Result

Search results for the GEO ID: GSE26213

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Title

Source name

Description

Characteristics

GSM643760

GPL570

early_black_upper_extremity_10.8_mpi_54_yr_s1

early, black, upper extremity, 10.8 mpi, 54 yr

scaring: early color: black location: upper extremity time: 10.8 mpi age: 54 yr

Sample_geo_accession	GSM643760
Sample_status	Public on Dec 31 2011
Sample_submission_date	Dec 20 2010
Sample_last_update_date	Dec 31 2011
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Homo sapiens
Sample_taxid_ch1	9606
Sample_treatment_protocol_ch1	After harvest, the sample was placed immediately in liquid nitrogen. The full-thickness human and porcine wound samples were snap-frozen in chilled Tissue-Tek® Optimal Cutting Temperature embedding medium (Sakura Finetechnical U.S.A., Torrance, CA). The biopsies were sectioned at 7μm, fixed in 75% ethanol, dehydrated and air dried. The slides were loaded into the Arcturus® AutoPix Laser Capture Microdissection system (Molecular Devices Corporation, Sunnyvale, CA). A laser spot size of 25 μm diameter was used with 85-95mW power and 8,500-10,000 ms duration. The offset and overlap was 25%. The efficiency of the microdissection was evaluated by examining the cap after capture and by examining the tissue before and after lift off from the cap. 10-20 sites were captured per sample or 500-1000 cells.
Sample_growth_protocol_ch1	NA
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Following laser capture microdissection, the cap was incubated in 50 μl PicoPureTM RNA extraction buffer (Molecular Devices Corporation, Sunnyvale, CA) at 42°C for 30 minutes. After DNase (Qiagen, Valencia, CA) treatment, total RNA was eluted in 12 μl of Elution Buffer. RNA quality was monitored with Agilent 2100 Bioanalyzer (Agilent Technologies, Inc., Santa Clara, CA), the Agilent RNA 6000 Pico chip, and Eukaryote Total RNA Pico by evaluating the features of the electropherogram and the RNA integrity numbers. 28S and 18S rRNA bands were expected and the intensity of the 28S bands was expected to be higher than the intensity of the 18S. The RNA Integrity Numbers (RIN) were expected to be greater than 6.0. Samples that failed these criteria were repeated. The LCM RNA and 500 pg control RNA were amplified using the RiboAmpTM HS kit (Molecular Devices Corporation, Sunnyvale, CA). RNA was reverse transcribed and double-stranded cDNAs synthesized and purified. The first-round cDNA was transcribed using T7 RNA polymerase. The resulting RNA was purified and used in the second round of amplification. The quality and quantity of amplified RNA was evaluated spectrophotometrically and with the Agilent 2100 Bioanalyzer (Agilent Technologies, Inc., Santa Clara, CA). The required A260/280 ratio was in the range 1.8-2.1. Samples that failed these criteria were repeated.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Transcription and labeling of complementary RNA was performed with biotinylated UTP and CTP (Affymetrix IVT labeling Kit). The target complementary RNA was fragmented, washed, and stained according to the manufacturer instructions. The quality and quantity of labeled complementary RNA was evaluated spectrophotometrically and with the Agilent 2100 Bioanalyzer (Agilent Technologies, Inc., Santa Clara, CA).
Sample_hyb_protocol	Labeled targets were hybridized to the Affymetrix Human GeneChip® Human Genome U133 plus 2.0 for 16–18 hours at 45 °C and 60 rounds per minute (Hybridization Oven 640, Affymetrix, Santa Clara, CA, USA). Spike controls were added to complementary RNA before hybridization. Washing and staining with streptavidine-phycoerythrine was performed in an automatic fluidics station (GeneChip® Fluidics Station 400, Affymetrix, Santa Clara, CA, USA).
Sample_scan_protocol	Scanning was performed with GeneChip® Scanner 3000 (Affymetrix, Santa Clara, CA, USA). The quality of the hybridization and overall chip performance was evaluated by visual inspection of the raw scanned data and the quality control measures in the Affymetrix *.RPT report file; except that we did not monitor the Affymetrix 3'5' ratios since there are no recommended values for amplified porcine tissues.
Sample_data_processing	Supplied in CHP files, Algorithm: ExpressionStat 5.0
Sample_platform_id	GPL570
Sample_contact_name	Oliver,,Couture
Sample_contact_institute	Iowa State University
Sample_contact_address	2255 Kildee
Sample_contact_city	Ames
Sample_contact_state	IA
Sample_contact_zip/postal_code	50011
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM643nnn/GSM643760/suppl/GSM643760.CEL.gz
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM643nnn/GSM643760/suppl/GSM643760.CHP.gz
Sample_series_id	GSE26095
Sample_series_id	GSE26213
Sample_data_row_count	54675

GSM643761

GPL570

early_white_neck_6.7_mpi_19_yr_s2

early, white, neck, 6.7 mpi, 19 yr

scaring: early color: white location: neck time: 6.7 mpi age: 19 yr

Sample_geo_accession	GSM643761
Sample_status	Public on Dec 31 2011
Sample_submission_date	Dec 20 2010
Sample_last_update_date	Dec 31 2011
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Homo sapiens
Sample_taxid_ch1	9606
Sample_treatment_protocol_ch1	After harvest, the sample was placed immediately in liquid nitrogen. The full-thickness human and porcine wound samples were snap-frozen in chilled Tissue-Tek® Optimal Cutting Temperature embedding medium (Sakura Finetechnical U.S.A., Torrance, CA). The biopsies were sectioned at 7μm, fixed in 75% ethanol, dehydrated and air dried. The slides were loaded into the Arcturus® AutoPix Laser Capture Microdissection system (Molecular Devices Corporation, Sunnyvale, CA). A laser spot size of 25 μm diameter was used with 85-95mW power and 8,500-10,000 ms duration. The offset and overlap was 25%. The efficiency of the microdissection was evaluated by examining the cap after capture and by examining the tissue before and after lift off from the cap. 10-20 sites were captured per sample or 500-1000 cells.
Sample_growth_protocol_ch1	NA
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Following laser capture microdissection, the cap was incubated in 50 μl PicoPureTM RNA extraction buffer (Molecular Devices Corporation, Sunnyvale, CA) at 42°C for 30 minutes. After DNase (Qiagen, Valencia, CA) treatment, total RNA was eluted in 12 μl of Elution Buffer. RNA quality was monitored with Agilent 2100 Bioanalyzer (Agilent Technologies, Inc., Santa Clara, CA), the Agilent RNA 6000 Pico chip, and Eukaryote Total RNA Pico by evaluating the features of the electropherogram and the RNA integrity numbers. 28S and 18S rRNA bands were expected and the intensity of the 28S bands was expected to be higher than the intensity of the 18S. The RNA Integrity Numbers (RIN) were expected to be greater than 6.0. Samples that failed these criteria were repeated. The LCM RNA and 500 pg control RNA were amplified using the RiboAmpTM HS kit (Molecular Devices Corporation, Sunnyvale, CA). RNA was reverse transcribed and double-stranded cDNAs synthesized and purified. The first-round cDNA was transcribed using T7 RNA polymerase. The resulting RNA was purified and used in the second round of amplification. The quality and quantity of amplified RNA was evaluated spectrophotometrically and with the Agilent 2100 Bioanalyzer (Agilent Technologies, Inc., Santa Clara, CA). The required A260/280 ratio was in the range 1.8-2.1. Samples that failed these criteria were repeated.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Transcription and labeling of complementary RNA was performed with biotinylated UTP and CTP (Affymetrix IVT labeling Kit). The target complementary RNA was fragmented, washed, and stained according to the manufacturer instructions. The quality and quantity of labeled complementary RNA was evaluated spectrophotometrically and with the Agilent 2100 Bioanalyzer (Agilent Technologies, Inc., Santa Clara, CA).
Sample_hyb_protocol	Labeled targets were hybridized to the Affymetrix Human GeneChip® Human Genome U133 plus 2.0 for 16–18 hours at 45 °C and 60 rounds per minute (Hybridization Oven 640, Affymetrix, Santa Clara, CA, USA). Spike controls were added to complementary RNA before hybridization. Washing and staining with streptavidine-phycoerythrine was performed in an automatic fluidics station (GeneChip® Fluidics Station 400, Affymetrix, Santa Clara, CA, USA).
Sample_scan_protocol	Scanning was performed with GeneChip® Scanner 3000 (Affymetrix, Santa Clara, CA, USA). The quality of the hybridization and overall chip performance was evaluated by visual inspection of the raw scanned data and the quality control measures in the Affymetrix *.RPT report file; except that we did not monitor the Affymetrix 3'5' ratios since there are no recommended values for amplified porcine tissues.
Sample_data_processing	Supplied in CHP files, Algorithm: ExpressionStat 5.0
Sample_platform_id	GPL570
Sample_contact_name	Oliver,,Couture
Sample_contact_institute	Iowa State University
Sample_contact_address	2255 Kildee
Sample_contact_city	Ames
Sample_contact_state	IA
Sample_contact_zip/postal_code	50011
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM643nnn/GSM643761/suppl/GSM643761.CEL.gz
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM643nnn/GSM643761/suppl/GSM643761.CHP.gz
Sample_series_id	GSE26095
Sample_series_id	GSE26213
Sample_data_row_count	54675

GSM643762

GPL570

early_black_upper_extremity_10.8_mpi_54_yr_s3

early, black, upper extremity, 10.8 mpi, 54 yr

scaring: early color: black location: upper extremity time: 10.8 mpi age: 54 yr

Sample_geo_accession	GSM643762
Sample_status	Public on Dec 31 2011
Sample_submission_date	Dec 20 2010
Sample_last_update_date	Dec 31 2011
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Homo sapiens
Sample_taxid_ch1	9606
Sample_treatment_protocol_ch1	After harvest, the sample was placed immediately in liquid nitrogen. The full-thickness human and porcine wound samples were snap-frozen in chilled Tissue-Tek® Optimal Cutting Temperature embedding medium (Sakura Finetechnical U.S.A., Torrance, CA). The biopsies were sectioned at 7μm, fixed in 75% ethanol, dehydrated and air dried. The slides were loaded into the Arcturus® AutoPix Laser Capture Microdissection system (Molecular Devices Corporation, Sunnyvale, CA). A laser spot size of 25 μm diameter was used with 85-95mW power and 8,500-10,000 ms duration. The offset and overlap was 25%. The efficiency of the microdissection was evaluated by examining the cap after capture and by examining the tissue before and after lift off from the cap. 10-20 sites were captured per sample or 500-1000 cells.
Sample_growth_protocol_ch1	NA
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Following laser capture microdissection, the cap was incubated in 50 μl PicoPureTM RNA extraction buffer (Molecular Devices Corporation, Sunnyvale, CA) at 42°C for 30 minutes. After DNase (Qiagen, Valencia, CA) treatment, total RNA was eluted in 12 μl of Elution Buffer. RNA quality was monitored with Agilent 2100 Bioanalyzer (Agilent Technologies, Inc., Santa Clara, CA), the Agilent RNA 6000 Pico chip, and Eukaryote Total RNA Pico by evaluating the features of the electropherogram and the RNA integrity numbers. 28S and 18S rRNA bands were expected and the intensity of the 28S bands was expected to be higher than the intensity of the 18S. The RNA Integrity Numbers (RIN) were expected to be greater than 6.0. Samples that failed these criteria were repeated. The LCM RNA and 500 pg control RNA were amplified using the RiboAmpTM HS kit (Molecular Devices Corporation, Sunnyvale, CA). RNA was reverse transcribed and double-stranded cDNAs synthesized and purified. The first-round cDNA was transcribed using T7 RNA polymerase. The resulting RNA was purified and used in the second round of amplification. The quality and quantity of amplified RNA was evaluated spectrophotometrically and with the Agilent 2100 Bioanalyzer (Agilent Technologies, Inc., Santa Clara, CA). The required A260/280 ratio was in the range 1.8-2.1. Samples that failed these criteria were repeated.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Transcription and labeling of complementary RNA was performed with biotinylated UTP and CTP (Affymetrix IVT labeling Kit). The target complementary RNA was fragmented, washed, and stained according to the manufacturer instructions. The quality and quantity of labeled complementary RNA was evaluated spectrophotometrically and with the Agilent 2100 Bioanalyzer (Agilent Technologies, Inc., Santa Clara, CA).
Sample_hyb_protocol	Labeled targets were hybridized to the Affymetrix Human GeneChip® Human Genome U133 plus 2.0 for 16–18 hours at 45 °C and 60 rounds per minute (Hybridization Oven 640, Affymetrix, Santa Clara, CA, USA). Spike controls were added to complementary RNA before hybridization. Washing and staining with streptavidine-phycoerythrine was performed in an automatic fluidics station (GeneChip® Fluidics Station 400, Affymetrix, Santa Clara, CA, USA).
Sample_scan_protocol	Scanning was performed with GeneChip® Scanner 3000 (Affymetrix, Santa Clara, CA, USA). The quality of the hybridization and overall chip performance was evaluated by visual inspection of the raw scanned data and the quality control measures in the Affymetrix *.RPT report file; except that we did not monitor the Affymetrix 3'5' ratios since there are no recommended values for amplified porcine tissues.
Sample_data_processing	Supplied in CHP files, Algorithm: ExpressionStat 5.0
Sample_platform_id	GPL570
Sample_contact_name	Oliver,,Couture
Sample_contact_institute	Iowa State University
Sample_contact_address	2255 Kildee
Sample_contact_city	Ames
Sample_contact_state	IA
Sample_contact_zip/postal_code	50011
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM643nnn/GSM643762/suppl/GSM643762.CEL.gz
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM643nnn/GSM643762/suppl/GSM643762.CHP.gz
Sample_series_id	GSE26095
Sample_series_id	GSE26213
Sample_data_row_count	54675

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