissue: Peripheral blood monocytes
Phenotype: severe periodontitis
|
Patients were recruited among the ones seeking treatment at the clinic for post-doctoral Periodontics, Columbia University College of Dental Medicine. To be eligible for enrollment, patients had to be diagnosed with severe periodontitis, with radiographic evidence of bone loss extending to greater or equal to 30% of the tooth length at several teeth. Additional inclusion criteria required: age greater or equal to 18 years; presence of greater or equal to 2 teeth/quadrant with a pocket depth of greater or equal to 6 mm and concomitant attachment loss of greater or equal to 3 mm; a minimum of 20 teeth present; no prior periodontal therapy; no systemic conditions or genetic disorders that entail the diagnosis of periodontitis as a manifestation of systemic diseases; no use of systemic antibiotics or regular use of anti-inflammatory drugs for the preceding 6-month period; no diabetes mellitus; no current use of tobacco products or of nicotine replacement medication; not currently pregnant. A total of 15 subjects, 7 male and 8 female, were enrolled. All participants were informed about the scope and procedures of the study and informed consent was obtained.
|
| Sample_geo_accession | GSM155487
| | Sample_status | Public on Dec 31 2007
| | Sample_submission_date | Jan 16 2007
| | Sample_last_update_date | Jan 16 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Fifty ml of blood were obtained by venipucture and collected in Vacutainer cell preparation tubes (Beckton-Dickinson, NJ, USA) with sodium heparin, and were used to harvest peripheral blood mononuclear cells (PBMCs). A 1:1 dilution with PBS was made and the diluted blood sample was centrifuged at 1,000 g in Ficoll tubes (Sigma Accuspin, St. Louis, MO). After washing and counting of the cells in a phase hemacytometer (Hauser Scientific, Horsham, PA), PBMCs were re-suspended in 80 microlitres of MACS buffer (PBS pH 7.2, 0.5% BSA and 2 mM EDTA) and incubated on ice with 20 microlitres of CD14 microbeads (Miltenyi Biotec, Auburn CA) per 107 total cells for 15 minutes. After washings, the cell suspension was applied to a MACS LS separation column (Miltenyi Biotec) placed in the magnetic field of a MACS separator (Miltenyi Biotec). Thereafter, the column was removed from the separator and CD14 positive cells were collected by washings in MACS buffer.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | CD14 positive cells were vigorously pipetted in Trizol (Invitrogen Life Technologies, Carlsbad, CA, USA). After incubation with chloroform and centrifugation at 12,000 g, RNA in the upper aqueous phase was precipitated by mixing with isopropyl alcohol, further centrifugation and washing in 75% ethanol. Further purification of the extracted RNA was achieved by the use of the RNeasy total RNA isolation kit (Qiagen, Valencia, CA, USA) according to the manufacturer.s instructions. The purified RNA was quantified spectrophotometrically. One hundred nanograms of total RNA were amplified and reverse transcribed using the GeneChip expression 3.-amplification two-cycle cDNA synthesis kit (Affymetrix, Santa Clara, CA, USA) and the MEGAscript T7 transcription kit (Ambion, Austin, TX, USA) according to the manufacturers. instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Synthesis of biotin-labeled cRNA and subsequent fragmentation were performed by the use of the IVT labeling kit (Affymetrix, Santa Clara, CA, USA). The cRNA yield was determined spectrophotometrically at 260 nm. Fragmented cRNA was stored at -80C until hybridization.
| | Sample_hyb_protocol | According to the manufacturer's instructions.
| | Sample_scan_protocol | According to the manufacturer's instructions.
| | Sample_data_processing | All CEL files in the series were processed using RMA in R using justRMA with default parameters.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Paul,,Pavlidis
| | Sample_contact_email | paul@chibi.ubc.ca
| | Sample_contact_department | Centre for High-Throughput Biology / Psychiatry
| | Sample_contact_institute | University of British Columbia
| | Sample_contact_address | 177 Michael Smith Laboratories 2185 East Mall
| | Sample_contact_city | Vancouver
| | Sample_contact_state | British Columbia
| | Sample_contact_zip/postal_code | V6T 1Z4
| | Sample_contact_country | Canada
| | Sample_contact_web_link | http://www.chibi.ubc.ca/faculty/pavlidis
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM155nnn/GSM155487/suppl/GSM155487.CEL.gz
| | Sample_series_id | GSE6751
| | Sample_data_row_count | 54675
| | |
|
GSM155488 | GPL570 |
|
Patient 40, time point 2
|
Patient 40 PBMC, collected at time point 2
|
Time: at commencement of periodontal therapy
Tissue: Peripheral blood monocytes
Phenotype: severe periodontitis
|
Patients were recruited among the ones seeking treatment at the clinic for post-doctoral Periodontics, Columbia University College of Dental Medicine. To be eligible for enrollment, patients had to be diagnosed with severe periodontitis, with radiographic evidence of bone loss extending to greater or equal to 30% of the tooth length at several teeth. Additional inclusion criteria required: age greater or equal to 18 years; presence of greater or equal to 2 teeth/quadrant with a pocket depth of greater or equal to 6 mm and concomitant attachment loss of greater or equal to 3 mm; a minimum of 20 teeth present; no prior periodontal therapy; no systemic conditions or genetic disorders that entail the diagnosis of periodontitis as a manifestation of systemic diseases; no use of systemic antibiotics or regular use of anti-inflammatory drugs for the preceding 6-month period; no diabetes mellitus; no current use of tobacco products or of nicotine replacement medication; not currently pregnant. A total of 15 subjects, 7 male and 8 female, were enrolled. All participants were informed about the scope and procedures of the study and informed consent was obtained.
|
| Sample_geo_accession | GSM155488
| | Sample_status | Public on Dec 31 2007
| | Sample_submission_date | Jan 16 2007
| | Sample_last_update_date | Jan 16 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Fifty ml of blood were obtained by venipucture and collected in Vacutainer cell preparation tubes (Beckton-Dickinson, NJ, USA) with sodium heparin, and were used to harvest peripheral blood mononuclear cells (PBMCs). A 1:1 dilution with PBS was made and the diluted blood sample was centrifuged at 1,000 g in Ficoll tubes (Sigma Accuspin, St. Louis, MO). After washing and counting of the cells in a phase hemacytometer (Hauser Scientific, Horsham, PA), PBMCs were re-suspended in 80 microlitres of MACS buffer (PBS pH 7.2, 0.5% BSA and 2 mM EDTA) and incubated on ice with 20 microlitres of CD14 microbeads (Miltenyi Biotec, Auburn CA) per 107 total cells for 15 minutes. After washings, the cell suspension was applied to a MACS LS separation column (Miltenyi Biotec) placed in the magnetic field of a MACS separator (Miltenyi Biotec). Thereafter, the column was removed from the separator and CD14 positive cells were collected by washings in MACS buffer.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | CD14 positive cells were vigorously pipetted in Trizol (Invitrogen Life Technologies, Carlsbad, CA, USA). After incubation with chloroform and centrifugation at 12,000 g, RNA in the upper aqueous phase was precipitated by mixing with isopropyl alcohol, further centrifugation and washing in 75% ethanol. Further purification of the extracted RNA was achieved by the use of the RNeasy total RNA isolation kit (Qiagen, Valencia, CA, USA) according to the manufacturer.s instructions. The purified RNA was quantified spectrophotometrically. One hundred nanograms of total RNA were amplified and reverse transcribed using the GeneChip expression 3.-amplification two-cycle cDNA synthesis kit (Affymetrix, Santa Clara, CA, USA) and the MEGAscript T7 transcription kit (Ambion, Austin, TX, USA) according to the manufacturers. instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Synthesis of biotin-labeled cRNA and subsequent fragmentation were performed by the use of the IVT labeling kit (Affymetrix, Santa Clara, CA, USA). The cRNA yield was determined spectrophotometrically at 260 nm. Fragmented cRNA was stored at -80C until hybridization.
| | Sample_hyb_protocol | According to the manufacturer's instructions.
| | Sample_scan_protocol | According to the manufacturer's instructions.
| | Sample_data_processing | All CEL files in the series were processed using RMA in R using justRMA with default parameters.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Paul,,Pavlidis
| | Sample_contact_email | paul@chibi.ubc.ca
| | Sample_contact_department | Centre for High-Throughput Biology / Psychiatry
| | Sample_contact_institute | University of British Columbia
| | Sample_contact_address | 177 Michael Smith Laboratories 2185 East Mall
| | Sample_contact_city | Vancouver
| | Sample_contact_state | British Columbia
| | Sample_contact_zip/postal_code | V6T 1Z4
| | Sample_contact_country | Canada
| | Sample_contact_web_link | http://www.chibi.ubc.ca/faculty/pavlidis
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM155nnn/GSM155488/suppl/GSM155488.CEL.gz
| | Sample_series_id | GSE6751
| | Sample_data_row_count | 54675
| | |
|
GSM155489 | GPL570 |
|
Patient 40, time point 3
|
Patient 40 PBMC, collected at time point 3
|
Time: six weeks after commencement of periodontal therapy (after treatment end)
Tissue: Peripheral blood monocytes
Phenotype: severe periodontitis
|
Patients were recruited among the ones seeking treatment at the clinic for post-doctoral Periodontics, Columbia University College of Dental Medicine. To be eligible for enrollment, patients had to be diagnosed with severe periodontitis, with radiographic evidence of bone loss extending to greater or equal to 30% of the tooth length at several teeth. Additional inclusion criteria required: age greater or equal to 18 years; presence of greater or equal to 2 teeth/quadrant with a pocket depth of greater or equal to 6 mm and concomitant attachment loss of greater or equal to 3 mm; a minimum of 20 teeth present; no prior periodontal therapy; no systemic conditions or genetic disorders that entail the diagnosis of periodontitis as a manifestation of systemic diseases; no use of systemic antibiotics or regular use of anti-inflammatory drugs for the preceding 6-month period; no diabetes mellitus; no current use of tobacco products or of nicotine replacement medication; not currently pregnant. A total of 15 subjects, 7 male and 8 female, were enrolled. All participants were informed about the scope and procedures of the study and informed consent was obtained.
|
| Sample_geo_accession | GSM155489
| | Sample_status | Public on Dec 31 2007
| | Sample_submission_date | Jan 16 2007
| | Sample_last_update_date | Jan 16 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Fifty ml of blood were obtained by venipucture and collected in Vacutainer cell preparation tubes (Beckton-Dickinson, NJ, USA) with sodium heparin, and were used to harvest peripheral blood mononuclear cells (PBMCs). A 1:1 dilution with PBS was made and the diluted blood sample was centrifuged at 1,000 g in Ficoll tubes (Sigma Accuspin, St. Louis, MO). After washing and counting of the cells in a phase hemacytometer (Hauser Scientific, Horsham, PA), PBMCs were re-suspended in 80 microlitres of MACS buffer (PBS pH 7.2, 0.5% BSA and 2 mM EDTA) and incubated on ice with 20 microlitres of CD14 microbeads (Miltenyi Biotec, Auburn CA) per 107 total cells for 15 minutes. After washings, the cell suspension was applied to a MACS LS separation column (Miltenyi Biotec) placed in the magnetic field of a MACS separator (Miltenyi Biotec). Thereafter, the column was removed from the separator and CD14 positive cells were collected by washings in MACS buffer.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | CD14 positive cells were vigorously pipetted in Trizol (Invitrogen Life Technologies, Carlsbad, CA, USA). After incubation with chloroform and centrifugation at 12,000 g, RNA in the upper aqueous phase was precipitated by mixing with isopropyl alcohol, further centrifugation and washing in 75% ethanol. Further purification of the extracted RNA was achieved by the use of the RNeasy total RNA isolation kit (Qiagen, Valencia, CA, USA) according to the manufacturer.s instructions. The purified RNA was quantified spectrophotometrically. One hundred nanograms of total RNA were amplified and reverse transcribed using the GeneChip expression 3.-amplification two-cycle cDNA synthesis kit (Affymetrix, Santa Clara, CA, USA) and the MEGAscript T7 transcription kit (Ambion, Austin, TX, USA) according to the manufacturers. instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Synthesis of biotin-labeled cRNA and subsequent fragmentation were performed by the use of the IVT labeling kit (Affymetrix, Santa Clara, CA, USA). The cRNA yield was determined spectrophotometrically at 260 nm. Fragmented cRNA was stored at -80C until hybridization.
| | Sample_hyb_protocol | According to the manufacturer's instructions.
| | Sample_scan_protocol | According to the manufacturer's instructions.
| | Sample_data_processing | All CEL files in the series were processed using RMA in R using justRMA with default parameters.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Paul,,Pavlidis
| | Sample_contact_email | paul@chibi.ubc.ca
| | Sample_contact_department | Centre for High-Throughput Biology / Psychiatry
| | Sample_contact_institute | University of British Columbia
| | Sample_contact_address | 177 Michael Smith Laboratories 2185 East Mall
| | Sample_contact_city | Vancouver
| | Sample_contact_state | British Columbia
| | Sample_contact_zip/postal_code | V6T 1Z4
| | Sample_contact_country | Canada
| | Sample_contact_web_link | http://www.chibi.ubc.ca/faculty/pavlidis
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM155nnn/GSM155489/suppl/GSM155489.CEL.gz
| | Sample_series_id | GSE6751
| | Sample_data_row_count | 54675
| | |
|
GSM155490 | GPL570 |
|
Patient 40, time point 4
|
Patient 40 PBMC, collected at time point 4
|
Time: ten weeks after prior to commencement of periodontal therapy (four weeks after treatment end)
Tissue: Peripheral blood monocytes
Phenotype: severe periodontitis
|
Patients were recruited among the ones seeking treatment at the clinic for post-doctoral Periodontics, Columbia University College of Dental Medicine. To be eligible for enrollment, patients had to be diagnosed with severe periodontitis, with radiographic evidence of bone loss extending to greater or equal to 30% of the tooth length at several teeth. Additional inclusion criteria required: age greater or equal to 18 years; presence of greater or equal to 2 teeth/quadrant with a pocket depth of greater or equal to 6 mm and concomitant attachment loss of greater or equal to 3 mm; a minimum of 20 teeth present; no prior periodontal therapy; no systemic conditions or genetic disorders that entail the diagnosis of periodontitis as a manifestation of systemic diseases; no use of systemic antibiotics or regular use of anti-inflammatory drugs for the preceding 6-month period; no diabetes mellitus; no current use of tobacco products or of nicotine replacement medication; not currently pregnant. A total of 15 subjects, 7 male and 8 female, were enrolled. All participants were informed about the scope and procedures of the study and informed consent was obtained.
|
| Sample_geo_accession | GSM155490
| | Sample_status | Public on Dec 31 2007
| | Sample_submission_date | Jan 16 2007
| | Sample_last_update_date | Jan 16 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Fifty ml of blood were obtained by venipucture and collected in Vacutainer cell preparation tubes (Beckton-Dickinson, NJ, USA) with sodium heparin, and were used to harvest peripheral blood mononuclear cells (PBMCs). A 1:1 dilution with PBS was made and the diluted blood sample was centrifuged at 1,000 g in Ficoll tubes (Sigma Accuspin, St. Louis, MO). After washing and counting of the cells in a phase hemacytometer (Hauser Scientific, Horsham, PA), PBMCs were re-suspended in 80 microlitres of MACS buffer (PBS pH 7.2, 0.5% BSA and 2 mM EDTA) and incubated on ice with 20 microlitres of CD14 microbeads (Miltenyi Biotec, Auburn CA) per 107 total cells for 15 minutes. After washings, the cell suspension was applied to a MACS LS separation column (Miltenyi Biotec) placed in the magnetic field of a MACS separator (Miltenyi Biotec). Thereafter, the column was removed from the separator and CD14 positive cells were collected by washings in MACS buffer.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | CD14 positive cells were vigorously pipetted in Trizol (Invitrogen Life Technologies, Carlsbad, CA, USA). After incubation with chloroform and centrifugation at 12,000 g, RNA in the upper aqueous phase was precipitated by mixing with isopropyl alcohol, further centrifugation and washing in 75% ethanol. Further purification of the extracted RNA was achieved by the use of the RNeasy total RNA isolation kit (Qiagen, Valencia, CA, USA) according to the manufacturer.s instructions. The purified RNA was quantified spectrophotometrically. One hundred nanograms of total RNA were amplified and reverse transcribed using the GeneChip expression 3.-amplification two-cycle cDNA synthesis kit (Affymetrix, Santa Clara, CA, USA) and the MEGAscript T7 transcription kit (Ambion, Austin, TX, USA) according to the manufacturers. instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Synthesis of biotin-labeled cRNA and subsequent fragmentation were performed by the use of the IVT labeling kit (Affymetrix, Santa Clara, CA, USA). The cRNA yield was determined spectrophotometrically at 260 nm. Fragmented cRNA was stored at -80C until hybridization.
| | Sample_hyb_protocol | According to the manufacturer's instructions.
| | Sample_scan_protocol | According to the manufacturer's instructions.
| | Sample_data_processing | All CEL files in the series were processed using RMA in R using justRMA with default parameters.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Paul,,Pavlidis
| | Sample_contact_email | paul@chibi.ubc.ca
| | Sample_contact_department | Centre for High-Throughput Biology / Psychiatry
| | Sample_contact_institute | University of British Columbia
| | Sample_contact_address | 177 Michael Smith Laboratories 2185 East Mall
| | Sample_contact_city | Vancouver
| | Sample_contact_state | British Columbia
| | Sample_contact_zip/postal_code | V6T 1Z4
| | Sample_contact_country | Canada
| | Sample_contact_web_link | http://www.chibi.ubc.ca/faculty/pavlidis
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM155nnn/GSM155490/suppl/GSM155490.CEL.gz
| | Sample_series_id | GSE6751
| | Sample_data_row_count | 54675
| | |
|
GSM155491 | GPL570 |
|
Patient 43, time point 1
|
Patient 43 PBMC, collected at time point 1
|
Time: one week prior to commencement of periodontal therapy
Tissue: Peripheral blood monocytes
Phenotype: severe periodontitis
|
Patients were recruited among the ones seeking treatment at the clinic for post-doctoral Periodontics, Columbia University College of Dental Medicine. To be eligible for enrollment, patients had to be diagnosed with severe periodontitis, with radiographic evidence of bone loss extending to greater or equal to 30% of the tooth length at several teeth. Additional inclusion criteria required: age greater or equal to 18 years; presence of greater or equal to 2 teeth/quadrant with a pocket depth of greater or equal to 6 mm and concomitant attachment loss of greater or equal to 3 mm; a minimum of 20 teeth present; no prior periodontal therapy; no systemic conditions or genetic disorders that entail the diagnosis of periodontitis as a manifestation of systemic diseases; no use of systemic antibiotics or regular use of anti-inflammatory drugs for the preceding 6-month period; no diabetes mellitus; no current use of tobacco products or of nicotine replacement medication; not currently pregnant. A total of 15 subjects, 7 male and 8 female, were enrolled. All participants were informed about the scope and procedures of the study and informed consent was obtained.
|
| Sample_geo_accession | GSM155491
| | Sample_status | Public on Dec 31 2007
| | Sample_submission_date | Jan 16 2007
| | Sample_last_update_date | Jan 16 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Fifty ml of blood were obtained by venipucture and collected in Vacutainer cell preparation tubes (Beckton-Dickinson, NJ, USA) with sodium heparin, and were used to harvest peripheral blood mononuclear cells (PBMCs). A 1:1 dilution with PBS was made and the diluted blood sample was centrifuged at 1,000 g in Ficoll tubes (Sigma Accuspin, St. Louis, MO). After washing and counting of the cells in a phase hemacytometer (Hauser Scientific, Horsham, PA), PBMCs were re-suspended in 80 microlitres of MACS buffer (PBS pH 7.2, 0.5% BSA and 2 mM EDTA) and incubated on ice with 20 microlitres of CD14 microbeads (Miltenyi Biotec, Auburn CA) per 107 total cells for 15 minutes. After washings, the cell suspension was applied to a MACS LS separation column (Miltenyi Biotec) placed in the magnetic field of a MACS separator (Miltenyi Biotec). Thereafter, the column was removed from the separator and CD14 positive cells were collected by washings in MACS buffer.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | CD14 positive cells were vigorously pipetted in Trizol (Invitrogen Life Technologies, Carlsbad, CA, USA). After incubation with chloroform and centrifugation at 12,000 g, RNA in the upper aqueous phase was precipitated by mixing with isopropyl alcohol, further centrifugation and washing in 75% ethanol. Further purification of the extracted RNA was achieved by the use of the RNeasy total RNA isolation kit (Qiagen, Valencia, CA, USA) according to the manufacturer.s instructions. The purified RNA was quantified spectrophotometrically. One hundred nanograms of total RNA were amplified and reverse transcribed using the GeneChip expression 3.-amplification two-cycle cDNA synthesis kit (Affymetrix, Santa Clara, CA, USA) and the MEGAscript T7 transcription kit (Ambion, Austin, TX, USA) according to the manufacturers. instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Synthesis of biotin-labeled cRNA and subsequent fragmentation were performed by the use of the IVT labeling kit (Affymetrix, Santa Clara, CA, USA). The cRNA yield was determined spectrophotometrically at 260 nm. Fragmented cRNA was stored at -80C until hybridization.
| | Sample_hyb_protocol | According to the manufacturer's instructions.
| | Sample_scan_protocol | According to the manufacturer's instructions.
| | Sample_data_processing | All CEL files in the series were processed using RMA in R using justRMA with default parameters.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Paul,,Pavlidis
| | Sample_contact_email | paul@chibi.ubc.ca
| | Sample_contact_department | Centre for High-Throughput Biology / Psychiatry
| | Sample_contact_institute | University of British Columbia
| | Sample_contact_address | 177 Michael Smith Laboratories 2185 East Mall
| | Sample_contact_city | Vancouver
| | Sample_contact_state | British Columbia
| | Sample_contact_zip/postal_code | V6T 1Z4
| | Sample_contact_country | Canada
| | Sample_contact_web_link | http://www.chibi.ubc.ca/faculty/pavlidis
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM155nnn/GSM155491/suppl/GSM155491.CEL.gz
| | Sample_series_id | GSE6751
| | Sample_data_row_count | 54675
| | |
|
GSM155492 | GPL570 |
|
Patient 43, time point 2
|
Patient 43 PBMC, collected at time point 2
|
Time: at commencement of periodontal therapy
Tissue: Peripheral blood monocytes
Phenotype: severe periodontitis
|
Patients were recruited among the ones seeking treatment at the clinic for post-doctoral Periodontics, Columbia University College of Dental Medicine. To be eligible for enrollment, patients had to be diagnosed with severe periodontitis, with radiographic evidence of bone loss extending to greater or equal to 30% of the tooth length at several teeth. Additional inclusion criteria required: age greater or equal to 18 years; presence of greater or equal to 2 teeth/quadrant with a pocket depth of greater or equal to 6 mm and concomitant attachment loss of greater or equal to 3 mm; a minimum of 20 teeth present; no prior periodontal therapy; no systemic conditions or genetic disorders that entail the diagnosis of periodontitis as a manifestation of systemic diseases; no use of systemic antibiotics or regular use of anti-inflammatory drugs for the preceding 6-month period; no diabetes mellitus; no current use of tobacco products or of nicotine replacement medication; not currently pregnant. A total of 15 subjects, 7 male and 8 female, were enrolled. All participants were informed about the scope and procedures of the study and informed consent was obtained.
|
| Sample_geo_accession | GSM155492
| | Sample_status | Public on Dec 31 2007
| | Sample_submission_date | Jan 16 2007
| | Sample_last_update_date | Jan 16 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Fifty ml of blood were obtained by venipucture and collected in Vacutainer cell preparation tubes (Beckton-Dickinson, NJ, USA) with sodium heparin, and were used to harvest peripheral blood mononuclear cells (PBMCs). A 1:1 dilution with PBS was made and the diluted blood sample was centrifuged at 1,000 g in Ficoll tubes (Sigma Accuspin, St. Louis, MO). After washing and counting of the cells in a phase hemacytometer (Hauser Scientific, Horsham, PA), PBMCs were re-suspended in 80 microlitres of MACS buffer (PBS pH 7.2, 0.5% BSA and 2 mM EDTA) and incubated on ice with 20 microlitres of CD14 microbeads (Miltenyi Biotec, Auburn CA) per 107 total cells for 15 minutes. After washings, the cell suspension was applied to a MACS LS separation column (Miltenyi Biotec) placed in the magnetic field of a MACS separator (Miltenyi Biotec). Thereafter, the column was removed from the separator and CD14 positive cells were collected by washings in MACS buffer.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | CD14 positive cells were vigorously pipetted in Trizol (Invitrogen Life Technologies, Carlsbad, CA, USA). After incubation with chloroform and centrifugation at 12,000 g, RNA in the upper aqueous phase was precipitated by mixing with isopropyl alcohol, further centrifugation and washing in 75% ethanol. Further purification of the extracted RNA was achieved by the use of the RNeasy total RNA isolation kit (Qiagen, Valencia, CA, USA) according to the manufacturer.s instructions. The purified RNA was quantified spectrophotometrically. One hundred nanograms of total RNA were amplified and reverse transcribed using the GeneChip expression 3.-amplification two-cycle cDNA synthesis kit (Affymetrix, Santa Clara, CA, USA) and the MEGAscript T7 transcription kit (Ambion, Austin, TX, USA) according to the manufacturers. instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Synthesis of biotin-labeled cRNA and subsequent fragmentation were performed by the use of the IVT labeling kit (Affymetrix, Santa Clara, CA, USA). The cRNA yield was determined spectrophotometrically at 260 nm. Fragmented cRNA was stored at -80C until hybridization.
| | Sample_hyb_protocol | According to the manufacturer's instructions.
| | Sample_scan_protocol | According to the manufacturer's instructions.
| | Sample_data_processing | All CEL files in the series were processed using RMA in R using justRMA with default parameters.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Paul,,Pavlidis
| | Sample_contact_email | paul@chibi.ubc.ca
| | Sample_contact_department | Centre for High-Throughput Biology / Psychiatry
| | Sample_contact_institute | University of British Columbia
| | Sample_contact_address | 177 Michael Smith Laboratories 2185 East Mall
| | Sample_contact_city | Vancouver
| | Sample_contact_state | British Columbia
| | Sample_contact_zip/postal_code | V6T 1Z4
| | Sample_contact_country | Canada
| | Sample_contact_web_link | http://www.chibi.ubc.ca/faculty/pavlidis
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM155nnn/GSM155492/suppl/GSM155492.CEL.gz
| | Sample_series_id | GSE6751
| | Sample_data_row_count | 54675
| | |
|
GSM155493 | GPL570 |
|
Patient 43, time point 3
|
Patient 43 PBMC, collected at time point 3
|
Time: six weeks after commencement of periodontal therapy (after treatment end)
Tissue: Peripheral blood monocytes
Phenotype: severe periodontitis
|
Patients were recruited among the ones seeking treatment at the clinic for post-doctoral Periodontics, Columbia University College of Dental Medicine. To be eligible for enrollment, patients had to be diagnosed with severe periodontitis, with radiographic evidence of bone loss extending to greater or equal to 30% of the tooth length at several teeth. Additional inclusion criteria required: age greater or equal to 18 years; presence of greater or equal to 2 teeth/quadrant with a pocket depth of greater or equal to 6 mm and concomitant attachment loss of greater or equal to 3 mm; a minimum of 20 teeth present; no prior periodontal therapy; no systemic conditions or genetic disorders that entail the diagnosis of periodontitis as a manifestation of systemic diseases; no use of systemic antibiotics or regular use of anti-inflammatory drugs for the preceding 6-month period; no diabetes mellitus; no current use of tobacco products or of nicotine replacement medication; not currently pregnant. A total of 15 subjects, 7 male and 8 female, were enrolled. All participants were informed about the scope and procedures of the study and informed consent was obtained.
|
| Sample_geo_accession | GSM155493
| | Sample_status | Public on Dec 31 2007
| | Sample_submission_date | Jan 16 2007
| | Sample_last_update_date | Jan 16 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Fifty ml of blood were obtained by venipucture and collected in Vacutainer cell preparation tubes (Beckton-Dickinson, NJ, USA) with sodium heparin, and were used to harvest peripheral blood mononuclear cells (PBMCs). A 1:1 dilution with PBS was made and the diluted blood sample was centrifuged at 1,000 g in Ficoll tubes (Sigma Accuspin, St. Louis, MO). After washing and counting of the cells in a phase hemacytometer (Hauser Scientific, Horsham, PA), PBMCs were re-suspended in 80 microlitres of MACS buffer (PBS pH 7.2, 0.5% BSA and 2 mM EDTA) and incubated on ice with 20 microlitres of CD14 microbeads (Miltenyi Biotec, Auburn CA) per 107 total cells for 15 minutes. After washings, the cell suspension was applied to a MACS LS separation column (Miltenyi Biotec) placed in the magnetic field of a MACS separator (Miltenyi Biotec). Thereafter, the column was removed from the separator and CD14 positive cells were collected by washings in MACS buffer.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | CD14 positive cells were vigorously pipetted in Trizol (Invitrogen Life Technologies, Carlsbad, CA, USA). After incubation with chloroform and centrifugation at 12,000 g, RNA in the upper aqueous phase was precipitated by mixing with isopropyl alcohol, further centrifugation and washing in 75% ethanol. Further purification of the extracted RNA was achieved by the use of the RNeasy total RNA isolation kit (Qiagen, Valencia, CA, USA) according to the manufacturer.s instructions. The purified RNA was quantified spectrophotometrically. One hundred nanograms of total RNA were amplified and reverse transcribed using the GeneChip expression 3.-amplification two-cycle cDNA synthesis kit (Affymetrix, Santa Clara, CA, USA) and the MEGAscript T7 transcription kit (Ambion, Austin, TX, USA) according to the manufacturers. instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Synthesis of biotin-labeled cRNA and subsequent fragmentation were performed by the use of the IVT labeling kit (Affymetrix, Santa Clara, CA, USA). The cRNA yield was determined spectrophotometrically at 260 nm. Fragmented cRNA was stored at -80C until hybridization.
| | Sample_hyb_protocol | According to the manufacturer's instructions.
| | Sample_scan_protocol | According to the manufacturer's instructions.
| | Sample_data_processing | All CEL files in the series were processed using RMA in R using justRMA with default parameters.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Paul,,Pavlidis
| | Sample_contact_email | paul@chibi.ubc.ca
| | Sample_contact_department | Centre for High-Throughput Biology / Psychiatry
| | Sample_contact_institute | University of British Columbia
| | Sample_contact_address | 177 Michael Smith Laboratories 2185 East Mall
| | Sample_contact_city | Vancouver
| | Sample_contact_state | British Columbia
| | Sample_contact_zip/postal_code | V6T 1Z4
| | Sample_contact_country | Canada
| | Sample_contact_web_link | http://www.chibi.ubc.ca/faculty/pavlidis
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM155nnn/GSM155493/suppl/GSM155493.CEL.gz
| | Sample_series_id | GSE6751
| | Sample_data_row_count | 54675
| | |
|
GSM155494 | GPL570 |
|
Patient 43, time point 4
|
Patient 43 PBMC, collected at time point 4
|
Time: ten weeks after prior to commencement of periodontal therapy (four weeks after treatment end)
Tissue: Peripheral blood monocytes
Phenotype: severe periodontitis
|
Patients were recruited among the ones seeking treatment at the clinic for post-doctoral Periodontics, Columbia University College of Dental Medicine. To be eligible for enrollment, patients had to be diagnosed with severe periodontitis, with radiographic evidence of bone loss extending to greater or equal to 30% of the tooth length at several teeth. Additional inclusion criteria required: age greater or equal to 18 years; presence of greater or equal to 2 teeth/quadrant with a pocket depth of greater or equal to 6 mm and concomitant attachment loss of greater or equal to 3 mm; a minimum of 20 teeth present; no prior periodontal therapy; no systemic conditions or genetic disorders that entail the diagnosis of periodontitis as a manifestation of systemic diseases; no use of systemic antibiotics or regular use of anti-inflammatory drugs for the preceding 6-month period; no diabetes mellitus; no current use of tobacco products or of nicotine replacement medication; not currently pregnant. A total of 15 subjects, 7 male and 8 female, were enrolled. All participants were informed about the scope and procedures of the study and informed consent was obtained.
|
| Sample_geo_accession | GSM155494
| | Sample_status | Public on Dec 31 2007
| | Sample_submission_date | Jan 16 2007
| | Sample_last_update_date | Jan 16 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Fifty ml of blood were obtained by venipucture and collected in Vacutainer cell preparation tubes (Beckton-Dickinson, NJ, USA) with sodium heparin, and were used to harvest peripheral blood mononuclear cells (PBMCs). A 1:1 dilution with PBS was made and the diluted blood sample was centrifuged at 1,000 g in Ficoll tubes (Sigma Accuspin, St. Louis, MO). After washing and counting of the cells in a phase hemacytometer (Hauser Scientific, Horsham, PA), PBMCs were re-suspended in 80 microlitres of MACS buffer (PBS pH 7.2, 0.5% BSA and 2 mM EDTA) and incubated on ice with 20 microlitres of CD14 microbeads (Miltenyi Biotec, Auburn CA) per 107 total cells for 15 minutes. After washings, the cell suspension was applied to a MACS LS separation column (Miltenyi Biotec) placed in the magnetic field of a MACS separator (Miltenyi Biotec). Thereafter, the column was removed from the separator and CD14 positive cells were collected by washings in MACS buffer.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | CD14 positive cells were vigorously pipetted in Trizol (Invitrogen Life Technologies, Carlsbad, CA, USA). After incubation with chloroform and centrifugation at 12,000 g, RNA in the upper aqueous phase was precipitated by mixing with isopropyl alcohol, further centrifugation and washing in 75% ethanol. Further purification of the extracted RNA was achieved by the use of the RNeasy total RNA isolation kit (Qiagen, Valencia, CA, USA) according to the manufacturer.s instructions. The purified RNA was quantified spectrophotometrically. One hundred nanograms of total RNA were amplified and reverse transcribed using the GeneChip expression 3.-amplification two-cycle cDNA synthesis kit (Affymetrix, Santa Clara, CA, USA) and the MEGAscript T7 transcription kit (Ambion, Austin, TX, USA) according to the manufacturers. instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Synthesis of biotin-labeled cRNA and subsequent fragmentation were performed by the use of the IVT labeling kit (Affymetrix, Santa Clara, CA, USA). The cRNA yield was determined spectrophotometrically at 260 nm. Fragmented cRNA was stored at -80C until hybridization.
| | Sample_hyb_protocol | According to the manufacturer's instructions.
| | Sample_scan_protocol | According to the manufacturer's instructions.
| | Sample_data_processing | All CEL files in the series were processed using RMA in R using justRMA with default parameters.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Paul,,Pavlidis
| | Sample_contact_email | paul@chibi.ubc.ca
| | Sample_contact_department | Centre for High-Throughput Biology / Psychiatry
| | Sample_contact_institute | University of British Columbia
| | Sample_contact_address | 177 Michael Smith Laboratories 2185 East Mall
| | Sample_contact_city | Vancouver
| | Sample_contact_state | British Columbia
| | Sample_contact_zip/postal_code | V6T 1Z4
| | Sample_contact_country | Canada
| | Sample_contact_web_link | http://www.chibi.ubc.ca/faculty/pavlidis
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM155nnn/GSM155494/suppl/GSM155494.CEL.gz
| | Sample_series_id | GSE6751
| | Sample_data_row_count | 54675
| | |
|
GSM155495 | GPL570 |
|
Patient 45, time point 1
|
Patient 45 PBMC, collected at time point 1
|
Time: one week prior to commencement of periodontal therapy
Tissue: Peripheral blood monocytes
Phenotype: severe periodontitis
|
Patients were recruited among the ones seeking treatment at the clinic for post-doctoral Periodontics, Columbia University College of Dental Medicine. To be eligible for enrollment, patients had to be diagnosed with severe periodontitis, with radiographic evidence of bone loss extending to greater or equal to 30% of the tooth length at several teeth. Additional inclusion criteria required: age greater or equal to 18 years; presence of greater or equal to 2 teeth/quadrant with a pocket depth of greater or equal to 6 mm and concomitant attachment loss of greater or equal to 3 mm; a minimum of 20 teeth present; no prior periodontal therapy; no systemic conditions or genetic disorders that entail the diagnosis of periodontitis as a manifestation of systemic diseases; no use of systemic antibiotics or regular use of anti-inflammatory drugs for the preceding 6-month period; no diabetes mellitus; no current use of tobacco products or of nicotine replacement medication; not currently pregnant. A total of 15 subjects, 7 male and 8 female, were enrolled. All participants were informed about the scope and procedures of the study and informed consent was obtained.
|
| Sample_geo_accession | GSM155495
| | Sample_status | Public on Dec 31 2007
| | Sample_submission_date | Jan 16 2007
| | Sample_last_update_date | Jan 16 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Fifty ml of blood were obtained by venipucture and collected in Vacutainer cell preparation tubes (Beckton-Dickinson, NJ, USA) with sodium heparin, and were used to harvest peripheral blood mononuclear cells (PBMCs). A 1:1 dilution with PBS was made and the diluted blood sample was centrifuged at 1,000 g in Ficoll tubes (Sigma Accuspin, St. Louis, MO). After washing and counting of the cells in a phase hemacytometer (Hauser Scientific, Horsham, PA), PBMCs were re-suspended in 80 microlitres of MACS buffer (PBS pH 7.2, 0.5% BSA and 2 mM EDTA) and incubated on ice with 20 microlitres of CD14 microbeads (Miltenyi Biotec, Auburn CA) per 107 total cells for 15 minutes. After washings, the cell suspension was applied to a MACS LS separation column (Miltenyi Biotec) placed in the magnetic field of a MACS separator (Miltenyi Biotec). Thereafter, the column was removed from the separator and CD14 positive cells were collected by washings in MACS buffer.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | CD14 positive cells were vigorously pipetted in Trizol (Invitrogen Life Technologies, Carlsbad, CA, USA). After incubation with chloroform and centrifugation at 12,000 g, RNA in the upper aqueous phase was precipitated by mixing with isopropyl alcohol, further centrifugation and washing in 75% ethanol. Further purification of the extracted RNA was achieved by the use of the RNeasy total RNA isolation kit (Qiagen, Valencia, CA, USA) according to the manufacturer.s instructions. The purified RNA was quantified spectrophotometrically. One hundred nanograms of total RNA were amplified and reverse transcribed using the GeneChip expression 3.-amplification two-cycle cDNA synthesis kit (Affymetrix, Santa Clara, CA, USA) and the MEGAscript T7 transcription kit (Ambion, Austin, TX, USA) according to the manufacturers. instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Synthesis of biotin-labeled cRNA and subsequent fragmentation were performed by the use of the IVT labeling kit (Affymetrix, Santa Clara, CA, USA). The cRNA yield was determined spectrophotometrically at 260 nm. Fragmented cRNA was stored at -80C until hybridization.
| | Sample_hyb_protocol | According to the manufacturer's instructions.
| | Sample_scan_protocol | According to the manufacturer's instructions.
| | Sample_data_processing | All CEL files in the series were processed using RMA in R using justRMA with default parameters.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Paul,,Pavlidis
| | Sample_contact_email | paul@chibi.ubc.ca
| | Sample_contact_department | Centre for High-Throughput Biology / Psychiatry
| | Sample_contact_institute | University of British Columbia
| | Sample_contact_address | 177 Michael Smith Laboratories 2185 East Mall
| | Sample_contact_city | Vancouver
| | Sample_contact_state | British Columbia
| | Sample_contact_zip/postal_code | V6T 1Z4
| | Sample_contact_country | Canada
| | Sample_contact_web_link | http://www.chibi.ubc.ca/faculty/pavlidis
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM155nnn/GSM155495/suppl/GSM155495.CEL.gz
| | Sample_series_id | GSE6751
| | Sample_data_row_count | 54675
| | |
|
GSM155496 | GPL570 |
|
Patient 45, time point 2
|
Patient 45 PBMC, collected at time point 2
|
Time: at commencement of periodontal therapy
Tissue: Peripheral blood monocytes
Phenotype: severe periodontitis
|
Patients were recruited among the ones seeking treatment at the clinic for post-doctoral Periodontics, Columbia University College of Dental Medicine. To be eligible for enrollment, patients had to be diagnosed with severe periodontitis, with radiographic evidence of bone loss extending to greater or equal to 30% of the tooth length at several teeth. Additional inclusion criteria required: age greater or equal to 18 years; presence of greater or equal to 2 teeth/quadrant with a pocket depth of greater or equal to 6 mm and concomitant attachment loss of greater or equal to 3 mm; a minimum of 20 teeth present; no prior periodontal therapy; no systemic conditions or genetic disorders that entail the diagnosis of periodontitis as a manifestation of systemic diseases; no use of systemic antibiotics or regular use of anti-inflammatory drugs for the preceding 6-month period; no diabetes mellitus; no current use of tobacco products or of nicotine replacement medication; not currently pregnant. A total of 15 subjects, 7 male and 8 female, were enrolled. All participants were informed about the scope and procedures of the study and informed consent was obtained.
|
| Sample_geo_accession | GSM155496
| | Sample_status | Public on Dec 31 2007
| | Sample_submission_date | Jan 16 2007
| | Sample_last_update_date | Jan 16 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Fifty ml of blood were obtained by venipucture and collected in Vacutainer cell preparation tubes (Beckton-Dickinson, NJ, USA) with sodium heparin, and were used to harvest peripheral blood mononuclear cells (PBMCs). A 1:1 dilution with PBS was made and the diluted blood sample was centrifuged at 1,000 g in Ficoll tubes (Sigma Accuspin, St. Louis, MO). After washing and counting of the cells in a phase hemacytometer (Hauser Scientific, Horsham, PA), PBMCs were re-suspended in 80 microlitres of MACS buffer (PBS pH 7.2, 0.5% BSA and 2 mM EDTA) and incubated on ice with 20 microlitres of CD14 microbeads (Miltenyi Biotec, Auburn CA) per 107 total cells for 15 minutes. After washings, the cell suspension was applied to a MACS LS separation column (Miltenyi Biotec) placed in the magnetic field of a MACS separator (Miltenyi Biotec). Thereafter, the column was removed from the separator and CD14 positive cells were collected by washings in MACS buffer.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | CD14 positive cells were vigorously pipetted in Trizol (Invitrogen Life Technologies, Carlsbad, CA, USA). After incubation with chloroform and centrifugation at 12,000 g, RNA in the upper aqueous phase was precipitated by mixing with isopropyl alcohol, further centrifugation and washing in 75% ethanol. Further purification of the extracted RNA was achieved by the use of the RNeasy total RNA isolation kit (Qiagen, Valencia, CA, USA) according to the manufacturer.s instructions. The purified RNA was quantified spectrophotometrically. One hundred nanograms of total RNA were amplified and reverse transcribed using the GeneChip expression 3.-amplification two-cycle cDNA synthesis kit (Affymetrix, Santa Clara, CA, USA) and the MEGAscript T7 transcription kit (Ambion, Austin, TX, USA) according to the manufacturers. instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Synthesis of biotin-labeled cRNA and subsequent fragmentation were performed by the use of the IVT labeling kit (Affymetrix, Santa Clara, CA, USA). The cRNA yield was determined spectrophotometrically at 260 nm. Fragmented cRNA was stored at -80C until hybridization.
| | Sample_hyb_protocol | According to the manufacturer's instructions.
| | Sample_scan_protocol | According to the manufacturer's instructions.
| | Sample_data_processing | All CEL files in the series were processed using RMA in R using justRMA with default parameters.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Paul,,Pavlidis
| | Sample_contact_email | paul@chibi.ubc.ca
| | Sample_contact_department | Centre for High-Throughput Biology / Psychiatry
| | Sample_contact_institute | University of British Columbia
| | Sample_contact_address | 177 Michael Smith Laboratories 2185 East Mall
| | Sample_contact_city | Vancouver
| | Sample_contact_state | British Columbia
| | Sample_contact_zip/postal_code | V6T 1Z4
| | Sample_contact_country | Canada
| | Sample_contact_web_link | http://www.chibi.ubc.ca/faculty/pavlidis
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM155nnn/GSM155496/suppl/GSM155496.CEL.gz
| | Sample_series_id | GSE6751
| | Sample_data_row_count | 54675
| | |
|
GSM155497 | GPL570 |
|
Patient 45, time point 3
|
Patient 45 PBMC, collected at time point 3
|
Time: six weeks after commencement of periodontal therapy (after treatment end)
Tissue: Peripheral blood monocytes
Phenotype: severe periodontitis
|
Patients were recruited among the ones seeking treatment at the clinic for post-doctoral Periodontics, Columbia University College of Dental Medicine. To be eligible for enrollment, patients had to be diagnosed with severe periodontitis, with radiographic evidence of bone loss extending to greater or equal to 30% of the tooth length at several teeth. Additional inclusion criteria required: age greater or equal to 18 years; presence of greater or equal to 2 teeth/quadrant with a pocket depth of greater or equal to 6 mm and concomitant attachment loss of greater or equal to 3 mm; a minimum of 20 teeth present; no prior periodontal therapy; no systemic conditions or genetic disorders that entail the diagnosis of periodontitis as a manifestation of systemic diseases; no use of systemic antibiotics or regular use of anti-inflammatory drugs for the preceding 6-month period; no diabetes mellitus; no current use of tobacco products or of nicotine replacement medication; not currently pregnant. A total of 15 subjects, 7 male and 8 female, were enrolled. All participants were informed about the scope and procedures of the study and informed consent was obtained.
|
| Sample_geo_accession | GSM155497
| | Sample_status | Public on Dec 31 2007
| | Sample_submission_date | Jan 16 2007
| | Sample_last_update_date | Jan 16 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Fifty ml of blood were obtained by venipucture and collected in Vacutainer cell preparation tubes (Beckton-Dickinson, NJ, USA) with sodium heparin, and were used to harvest peripheral blood mononuclear cells (PBMCs). A 1:1 dilution with PBS was made and the diluted blood sample was centrifuged at 1,000 g in Ficoll tubes (Sigma Accuspin, St. Louis, MO). After washing and counting of the cells in a phase hemacytometer (Hauser Scientific, Horsham, PA), PBMCs were re-suspended in 80 microlitres of MACS buffer (PBS pH 7.2, 0.5% BSA and 2 mM EDTA) and incubated on ice with 20 microlitres of CD14 microbeads (Miltenyi Biotec, Auburn CA) per 107 total cells for 15 minutes. After washings, the cell suspension was applied to a MACS LS separation column (Miltenyi Biotec) placed in the magnetic field of a MACS separator (Miltenyi Biotec). Thereafter, the column was removed from the separator and CD14 positive cells were collected by washings in MACS buffer.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | CD14 positive cells were vigorously pipetted in Trizol (Invitrogen Life Technologies, Carlsbad, CA, USA). After incubation with chloroform and centrifugation at 12,000 g, RNA in the upper aqueous phase was precipitated by mixing with isopropyl alcohol, further centrifugation and washing in 75% ethanol. Further purification of the extracted RNA was achieved by the use of the RNeasy total RNA isolation kit (Qiagen, Valencia, CA, USA) according to the manufacturer.s instructions. The purified RNA was quantified spectrophotometrically. One hundred nanograms of total RNA were amplified and reverse transcribed using the GeneChip expression 3.-amplification two-cycle cDNA synthesis kit (Affymetrix, Santa Clara, CA, USA) and the MEGAscript T7 transcription kit (Ambion, Austin, TX, USA) according to the manufacturers. instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Synthesis of biotin-labeled cRNA and subsequent fragmentation were performed by the use of the IVT labeling kit (Affymetrix, Santa Clara, CA, USA). The cRNA yield was determined spectrophotometrically at 260 nm. Fragmented cRNA was stored at -80C until hybridization.
| | Sample_hyb_protocol | According to the manufacturer's instructions.
| | Sample_scan_protocol | According to the manufacturer's instructions.
| | Sample_data_processing | All CEL files in the series were processed using RMA in R using justRMA with default parameters.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Paul,,Pavlidis
| | Sample_contact_email | paul@chibi.ubc.ca
| | Sample_contact_department | Centre for High-Throughput Biology / Psychiatry
| | Sample_contact_institute | University of British Columbia
| | Sample_contact_address | 177 Michael Smith Laboratories 2185 East Mall
| | Sample_contact_city | Vancouver
| | Sample_contact_state | British Columbia
| | Sample_contact_zip/postal_code | V6T 1Z4
| | Sample_contact_country | Canada
| | Sample_contact_web_link | http://www.chibi.ubc.ca/faculty/pavlidis
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM155nnn/GSM155497/suppl/GSM155497.CEL.gz
| | Sample_series_id | GSE6751
| | Sample_data_row_count | 54675
| | |
|
GSM155498 | GPL570 |
|
Patient 45, time point 4
|
Patient 45 PBMC, collected at time point 4
|
Time: ten weeks after prior to commencement of periodontal therapy (four weeks after treatment end)
Tissue: Peripheral blood monocytes
Phenotype: severe periodontitis
|
Patients were recruited among the ones seeking treatment at the clinic for post-doctoral Periodontics, Columbia University College of Dental Medicine. To be eligible for enrollment, patients had to be diagnosed with severe periodontitis, with radiographic evidence of bone loss extending to greater or equal to 30% of the tooth length at several teeth. Additional inclusion criteria required: age greater or equal to 18 years; presence of greater or equal to 2 teeth/quadrant with a pocket depth of greater or equal to 6 mm and concomitant attachment loss of greater or equal to 3 mm; a minimum of 20 teeth present; no prior periodontal therapy; no systemic conditions or genetic disorders that entail the diagnosis of periodontitis as a manifestation of systemic diseases; no use of systemic antibiotics or regular use of anti-inflammatory drugs for the preceding 6-month period; no diabetes mellitus; no current use of tobacco products or of nicotine replacement medication; not currently pregnant. A total of 15 subjects, 7 male and 8 female, were enrolled. All participants were informed about the scope and procedures of the study and informed consent was obtained.
|
| Sample_geo_accession | GSM155498
| | Sample_status | Public on Dec 31 2007
| | Sample_submission_date | Jan 16 2007
| | Sample_last_update_date | Jan 16 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Fifty ml of blood were obtained by venipucture and collected in Vacutainer cell preparation tubes (Beckton-Dickinson, NJ, USA) with sodium heparin, and were used to harvest peripheral blood mononuclear cells (PBMCs). A 1:1 dilution with PBS was made and the diluted blood sample was centrifuged at 1,000 g in Ficoll tubes (Sigma Accuspin, St. Louis, MO). After washing and counting of the cells in a phase hemacytometer (Hauser Scientific, Horsham, PA), PBMCs were re-suspended in 80 microlitres of MACS buffer (PBS pH 7.2, 0.5% BSA and 2 mM EDTA) and incubated on ice with 20 microlitres of CD14 microbeads (Miltenyi Biotec, Auburn CA) per 107 total cells for 15 minutes. After washings, the cell suspension was applied to a MACS LS separation column (Miltenyi Biotec) placed in the magnetic field of a MACS separator (Miltenyi Biotec). Thereafter, the column was removed from the separator and CD14 positive cells were collected by washings in MACS buffer.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | CD14 positive cells were vigorously pipetted in Trizol (Invitrogen Life Technologies, Carlsbad, CA, USA). After incubation with chloroform and centrifugation at 12,000 g, RNA in the upper aqueous phase was precipitated by mixing with isopropyl alcohol, further centrifugation and washing in 75% ethanol. Further purification of the extracted RNA was achieved by the use of the RNeasy total RNA isolation kit (Qiagen, Valencia, CA, USA) according to the manufacturer.s instructions. The purified RNA was quantified spectrophotometrically. One hundred nanograms of total RNA were amplified and reverse transcribed using the GeneChip expression 3.-amplification two-cycle cDNA synthesis kit (Affymetrix, Santa Clara, CA, USA) and the MEGAscript T7 transcription kit (Ambion, Austin, TX, USA) according to the manufacturers. instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Synthesis of biotin-labeled cRNA and subsequent fragmentation were performed by the use of the IVT labeling kit (Affymetrix, Santa Clara, CA, USA). The cRNA yield was determined spectrophotometrically at 260 nm. Fragmented cRNA was stored at -80C until hybridization.
| | Sample_hyb_protocol | According to the manufacturer's instructions.
| | Sample_scan_protocol | According to the manufacturer's instructions.
| | Sample_data_processing | All CEL files in the series were processed using RMA in R using justRMA with default parameters.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Paul,,Pavlidis
| | Sample_contact_email | paul@chibi.ubc.ca
| | Sample_contact_department | Centre for High-Throughput Biology / Psychiatry
| | Sample_contact_institute | University of British Columbia
| | Sample_contact_address | 177 Michael Smith Laboratories 2185 East Mall
| | Sample_contact_city | Vancouver
| | Sample_contact_state | British Columbia
| | Sample_contact_zip/postal_code | V6T 1Z4
| | Sample_contact_country | Canada
| | Sample_contact_web_link | http://www.chibi.ubc.ca/faculty/pavlidis
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM155nnn/GSM155498/suppl/GSM155498.CEL.gz
| | Sample_series_id | GSE6751
| | Sample_data_row_count | 54675
| | |
|
GSM155499 | GPL570 |
|
Patient 54, time point 1
|
Patient 54 PBMC, collected at time point 1
|
Time: one week prior to commencement of periodontal therapy
Tissue: Peripheral blood monocytes
Phenotype: severe periodontitis
|
Patients were recruited among the ones seeking treatment at the clinic for post-doctoral Periodontics, Columbia University College of Dental Medicine. To be eligible for enrollment, patients had to be diagnosed with severe periodontitis, with radiographic evidence of bone loss extending to greater or equal to 30% of the tooth length at several teeth. Additional inclusion criteria required: age greater or equal to 18 years; presence of greater or equal to 2 teeth/quadrant with a pocket depth of greater or equal to 6 mm and concomitant attachment loss of greater or equal to 3 mm; a minimum of 20 teeth present; no prior periodontal therapy; no systemic conditions or genetic disorders that entail the diagnosis of periodontitis as a manifestation of systemic diseases; no use of systemic antibiotics or regular use of anti-inflammatory drugs for the preceding 6-month period; no diabetes mellitus; no current use of tobacco products or of nicotine replacement medication; not currently pregnant. A total of 15 subjects, 7 male and 8 female, were enrolled. All participants were informed about the scope and procedures of the study and informed consent was obtained.
|
| Sample_geo_accession | GSM155499
| | Sample_status | Public on Dec 31 2007
| | Sample_submission_date | Jan 16 2007
| | Sample_last_update_date | Jan 16 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Fifty ml of blood were obtained by venipucture and collected in Vacutainer cell preparation tubes (Beckton-Dickinson, NJ, USA) with sodium heparin, and were used to harvest peripheral blood mononuclear cells (PBMCs). A 1:1 dilution with PBS was made and the diluted blood sample was centrifuged at 1,000 g in Ficoll tubes (Sigma Accuspin, St. Louis, MO). After washing and counting of the cells in a phase hemacytometer (Hauser Scientific, Horsham, PA), PBMCs were re-suspended in 80 microlitres of MACS buffer (PBS pH 7.2, 0.5% BSA and 2 mM EDTA) and incubated on ice with 20 microlitres of CD14 microbeads (Miltenyi Biotec, Auburn CA) per 107 total cells for 15 minutes. After washings, the cell suspension was applied to a MACS LS separation column (Miltenyi Biotec) placed in the magnetic field of a MACS separator (Miltenyi Biotec). Thereafter, the column was removed from the separator and CD14 positive cells were collected by washings in MACS buffer.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | CD14 positive cells were vigorously pipetted in Trizol (Invitrogen Life Technologies, Carlsbad, CA, USA). After incubation with chloroform and centrifugation at 12,000 g, RNA in the upper aqueous phase was precipitated by mixing with isopropyl alcohol, further centrifugation and washing in 75% ethanol. Further purification of the extracted RNA was achieved by the use of the RNeasy total RNA isolation kit (Qiagen, Valencia, CA, USA) according to the manufacturer.s instructions. The purified RNA was quantified spectrophotometrically. One hundred nanograms of total RNA were amplified and reverse transcribed using the GeneChip expression 3.-amplification two-cycle cDNA synthesis kit (Affymetrix, Santa Clara, CA, USA) and the MEGAscript T7 transcription kit (Ambion, Austin, TX, USA) according to the manufacturers. instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Synthesis of biotin-labeled cRNA and subsequent fragmentation were performed by the use of the IVT labeling kit (Affymetrix, Santa Clara, CA, USA). The cRNA yield was determined spectrophotometrically at 260 nm. Fragmented cRNA was stored at -80C until hybridization.
| | Sample_hyb_protocol | According to the manufacturer's instructions.
| | Sample_scan_protocol | According to the manufacturer's instructions.
| | Sample_data_processing | All CEL files in the series were processed using RMA in R using justRMA with default parameters.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Paul,,Pavlidis
| | Sample_contact_email | paul@chibi.ubc.ca
| | Sample_contact_department | Centre for High-Throughput Biology / Psychiatry
| | Sample_contact_institute | University of British Columbia
| | Sample_contact_address | 177 Michael Smith Laboratories 2185 East Mall
| | Sample_contact_city | Vancouver
| | Sample_contact_state | British Columbia
| | Sample_contact_zip/postal_code | V6T 1Z4
| | Sample_contact_country | Canada
| | Sample_contact_web_link | http://www.chibi.ubc.ca/faculty/pavlidis
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM155nnn/GSM155499/suppl/GSM155499.CEL.gz
| | Sample_series_id | GSE6751
| | Sample_data_row_count | 54675
| | |
|
GSM155500 | GPL570 |
|
Patient 54, time point 2
|
Patient 54 PBMC, collected at time point 2
|
Time: at commencement of periodontal therapy
Tissue: Peripheral blood monocytes
Phenotype: severe periodontitis
|
Patients were recruited among the ones seeking treatment at the clinic for post-doctoral Periodontics, Columbia University College of Dental Medicine. To be eligible for enrollment, patients had to be diagnosed with severe periodontitis, with radiographic evidence of bone loss extending to greater or equal to 30% of the tooth length at several teeth. Additional inclusion criteria required: age greater or equal to 18 years; presence of greater or equal to 2 teeth/quadrant with a pocket depth of greater or equal to 6 mm and concomitant attachment loss of greater or equal to 3 mm; a minimum of 20 teeth present; no prior periodontal therapy; no systemic conditions or genetic disorders that entail the diagnosis of periodontitis as a manifestation of systemic diseases; no use of systemic antibiotics or regular use of anti-inflammatory drugs for the preceding 6-month period; no diabetes mellitus; no current use of tobacco products or of nicotine replacement medication; not currently pregnant. A total of 15 subjects, 7 male and 8 female, were enrolled. All participants were informed about the scope and procedures of the study and informed consent was obtained.
|
| Sample_geo_accession | GSM155500
| | Sample_status | Public on Dec 31 2007
| | Sample_submission_date | Jan 16 2007
| | Sample_last_update_date | Jan 16 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Fifty ml of blood were obtained by venipucture and collected in Vacutainer cell preparation tubes (Beckton-Dickinson, NJ, USA) with sodium heparin, and were used to harvest peripheral blood mononuclear cells (PBMCs). A 1:1 dilution with PBS was made and the diluted blood sample was centrifuged at 1,000 g in Ficoll tubes (Sigma Accuspin, St. Louis, MO). After washing and counting of the cells in a phase hemacytometer (Hauser Scientific, Horsham, PA), PBMCs were re-suspended in 80 microlitres of MACS buffer (PBS pH 7.2, 0.5% BSA and 2 mM EDTA) and incubated on ice with 20 microlitres of CD14 microbeads (Miltenyi Biotec, Auburn CA) per 107 total cells for 15 minutes. After washings, the cell suspension was applied to a MACS LS separation column (Miltenyi Biotec) placed in the magnetic field of a MACS separator (Miltenyi Biotec). Thereafter, the column was removed from the separator and CD14 positive cells were collected by washings in MACS buffer.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | CD14 positive cells were vigorously pipetted in Trizol (Invitrogen Life Technologies, Carlsbad, CA, USA). After incubation with chloroform and centrifugation at 12,000 g, RNA in the upper aqueous phase was precipitated by mixing with isopropyl alcohol, further centrifugation and washing in 75% ethanol. Further purification of the extracted RNA was achieved by the use of the RNeasy total RNA isolation kit (Qiagen, Valencia, CA, USA) according to the manufacturer.s instructions. The purified RNA was quantified spectrophotometrically. One hundred nanograms of total RNA were amplified and reverse transcribed using the GeneChip expression 3.-amplification two-cycle cDNA synthesis kit (Affymetrix, Santa Clara, CA, USA) and the MEGAscript T7 transcription kit (Ambion, Austin, TX, USA) according to the manufacturers. instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Synthesis of biotin-labeled cRNA and subsequent fragmentation were performed by the use of the IVT labeling kit (Affymetrix, Santa Clara, CA, USA). The cRNA yield was determined spectrophotometrically at 260 nm. Fragmented cRNA was stored at -80C until hybridization.
| | Sample_hyb_protocol | According to the manufacturer's instructions.
| | Sample_scan_protocol | According to the manufacturer's instructions.
| | Sample_data_processing | All CEL files in the series were processed using RMA in R using justRMA with default parameters.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Paul,,Pavlidis
| | Sample_contact_email | paul@chibi.ubc.ca
| | Sample_contact_department | Centre for High-Throughput Biology / Psychiatry
| | Sample_contact_institute | University of British Columbia
| | Sample_contact_address | 177 Michael Smith Laboratories 2185 East Mall
| | Sample_contact_city | Vancouver
| | Sample_contact_state | British Columbia
| | Sample_contact_zip/postal_code | V6T 1Z4
| | Sample_contact_country | Canada
| | Sample_contact_web_link | http://www.chibi.ubc.ca/faculty/pavlidis
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM155nnn/GSM155500/suppl/GSM155500.CEL.gz
| | Sample_series_id | GSE6751
| | Sample_data_row_count | 54675
| | |
|
GSM155501 | GPL570 |
|
Patient 54, time point 3
|
Patient 54 PBMC, collected at time point 3
|
Time: six weeks after commencement of periodontal therapy (after treatment end)
Tissue: Peripheral blood monocytes
Phenotype: severe periodontitis
|
Patients were recruited among the ones seeking treatment at the clinic for post-doctoral Periodontics, Columbia University College of Dental Medicine. To be eligible for enrollment, patients had to be diagnosed with severe periodontitis, with radiographic evidence of bone loss extending to greater or equal to 30% of the tooth length at several teeth. Additional inclusion criteria required: age greater or equal to 18 years; presence of greater or equal to 2 teeth/quadrant with a pocket depth of greater or equal to 6 mm and concomitant attachment loss of greater or equal to 3 mm; a minimum of 20 teeth present; no prior periodontal therapy; no systemic conditions or genetic disorders that entail the diagnosis of periodontitis as a manifestation of systemic diseases; no use of systemic antibiotics or regular use of anti-inflammatory drugs for the preceding 6-month period; no diabetes mellitus; no current use of tobacco products or of nicotine replacement medication; not currently pregnant. A total of 15 subjects, 7 male and 8 female, were enrolled. All participants were informed about the scope and procedures of the study and informed consent was obtained.
|
| Sample_geo_accession | GSM155501
| | Sample_status | Public on Dec 31 2007
| | Sample_submission_date | Jan 16 2007
| | Sample_last_update_date | Jan 16 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Fifty ml of blood were obtained by venipucture and collected in Vacutainer cell preparation tubes (Beckton-Dickinson, NJ, USA) with sodium heparin, and were used to harvest peripheral blood mononuclear cells (PBMCs). A 1:1 dilution with PBS was made and the diluted blood sample was centrifuged at 1,000 g in Ficoll tubes (Sigma Accuspin, St. Louis, MO). After washing and counting of the cells in a phase hemacytometer (Hauser Scientific, Horsham, PA), PBMCs were re-suspended in 80 microlitres of MACS buffer (PBS pH 7.2, 0.5% BSA and 2 mM EDTA) and incubated on ice with 20 microlitres of CD14 microbeads (Miltenyi Biotec, Auburn CA) per 107 total cells for 15 minutes. After washings, the cell suspension was applied to a MACS LS separation column (Miltenyi Biotec) placed in the magnetic field of a MACS separator (Miltenyi Biotec). Thereafter, the column was removed from the separator and CD14 positive cells were collected by washings in MACS buffer.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | CD14 positive cells were vigorously pipetted in Trizol (Invitrogen Life Technologies, Carlsbad, CA, USA). After incubation with chloroform and centrifugation at 12,000 g, RNA in the upper aqueous phase was precipitated by mixing with isopropyl alcohol, further centrifugation and washing in 75% ethanol. Further purification of the extracted RNA was achieved by the use of the RNeasy total RNA isolation kit (Qiagen, Valencia, CA, USA) according to the manufacturer.s instructions. The purified RNA was quantified spectrophotometrically. One hundred nanograms of total RNA were amplified and reverse transcribed using the GeneChip expression 3.-amplification two-cycle cDNA synthesis kit (Affymetrix, Santa Clara, CA, USA) and the MEGAscript T7 transcription kit (Ambion, Austin, TX, USA) according to the manufacturers. instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Synthesis of biotin-labeled cRNA and subsequent fragmentation were performed by the use of the IVT labeling kit (Affymetrix, Santa Clara, CA, USA). The cRNA yield was determined spectrophotometrically at 260 nm. Fragmented cRNA was stored at -80C until hybridization.
| | Sample_hyb_protocol | According to the manufacturer's instructions.
| | Sample_scan_protocol | According to the manufacturer's instructions.
| | Sample_data_processing | All CEL files in the series were processed using RMA in R using justRMA with default parameters.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Paul,,Pavlidis
| | Sample_contact_email | paul@chibi.ubc.ca
| | Sample_contact_department | Centre for High-Throughput Biology / Psychiatry
| | Sample_contact_institute | University of British Columbia
| | Sample_contact_address | 177 Michael Smith Laboratories 2185 East Mall
| | Sample_contact_city | Vancouver
| | Sample_contact_state | British Columbia
| | Sample_contact_zip/postal_code | V6T 1Z4
| | Sample_contact_country | Canada
| | Sample_contact_web_link | http://www.chibi.ubc.ca/faculty/pavlidis
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM155nnn/GSM155501/suppl/GSM155501.CEL.gz
| | Sample_series_id | GSE6751
| | Sample_data_row_count | 54675
| | |
|
GSM155502 | GPL570 |
|
Patient 54, time point 4
|
Patient 54 PBMC, collected at time point 4
|
Time: ten weeks after prior to commencement of periodontal therapy (four weeks after treatment end)
Tissue: Peripheral blood monocytes
Phenotype: severe periodontitis
|
Patients were recruited among the ones seeking treatment at the clinic for post-doctoral Periodontics, Columbia University College of Dental Medicine. To be eligible for enrollment, patients had to be diagnosed with severe periodontitis, with radiographic evidence of bone loss extending to greater or equal to 30% of the tooth length at several teeth. Additional inclusion criteria required: age greater or equal to 18 years; presence of greater or equal to 2 teeth/quadrant with a pocket depth of greater or equal to 6 mm and concomitant attachment loss of greater or equal to 3 mm; a minimum of 20 teeth present; no prior periodontal therapy; no systemic conditions or genetic disorders that entail the diagnosis of periodontitis as a manifestation of systemic diseases; no use of systemic antibiotics or regular use of anti-inflammatory drugs for the preceding 6-month period; no diabetes mellitus; no current use of tobacco products or of nicotine replacement medication; not currently pregnant. A total of 15 subjects, 7 male and 8 female, were enrolled. All participants were informed about the scope and procedures of the study and informed consent was obtained.
|
| Sample_geo_accession | GSM155502
| | Sample_status | Public on Dec 31 2007
| | Sample_submission_date | Jan 16 2007
| | Sample_last_update_date | Jan 16 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Fifty ml of blood were obtained by venipucture and collected in Vacutainer cell preparation tubes (Beckton-Dickinson, NJ, USA) with sodium heparin, and were used to harvest peripheral blood mononuclear cells (PBMCs). A 1:1 dilution with PBS was made and the diluted blood sample was centrifuged at 1,000 g in Ficoll tubes (Sigma Accuspin, St. Louis, MO). After washing and counting of the cells in a phase hemacytometer (Hauser Scientific, Horsham, PA), PBMCs were re-suspended in 80 microlitres of MACS buffer (PBS pH 7.2, 0.5% BSA and 2 mM EDTA) and incubated on ice with 20 microlitres of CD14 microbeads (Miltenyi Biotec, Auburn CA) per 107 total cells for 15 minutes. After washings, the cell suspension was applied to a MACS LS separation column (Miltenyi Biotec) placed in the magnetic field of a MACS separator (Miltenyi Biotec). Thereafter, the column was removed from the separator and CD14 positive cells were collected by washings in MACS buffer.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | CD14 positive cells were vigorously pipetted in Trizol (Invitrogen Life Technologies, Carlsbad, CA, USA). After incubation with chloroform and centrifugation at 12,000 g, RNA in the upper aqueous phase was precipitated by mixing with isopropyl alcohol, further centrifugation and washing in 75% ethanol. Further purification of the extracted RNA was achieved by the use of the RNeasy total RNA isolation kit (Qiagen, Valencia, CA, USA) according to the manufacturer.s instructions. The purified RNA was quantified spectrophotometrically. One hundred nanograms of total RNA were amplified and reverse transcribed using the GeneChip expression 3.-amplification two-cycle cDNA synthesis kit (Affymetrix, Santa Clara, CA, USA) and the MEGAscript T7 transcription kit (Ambion, Austin, TX, USA) according to the manufacturers. instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Synthesis of biotin-labeled cRNA and subsequent fragmentation were performed by the use of the IVT labeling kit (Affymetrix, Santa Clara, CA, USA). The cRNA yield was determined spectrophotometrically at 260 nm. Fragmented cRNA was stored at -80C until hybridization.
| | Sample_hyb_protocol | According to the manufacturer's instructions.
| | Sample_scan_protocol | According to the manufacturer's instructions.
| | Sample_data_processing | All CEL files in the series were processed using RMA in R using justRMA with default parameters.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Paul,,Pavlidis
| | Sample_contact_email | paul@chibi.ubc.ca
| | Sample_contact_department | Centre for High-Throughput Biology / Psychiatry
| | Sample_contact_institute | University of British Columbia
| | Sample_contact_address | 177 Michael Smith Laboratories 2185 East Mall
| | Sample_contact_city | Vancouver
| | Sample_contact_state | British Columbia
| | Sample_contact_zip/postal_code | V6T 1Z4
| | Sample_contact_country | Canada
| | Sample_contact_web_link | http://www.chibi.ubc.ca/faculty/pavlidis
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM155nnn/GSM155502/suppl/GSM155502.CEL.gz
| | Sample_series_id | GSE6751
| | Sample_data_row_count | 54675
| | |
|
GSM155503 | GPL570 |
|
Patient 55, time point 1
|
Patient 55 PBMC, collected at time point 1
|
Time: one week prior to commencement of periodontal therapy
Tissue: Peripheral blood monocytes
Phenotype: severe periodontitis
|
Patients were recruited among the ones seeking treatment at the clinic for post-doctoral Periodontics, Columbia University College of Dental Medicine. To be eligible for enrollment, patients had to be diagnosed with severe periodontitis, with radiographic evidence of bone loss extending to greater or equal to 30% of the tooth length at several teeth. Additional inclusion criteria required: age greater or equal to 18 years; presence of greater or equal to 2 teeth/quadrant with a pocket depth of greater or equal to 6 mm and concomitant attachment loss of greater or equal to 3 mm; a minimum of 20 teeth present; no prior periodontal therapy; no systemic conditions or genetic disorders that entail the diagnosis of periodontitis as a manifestation of systemic diseases; no use of systemic antibiotics or regular use of anti-inflammatory drugs for the preceding 6-month period; no diabetes mellitus; no current use of tobacco products or of nicotine replacement medication; not currently pregnant. A total of 15 subjects, 7 male and 8 female, were enrolled. All participants were informed about the scope and procedures of the study and informed consent was obtained.
|
| Sample_geo_accession | GSM155503
| | Sample_status | Public on Dec 31 2007
| | Sample_submission_date | Jan 16 2007
| | Sample_last_update_date | Jan 16 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Fifty ml of blood were obtained by venipucture and collected in Vacutainer cell preparation tubes (Beckton-Dickinson, NJ, USA) with sodium heparin, and were used to harvest peripheral blood mononuclear cells (PBMCs). A 1:1 dilution with PBS was made and the diluted blood sample was centrifuged at 1,000 g in Ficoll tubes (Sigma Accuspin, St. Louis, MO). After washing and counting of the cells in a phase hemacytometer (Hauser Scientific, Horsham, PA), PBMCs were re-suspended in 80 microlitres of MACS buffer (PBS pH 7.2, 0.5% BSA and 2 mM EDTA) and incubated on ice with 20 microlitres of CD14 microbeads (Miltenyi Biotec, Auburn CA) per 107 total cells for 15 minutes. After washings, the cell suspension was applied to a MACS LS separation column (Miltenyi Biotec) placed in the magnetic field of a MACS separator (Miltenyi Biotec). Thereafter, the column was removed from the separator and CD14 positive cells were collected by washings in MACS buffer.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | CD14 positive cells were vigorously pipetted in Trizol (Invitrogen Life Technologies, Carlsbad, CA, USA). After incubation with chloroform and centrifugation at 12,000 g, RNA in the upper aqueous phase was precipitated by mixing with isopropyl alcohol, further centrifugation and washing in 75% ethanol. Further purification of the extracted RNA was achieved by the use of the RNeasy total RNA isolation kit (Qiagen, Valencia, CA, USA) according to the manufacturer.s instructions. The purified RNA was quantified spectrophotometrically. One hundred nanograms of total RNA were amplified and reverse transcribed using the GeneChip expression 3.-amplification two-cycle cDNA synthesis kit (Affymetrix, Santa Clara, CA, USA) and the MEGAscript T7 transcription kit (Ambion, Austin, TX, USA) according to the manufacturers. instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Synthesis of biotin-labeled cRNA and subsequent fragmentation were performed by the use of the IVT labeling kit (Affymetrix, Santa Clara, CA, USA). The cRNA yield was determined spectrophotometrically at 260 nm. Fragmented cRNA was stored at -80C until hybridization.
| | Sample_hyb_protocol | According to the manufacturer's instructions.
| | Sample_scan_protocol | According to the manufacturer's instructions.
| | Sample_data_processing | All CEL files in the series were processed using RMA in R using justRMA with default parameters.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Paul,,Pavlidis
| | Sample_contact_email | paul@chibi.ubc.ca
| | Sample_contact_department | Centre for High-Throughput Biology / Psychiatry
| | Sample_contact_institute | University of British Columbia
| | Sample_contact_address | 177 Michael Smith Laboratories 2185 East Mall
| | Sample_contact_city | Vancouver
| | Sample_contact_state | British Columbia
| | Sample_contact_zip/postal_code | V6T 1Z4
| | Sample_contact_country | Canada
| | Sample_contact_web_link | http://www.chibi.ubc.ca/faculty/pavlidis
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM155nnn/GSM155503/suppl/GSM155503.CEL.gz
| | Sample_series_id | GSE6751
| | Sample_data_row_count | 54675
| | |
|
GSM155504 | GPL570 |
|
Patient 55, time point 2
|
Patient 55 PBMC, collected at time point 2
|
Time: at commencement of periodontal therapy
Tissue: Peripheral blood monocytes
Phenotype: severe periodontitis
|
Patients were recruited among the ones seeking treatment at the clinic for post-doctoral Periodontics, Columbia University College of Dental Medicine. To be eligible for enrollment, patients had to be diagnosed with severe periodontitis, with radiographic evidence of bone loss extending to greater or equal to 30% of the tooth length at several teeth. Additional inclusion criteria required: age greater or equal to 18 years; presence of greater or equal to 2 teeth/quadrant with a pocket depth of greater or equal to 6 mm and concomitant attachment loss of greater or equal to 3 mm; a minimum of 20 teeth present; no prior periodontal therapy; no systemic conditions or genetic disorders that entail the diagnosis of periodontitis as a manifestation of systemic diseases; no use of systemic antibiotics or regular use of anti-inflammatory drugs for the preceding 6-month period; no diabetes mellitus; no current use of tobacco products or of nicotine replacement medication; not currently pregnant. A total of 15 subjects, 7 male and 8 female, were enrolled. All participants were informed about the scope and procedures of the study and informed consent was obtained.
|
| Sample_geo_accession | GSM155504
| | Sample_status | Public on Dec 31 2007
| | Sample_submission_date | Jan 16 2007
| | Sample_last_update_date | Jan 16 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Fifty ml of blood were obtained by venipucture and collected in Vacutainer cell preparation tubes (Beckton-Dickinson, NJ, USA) with sodium heparin, and were used to harvest peripheral blood mononuclear cells (PBMCs). A 1:1 dilution with PBS was made and the diluted blood sample was centrifuged at 1,000 g in Ficoll tubes (Sigma Accuspin, St. Louis, MO). After washing and counting of the cells in a phase hemacytometer (Hauser Scientific, Horsham, PA), PBMCs were re-suspended in 80 microlitres of MACS buffer (PBS pH 7.2, 0.5% BSA and 2 mM EDTA) and incubated on ice with 20 microlitres of CD14 microbeads (Miltenyi Biotec, Auburn CA) per 107 total cells for 15 minutes. After washings, the cell suspension was applied to a MACS LS separation column (Miltenyi Biotec) placed in the magnetic field of a MACS separator (Miltenyi Biotec). Thereafter, the column was removed from the separator and CD14 positive cells were collected by washings in MACS buffer.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | CD14 positive cells were vigorously pipetted in Trizol (Invitrogen Life Technologies, Carlsbad, CA, USA). After incubation with chloroform and centrifugation at 12,000 g, RNA in the upper aqueous phase was precipitated by mixing with isopropyl alcohol, further centrifugation and washing in 75% ethanol. Further purification of the extracted RNA was achieved by the use of the RNeasy total RNA isolation kit (Qiagen, Valencia, CA, USA) according to the manufacturer.s instructions. The purified RNA was quantified spectrophotometrically. One hundred nanograms of total RNA were amplified and reverse transcribed using the GeneChip expression 3.-amplification two-cycle cDNA synthesis kit (Affymetrix, Santa Clara, CA, USA) and the MEGAscript T7 transcription kit (Ambion, Austin, TX, USA) according to the manufacturers. instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Synthesis of biotin-labeled cRNA and subsequent fragmentation were performed by the use of the IVT labeling kit (Affymetrix, Santa Clara, CA, USA). The cRNA yield was determined spectrophotometrically at 260 nm. Fragmented cRNA was stored at -80C until hybridization.
| | Sample_hyb_protocol | According to the manufacturer's instructions.
| | Sample_scan_protocol | According to the manufacturer's instructions.
| | Sample_data_processing | All CEL files in the series were processed using RMA in R using justRMA with default parameters.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Paul,,Pavlidis
| | Sample_contact_email | paul@chibi.ubc.ca
| | Sample_contact_department | Centre for High-Throughput Biology / Psychiatry
| | Sample_contact_institute | University of British Columbia
| | Sample_contact_address | 177 Michael Smith Laboratories 2185 East Mall
| | Sample_contact_city | Vancouver
| | Sample_contact_state | British Columbia
| | Sample_contact_zip/postal_code | V6T 1Z4
| | Sample_contact_country | Canada
| | Sample_contact_web_link | http://www.chibi.ubc.ca/faculty/pavlidis
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM155nnn/GSM155504/suppl/GSM155504.CEL.gz
| | Sample_series_id | GSE6751
| | Sample_data_row_count | 54675
| | |
|
GSM155505 | GPL570 |
|
Patient 55, time point 3
|
Patient 55 PBMC, collected at time point 3
|
Time: six weeks after commencement of periodontal therapy (after treatment end)
Tissue: Peripheral blood monocytes
Phenotype: severe periodontitis
|
Patients were recruited among the ones seeking treatment at the clinic for post-doctoral Periodontics, Columbia University College of Dental Medicine. To be eligible for enrollment, patients had to be diagnosed with severe periodontitis, with radiographic evidence of bone loss extending to greater or equal to 30% of the tooth length at several teeth. Additional inclusion criteria required: age greater or equal to 18 years; presence of greater or equal to 2 teeth/quadrant with a pocket depth of greater or equal to 6 mm and concomitant attachment loss of greater or equal to 3 mm; a minimum of 20 teeth present; no prior periodontal therapy; no systemic conditions or genetic disorders that entail the diagnosis of periodontitis as a manifestation of systemic diseases; no use of systemic antibiotics or regular use of anti-inflammatory drugs for the preceding 6-month period; no diabetes mellitus; no current use of tobacco products or of nicotine replacement medication; not currently pregnant. A total of 15 subjects, 7 male and 8 female, were enrolled. All participants were informed about the scope and procedures of the study and informed consent was obtained.
|
| Sample_geo_accession | GSM155505
| | Sample_status | Public on Dec 31 2007
| | Sample_submission_date | Jan 16 2007
| | Sample_last_update_date | Jan 16 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Fifty ml of blood were obtained by venipucture and collected in Vacutainer cell preparation tubes (Beckton-Dickinson, NJ, USA) with sodium heparin, and were used to harvest peripheral blood mononuclear cells (PBMCs). A 1:1 dilution with PBS was made and the diluted blood sample was centrifuged at 1,000 g in Ficoll tubes (Sigma Accuspin, St. Louis, MO). After washing and counting of the cells in a phase hemacytometer (Hauser Scientific, Horsham, PA), PBMCs were re-suspended in 80 microlitres of MACS buffer (PBS pH 7.2, 0.5% BSA and 2 mM EDTA) and incubated on ice with 20 microlitres of CD14 microbeads (Miltenyi Biotec, Auburn CA) per 107 total cells for 15 minutes. After washings, the cell suspension was applied to a MACS LS separation column (Miltenyi Biotec) placed in the magnetic field of a MACS separator (Miltenyi Biotec). Thereafter, the column was removed from the separator and CD14 positive cells were collected by washings in MACS buffer.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | CD14 positive cells were vigorously pipetted in Trizol (Invitrogen Life Technologies, Carlsbad, CA, USA). After incubation with chloroform and centrifugation at 12,000 g, RNA in the upper aqueous phase was precipitated by mixing with isopropyl alcohol, further centrifugation and washing in 75% ethanol. Further purification of the extracted RNA was achieved by the use of the RNeasy total RNA isolation kit (Qiagen, Valencia, CA, USA) according to the manufacturer.s instructions. The purified RNA was quantified spectrophotometrically. One hundred nanograms of total RNA were amplified and reverse transcribed using the GeneChip expression 3.-amplification two-cycle cDNA synthesis kit (Affymetrix, Santa Clara, CA, USA) and the MEGAscript T7 transcription kit (Ambion, Austin, TX, USA) according to the manufacturers. instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Synthesis of biotin-labeled cRNA and subsequent fragmentation were performed by the use of the IVT labeling kit (Affymetrix, Santa Clara, CA, USA). The cRNA yield was determined spectrophotometrically at 260 nm. Fragmented cRNA was stored at -80C until hybridization.
| | Sample_hyb_protocol | According to the manufacturer's instructions.
| | Sample_scan_protocol | According to the manufacturer's instructions.
| | Sample_data_processing | All CEL files in the series were processed using RMA in R using justRMA with default parameters.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Paul,,Pavlidis
| | Sample_contact_email | paul@chibi.ubc.ca
| | Sample_contact_department | Centre for High-Throughput Biology / Psychiatry
| | Sample_contact_institute | University of British Columbia
| | Sample_contact_address | 177 Michael Smith Laboratories 2185 East Mall
| | Sample_contact_city | Vancouver
| | Sample_contact_state | British Columbia
| | Sample_contact_zip/postal_code | V6T 1Z4
| | Sample_contact_country | Canada
| | Sample_contact_web_link | http://www.chibi.ubc.ca/faculty/pavlidis
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM155nnn/GSM155505/suppl/GSM155505.CEL.gz
| | Sample_series_id | GSE6751
| | Sample_data_row_count | 54675
| | |
|
GSM155506 | GPL570 |
|
Patient 55, time point 4
|
Patient 55 PBMC, collected at time point 4
|
Time: ten weeks after prior to commencement of periodontal therapy (four weeks after treatment end)
Tissue: Peripheral blood monocytes
Phenotype: severe periodontitis
|
Patients were recruited among the ones seeking treatment at the clinic for post-doctoral Periodontics, Columbia University College of Dental Medicine. To be eligible for enrollment, patients had to be diagnosed with severe periodontitis, with radiographic evidence of bone loss extending to greater or equal to 30% of the tooth length at several teeth. Additional inclusion criteria required: age greater or equal to 18 years; presence of greater or equal to 2 teeth/quadrant with a pocket depth of greater or equal to 6 mm and concomitant attachment loss of greater or equal to 3 mm; a minimum of 20 teeth present; no prior periodontal therapy; no systemic conditions or genetic disorders that entail the diagnosis of periodontitis as a manifestation of systemic diseases; no use of systemic antibiotics or regular use of anti-inflammatory drugs for the preceding 6-month period; no diabetes mellitus; no current use of tobacco products or of nicotine replacement medication; not currently pregnant. A total of 15 subjects, 7 male and 8 female, were enrolled. All participants were informed about the scope and procedures of the study and informed consent was obtained.
|
| Sample_geo_accession | GSM155506
| | Sample_status | Public on Dec 31 2007
| | Sample_submission_date | Jan 16 2007
| | Sample_last_update_date | Jan 16 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Fifty ml of blood were obtained by venipucture and collected in Vacutainer cell preparation tubes (Beckton-Dickinson, NJ, USA) with sodium heparin, and were used to harvest peripheral blood mononuclear cells (PBMCs). A 1:1 dilution with PBS was made and the diluted blood sample was centrifuged at 1,000 g in Ficoll tubes (Sigma Accuspin, St. Louis, MO). After washing and counting of the cells in a phase hemacytometer (Hauser Scientific, Horsham, PA), PBMCs were re-suspended in 80 microlitres of MACS buffer (PBS pH 7.2, 0.5% BSA and 2 mM EDTA) and incubated on ice with 20 microlitres of CD14 microbeads (Miltenyi Biotec, Auburn CA) per 107 total cells for 15 minutes. After washings, the cell suspension was applied to a MACS LS separation column (Miltenyi Biotec) placed in the magnetic field of a MACS separator (Miltenyi Biotec). Thereafter, the column was removed from the separator and CD14 positive cells were collected by washings in MACS buffer.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | CD14 positive cells were vigorously pipetted in Trizol (Invitrogen Life Technologies, Carlsbad, CA, USA). After incubation with chloroform and centrifugation at 12,000 g, RNA in the upper aqueous phase was precipitated by mixing with isopropyl alcohol, further centrifugation and washing in 75% ethanol. Further purification of the extracted RNA was achieved by the use of the RNeasy total RNA isolation kit (Qiagen, Valencia, CA, USA) according to the manufacturer.s instructions. The purified RNA was quantified spectrophotometrically. One hundred nanograms of total RNA were amplified and reverse transcribed using the GeneChip expression 3.-amplification two-cycle cDNA synthesis kit (Affymetrix, Santa Clara, CA, USA) and the MEGAscript T7 transcription kit (Ambion, Austin, TX, USA) according to the manufacturers. instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Synthesis of biotin-labeled cRNA and subsequent fragmentation were performed by the use of the IVT labeling kit (Affymetrix, Santa Clara, CA, USA). The cRNA yield was determined spectrophotometrically at 260 nm. Fragmented cRNA was stored at -80C until hybridization.
| | Sample_hyb_protocol | According to the manufacturer's instructions.
| | Sample_scan_protocol | According to the manufacturer's instructions.
| | Sample_data_processing | All CEL files in the series were processed using RMA in R using justRMA with default parameters.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Paul,,Pavlidis
| | Sample_contact_email | paul@chibi.ubc.ca
| | Sample_contact_department | Centre for High-Throughput Biology / Psychiatry
| | Sample_contact_institute | University of British Columbia
| | Sample_contact_address | 177 Michael Smith Laboratories 2185 East Mall
| | Sample_contact_city | Vancouver
| | Sample_contact_state | British Columbia
| | Sample_contact_zip/postal_code | V6T 1Z4
| | Sample_contact_country | Canada
| | Sample_contact_web_link | http://www.chibi.ubc.ca/faculty/pavlidis
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM155nnn/GSM155506/suppl/GSM155506.CEL.gz
| | Sample_series_id | GSE6751
| | Sample_data_row_count | 54675
| | |
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