Search results for the GEO ID: GSE9723  |
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|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM245725 | GPL96 |
|
HIGK cells infected with Porphyromonas gingivalis, biological rep1
|
Human Immortalized Gingival Keratinocyte
|
HIGK cells were originally obtained by transfection of primary gingival epithelial cells with E6/E7 from HPV (Oda et al., 1990).
HIGK cells were reported to be stable for over 350 passages (Oda et al., 1996). They were originally obtained at passage number 82, and used by passage number 90 for the the experiments described herein.
|
Gene expression data from Porphyromonas gingivalis-infected HIGK cells.
Human Immortalized Gingival Keratinocyte (Oda, D., and Watson, E. (1990) Human oral epithelial cell culture. Improved conditions for reproducible culture in serum-free medium. In Vitro Cell Dev Biol Anim 26: 589–595. Oda, D., Bigler, L., Lee, P., and Blanton, R. (1996) HPV immortalization of human oral epithelial cells: a model for carcinogenesis. Exp Cell Res 226: 164–169.)
|
| Sample_geo_accession | GSM245725
| | Sample_status | Public on Apr 15 2008
| | Sample_submission_date | Nov 28 2007
| | Sample_last_update_date | Aug 14 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Bacteria at mid-log phase were harvested and washed by centrifugation, and resuspended in antibiotic-free K-SFM media. HIGK cells (10e7) were co-cultured with bacteria to give a total association (adhered plus invaded) of approximately 100 organisms per epithelial cell. Numbers of adhered and invaded organisms were confirmed in parallel experiments by plate counting. After 2 hours at 37C in 5% CO2, the HIGK cells were lysed with Trizol (Invitrogen) prior to RNA extraction.
| | Sample_growth_protocol_ch1 | HIGK cells were cultured under 5% CO2 in keratinocyte serum-free medium (K-SFM, Gibco/Invitrogen, Carlsbad, CA) supplemented with: 0.05 mM calcium chloride, 200 mM L-glutamine (Gibco/Invitrogen, Carlsbad, CA).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted, DNAse-treated, purified and quantified according to standard methods (Qiagen and Affymetrix).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cRNA synthesis was performed with 10 ug of total cellular RNA, based on the Affymetrix protocol. Double-stranded cDNA was synthesized according to a standardized protocol (SuperScript doublestranded cDNA synthesis kit; Invitrogen, Carlsbad, CA). cRNA was transcribed in vitro, incorporating biotinylated nucleotides by using a BioArray high-yield RNA transcript labeling kit (T7) (Enzo Life Sciences, Farmingdale, NY).
| | Sample_hyb_protocol | Following fragmentation, human HG U133-A oligonucleotide microarrays (Affymetrix) were hybridized for 16 h at 45C, stained with phycoerythrin-conjugated streptavidin and washed according to the Affymetrix protocol (EukGE-WS2v4).
| | Sample_scan_protocol | GeneChips were scanned with an Affymetrix fluidics station, and scanned with an Affymetrix GeneChip 3000 scanner.
| | Sample_data_processing | The data were analyzed with Affymetrix GCOS using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.
| | Sample_platform_id | GPL96
| | Sample_contact_name | Martin,,Handfield
| | Sample_contact_email | mhandfield@dental.ufl.edu
| | Sample_contact_phone | 352-846-0763
| | Sample_contact_laboratory | Handfield Lab
| | Sample_contact_department | Oral Biology
| | Sample_contact_institute | University of Florida
| | Sample_contact_address | 1600 SW Archer Road, BOX 100424
| | Sample_contact_city | Gainesville
| | Sample_contact_state | FL
| | Sample_contact_zip/postal_code | 32610-0424
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM245nnn/GSM245725/suppl/GSM245725.CEL.gz
| | Sample_series_id | GSE9723
| | Sample_series_id | GSE10526
| | Sample_data_row_count | 22283
| | |
|
GSM245726 | GPL96 |
|
HIGK cells infected with Porphyromonas gingivalis, biological rep2
|
Human Immortalized Gingival Keratinocyte
|
HIGK cells were originally obtained by transfection of primary gingival epithelial cells with E6/E7 from HPV (Oda et al., 1990).
HIGK cells were reported to be stable for over 350 passages (Oda et al., 1996). They were originally obtained at passage number 82, and used by passage number 90 for the the experiments described herein.
|
Gene expression data from Porphyromonas gingivalis-infected HIGK cells.
Human Immortalized Gingival Keratinocyte (Oda, D., and Watson, E. (1990) Human oral epithelial cell culture. Improved conditions for reproducible culture in serum-free medium. In Vitro Cell Dev Biol Anim 26: 589–595. Oda, D., Bigler, L., Lee, P., and Blanton, R. (1996) HPV immortalization of human oral epithelial cells: a model for carcinogenesis. Exp Cell Res 226: 164–169.)
|
| Sample_geo_accession | GSM245726
| | Sample_status | Public on Apr 15 2008
| | Sample_submission_date | Nov 28 2007
| | Sample_last_update_date | Aug 14 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Bacteria at mid-log phase were harvested and washed by centrifugation, and resuspended in antibiotic-free K-SFM media. HIGK cells (10e7) were co-cultured with bacteria to give a total association (adhered plus invaded) of approximately 100 organisms per epithelial cell. Numbers of adhered and invaded organisms were confirmed in parallel experiments by plate counting. After 2 hours at 37C in 5% CO2, the HIGK cells were lysed with Trizol (Invitrogen) prior to RNA extraction.
| | Sample_growth_protocol_ch1 | HIGK cells were cultured under 5% CO2 in keratinocyte serum-free medium (K-SFM, Gibco/Invitrogen, Carlsbad, CA) supplemented with: 0.05 mM calcium chloride, 200 mM L-glutamine (Gibco/Invitrogen, Carlsbad, CA).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted, DNAse-treated, purified and quantified according to standard methods (Qiagen and Affymetrix).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cRNA synthesis was performed with 10 ug of total cellular RNA, based on the Affymetrix protocol. Double-stranded cDNA was synthesized according to a standardized protocol (SuperScript doublestranded cDNA synthesis kit; Invitrogen, Carlsbad, CA). cRNA was transcribed in vitro, incorporating biotinylated nucleotides by using a BioArray high-yield RNA transcript labeling kit (T7) (Enzo Life Sciences, Farmingdale, NY).
| | Sample_hyb_protocol | Following fragmentation, human HG U133-A oligonucleotide microarrays (Affymetrix) were hybridized for 16 h at 45C, stained with phycoerythrin-conjugated streptavidin and washed according to the Affymetrix protocol (EukGE-WS2v4).
| | Sample_scan_protocol | GeneChips were scanned with an Affymetrix fluidics station, and scanned with an Affymetrix GeneChip 3000 scanner.
| | Sample_data_processing | The data were analyzed with Affymetrix GCOS using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.
| | Sample_platform_id | GPL96
| | Sample_contact_name | Martin,,Handfield
| | Sample_contact_email | mhandfield@dental.ufl.edu
| | Sample_contact_phone | 352-846-0763
| | Sample_contact_laboratory | Handfield Lab
| | Sample_contact_department | Oral Biology
| | Sample_contact_institute | University of Florida
| | Sample_contact_address | 1600 SW Archer Road, BOX 100424
| | Sample_contact_city | Gainesville
| | Sample_contact_state | FL
| | Sample_contact_zip/postal_code | 32610-0424
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM245nnn/GSM245726/suppl/GSM245726.CEL.gz
| | Sample_series_id | GSE9723
| | Sample_series_id | GSE10526
| | Sample_data_row_count | 22283
| | |
|
GSM245727 | GPL96 |
|
HIGK cells infected with Porphyromonas gingivalis, biological rep3
|
Human Immortalized Gingival Keratinocyte
|
HIGK cells were originally obtained by transfection of primary gingival epithelial cells with E6/E7 from HPV (Oda et al., 1990).
HIGK cells were reported to be stable for over 350 passages (Oda et al., 1996). They were originally obtained at passage number 82, and used by passage number 90 for the the experiments described herein.
|
Gene expression data from Porphyromonas gingivalis-infected HIGK cells.
Human Immortalized Gingival Keratinocyte (Oda, D., and Watson, E. (1990) Human oral epithelial cell culture. Improved conditions for reproducible culture in serum-free medium. In Vitro Cell Dev Biol Anim 26: 589–595. Oda, D., Bigler, L., Lee, P., and Blanton, R. (1996) HPV immortalization of human oral epithelial cells: a model for carcinogenesis. Exp Cell Res 226: 164–169.)
|
| Sample_geo_accession | GSM245727
| | Sample_status | Public on Apr 15 2008
| | Sample_submission_date | Nov 28 2007
| | Sample_last_update_date | Aug 14 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Bacteria at mid-log phase were harvested and washed by centrifugation, and resuspended in antibiotic-free K-SFM media. HIGK cells (10e7) were co-cultured with bacteria to give a total association (adhered plus invaded) of approximately 100 organisms per epithelial cell. Numbers of adhered and invaded organisms were confirmed in parallel experiments by plate counting. After 2 hours at 37C in 5% CO2, the HIGK cells were lysed with Trizol (Invitrogen) prior to RNA extraction.
| | Sample_growth_protocol_ch1 | HIGK cells were cultured under 5% CO2 in keratinocyte serum-free medium (K-SFM, Gibco/Invitrogen, Carlsbad, CA) supplemented with: 0.05 mM calcium chloride, 200 mM L-glutamine (Gibco/Invitrogen, Carlsbad, CA).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted, DNAse-treated, purified and quantified according to standard methods (Qiagen and Affymetrix).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cRNA synthesis was performed with 10 ug of total cellular RNA, based on the Affymetrix protocol. Double-stranded cDNA was synthesized according to a standardized protocol (SuperScript doublestranded cDNA synthesis kit; Invitrogen, Carlsbad, CA). cRNA was transcribed in vitro, incorporating biotinylated nucleotides by using a BioArray high-yield RNA transcript labeling kit (T7) (Enzo Life Sciences, Farmingdale, NY).
| | Sample_hyb_protocol | Following fragmentation, human HG U133-A oligonucleotide microarrays (Affymetrix) were hybridized for 16 h at 45C, stained with phycoerythrin-conjugated streptavidin and washed according to the Affymetrix protocol (EukGE-WS2v4).
| | Sample_scan_protocol | GeneChips were scanned with an Affymetrix fluidics station, and scanned with an Affymetrix GeneChip 3000 scanner.
| | Sample_data_processing | The data were analyzed with Affymetrix GCOS using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.
| | Sample_platform_id | GPL96
| | Sample_contact_name | Martin,,Handfield
| | Sample_contact_email | mhandfield@dental.ufl.edu
| | Sample_contact_phone | 352-846-0763
| | Sample_contact_laboratory | Handfield Lab
| | Sample_contact_department | Oral Biology
| | Sample_contact_institute | University of Florida
| | Sample_contact_address | 1600 SW Archer Road, BOX 100424
| | Sample_contact_city | Gainesville
| | Sample_contact_state | FL
| | Sample_contact_zip/postal_code | 32610-0424
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM245nnn/GSM245727/suppl/GSM245727.CEL.gz
| | Sample_series_id | GSE9723
| | Sample_series_id | GSE10526
| | Sample_data_row_count | 22283
| | |
|
GSM245728 | GPL96 |
|
HIGK cells infected with Porphyromonas gingivalis, biological rep4
|
Human Immortalized Gingival Keratinocyte
|
HIGK cells were originally obtained by transfection of primary gingival epithelial cells with E6/E7 from HPV (Oda et al., 1990).
HIGK cells were reported to be stable for over 350 passages (Oda et al., 1996). They were originally obtained at passage number 82, and used by passage number 90 for the the experiments described herein.
|
Gene expression data from Porphyromonas gingivalis-infected HIGK cells.
Human Immortalized Gingival Keratinocyte (Oda, D., and Watson, E. (1990) Human oral epithelial cell culture. Improved conditions for reproducible culture in serum-free medium. In Vitro Cell Dev Biol Anim 26: 589–595. Oda, D., Bigler, L., Lee, P., and Blanton, R. (1996) HPV immortalization of human oral epithelial cells: a model for carcinogenesis. Exp Cell Res 226: 164–169.)
|
| Sample_geo_accession | GSM245728
| | Sample_status | Public on Apr 15 2008
| | Sample_submission_date | Nov 28 2007
| | Sample_last_update_date | Aug 14 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Bacteria at mid-log phase were harvested and washed by centrifugation, and resuspended in antibiotic-free K-SFM media. HIGK cells (10e7) were co-cultured with bacteria to give a total association (adhered plus invaded) of approximately 100 organisms per epithelial cell. Numbers of adhered and invaded organisms were confirmed in parallel experiments by plate counting. After 2 hours at 37C in 5% CO2, the HIGK cells were lysed with Trizol (Invitrogen) prior to RNA extraction.
| | Sample_growth_protocol_ch1 | HIGK cells were cultured under 5% CO2 in keratinocyte serum-free medium (K-SFM, Gibco/Invitrogen, Carlsbad, CA) supplemented with: 0.05 mM calcium chloride, 200 mM L-glutamine (Gibco/Invitrogen, Carlsbad, CA).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted, DNAse-treated, purified and quantified according to standard methods (Qiagen and Affymetrix).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cRNA synthesis was performed with 10 ug of total cellular RNA, based on the Affymetrix protocol. Double-stranded cDNA was synthesized according to a standardized protocol (SuperScript doublestranded cDNA synthesis kit; Invitrogen, Carlsbad, CA). cRNA was transcribed in vitro, incorporating biotinylated nucleotides by using a BioArray high-yield RNA transcript labeling kit (T7) (Enzo Life Sciences, Farmingdale, NY).
| | Sample_hyb_protocol | Following fragmentation, human HG U133-A oligonucleotide microarrays (Affymetrix) were hybridized for 16 h at 45C, stained with phycoerythrin-conjugated streptavidin and washed according to the Affymetrix protocol (EukGE-WS2v4).
| | Sample_scan_protocol | GeneChips were scanned with an Affymetrix fluidics station, and scanned with an Affymetrix GeneChip 3000 scanner.
| | Sample_data_processing | The data were analyzed with Affymetrix GCOS using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.
| | Sample_platform_id | GPL96
| | Sample_contact_name | Martin,,Handfield
| | Sample_contact_email | mhandfield@dental.ufl.edu
| | Sample_contact_phone | 352-846-0763
| | Sample_contact_laboratory | Handfield Lab
| | Sample_contact_department | Oral Biology
| | Sample_contact_institute | University of Florida
| | Sample_contact_address | 1600 SW Archer Road, BOX 100424
| | Sample_contact_city | Gainesville
| | Sample_contact_state | FL
| | Sample_contact_zip/postal_code | 32610-0424
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM245nnn/GSM245728/suppl/GSM245728.CEL.gz
| | Sample_series_id | GSE9723
| | Sample_series_id | GSE10526
| | Sample_data_row_count | 22283
| | |
|
GSM245729 | GPL96 |
|
Sham infected HIGK cells, biological rep1 (1777)
|
Human Immortalized Gingival Keratinocyte
|
HIGK cells were originally obtained by transfection of primary gingival epithelial cells with E6/E7 from HPV (Oda et al., 1990).
HIGK cells were reported to be stable for over 350 passages (Oda et al., 1996). They were originally obtained at passage number 82, and used by passage number 90 for the the experiments described herein.
|
Gene expression data from uninfected HIGK cells.
Human Immortalized Gingival Keratinocyte (Oda, D., and Watson, E. (1990) Human oral epithelial cell culture. Improved conditions for reproducible culture in serum-free medium. In Vitro Cell Dev Biol Anim 26: 589–595. Oda, D., Bigler, L., Lee, P., and Blanton, R. (1996) HPV immortalization of human oral epithelial cells: a model for carcinogenesis. Exp Cell Res 226: 164–169.)
|
| Sample_geo_accession | GSM245729
| | Sample_status | Public on Mar 01 2008
| | Sample_submission_date | Nov 28 2007
| | Sample_last_update_date | Aug 14 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | HIGK cells were sham infected with antibiotic-free K-SFM media. HIGK cells (10e7) were cultured for 2 hours at 37C in 5% CO2, and were lysed with Trizol (Invitrogen) prior to RNA extraction.
| | Sample_growth_protocol_ch1 | HIGK cells were cultured under 5% CO2 in keratinocyte serum-free medium (K-SFM, Gibco/Invitrogen, Carlsbad, CA) supplemented with: 0.05 mM calcium chloride, 200 mM L-glutamine (Gibco/Invitrogen, Carlsbad, CA).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted, DNAse-treated, purified and quantified according to standard methods (Qiagen and Affymetrix).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cRNA synthesis was performed with 10 ug of total cellular RNA, based on the Affymetrix protocol. Double-stranded cDNA was synthesized according to a standardized protocol (SuperScript doublestranded cDNA synthesis kit; Invitrogen, Carlsbad, CA). cRNA was transcribed in vitro, incorporating biotinylated nucleotides by using a BioArray high-yield RNA transcript labeling kit (T7) (Enzo Life Sciences, Farmingdale, NY).
| | Sample_hyb_protocol | Following fragmentation, human HG U133-A oligonucleotide microarrays (Affymetrix) were hybridized for 16 h at 45C, stained with phycoerythrin-conjugated streptavidin and washed according to the Affymetrix protocol (EukGE-WS2v4).
| | Sample_scan_protocol | GeneChips were scanned with an Affymetrix fluidics station, and scanned with an Affymetrix GeneChip 3000 scanner.
| | Sample_data_processing | The data were analyzed with Affymetrix GCOS using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.
| | Sample_platform_id | GPL96
| | Sample_contact_name | Martin,,Handfield
| | Sample_contact_email | mhandfield@dental.ufl.edu
| | Sample_contact_phone | 352-846-0763
| | Sample_contact_laboratory | Handfield Lab
| | Sample_contact_department | Oral Biology
| | Sample_contact_institute | University of Florida
| | Sample_contact_address | 1600 SW Archer Road, BOX 100424
| | Sample_contact_city | Gainesville
| | Sample_contact_state | FL
| | Sample_contact_zip/postal_code | 32610-0424
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM245nnn/GSM245729/suppl/GSM245729.CEL.gz
| | Sample_series_id | GSE9723
| | Sample_data_row_count | 22283
| | |
|
GSM245730 | GPL96 |
|
Sham infected HIGK cells, biological rep2 (1778)
|
Human Immortalized Gingival Keratinocyte
|
HIGK cells were originally obtained by transfection of primary gingival epithelial cells with E6/E7 from HPV (Oda et al., 1990).
HIGK cells were reported to be stable for over 350 passages (Oda et al., 1996). They were originally obtained at passage number 82, and used by passage number 90 for the the experiments described herein.
|
Gene expression data from uninfected HIGK cells.
Human Immortalized Gingival Keratinocyte (Oda, D., and Watson, E. (1990) Human oral epithelial cell culture. Improved conditions for reproducible culture in serum-free medium. In Vitro Cell Dev Biol Anim 26: 589–595. Oda, D., Bigler, L., Lee, P., and Blanton, R. (1996) HPV immortalization of human oral epithelial cells: a model for carcinogenesis. Exp Cell Res 226: 164–169.)
|
| Sample_geo_accession | GSM245730
| | Sample_status | Public on Mar 01 2008
| | Sample_submission_date | Nov 28 2007
| | Sample_last_update_date | Aug 14 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | HIGK cells were sham infected with antibiotic-free K-SFM media. HIGK cells (10e7) were cultured for 2 hours at 37C in 5% CO2, and were lysed with Trizol (Invitrogen) prior to RNA extraction.
| | Sample_growth_protocol_ch1 | HIGK cells were cultured under 5% CO2 in keratinocyte serum-free medium (K-SFM, Gibco/Invitrogen, Carlsbad, CA) supplemented with: 0.05 mM calcium chloride, 200 mM L-glutamine (Gibco/Invitrogen, Carlsbad, CA).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted, DNAse-treated, purified and quantified according to standard methods (Qiagen and Affymetrix).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cRNA synthesis was performed with 10 ug of total cellular RNA, based on the Affymetrix protocol. Double-stranded cDNA was synthesized according to a standardized protocol (SuperScript doublestranded cDNA synthesis kit; Invitrogen, Carlsbad, CA). cRNA was transcribed in vitro, incorporating biotinylated nucleotides by using a BioArray high-yield RNA transcript labeling kit (T7) (Enzo Life Sciences, Farmingdale, NY).
| | Sample_hyb_protocol | Following fragmentation, human HG U133-A oligonucleotide microarrays (Affymetrix) were hybridized for 16 h at 45C, stained with phycoerythrin-conjugated streptavidin and washed according to the Affymetrix protocol (EukGE-WS2v4).
| | Sample_scan_protocol | GeneChips were scanned with an Affymetrix fluidics station, and scanned with an Affymetrix GeneChip 3000 scanner.
| | Sample_data_processing | The data were analyzed with Affymetrix GCOS using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.
| | Sample_platform_id | GPL96
| | Sample_contact_name | Martin,,Handfield
| | Sample_contact_email | mhandfield@dental.ufl.edu
| | Sample_contact_phone | 352-846-0763
| | Sample_contact_laboratory | Handfield Lab
| | Sample_contact_department | Oral Biology
| | Sample_contact_institute | University of Florida
| | Sample_contact_address | 1600 SW Archer Road, BOX 100424
| | Sample_contact_city | Gainesville
| | Sample_contact_state | FL
| | Sample_contact_zip/postal_code | 32610-0424
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM245nnn/GSM245730/suppl/GSM245730.CEL.gz
| | Sample_series_id | GSE9723
| | Sample_data_row_count | 22283
| | |
|
GSM245731 | GPL96 |
|
Sham infected HIGK cells, biological rep3 (1779)
|
Human Immortalized Gingival Keratinocyte
|
HIGK cells were originally obtained by transfection of primary gingival epithelial cells with E6/E7 from HPV (Oda et al., 1990).
HIGK cells were reported to be stable for over 350 passages (Oda et al., 1996). They were originally obtained at passage number 82, and used by passage number 90 for the the experiments described herein.
|
Gene expression data from uninfected HIGK cells.
Human Immortalized Gingival Keratinocyte (Oda, D., and Watson, E. (1990) Human oral epithelial cell culture. Improved conditions for reproducible culture in serum-free medium. In Vitro Cell Dev Biol Anim 26: 589–595. Oda, D., Bigler, L., Lee, P., and Blanton, R. (1996) HPV immortalization of human oral epithelial cells: a model for carcinogenesis. Exp Cell Res 226: 164–169.)
|
| Sample_geo_accession | GSM245731
| | Sample_status | Public on Mar 01 2008
| | Sample_submission_date | Nov 28 2007
| | Sample_last_update_date | Aug 14 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | HIGK cells were sham infected with antibiotic-free K-SFM media. HIGK cells (10e7) were cultured for 2 hours at 37C in 5% CO2, and were lysed with Trizol (Invitrogen) prior to RNA extraction.
| | Sample_growth_protocol_ch1 | HIGK cells were cultured under 5% CO2 in keratinocyte serum-free medium (K-SFM, Gibco/Invitrogen, Carlsbad, CA) supplemented with: 0.05 mM calcium chloride, 200 mM L-glutamine (Gibco/Invitrogen, Carlsbad, CA).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted, DNAse-treated, purified and quantified according to standard methods (Qiagen and Affymetrix).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cRNA synthesis was performed with 10 ug of total cellular RNA, based on the Affymetrix protocol. Double-stranded cDNA was synthesized according to a standardized protocol (SuperScript doublestranded cDNA synthesis kit; Invitrogen, Carlsbad, CA). cRNA was transcribed in vitro, incorporating biotinylated nucleotides by using a BioArray high-yield RNA transcript labeling kit (T7) (Enzo Life Sciences, Farmingdale, NY).
| | Sample_hyb_protocol | Following fragmentation, human HG U133-A oligonucleotide microarrays (Affymetrix) were hybridized for 16 h at 45C, stained with phycoerythrin-conjugated streptavidin and washed according to the Affymetrix protocol (EukGE-WS2v4).
| | Sample_scan_protocol | GeneChips were scanned with an Affymetrix fluidics station, and scanned with an Affymetrix GeneChip 3000 scanner.
| | Sample_data_processing | The data were analyzed with Affymetrix GCOS using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.
| | Sample_platform_id | GPL96
| | Sample_contact_name | Martin,,Handfield
| | Sample_contact_email | mhandfield@dental.ufl.edu
| | Sample_contact_phone | 352-846-0763
| | Sample_contact_laboratory | Handfield Lab
| | Sample_contact_department | Oral Biology
| | Sample_contact_institute | University of Florida
| | Sample_contact_address | 1600 SW Archer Road, BOX 100424
| | Sample_contact_city | Gainesville
| | Sample_contact_state | FL
| | Sample_contact_zip/postal_code | 32610-0424
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM245nnn/GSM245731/suppl/GSM245731.CEL.gz
| | Sample_series_id | GSE9723
| | Sample_data_row_count | 22283
| | |
|
GSM245732 | GPL96 |
|
Sham infected HIGK cells, biological rep4 (1780)
|
Human Immortalized Gingival Keratinocyte
|
HIGK cells were originally obtained by transfection of primary gingival epithelial cells with E6/E7 from HPV (Oda et al., 1990).
HIGK cells were reported to be stable for over 350 passages (Oda et al., 1996). They were originally obtained at passage number 82, and used by passage number 90 for the the experiments described herein.
|
Gene expression data from uninfected HIGK cells.
Human Immortalized Gingival Keratinocyte (Oda, D., and Watson, E. (1990) Human oral epithelial cell culture. Improved conditions for reproducible culture in serum-free medium. In Vitro Cell Dev Biol Anim 26: 589–595. Oda, D., Bigler, L., Lee, P., and Blanton, R. (1996) HPV immortalization of human oral epithelial cells: a model for carcinogenesis. Exp Cell Res 226: 164–169.)
|
| Sample_geo_accession | GSM245732
| | Sample_status | Public on Mar 01 2008
| | Sample_submission_date | Nov 28 2007
| | Sample_last_update_date | Aug 14 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | HIGK cells were sham infected with antibiotic-free K-SFM media. HIGK cells (10e7) were cultured for 2 hours at 37C in 5% CO2, and were lysed with Trizol (Invitrogen) prior to RNA extraction.
| | Sample_growth_protocol_ch1 | HIGK cells were cultured under 5% CO2 in keratinocyte serum-free medium (K-SFM, Gibco/Invitrogen, Carlsbad, CA) supplemented with: 0.05 mM calcium chloride, 200 mM L-glutamine (Gibco/Invitrogen, Carlsbad, CA).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted, DNAse-treated, purified and quantified according to standard methods (Qiagen and Affymetrix).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cRNA synthesis was performed with 10 ug of total cellular RNA, based on the Affymetrix protocol. Double-stranded cDNA was synthesized according to a standardized protocol (SuperScript doublestranded cDNA synthesis kit; Invitrogen, Carlsbad, CA). cRNA was transcribed in vitro, incorporating biotinylated nucleotides by using a BioArray high-yield RNA transcript labeling kit (T7) (Enzo Life Sciences, Farmingdale, NY).
| | Sample_hyb_protocol | Following fragmentation, human HG U133-A oligonucleotide microarrays (Affymetrix) were hybridized for 16 h at 45C, stained with phycoerythrin-conjugated streptavidin and washed according to the Affymetrix protocol (EukGE-WS2v4).
| | Sample_scan_protocol | GeneChips were scanned with an Affymetrix fluidics station, and scanned with an Affymetrix GeneChip 3000 scanner.
| | Sample_data_processing | The data were analyzed with Affymetrix GCOS using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.
| | Sample_platform_id | GPL96
| | Sample_contact_name | Martin,,Handfield
| | Sample_contact_email | mhandfield@dental.ufl.edu
| | Sample_contact_phone | 352-846-0763
| | Sample_contact_laboratory | Handfield Lab
| | Sample_contact_department | Oral Biology
| | Sample_contact_institute | University of Florida
| | Sample_contact_address | 1600 SW Archer Road, BOX 100424
| | Sample_contact_city | Gainesville
| | Sample_contact_state | FL
| | Sample_contact_zip/postal_code | 32610-0424
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM245nnn/GSM245732/suppl/GSM245732.CEL.gz
| | Sample_series_id | GSE9723
| | Sample_data_row_count | 22283
| | |
|
GSM245733 | GPL96 |
|
HIGK cells infected with Aggregatibacter actinomycetemcomitans, biological rep1
|
Human Immortalized Gingival Keratinocyte
|
HIGK cells were originally obtained by transfection of primary gingival epithelial cells with E6/E7 from HPV (Oda et al., 1990).
HIGK cells were reported to be stable for over 350 passages (Oda et al., 1996). They were originally obtained at passage number 82, and used by passage number 90 for the the experiments described herein.
|
Gene expression data from Aggregatibacter actinomycetemcomitans-infected HIGK cells.
Human Immortalized Gingival Keratinocyte (Oda, D., and Watson, E. (1990) Human oral epithelial cell culture. Improved conditions for reproducible culture in serum-free medium. In Vitro Cell Dev Biol Anim 26: 589–595. Oda, D., Bigler, L., Lee, P., and Blanton, R. (1996) HPV immortalization of human oral epithelial cells: a model for carcinogenesis. Exp Cell Res 226: 164–169.)
|
| Sample_geo_accession | GSM245733
| | Sample_status | Public on Mar 01 2008
| | Sample_submission_date | Nov 28 2007
| | Sample_last_update_date | Aug 14 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Bacteria at mid-log phase were harvested and washed by centrifugation, and resuspended in antibiotic-free K-SFM media. HIGK cells (10e7) were co-cultured with bacteria to give a total association (adhered plus invaded) of approximately 2500 organisms per epithelial cell. Numbers of adhered and invaded organisms were confirmed in parallel experiments by plate counting. After 2 hours at 37C in 5% CO2, the HIGK cells were lysed with Trizol (Invitrogen) prior to RNA extraction.
| | Sample_growth_protocol_ch1 | HIGK cells were cultured under 5% CO2 in keratinocyte serum-free medium (K-SFM, Gibco/Invitrogen, Carlsbad, CA) supplemented with: 0.05 mM calcium chloride, 200 mM L-glutamine (Gibco/Invitrogen, Carlsbad, CA).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted, DNAse-treated, purified and quantified according to standard methods (Qiagen and Affymetrix).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cRNA synthesis was performed with 10 ug of total cellular RNA, based on the Affymetrix protocol. Double-stranded cDNA was synthesized according to a standardized protocol (SuperScript doublestranded cDNA synthesis kit; Invitrogen, Carlsbad, CA). cRNA was transcribed in vitro, incorporating biotinylated nucleotides by using a BioArray high-yield RNA transcript labeling kit (T7) (Enzo Life Sciences, Farmingdale, NY).
| | Sample_hyb_protocol | Following fragmentation, human HG U133-A oligonucleotide microarrays (Affymetrix) were hybridized for 16 h at 45C, stained with phycoerythrin-conjugated streptavidin and washed according to the Affymetrix protocol (EukGE-WS2v4).
| | Sample_scan_protocol | GeneChips were scanned with an Affymetrix fluidics station, and scanned with an Affymetrix GeneChip 3000 scanner.
| | Sample_data_processing | The data were analyzed with Affymetrix GCOS using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.
| | Sample_platform_id | GPL96
| | Sample_contact_name | Martin,,Handfield
| | Sample_contact_email | mhandfield@dental.ufl.edu
| | Sample_contact_phone | 352-846-0763
| | Sample_contact_laboratory | Handfield Lab
| | Sample_contact_department | Oral Biology
| | Sample_contact_institute | University of Florida
| | Sample_contact_address | 1600 SW Archer Road, BOX 100424
| | Sample_contact_city | Gainesville
| | Sample_contact_state | FL
| | Sample_contact_zip/postal_code | 32610-0424
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM245nnn/GSM245733/suppl/GSM245733.CEL.gz
| | Sample_series_id | GSE9723
| | Sample_data_row_count | 22283
| | |
|
GSM245734 | GPL96 |
|
HIGK cells infected with Aggregatibacter actinomycetemcomitans, biological rep2
|
Human Immortalized Gingival Keratinocyte
|
HIGK cells were originally obtained by transfection of primary gingival epithelial cells with E6/E7 from HPV (Oda et al., 1990).
HIGK cells were reported to be stable for over 350 passages (Oda et al., 1996). They were originally obtained at passage number 82, and used by passage number 90 for the the experiments described herein.
|
Gene expression data from Aggregatibacter actinomycetemcomitans-infected HIGK cells.
Human Immortalized Gingival Keratinocyte (Oda, D., and Watson, E. (1990) Human oral epithelial cell culture. Improved conditions for reproducible culture in serum-free medium. In Vitro Cell Dev Biol Anim 26: 589–595. Oda, D., Bigler, L., Lee, P., and Blanton, R. (1996) HPV immortalization of human oral epithelial cells: a model for carcinogenesis. Exp Cell Res 226: 164–169.)
|
| Sample_geo_accession | GSM245734
| | Sample_status | Public on Mar 01 2008
| | Sample_submission_date | Nov 28 2007
| | Sample_last_update_date | Aug 14 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Bacteria at mid-log phase were harvested and washed by centrifugation, and resuspended in antibiotic-free K-SFM media. HIGK cells (10e7) were co-cultured with bacteria to give a total association (adhered plus invaded) of approximately 2500 organisms per epithelial cell. Numbers of adhered and invaded organisms were confirmed in parallel experiments by plate counting. After 2 hours at 37C in 5% CO2, the HIGK cells were lysed with Trizol (Invitrogen) prior to RNA extraction.
| | Sample_growth_protocol_ch1 | HIGK cells were cultured under 5% CO2 in keratinocyte serum-free medium (K-SFM, Gibco/Invitrogen, Carlsbad, CA) supplemented with: 0.05 mM calcium chloride, 200 mM L-glutamine (Gibco/Invitrogen, Carlsbad, CA).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted, DNAse-treated, purified and quantified according to standard methods (Qiagen and Affymetrix).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cRNA synthesis was performed with 10 ug of total cellular RNA, based on the Affymetrix protocol. Double-stranded cDNA was synthesized according to a standardized protocol (SuperScript doublestranded cDNA synthesis kit; Invitrogen, Carlsbad, CA). cRNA was transcribed in vitro, incorporating biotinylated nucleotides by using a BioArray high-yield RNA transcript labeling kit (T7) (Enzo Life Sciences, Farmingdale, NY).
| | Sample_hyb_protocol | Following fragmentation, human HG U133-A oligonucleotide microarrays (Affymetrix) were hybridized for 16 h at 45C, stained with phycoerythrin-conjugated streptavidin and washed according to the Affymetrix protocol (EukGE-WS2v4).
| | Sample_scan_protocol | GeneChips were scanned with an Affymetrix fluidics station, and scanned with an Affymetrix GeneChip 3000 scanner.
| | Sample_data_processing | The data were analyzed with Affymetrix GCOS using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.
| | Sample_platform_id | GPL96
| | Sample_contact_name | Martin,,Handfield
| | Sample_contact_email | mhandfield@dental.ufl.edu
| | Sample_contact_phone | 352-846-0763
| | Sample_contact_laboratory | Handfield Lab
| | Sample_contact_department | Oral Biology
| | Sample_contact_institute | University of Florida
| | Sample_contact_address | 1600 SW Archer Road, BOX 100424
| | Sample_contact_city | Gainesville
| | Sample_contact_state | FL
| | Sample_contact_zip/postal_code | 32610-0424
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM245nnn/GSM245734/suppl/GSM245734.CEL.gz
| | Sample_series_id | GSE9723
| | Sample_data_row_count | 22283
| | |
|
GSM245735 | GPL96 |
|
HIGK cells infected with Aggregatibacter actinomycetemcomitans, biological rep3
|
Human Immortalized Gingival Keratinocyte
|
HIGK cells were originally obtained by transfection of primary gingival epithelial cells with E6/E7 from HPV (Oda et al., 1990).
HIGK cells were reported to be stable for over 350 passages (Oda et al., 1996). They were originally obtained at passage number 82, and used by passage number 90 for the the experiments described herein.
|
Gene expression data from Aggregatibacter actinomycetemcomitans-infected HIGK cells.
Human Immortalized Gingival Keratinocyte (Oda, D., and Watson, E. (1990) Human oral epithelial cell culture. Improved conditions for reproducible culture in serum-free medium. In Vitro Cell Dev Biol Anim 26: 589–595. Oda, D., Bigler, L., Lee, P., and Blanton, R. (1996) HPV immortalization of human oral epithelial cells: a model for carcinogenesis. Exp Cell Res 226: 164–169.)
|
| Sample_geo_accession | GSM245735
| | Sample_status | Public on Mar 01 2008
| | Sample_submission_date | Nov 28 2007
| | Sample_last_update_date | Aug 14 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Bacteria at mid-log phase were harvested and washed by centrifugation, and resuspended in antibiotic-free K-SFM media. HIGK cells (10e7) were co-cultured with bacteria to give a total association (adhered plus invaded) of approximately 2500 organisms per epithelial cell. Numbers of adhered and invaded organisms were confirmed in parallel experiments by plate counting. After 2 hours at 37C in 5% CO2, the HIGK cells were lysed with Trizol (Invitrogen) prior to RNA extraction.
| | Sample_growth_protocol_ch1 | HIGK cells were cultured under 5% CO2 in keratinocyte serum-free medium (K-SFM, Gibco/Invitrogen, Carlsbad, CA) supplemented with: 0.05 mM calcium chloride, 200 mM L-glutamine (Gibco/Invitrogen, Carlsbad, CA).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted, DNAse-treated, purified and quantified according to standard methods (Qiagen and Affymetrix).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cRNA synthesis was performed with 10 ug of total cellular RNA, based on the Affymetrix protocol. Double-stranded cDNA was synthesized according to a standardized protocol (SuperScript doublestranded cDNA synthesis kit; Invitrogen, Carlsbad, CA). cRNA was transcribed in vitro, incorporating biotinylated nucleotides by using a BioArray high-yield RNA transcript labeling kit (T7) (Enzo Life Sciences, Farmingdale, NY).
| | Sample_hyb_protocol | Following fragmentation, human HG U133-A oligonucleotide microarrays (Affymetrix) were hybridized for 16 h at 45C, stained with phycoerythrin-conjugated streptavidin and washed according to the Affymetrix protocol (EukGE-WS2v4).
| | Sample_scan_protocol | GeneChips were scanned with an Affymetrix fluidics station, and scanned with an Affymetrix GeneChip 3000 scanner.
| | Sample_data_processing | The data were analyzed with Affymetrix GCOS using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.
| | Sample_platform_id | GPL96
| | Sample_contact_name | Martin,,Handfield
| | Sample_contact_email | mhandfield@dental.ufl.edu
| | Sample_contact_phone | 352-846-0763
| | Sample_contact_laboratory | Handfield Lab
| | Sample_contact_department | Oral Biology
| | Sample_contact_institute | University of Florida
| | Sample_contact_address | 1600 SW Archer Road, BOX 100424
| | Sample_contact_city | Gainesville
| | Sample_contact_state | FL
| | Sample_contact_zip/postal_code | 32610-0424
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM245nnn/GSM245735/suppl/GSM245735.CEL.gz
| | Sample_series_id | GSE9723
| | Sample_data_row_count | 22283
| | |
|
GSM245736 | GPL96 |
|
HIGK cells infected with Aggregatibacter actinomycetemcomitans, biological rep4
|
Human Immortalized Gingival Keratinocyte
|
HIGK cells were originally obtained by transfection of primary gingival epithelial cells with E6/E7 from HPV (Oda et al., 1990).
HIGK cells were reported to be stable for over 350 passages (Oda et al., 1996). They were originally obtained at passage number 82, and used by passage number 90 for the the experiments described herein.
|
Gene expression data from Aggregatibacter actinomycetemcomitans-infected HIGK cells.
Human Immortalized Gingival Keratinocyte (Oda, D., and Watson, E. (1990) Human oral epithelial cell culture. Improved conditions for reproducible culture in serum-free medium. In Vitro Cell Dev Biol Anim 26: 589–595. Oda, D., Bigler, L., Lee, P., and Blanton, R. (1996) HPV immortalization of human oral epithelial cells: a model for carcinogenesis. Exp Cell Res 226: 164–169.)
|
| Sample_geo_accession | GSM245736
| | Sample_status | Public on Mar 01 2008
| | Sample_submission_date | Nov 28 2007
| | Sample_last_update_date | Aug 14 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Bacteria at mid-log phase were harvested and washed by centrifugation, and resuspended in antibiotic-free K-SFM media. HIGK cells (10e7) were co-cultured with bacteria to give a total association (adhered plus invaded) of approximately 2500 organisms per epithelial cell. Numbers of adhered and invaded organisms were confirmed in parallel experiments by plate counting. After 2 hours at 37C in 5% CO2, the HIGK cells were lysed with Trizol (Invitrogen) prior to RNA extraction.
| | Sample_growth_protocol_ch1 | HIGK cells were cultured under 5% CO2 in keratinocyte serum-free medium (K-SFM, Gibco/Invitrogen, Carlsbad, CA) supplemented with: 0.05 mM calcium chloride, 200 mM L-glutamine (Gibco/Invitrogen, Carlsbad, CA).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted, DNAse-treated, purified and quantified according to standard methods (Qiagen and Affymetrix).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cRNA synthesis was performed with 10 ug of total cellular RNA, based on the Affymetrix protocol. Double-stranded cDNA was synthesized according to a standardized protocol (SuperScript doublestranded cDNA synthesis kit; Invitrogen, Carlsbad, CA). cRNA was transcribed in vitro, incorporating biotinylated nucleotides by using a BioArray high-yield RNA transcript labeling kit (T7) (Enzo Life Sciences, Farmingdale, NY).
| | Sample_hyb_protocol | Following fragmentation, human HG U133-A oligonucleotide microarrays (Affymetrix) were hybridized for 16 h at 45C, stained with phycoerythrin-conjugated streptavidin and washed according to the Affymetrix protocol (EukGE-WS2v4).
| | Sample_scan_protocol | GeneChips were scanned with an Affymetrix fluidics station, and scanned with an Affymetrix GeneChip 3000 scanner.
| | Sample_data_processing | The data were analyzed with Affymetrix GCOS using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.
| | Sample_platform_id | GPL96
| | Sample_contact_name | Martin,,Handfield
| | Sample_contact_email | mhandfield@dental.ufl.edu
| | Sample_contact_phone | 352-846-0763
| | Sample_contact_laboratory | Handfield Lab
| | Sample_contact_department | Oral Biology
| | Sample_contact_institute | University of Florida
| | Sample_contact_address | 1600 SW Archer Road, BOX 100424
| | Sample_contact_city | Gainesville
| | Sample_contact_state | FL
| | Sample_contact_zip/postal_code | 32610-0424
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM245nnn/GSM245736/suppl/GSM245736.CEL.gz
| | Sample_series_id | GSE9723
| | Sample_data_row_count | 22283
| | |
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