Search results for the GEO ID: GSE8056  |
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|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM198866 | GPL570 |
|
Burn wound margin pool 0-3 days post-thermal injury-3
|
Burn wound margin of human skin, replicate #3 of pooled time group 0-3 days post-thermal injury
|
median age: 42
mean age: 44.2
Procedure: excision, left hand; excision, back; excision, right upper extremity; excision, back; excision, right thigh
Total Body Surface Are Burned: 2%; 10%; 3%; 50%; 4%
Post Burn Day: 1; 2; 3; 3; 3
Sex: F; M; F; M; F
|
All skin specimens were obtained in the operating room within minutes of being removed from the patient. Specimens were placed in aluminum foil and immediately snap-frozen in liquid nitrogen to preserve molecular content. Burn specimens were taken from wound margins since there was little point in trying to detect gene expression profiles in areas of full thickness injury where skin is undergoing necrosis. Harvested tissue at the burn wound margin maximized the capture of viable cells from the multiple lineages important to the healing process and minimized the inclusion of non-viable cells destroyed by full-thickness injury. The samples were stored at -80 C until RNA isolation.
|
| Sample_geo_accession | GSM198866
| | Sample_status | Public on May 23 2010
| | Sample_submission_date | Jun 07 2007
| | Sample_last_update_date | May 23 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | At the time of isolation, tissues were chopped into small pieces at -20°C. Samples were weighed and 1ml Trizol (Invitrogen, Carlsbad, CA) was added per 100mg of sample. RNA was extracted using Qiagen’s Rnase-free DNase Set (Valencia, CA) supplied protocol with the following modification. RNA was precipitated with 0.25 volumes isopropanol (Fisher Scientific, Fairlawn, NJ) and 0.25 volumes of RNA precipitation solution (7% NaCl / 21% disodium citrate). DNase treatment was performed following the first Trizol isolation using Qiagen’s RNase-free DNase Set. Manufacturer’s protocol was modified and 10µl DNase in 70µl Buffer RDD was added to every 100µl of sample. Following DNase treatment the Trizol isolation was repeated once or occasionally twice to remove the DNase as well as any remaining fats or salts. RNA was re-suspended in RNase/DNase free H2O. A small aliquot of each sample was sent to the Microarray Core for quantification and bioanalysis. If the sample met the Microarray Core’s standards, samples were pooled equally by mass as to contain RNA from 5 tissue specimens for each array replicate. Pooled RNA samples were then resubmitted for bioanalysis quality assurance followed by microarray labeling and replicate hybridization.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Following quality control, the RNA was prepared for microarray analysis using the standard Affymetrix protocol (Affymetrix Inc, Santa Clara, CA). Briefly, a total of 5 µg of total RNA was reverse transcribed to double-stranded (ds) cDNA using an oligo-dT primer coupled to a T7 promoter. In vitro transcription from the ds cDNA was then carried out using T7 polymerase and incorporating biotin-modified CTP and UTP ribonucleotides.
| | Sample_hyb_protocol | Hybridized cRNA was detected using streptavidin coupled to phycoerythrin and visualized using GeneChip Scanner 3000 7G.
| | Sample_scan_protocol | GeneChips were scanned using GeneChip Scanner 3000 7G and GeneChip Operating System (GCOS, Affymetrix, Santa Clara, CA). Default values were used to grid images (.DAT) and generate .CEL and .CHP files and to generate gene expression values and ratios of gene expression between the hybridized samples
| | Sample_data_processing | For statistical analysis, CEL files (raw Affymetrix data) were imported in GeneSpring 7.0 (Agilent Technologies) and transformed by RMA (Robust Multichip Analysis).
| | Sample_platform_id | GPL570
| | Sample_contact_name | Lillian,B,Nanney
| | Sample_contact_email | lillian.nanney@vanderbilt.edu, joseph.a.greco@vanderbilt.edu
| | Sample_contact_department | Plastic Surgery
| | Sample_contact_institute | Vanderbilt University
| | Sample_contact_address | 1161 21st Ave S/S2221 MCN
| | Sample_contact_city | Nashville
| | Sample_contact_state | TN
| | Sample_contact_zip/postal_code | 37232
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM198nnn/GSM198866/suppl/GSM198866.CEL.gz
| | Sample_series_id | GSE8056
| | Sample_data_row_count | 54675
| | |
|
GSM198867 | GPL570 |
|
Burn wound margin pool 0-3 days post-thermal injury-1
|
Burn wound margin of human skin, replicate #1 of pooled time group 0-3 days post-thermal injury
|
median age: 39
mean age: 42.8
Procedure: excision, abdomen; excision, right arm; excision, bilateral lower extremities; excision, back; excision, left hand
Total Body Surface Are Burned: 30%; 40%; 23%; 20%; 2%
Post Burn Day: 3; 3; 3; 3; 3
Sex: F; F; M; M; M
|
All skin specimens were obtained in the operating room within minutes of being removed from the patient. Specimens were placed in aluminum foil and immediately snap-frozen in liquid nitrogen to preserve molecular content. Burn specimens were taken from wound margins since there was little point in trying to detect gene expression profiles in areas of full thickness injury where skin is undergoing necrosis. Harvested tissue at the burn wound margin maximized the capture of viable cells from the multiple lineages important to the healing process and minimized the inclusion of non-viable cells destroyed by full-thickness injury. The samples were stored at -80 C until RNA isolation.
|
| Sample_geo_accession | GSM198867
| | Sample_status | Public on May 23 2010
| | Sample_submission_date | Jun 07 2007
| | Sample_last_update_date | May 23 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | At the time of isolation, tissues were chopped into small pieces at -20°C. Samples were weighed and 1ml Trizol (Invitrogen, Carlsbad, CA) was added per 100mg of sample. RNA was extracted using Qiagen’s Rnase-free DNase Set (Valencia, CA) supplied protocol with the following modification. RNA was precipitated with 0.25 volumes isopropanol (Fisher Scientific, Fairlawn, NJ) and 0.25 volumes of RNA precipitation solution (7% NaCl / 21% disodium citrate). DNase treatment was performed following the first Trizol isolation using Qiagen’s RNase-free DNase Set. Manufacturer’s protocol was modified and 10µl DNase in 70µl Buffer RDD was added to every 100µl of sample. Following DNase treatment the Trizol isolation was repeated once or occasionally twice to remove the DNase as well as any remaining fats or salts. RNA was re-suspended in RNase/DNase free H2O. A small aliquot of each sample was sent to the Microarray Core for quantification and bioanalysis. If the sample met the Microarray Core’s standards, samples were pooled equally by mass as to contain RNA from 5 tissue specimens for each array replicate. Pooled RNA samples were then resubmitted for bioanalysis quality assurance followed by microarray labeling and replicate hybridization.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Following quality control, the RNA was prepared for microarray analysis using the standard Affymetrix protocol (Affymetrix Inc, Santa Clara, CA). Briefly, a total of 5 µg of total RNA was reverse transcribed to double-stranded (ds) cDNA using an oligo-dT primer coupled to a T7 promoter. In vitro transcription from the ds cDNA was then carried out using T7 polymerase and incorporating biotin-modified CTP and UTP ribonucleotides.
| | Sample_hyb_protocol | Hybridized cRNA was detected using streptavidin coupled to phycoerythrin and visualized using GeneChip Scanner 3000 7G.
| | Sample_scan_protocol | GeneChips were scanned using GeneChip Scanner 3000 7G and GeneChip Operating System (GCOS, Affymetrix, Santa Clara, CA). Default values were used to grid images (.DAT) and generate .CEL and .CHP files and to generate gene expression values and ratios of gene expression between the hybridized samples
| | Sample_data_processing | For statistical analysis, CEL files (raw Affymetrix data) were imported in GeneSpring 7.0 (Agilent Technologies) and transformed by RMA (Robust Multichip Analysis).
| | Sample_platform_id | GPL570
| | Sample_contact_name | Lillian,B,Nanney
| | Sample_contact_email | lillian.nanney@vanderbilt.edu, joseph.a.greco@vanderbilt.edu
| | Sample_contact_department | Plastic Surgery
| | Sample_contact_institute | Vanderbilt University
| | Sample_contact_address | 1161 21st Ave S/S2221 MCN
| | Sample_contact_city | Nashville
| | Sample_contact_state | TN
| | Sample_contact_zip/postal_code | 37232
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM198nnn/GSM198867/suppl/GSM198867.CEL.gz
| | Sample_series_id | GSE8056
| | Sample_data_row_count | 54675
| | |
|
GSM198868 | GPL570 |
|
Burn wound margin pool 0-3 days post-thermal injury-2
|
Burn wound margin of human skin, replicate #2 of pooled time group 0-3 days post-thermal injury
|
median age: 51
mean age: 48
Procedure: excision, abdomen; excision, left lower extremity; excision, abdomen; excision, right foot; excision, left upper extremity
Total Body Surface Are Burned: 80%; 5%; 15%; 3%; 15%
Post Burn Day: 1; 2; 3; 3; 3
Sex: F; M; M; F; M
|
All skin specimens were obtained in the operating room within minutes of being removed from the patient. Specimens were placed in aluminum foil and immediately snap-frozen in liquid nitrogen to preserve molecular content. Burn specimens were taken from wound margins since there was little point in trying to detect gene expression profiles in areas of full thickness injury where skin is undergoing necrosis. Harvested tissue at the burn wound margin maximized the capture of viable cells from the multiple lineages important to the healing process and minimized the inclusion of non-viable cells destroyed by full-thickness injury. The samples were stored at -80 C until RNA isolation.
|
| Sample_geo_accession | GSM198868
| | Sample_status | Public on May 23 2010
| | Sample_submission_date | Jun 07 2007
| | Sample_last_update_date | May 23 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | At the time of isolation, tissues were chopped into small pieces at -20°C. Samples were weighed and 1ml Trizol (Invitrogen, Carlsbad, CA) was added per 100mg of sample. RNA was extracted using Qiagen’s Rnase-free DNase Set (Valencia, CA) supplied protocol with the following modification. RNA was precipitated with 0.25 volumes isopropanol (Fisher Scientific, Fairlawn, NJ) and 0.25 volumes of RNA precipitation solution (7% NaCl / 21% disodium citrate). DNase treatment was performed following the first Trizol isolation using Qiagen’s RNase-free DNase Set. Manufacturer’s protocol was modified and 10µl DNase in 70µl Buffer RDD was added to every 100µl of sample. Following DNase treatment the Trizol isolation was repeated once or occasionally twice to remove the DNase as well as any remaining fats or salts. RNA was re-suspended in RNase/DNase free H2O. A small aliquot of each sample was sent to the Microarray Core for quantification and bioanalysis. If the sample met the Microarray Core’s standards, samples were pooled equally by mass as to contain RNA from 5 tissue specimens for each array replicate. Pooled RNA samples were then resubmitted for bioanalysis quality assurance followed by microarray labeling and replicate hybridization.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Following quality control, the RNA was prepared for microarray analysis using the standard Affymetrix protocol (Affymetrix Inc, Santa Clara, CA). Briefly, a total of 5 µg of total RNA was reverse transcribed to double-stranded (ds) cDNA using an oligo-dT primer coupled to a T7 promoter. In vitro transcription from the ds cDNA was then carried out using T7 polymerase and incorporating biotin-modified CTP and UTP ribonucleotides.
| | Sample_hyb_protocol | Hybridized cRNA was detected using streptavidin coupled to phycoerythrin and visualized using GeneChip Scanner 3000 7G.
| | Sample_scan_protocol | GeneChips were scanned using GeneChip Scanner 3000 7G and GeneChip Operating System (GCOS, Affymetrix, Santa Clara, CA). Default values were used to grid images (.DAT) and generate .CEL and .CHP files and to generate gene expression values and ratios of gene expression between the hybridized samples
| | Sample_data_processing | For statistical analysis, CEL files (raw Affymetrix data) were imported in GeneSpring 7.0 (Agilent Technologies) and transformed by RMA (Robust Multichip Analysis).
| | Sample_platform_id | GPL570
| | Sample_contact_name | Lillian,B,Nanney
| | Sample_contact_email | lillian.nanney@vanderbilt.edu, joseph.a.greco@vanderbilt.edu
| | Sample_contact_department | Plastic Surgery
| | Sample_contact_institute | Vanderbilt University
| | Sample_contact_address | 1161 21st Ave S/S2221 MCN
| | Sample_contact_city | Nashville
| | Sample_contact_state | TN
| | Sample_contact_zip/postal_code | 37232
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM198nnn/GSM198868/suppl/GSM198868.CEL.gz
| | Sample_series_id | GSE8056
| | Sample_data_row_count | 54675
| | |
|
GSM198869 | GPL570 |
|
Burn wound margin pool 4-7 days post-thermal injury-1
|
Burn wound margin of human skin, replicate #1 of pooled time group 4-7 days post-thermal injury
|
median age: 30
mean age: 27
Procedure: excision, right upper extremity; excision, right upper extremity; excision, right flank; excision, chest; excision, chest
Total Body Surface Are Burned: 6%; 8%; 10%; 5%; 15%
Post Burn Day: 4; 4; 4; 5; 5
Sex: M; M; M; F; F
|
All skin specimens were obtained in the operating room within minutes of being removed from the patient. Specimens were placed in aluminum foil and immediately snap-frozen in liquid nitrogen to preserve molecular content. Burn specimens were taken from wound margins since there was little point in trying to detect gene expression profiles in areas of full thickness injury where skin is undergoing necrosis. Harvested tissue at the burn wound margin maximized the capture of viable cells from the multiple lineages important to the healing process and minimized the inclusion of non-viable cells destroyed by full-thickness injury. The samples were stored at -80 C until RNA isolation.
|
| Sample_geo_accession | GSM198869
| | Sample_status | Public on May 23 2010
| | Sample_submission_date | Jun 07 2007
| | Sample_last_update_date | May 23 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | At the time of isolation, tissues were chopped into small pieces at -20°C. Samples were weighed and 1ml Trizol (Invitrogen, Carlsbad, CA) was added per 100mg of sample. RNA was extracted using Qiagen’s Rnase-free DNase Set (Valencia, CA) supplied protocol with the following modification. RNA was precipitated with 0.25 volumes isopropanol (Fisher Scientific, Fairlawn, NJ) and 0.25 volumes of RNA precipitation solution (7% NaCl / 21% disodium citrate). DNase treatment was performed following the first Trizol isolation using Qiagen’s RNase-free DNase Set. Manufacturer’s protocol was modified and 10µl DNase in 70µl Buffer RDD was added to every 100µl of sample. Following DNase treatment the Trizol isolation was repeated once or occasionally twice to remove the DNase as well as any remaining fats or salts. RNA was re-suspended in RNase/DNase free H2O. A small aliquot of each sample was sent to the Microarray Core for quantification and bioanalysis. If the sample met the Microarray Core’s standards, samples were pooled equally by mass as to contain RNA from 5 tissue specimens for each array replicate. Pooled RNA samples were then resubmitted for bioanalysis quality assurance followed by microarray labeling and replicate hybridization.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Following quality control, the RNA was prepared for microarray analysis using the standard Affymetrix protocol (Affymetrix Inc, Santa Clara, CA). Briefly, a total of 5 µg of total RNA was reverse transcribed to double-stranded (ds) cDNA using an oligo-dT primer coupled to a T7 promoter. In vitro transcription from the ds cDNA was then carried out using T7 polymerase and incorporating biotin-modified CTP and UTP ribonucleotides.
| | Sample_hyb_protocol | Hybridized cRNA was detected using streptavidin coupled to phycoerythrin and visualized using GeneChip Scanner 3000 7G.
| | Sample_scan_protocol | GeneChips were scanned using GeneChip Scanner 3000 7G and GeneChip Operating System (GCOS, Affymetrix, Santa Clara, CA). Default values were used to grid images (.DAT) and generate .CEL and .CHP files and to generate gene expression values and ratios of gene expression between the hybridized samples
| | Sample_data_processing | For statistical analysis, CEL files (raw Affymetrix data) were imported in GeneSpring 7.0 (Agilent Technologies) and transformed by RMA (Robust Multichip Analysis).
| | Sample_platform_id | GPL570
| | Sample_contact_name | Lillian,B,Nanney
| | Sample_contact_email | lillian.nanney@vanderbilt.edu, joseph.a.greco@vanderbilt.edu
| | Sample_contact_department | Plastic Surgery
| | Sample_contact_institute | Vanderbilt University
| | Sample_contact_address | 1161 21st Ave S/S2221 MCN
| | Sample_contact_city | Nashville
| | Sample_contact_state | TN
| | Sample_contact_zip/postal_code | 37232
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM198nnn/GSM198869/suppl/GSM198869.CEL.gz
| | Sample_series_id | GSE8056
| | Sample_data_row_count | 54675
| | |
|
GSM198870 | GPL570 |
|
Burn wound margin pool 4-7 days post-thermal injury-2
|
Burn wound margin of human skin, replicate #2 of pooled time group 4-7 days post-thermal injury
|
median age: 33
mean age: 32.8
Procedure: excision, trunk; excision, left upper extremity; excision, right lower extremity; excision, trunk; excision, back
Total Body Surface Are Burned: 30%; 4%; 8%; 25%; 20%
Post Burn Day: 4; 4; 6; 7; 7
Sex: M; M; F; F; M
|
All skin specimens were obtained in the operating room within minutes of being removed from the patient. Specimens were placed in aluminum foil and immediately snap-frozen in liquid nitrogen to preserve molecular content. Burn specimens were taken from wound margins since there was little point in trying to detect gene expression profiles in areas of full thickness injury where skin is undergoing necrosis. Harvested tissue at the burn wound margin maximized the capture of viable cells from the multiple lineages important to the healing process and minimized the inclusion of non-viable cells destroyed by full-thickness injury. The samples were stored at -80 C until RNA isolation.
|
| Sample_geo_accession | GSM198870
| | Sample_status | Public on May 23 2010
| | Sample_submission_date | Jun 07 2007
| | Sample_last_update_date | May 23 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | At the time of isolation, tissues were chopped into small pieces at -20°C. Samples were weighed and 1ml Trizol (Invitrogen, Carlsbad, CA) was added per 100mg of sample. RNA was extracted using Qiagen’s Rnase-free DNase Set (Valencia, CA) supplied protocol with the following modification. RNA was precipitated with 0.25 volumes isopropanol (Fisher Scientific, Fairlawn, NJ) and 0.25 volumes of RNA precipitation solution (7% NaCl / 21% disodium citrate). DNase treatment was performed following the first Trizol isolation using Qiagen’s RNase-free DNase Set. Manufacturer’s protocol was modified and 10µl DNase in 70µl Buffer RDD was added to every 100µl of sample. Following DNase treatment the Trizol isolation was repeated once or occasionally twice to remove the DNase as well as any remaining fats or salts. RNA was re-suspended in RNase/DNase free H2O. A small aliquot of each sample was sent to the Microarray Core for quantification and bioanalysis. If the sample met the Microarray Core’s standards, samples were pooled equally by mass as to contain RNA from 5 tissue specimens for each array replicate. Pooled RNA samples were then resubmitted for bioanalysis quality assurance followed by microarray labeling and replicate hybridization.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Following quality control, the RNA was prepared for microarray analysis using the standard Affymetrix protocol (Affymetrix Inc, Santa Clara, CA). Briefly, a total of 5 µg of total RNA was reverse transcribed to double-stranded (ds) cDNA using an oligo-dT primer coupled to a T7 promoter. In vitro transcription from the ds cDNA was then carried out using T7 polymerase and incorporating biotin-modified CTP and UTP ribonucleotides.
| | Sample_hyb_protocol | Hybridized cRNA was detected using streptavidin coupled to phycoerythrin and visualized using GeneChip Scanner 3000 7G.
| | Sample_scan_protocol | GeneChips were scanned using GeneChip Scanner 3000 7G and GeneChip Operating System (GCOS, Affymetrix, Santa Clara, CA). Default values were used to grid images (.DAT) and generate .CEL and .CHP files and to generate gene expression values and ratios of gene expression between the hybridized samples
| | Sample_data_processing | For statistical analysis, CEL files (raw Affymetrix data) were imported in GeneSpring 7.0 (Agilent Technologies) and transformed by RMA (Robust Multichip Analysis).
| | Sample_platform_id | GPL570
| | Sample_contact_name | Lillian,B,Nanney
| | Sample_contact_email | lillian.nanney@vanderbilt.edu, joseph.a.greco@vanderbilt.edu
| | Sample_contact_department | Plastic Surgery
| | Sample_contact_institute | Vanderbilt University
| | Sample_contact_address | 1161 21st Ave S/S2221 MCN
| | Sample_contact_city | Nashville
| | Sample_contact_state | TN
| | Sample_contact_zip/postal_code | 37232
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM198nnn/GSM198870/suppl/GSM198870.CEL.gz
| | Sample_series_id | GSE8056
| | Sample_data_row_count | 54675
| | |
|
GSM198871 | GPL570 |
|
Burn wound margin pool 4-7 days post-thermal injury-3
|
Burn wound margin of human skin, replicate #3 of pooled time group 4-7 days post-thermal injury
|
median age: 42
mean age: 42.8
Procedure: excision, abdomen; excision, right upper extremity; excision, abdomen; excision, back; excision, right upper extremity
Total Body Surface Are Burned: 50%; 10%; 27%; 5%; 5%
Post Burn Day: 4; 5; 5; 6; 6
Sex: M; M; M; M; M
|
All skin specimens were obtained in the operating room within minutes of being removed from the patient. Specimens were placed in aluminum foil and immediately snap-frozen in liquid nitrogen to preserve molecular content. Burn specimens were taken from wound margins since there was little point in trying to detect gene expression profiles in areas of full thickness injury where skin is undergoing necrosis. Harvested tissue at the burn wound margin maximized the capture of viable cells from the multiple lineages important to the healing process and minimized the inclusion of non-viable cells destroyed by full-thickness injury. The samples were stored at -80 C until RNA isolation.
|
| Sample_geo_accession | GSM198871
| | Sample_status | Public on May 23 2010
| | Sample_submission_date | Jun 07 2007
| | Sample_last_update_date | May 23 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | At the time of isolation, tissues were chopped into small pieces at -20°C. Samples were weighed and 1ml Trizol (Invitrogen, Carlsbad, CA) was added per 100mg of sample. RNA was extracted using Qiagen’s Rnase-free DNase Set (Valencia, CA) supplied protocol with the following modification. RNA was precipitated with 0.25 volumes isopropanol (Fisher Scientific, Fairlawn, NJ) and 0.25 volumes of RNA precipitation solution (7% NaCl / 21% disodium citrate). DNase treatment was performed following the first Trizol isolation using Qiagen’s RNase-free DNase Set. Manufacturer’s protocol was modified and 10µl DNase in 70µl Buffer RDD was added to every 100µl of sample. Following DNase treatment the Trizol isolation was repeated once or occasionally twice to remove the DNase as well as any remaining fats or salts. RNA was re-suspended in RNase/DNase free H2O. A small aliquot of each sample was sent to the Microarray Core for quantification and bioanalysis. If the sample met the Microarray Core’s standards, samples were pooled equally by mass as to contain RNA from 5 tissue specimens for each array replicate. Pooled RNA samples were then resubmitted for bioanalysis quality assurance followed by microarray labeling and replicate hybridization.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Following quality control, the RNA was prepared for microarray analysis using the standard Affymetrix protocol (Affymetrix Inc, Santa Clara, CA). Briefly, a total of 5 µg of total RNA was reverse transcribed to double-stranded (ds) cDNA using an oligo-dT primer coupled to a T7 promoter. In vitro transcription from the ds cDNA was then carried out using T7 polymerase and incorporating biotin-modified CTP and UTP ribonucleotides.
| | Sample_hyb_protocol | Hybridized cRNA was detected using streptavidin coupled to phycoerythrin and visualized using GeneChip Scanner 3000 7G.
| | Sample_scan_protocol | GeneChips were scanned using GeneChip Scanner 3000 7G and GeneChip Operating System (GCOS, Affymetrix, Santa Clara, CA). Default values were used to grid images (.DAT) and generate .CEL and .CHP files and to generate gene expression values and ratios of gene expression between the hybridized samples
| | Sample_data_processing | For statistical analysis, CEL files (raw Affymetrix data) were imported in GeneSpring 7.0 (Agilent Technologies) and transformed by RMA (Robust Multichip Analysis).
| | Sample_platform_id | GPL570
| | Sample_contact_name | Lillian,B,Nanney
| | Sample_contact_email | lillian.nanney@vanderbilt.edu, joseph.a.greco@vanderbilt.edu
| | Sample_contact_department | Plastic Surgery
| | Sample_contact_institute | Vanderbilt University
| | Sample_contact_address | 1161 21st Ave S/S2221 MCN
| | Sample_contact_city | Nashville
| | Sample_contact_state | TN
| | Sample_contact_zip/postal_code | 37232
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM198nnn/GSM198871/suppl/GSM198871.CEL.gz
| | Sample_series_id | GSE8056
| | Sample_data_row_count | 54675
| | |
|
GSM198872 | GPL570 |
|
Burn wound margin pool >7 days post-thermal injury-3
|
Burn wound margin of human skin, replicate #3 of pooled time group >7 days post-thermal injury
|
median age: 40
mean age: 46
Procedure: excision, right lower extremity; excision, left foot; excision, abdomen; excision, right foot; excision, left upper extremity
Total Body Surface Are Burned: 60%; 10%; 50%; 5%; 45%
Post Burn Day: 8; 9; 9; 9; 11
Sex: M; M; M; M; M
|
All skin specimens were obtained in the operating room within minutes of being removed from the patient. Specimens were placed in aluminum foil and immediately snap-frozen in liquid nitrogen to preserve molecular content. Burn specimens were taken from wound margins since there was little point in trying to detect gene expression profiles in areas of full thickness injury where skin is undergoing necrosis. Harvested tissue at the burn wound margin maximized the capture of viable cells from the multiple lineages important to the healing process and minimized the inclusion of non-viable cells destroyed by full-thickness injury. The samples were stored at -80 C until RNA isolation.
|
| Sample_geo_accession | GSM198872
| | Sample_status | Public on May 23 2010
| | Sample_submission_date | Jun 07 2007
| | Sample_last_update_date | May 23 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | At the time of isolation, tissues were chopped into small pieces at -20°C. Samples were weighed and 1ml Trizol (Invitrogen, Carlsbad, CA) was added per 100mg of sample. RNA was extracted using Qiagen’s Rnase-free DNase Set (Valencia, CA) supplied protocol with the following modification. RNA was precipitated with 0.25 volumes isopropanol (Fisher Scientific, Fairlawn, NJ) and 0.25 volumes of RNA precipitation solution (7% NaCl / 21% disodium citrate). DNase treatment was performed following the first Trizol isolation using Qiagen’s RNase-free DNase Set. Manufacturer’s protocol was modified and 10µl DNase in 70µl Buffer RDD was added to every 100µl of sample. Following DNase treatment the Trizol isolation was repeated once or occasionally twice to remove the DNase as well as any remaining fats or salts. RNA was re-suspended in RNase/DNase free H2O. A small aliquot of each sample was sent to the Microarray Core for quantification and bioanalysis. If the sample met the Microarray Core’s standards, samples were pooled equally by mass as to contain RNA from 5 tissue specimens for each array replicate. Pooled RNA samples were then resubmitted for bioanalysis quality assurance followed by microarray labeling and replicate hybridization.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Following quality control, the RNA was prepared for microarray analysis using the standard Affymetrix protocol (Affymetrix Inc, Santa Clara, CA). Briefly, a total of 5 µg of total RNA was reverse transcribed to double-stranded (ds) cDNA using an oligo-dT primer coupled to a T7 promoter. In vitro transcription from the ds cDNA was then carried out using T7 polymerase and incorporating biotin-modified CTP and UTP ribonucleotides.
| | Sample_hyb_protocol | Hybridized cRNA was detected using streptavidin coupled to phycoerythrin and visualized using GeneChip Scanner 3000 7G.
| | Sample_scan_protocol | GeneChips were scanned using GeneChip Scanner 3000 7G and GeneChip Operating System (GCOS, Affymetrix, Santa Clara, CA). Default values were used to grid images (.DAT) and generate .CEL and .CHP files and to generate gene expression values and ratios of gene expression between the hybridized samples
| | Sample_data_processing | For statistical analysis, CEL files (raw Affymetrix data) were imported in GeneSpring 7.0 (Agilent Technologies) and transformed by RMA (Robust Multichip Analysis).
| | Sample_platform_id | GPL570
| | Sample_contact_name | Lillian,B,Nanney
| | Sample_contact_email | lillian.nanney@vanderbilt.edu, joseph.a.greco@vanderbilt.edu
| | Sample_contact_department | Plastic Surgery
| | Sample_contact_institute | Vanderbilt University
| | Sample_contact_address | 1161 21st Ave S/S2221 MCN
| | Sample_contact_city | Nashville
| | Sample_contact_state | TN
| | Sample_contact_zip/postal_code | 37232
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM198nnn/GSM198872/suppl/GSM198872.CEL.gz
| | Sample_series_id | GSE8056
| | Sample_data_row_count | 54675
| | |
|
GSM198873 | GPL570 |
|
Burn wound margin pool >7 days post-thermal injury-1
|
Burn wound margin of human skin, replicate #1 of pooled time group >7 days post-thermal injury
|
median age: 30
mean age: 36.2
Procedure: excision, right abdomen; excision, back; excision, chest; excision, right lower extremity; excision, right upper extremity
Total Body Surface Are Burned: 20%; 15%; 50%; 12%; 33%
Post Burn Day: 10; 12; 13; 14; 17
Sex: M; M; M; M; F
|
All skin specimens were obtained in the operating room within minutes of being removed from the patient. Specimens were placed in aluminum foil and immediately snap-frozen in liquid nitrogen to preserve molecular content. Burn specimens were taken from wound margins since there was little point in trying to detect gene expression profiles in areas of full thickness injury where skin is undergoing necrosis. Harvested tissue at the burn wound margin maximized the capture of viable cells from the multiple lineages important to the healing process and minimized the inclusion of non-viable cells destroyed by full-thickness injury. The samples were stored at -80 C until RNA isolation.
|
| Sample_geo_accession | GSM198873
| | Sample_status | Public on May 23 2010
| | Sample_submission_date | Jun 07 2007
| | Sample_last_update_date | May 23 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | At the time of isolation, tissues were chopped into small pieces at -20°C. Samples were weighed and 1ml Trizol (Invitrogen, Carlsbad, CA) was added per 100mg of sample. RNA was extracted using Qiagen’s Rnase-free DNase Set (Valencia, CA) supplied protocol with the following modification. RNA was precipitated with 0.25 volumes isopropanol (Fisher Scientific, Fairlawn, NJ) and 0.25 volumes of RNA precipitation solution (7% NaCl / 21% disodium citrate). DNase treatment was performed following the first Trizol isolation using Qiagen’s RNase-free DNase Set. Manufacturer’s protocol was modified and 10µl DNase in 70µl Buffer RDD was added to every 100µl of sample. Following DNase treatment the Trizol isolation was repeated once or occasionally twice to remove the DNase as well as any remaining fats or salts. RNA was re-suspended in RNase/DNase free H2O. A small aliquot of each sample was sent to the Microarray Core for quantification and bioanalysis. If the sample met the Microarray Core’s standards, samples were pooled equally by mass as to contain RNA from 5 tissue specimens for each array replicate. Pooled RNA samples were then resubmitted for bioanalysis quality assurance followed by microarray labeling and replicate hybridization.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Following quality control, the RNA was prepared for microarray analysis using the standard Affymetrix protocol (Affymetrix Inc, Santa Clara, CA). Briefly, a total of 5 µg of total RNA was reverse transcribed to double-stranded (ds) cDNA using an oligo-dT primer coupled to a T7 promoter. In vitro transcription from the ds cDNA was then carried out using T7 polymerase and incorporating biotin-modified CTP and UTP ribonucleotides.
| | Sample_hyb_protocol | Hybridized cRNA was detected using streptavidin coupled to phycoerythrin and visualized using GeneChip Scanner 3000 7G.
| | Sample_scan_protocol | GeneChips were scanned using GeneChip Scanner 3000 7G and GeneChip Operating System (GCOS, Affymetrix, Santa Clara, CA). Default values were used to grid images (.DAT) and generate .CEL and .CHP files and to generate gene expression values and ratios of gene expression between the hybridized samples
| | Sample_data_processing | For statistical analysis, CEL files (raw Affymetrix data) were imported in GeneSpring 7.0 (Agilent Technologies) and transformed by RMA (Robust Multichip Analysis).
| | Sample_platform_id | GPL570
| | Sample_contact_name | Lillian,B,Nanney
| | Sample_contact_email | lillian.nanney@vanderbilt.edu, joseph.a.greco@vanderbilt.edu
| | Sample_contact_department | Plastic Surgery
| | Sample_contact_institute | Vanderbilt University
| | Sample_contact_address | 1161 21st Ave S/S2221 MCN
| | Sample_contact_city | Nashville
| | Sample_contact_state | TN
| | Sample_contact_zip/postal_code | 37232
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM198nnn/GSM198873/suppl/GSM198873.CEL.gz
| | Sample_series_id | GSE8056
| | Sample_data_row_count | 54675
| | |
|
GSM198874 | GPL570 |
|
Burn wound margin pool >7 days post-thermal injury-2
|
Burn wound margin of human skin, replicate #2 of pooled time group >7 days post-thermal injury
|
median age: 33
mean age: 37.8
Procedure: excision, right upper extremity; excision, chest; excision, right lower extremity; excision, right foot; excision, right hand
Total Body Surface Are Burned: 20%; 10%; 5%; 3%; 45%
Post Burn Day: 8; 12; 14; 15; 16
Sex: M; M; F; M; M
|
All skin specimens were obtained in the operating room within minutes of being removed from the patient. Specimens were placed in aluminum foil and immediately snap-frozen in liquid nitrogen to preserve molecular content. Burn specimens were taken from wound margins since there was little point in trying to detect gene expression profiles in areas of full thickness injury where skin is undergoing necrosis. Harvested tissue at the burn wound margin maximized the capture of viable cells from the multiple lineages important to the healing process and minimized the inclusion of non-viable cells destroyed by full-thickness injury. The samples were stored at -80 C until RNA isolation.
|
| Sample_geo_accession | GSM198874
| | Sample_status | Public on May 23 2010
| | Sample_submission_date | Jun 07 2007
| | Sample_last_update_date | May 23 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | At the time of isolation, tissues were chopped into small pieces at -20°C. Samples were weighed and 1ml Trizol (Invitrogen, Carlsbad, CA) was added per 100mg of sample. RNA was extracted using Qiagen’s Rnase-free DNase Set (Valencia, CA) supplied protocol with the following modification. RNA was precipitated with 0.25 volumes isopropanol (Fisher Scientific, Fairlawn, NJ) and 0.25 volumes of RNA precipitation solution (7% NaCl / 21% disodium citrate). DNase treatment was performed following the first Trizol isolation using Qiagen’s RNase-free DNase Set. Manufacturer’s protocol was modified and 10µl DNase in 70µl Buffer RDD was added to every 100µl of sample. Following DNase treatment the Trizol isolation was repeated once or occasionally twice to remove the DNase as well as any remaining fats or salts. RNA was re-suspended in RNase/DNase free H2O. A small aliquot of each sample was sent to the Microarray Core for quantification and bioanalysis. If the sample met the Microarray Core’s standards, samples were pooled equally by mass as to contain RNA from 5 tissue specimens for each array replicate. Pooled RNA samples were then resubmitted for bioanalysis quality assurance followed by microarray labeling and replicate hybridization.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Following quality control, the RNA was prepared for microarray analysis using the standard Affymetrix protocol (Affymetrix Inc, Santa Clara, CA). Briefly, a total of 5 µg of total RNA was reverse transcribed to double-stranded (ds) cDNA using an oligo-dT primer coupled to a T7 promoter. In vitro transcription from the ds cDNA was then carried out using T7 polymerase and incorporating biotin-modified CTP and UTP ribonucleotides.
| | Sample_hyb_protocol | Hybridized cRNA was detected using streptavidin coupled to phycoerythrin and visualized using GeneChip Scanner 3000 7G.
| | Sample_scan_protocol | GeneChips were scanned using GeneChip Scanner 3000 7G and GeneChip Operating System (GCOS, Affymetrix, Santa Clara, CA). Default values were used to grid images (.DAT) and generate .CEL and .CHP files and to generate gene expression values and ratios of gene expression between the hybridized samples
| | Sample_data_processing | For statistical analysis, CEL files (raw Affymetrix data) were imported in GeneSpring 7.0 (Agilent Technologies) and transformed by RMA (Robust Multichip Analysis).
| | Sample_platform_id | GPL570
| | Sample_contact_name | Lillian,B,Nanney
| | Sample_contact_email | lillian.nanney@vanderbilt.edu, joseph.a.greco@vanderbilt.edu
| | Sample_contact_department | Plastic Surgery
| | Sample_contact_institute | Vanderbilt University
| | Sample_contact_address | 1161 21st Ave S/S2221 MCN
| | Sample_contact_city | Nashville
| | Sample_contact_state | TN
| | Sample_contact_zip/postal_code | 37232
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM198nnn/GSM198874/suppl/GSM198874.CEL.gz
| | Sample_series_id | GSE8056
| | Sample_data_row_count | 54675
| | |
|
GSM198875 | GPL570 |
|
Normal human (no thermal injury) skin pool control-2
|
Normal human skin, pooled replicate #2 of normal (no thermal injury) skin control
|
median age: 26
mean age: 28.8
Procedure: reduction mammoplasty; reduction mammoplasty; blepharoplasty; reduction mammoplasty; excision of redundant tissue (back)
Total Body Surface Are Burned: 0% (all samples)
Post Burn Day: NA
Sex: F; F; F; F; F
|
All skin specimens were obtained in the operating room within minutes of being removed from the patient. Specimens were placed in aluminum foil and immediately snap-frozen in liquid nitrogen to preserve molecular content. Burn specimens were taken from wound margins since there was little point in trying to detect gene expression profiles in areas of full thickness injury where skin is undergoing necrosis. Harvested tissue at the burn wound margin maximized the capture of viable cells from the multiple lineages important to the healing process and minimized the inclusion of non-viable cells destroyed by full-thickness injury. The samples were stored at -80 C until RNA isolation.
|
| Sample_geo_accession | GSM198875
| | Sample_status | Public on May 23 2010
| | Sample_submission_date | Jun 07 2007
| | Sample_last_update_date | May 23 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | At the time of isolation, tissues were chopped into small pieces at -20°C. Samples were weighed and 1ml Trizol (Invitrogen, Carlsbad, CA) was added per 100mg of sample. RNA was extracted using Qiagen’s Rnase-free DNase Set (Valencia, CA) supplied protocol with the following modification. RNA was precipitated with 0.25 volumes isopropanol (Fisher Scientific, Fairlawn, NJ) and 0.25 volumes of RNA precipitation solution (7% NaCl / 21% disodium citrate). DNase treatment was performed following the first Trizol isolation using Qiagen’s RNase-free DNase Set. Manufacturer’s protocol was modified and 10µl DNase in 70µl Buffer RDD was added to every 100µl of sample. Following DNase treatment the Trizol isolation was repeated once or occasionally twice to remove the DNase as well as any remaining fats or salts. RNA was re-suspended in RNase/DNase free H2O. A small aliquot of each sample was sent to the Microarray Core for quantification and bioanalysis. If the sample met the Microarray Core’s standards, samples were pooled equally by mass as to contain RNA from 5 tissue specimens for each array replicate. Pooled RNA samples were then resubmitted for bioanalysis quality assurance followed by microarray labeling and replicate hybridization.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Following quality control, the RNA was prepared for microarray analysis using the standard Affymetrix protocol (Affymetrix Inc, Santa Clara, CA). Briefly, a total of 5 µg of total RNA was reverse transcribed to double-stranded (ds) cDNA using an oligo-dT primer coupled to a T7 promoter. In vitro transcription from the ds cDNA was then carried out using T7 polymerase and incorporating biotin-modified CTP and UTP ribonucleotides.
| | Sample_hyb_protocol | Hybridized cRNA was detected using streptavidin coupled to phycoerythrin and visualized using GeneChip Scanner 3000 7G.
| | Sample_scan_protocol | GeneChips were scanned using GeneChip Scanner 3000 7G and GeneChip Operating System (GCOS, Affymetrix, Santa Clara, CA). Default values were used to grid images (.DAT) and generate .CEL and .CHP files and to generate gene expression values and ratios of gene expression between the hybridized samples
| | Sample_data_processing | For statistical analysis, CEL files (raw Affymetrix data) were imported in GeneSpring 7.0 (Agilent Technologies) and transformed by RMA (Robust Multichip Analysis).
| | Sample_platform_id | GPL570
| | Sample_contact_name | Lillian,B,Nanney
| | Sample_contact_email | lillian.nanney@vanderbilt.edu, joseph.a.greco@vanderbilt.edu
| | Sample_contact_department | Plastic Surgery
| | Sample_contact_institute | Vanderbilt University
| | Sample_contact_address | 1161 21st Ave S/S2221 MCN
| | Sample_contact_city | Nashville
| | Sample_contact_state | TN
| | Sample_contact_zip/postal_code | 37232
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM198nnn/GSM198875/suppl/GSM198875.CEL.gz
| | Sample_series_id | GSE8056
| | Sample_data_row_count | 54675
| | |
|
GSM198876 | GPL570 |
|
Normal human (no thermal injury) skin pool control-3
|
Normal human skin, pooled replicate #3 of normal (no thermal injury) skin control
|
median age: 44
mean age: 45.4
Procedure: reduction mammoplasty; reduction mammoplasty; reduction mammoplasty; reduction mammoplasty; thigh lift
Total Body Surface Are Burned: 0% (all samples)
Post Burn Day: NA
Sex: F; F; F; F; F
|
All skin specimens were obtained in the operating room within minutes of being removed from the patient. Specimens were placed in aluminum foil and immediately snap-frozen in liquid nitrogen to preserve molecular content. Burn specimens were taken from wound margins since there was little point in trying to detect gene expression profiles in areas of full thickness injury where skin is undergoing necrosis. Harvested tissue at the burn wound margin maximized the capture of viable cells from the multiple lineages important to the healing process and minimized the inclusion of non-viable cells destroyed by full-thickness injury. The samples were stored at -80 C until RNA isolation.
|
| Sample_geo_accession | GSM198876
| | Sample_status | Public on May 23 2010
| | Sample_submission_date | Jun 07 2007
| | Sample_last_update_date | May 23 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | At the time of isolation, tissues were chopped into small pieces at -20°C. Samples were weighed and 1ml Trizol (Invitrogen, Carlsbad, CA) was added per 100mg of sample. RNA was extracted using Qiagen’s Rnase-free DNase Set (Valencia, CA) supplied protocol with the following modification. RNA was precipitated with 0.25 volumes isopropanol (Fisher Scientific, Fairlawn, NJ) and 0.25 volumes of RNA precipitation solution (7% NaCl / 21% disodium citrate). DNase treatment was performed following the first Trizol isolation using Qiagen’s RNase-free DNase Set. Manufacturer’s protocol was modified and 10µl DNase in 70µl Buffer RDD was added to every 100µl of sample. Following DNase treatment the Trizol isolation was repeated once or occasionally twice to remove the DNase as well as any remaining fats or salts. RNA was re-suspended in RNase/DNase free H2O. A small aliquot of each sample was sent to the Microarray Core for quantification and bioanalysis. If the sample met the Microarray Core’s standards, samples were pooled equally by mass as to contain RNA from 5 tissue specimens for each array replicate. Pooled RNA samples were then resubmitted for bioanalysis quality assurance followed by microarray labeling and replicate hybridization.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Following quality control, the RNA was prepared for microarray analysis using the standard Affymetrix protocol (Affymetrix Inc, Santa Clara, CA). Briefly, a total of 5 µg of total RNA was reverse transcribed to double-stranded (ds) cDNA using an oligo-dT primer coupled to a T7 promoter. In vitro transcription from the ds cDNA was then carried out using T7 polymerase and incorporating biotin-modified CTP and UTP ribonucleotides.
| | Sample_hyb_protocol | Hybridized cRNA was detected using streptavidin coupled to phycoerythrin and visualized using GeneChip Scanner 3000 7G.
| | Sample_scan_protocol | GeneChips were scanned using GeneChip Scanner 3000 7G and GeneChip Operating System (GCOS, Affymetrix, Santa Clara, CA). Default values were used to grid images (.DAT) and generate .CEL and .CHP files and to generate gene expression values and ratios of gene expression between the hybridized samples
| | Sample_data_processing | For statistical analysis, CEL files (raw Affymetrix data) were imported in GeneSpring 7.0 (Agilent Technologies) and transformed by RMA (Robust Multichip Analysis).
| | Sample_platform_id | GPL570
| | Sample_contact_name | Lillian,B,Nanney
| | Sample_contact_email | lillian.nanney@vanderbilt.edu, joseph.a.greco@vanderbilt.edu
| | Sample_contact_department | Plastic Surgery
| | Sample_contact_institute | Vanderbilt University
| | Sample_contact_address | 1161 21st Ave S/S2221 MCN
| | Sample_contact_city | Nashville
| | Sample_contact_state | TN
| | Sample_contact_zip/postal_code | 37232
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM198nnn/GSM198876/suppl/GSM198876.CEL.gz
| | Sample_series_id | GSE8056
| | Sample_data_row_count | 54675
| | |
|
GSM198877 | GPL570 |
|
Normal human (no thermal injury) skin pool control-1
|
Normal human skin, pooled replicate #1 of normal (no thermal injury) skin control
|
median age: 51
mean age: 44.2
Procedure: blepharoplasty; blepharoplasty; reduction mammoplasty; split-thickness skin grafting; blepharoplasty
Total Body Surface Are Burned: 0% (all samples)
Post Burn Day: NA
Sex: F; M; F; M; F
|
All skin specimens were obtained in the operating room within minutes of being removed from the patient. Specimens were placed in aluminum foil and immediately snap-frozen in liquid nitrogen to preserve molecular content. Burn specimens were taken from wound margins since there was little point in trying to detect gene expression profiles in areas of full thickness injury where skin is undergoing necrosis. Harvested tissue at the burn wound margin maximized the capture of viable cells from the multiple lineages important to the healing process and minimized the inclusion of non-viable cells destroyed by full-thickness injury. The samples were stored at -80 C until RNA isolation.
|
| Sample_geo_accession | GSM198877
| | Sample_status | Public on May 23 2010
| | Sample_submission_date | Jun 07 2007
| | Sample_last_update_date | May 23 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | At the time of isolation, tissues were chopped into small pieces at -20°C. Samples were weighed and 1ml Trizol (Invitrogen, Carlsbad, CA) was added per 100mg of sample. RNA was extracted using Qiagen’s Rnase-free DNase Set (Valencia, CA) supplied protocol with the following modification. RNA was precipitated with 0.25 volumes isopropanol (Fisher Scientific, Fairlawn, NJ) and 0.25 volumes of RNA precipitation solution (7% NaCl / 21% disodium citrate). DNase treatment was performed following the first Trizol isolation using Qiagen’s RNase-free DNase Set. Manufacturer’s protocol was modified and 10µl DNase in 70µl Buffer RDD was added to every 100µl of sample. Following DNase treatment the Trizol isolation was repeated once or occasionally twice to remove the DNase as well as any remaining fats or salts. RNA was re-suspended in RNase/DNase free H2O. A small aliquot of each sample was sent to the Microarray Core for quantification and bioanalysis. If the sample met the Microarray Core’s standards, samples were pooled equally by mass as to contain RNA from 5 tissue specimens for each array replicate. Pooled RNA samples were then resubmitted for bioanalysis quality assurance followed by microarray labeling and replicate hybridization.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Following quality control, the RNA was prepared for microarray analysis using the standard Affymetrix protocol (Affymetrix Inc, Santa Clara, CA). Briefly, a total of 5 µg of total RNA was reverse transcribed to double-stranded (ds) cDNA using an oligo-dT primer coupled to a T7 promoter. In vitro transcription from the ds cDNA was then carried out using T7 polymerase and incorporating biotin-modified CTP and UTP ribonucleotides.
| | Sample_hyb_protocol | Hybridized cRNA was detected using streptavidin coupled to phycoerythrin and visualized using GeneChip Scanner 3000 7G.
| | Sample_scan_protocol | GeneChips were scanned using GeneChip Scanner 3000 7G and GeneChip Operating System (GCOS, Affymetrix, Santa Clara, CA). Default values were used to grid images (.DAT) and generate .CEL and .CHP files and to generate gene expression values and ratios of gene expression between the hybridized samples
| | Sample_data_processing | For statistical analysis, CEL files (raw Affymetrix data) were imported in GeneSpring 7.0 (Agilent Technologies) and transformed by RMA (Robust Multichip Analysis).
| | Sample_platform_id | GPL570
| | Sample_contact_name | Lillian,B,Nanney
| | Sample_contact_email | lillian.nanney@vanderbilt.edu, joseph.a.greco@vanderbilt.edu
| | Sample_contact_department | Plastic Surgery
| | Sample_contact_institute | Vanderbilt University
| | Sample_contact_address | 1161 21st Ave S/S2221 MCN
| | Sample_contact_city | Nashville
| | Sample_contact_state | TN
| | Sample_contact_zip/postal_code | 37232
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM198nnn/GSM198877/suppl/GSM198877.CEL.gz
| | Sample_series_id | GSE8056
| | Sample_data_row_count | 54675
| | |
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(2 groups will be compared at a time) |
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| Select GSMs and click on "Add groups" |
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