Search results for the GEO ID: GSE7741  |
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GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM182149 | GPL570 |
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HCV infected liver _Fibrosis Stage 0_pool1
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Pooled early fibrosis Stage 0 of chronic HCV infected liver
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Tissue: Liver biopsy tissue
Disease stage: A pooled RNA sample from 4 liver tissues with chronic hepatitis C, fibrosis stage 0, grade of inflammation 0-1.
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Experiment ID: Rag208 HG U133Plus 2.0
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| Sample_geo_accession | GSM182149
| | Sample_status | Public on Nov 01 2007
| | Sample_submission_date | Apr 14 2007
| | Sample_last_update_date | Sep 27 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | All liver biopsy specimens were collected at Aga Khan University & Hospital following institutional ethics committee guidelines, from 3-10-2005 to 10-9-2005
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated from frozen liver tissues using TRIzol reagent (Invitrogen, MD) and purified using affinity resin column (Rneasy Qiagen, Chatsworth, CA). Equal amounts of total RNA from 4 individuals with fibrosis stage 0 were pooled. The quality of RNA was checked using the Agilent 2100 Bioanalyzer (Agilent Technologies).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | 50ng of the isolated total RNA was converted to cDNA and amplified according to the manufacturer’s instructions for the Affymetrix GeneChipTM System (Santa Clara, CA) at the Microarray Facilities, Mayo Foundation General Clinic Research (Rochester, MN). Double stranded cDNA was then purified by phase lock gel (Eppendorf, Westbury, NY) with phenol/chloroform extraction. Purified cDNA was used as a template for an in vitro transcription reaction for the synthesis of biotinylated cRNA using RNA transcript labeling reagent (affymetrix, Inc., Santa Clara, CA).
| | Sample_hyb_protocol | The labeled cRNAs were then fragmented and hybridized onto the Affymetrix GeneChipTM arrays (Affymetrix HG U133 plus 2.0), according to manufacturer’s instructions. Briefly, appropriate amounts of fragmented cRNA and control oligonucleotide B2 were added to the hybridization buffer along with control cRNA (BioB, BioC, BioD), herring sperm DNA, and bovine serum albumin (BSA). The hybridization mixture was heated at 99o C for 5 min followed by incubation at 45o C for 5 min before injecting the sample into the GeneChipTM. Then the hybridization was done at 45oC for 16 h with mixing on a rotisserie at 60 rpm. After hybridization, the solution was removed and arrays were washed and stained with streptavidin-phycoerythrin (Molecular Probes, Eugene, OR).
| | Sample_hyb_protocol | The quality of the fragmented biotin-labeled cRNA in each experiment was evaluated by both gel electrophoresis and hybridization (fraction of the sample) onto test-3 microarray as a measure of quality control before hybridizing onto the Affymetrix Gene Expression Arrays.
| | Sample_scan_protocol | Probe arrays were scanned in the Affymetrix GeneChipTM system confocal scanner by using Affymetrix GeneChipTM Operating System v1.3 software. Chips were scaled to a value of 500 to allow array-to-array comparisons.
| | Sample_data_processing | The CEL files generated by Gene Chip Operating Software (GCOS) were uploaded to Genespring GX software. Gene expression measures were computed using the Robust Multi-chip average method (RMA) that includes background correction, probe-level quantile normalization and calculation of expression measures.
| | Sample_data_processing |
| | Sample_platform_id | GPL570
| | Sample_contact_name | Saira,,Sarfraz
| | Sample_contact_email | saira.sarfraz@aku.edu
| | Sample_contact_laboratory | Juma Research lab. BSL-2
| | Sample_contact_department | Biological & Biomedical Sciences
| | Sample_contact_institute | Aga Khan University
| | Sample_contact_address | Stadium road
| | Sample_contact_city | Karachi
| | Sample_contact_zip/postal_code | 74800
| | Sample_contact_country | Pakistan
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM182nnn/GSM182149/suppl/GSM182149.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM182nnn/GSM182149/suppl/GSM182149.CHP.gz
| | Sample_series_id | GSE7741
| | Sample_data_row_count | 54675
| | |
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GSM182150 | GPL570 |
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Non-viral hepatic liver_pool1
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Pooled Non-viral hepatitis
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Tissue: Liver biopsy tissue
Disease state: A pooled RNA sample from 3 liver tissues with non-viral hepatitis fibrosis stage 3, grade of inflammation II
Male to female ratio: 1/2
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Experiment ID: Rag209 HG U133Plus 2.0
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| Sample_geo_accession | GSM182150
| | Sample_status | Public on Nov 01 2007
| | Sample_submission_date | Apr 14 2007
| | Sample_last_update_date | Sep 27 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | All liver biopsy specimens were collected at Aga Khan University & Hospital following institutional ethics committee guidelines, from 3-10-2005 to 10-9-2005
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated from frozen liver tissues using TRIzol reagent (Invitrogen, MD) and purified using affinity resin column (Rneasy Qiagen, Chatsworth, CA). Equal amounts of total RNA from 4 individuals with fibrosis stage 0 were pooled. The quality of RNA was checked using the Agilent 2100 Bioanalyzer (Agilent Technologies).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | 50ng of the isolated total RNA was converted to cDNA and amplified according to the manufacturer’s instructions for the Affymetrix GeneChipTM System (Santa Clara, CA) at the Microarray Facilities, Mayo Foundation General Clinic Research (Rochester, MN). Double stranded cDNA was then purified by phase lock gel (Eppendorf, Westbury, NY) with phenol/chloroform extraction. Purified cDNA was used as a template for an in vitro transcription reaction for the synthesis of biotinylated cRNA using RNA transcript labeling reagent (affymetrix, Inc., Santa Clara, CA).
| | Sample_hyb_protocol | The labeled cRNAs were then fragmented and hybridized onto the Affymetrix GeneChipTM arrays (Affymetrix HG U133 plus 2.0), according to manufacturer’s instructions. Briefly, appropriate amounts of fragmented cRNA and control oligonucleotide B2 were added to the hybridization buffer along with control cRNA (BioB, BioC, BioD), herring sperm DNA, and bovine serum albumin (BSA). The hybridization mixture was heated at 99o C for 5 min followed by incubation at 45o C for 5 min before injecting the sample into the GeneChipTM. Then the hybridization was done at 45oC for 16 h with mixing on a rotisserie at 60 rpm. After hybridization, the solution was removed and arrays were washed and stained with streptavidin-phycoerythrin (Molecular Probes, Eugene, OR).
| | Sample_hyb_protocol | The quality of the fragmented biotin-labeled cRNA in each experiment was evaluated by both gel electrophoresis and hybridization (fraction of the sample) onto test-3 microarray as a measure of quality control before hybridizing onto the Affymetrix Gene Expression Arrays.
| | Sample_scan_protocol | Probe arrays were scanned in the Affymetrix GeneChipTM system confocal scanner by using Affymetrix GeneChipTM Operating System v1.3 software. Chips were scaled to a value of 500 to allow array-to-array comparisons.
| | Sample_data_processing | The CEL files generated by Gene Chip Operating Software (GCOS) were uploaded to Genespring GX software. Gene expression measures were computed using the Robust Multi-chip average method (RMA) that includes background correction, probe-level quantile normalization and calculation of expression measures.
| | Sample_data_processing |
| | Sample_platform_id | GPL570
| | Sample_contact_name | Saira,,Sarfraz
| | Sample_contact_email | saira.sarfraz@aku.edu
| | Sample_contact_laboratory | Juma Research lab. BSL-2
| | Sample_contact_department | Biological & Biomedical Sciences
| | Sample_contact_institute | Aga Khan University
| | Sample_contact_address | Stadium road
| | Sample_contact_city | Karachi
| | Sample_contact_zip/postal_code | 74800
| | Sample_contact_country | Pakistan
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM182nnn/GSM182150/suppl/GSM182150.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM182nnn/GSM182150/suppl/GSM182150.CHP.gz
| | Sample_series_id | GSE7741
| | Sample_data_row_count | 54675
| | |
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GSM182151 | GPL570 |
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HCV infected liver_Advance Fibrosis pool
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Pooled advance fibrosis stage III-IV chronic HCV infected liver
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Tissue: Liver tissues
Disease state: A pooled RNA sample from 4 liver tissues with chronic hepatitis C fibrosis stage III and IV, grade of inflammation III-IV
Male to female ratio: 1/3
|
Experiment ID: Rag210 HG U133Plus 2.0
|
| Sample_geo_accession | GSM182151
| | Sample_status | Public on Nov 01 2007
| | Sample_submission_date | Apr 14 2007
| | Sample_last_update_date | Sep 27 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | All liver biopsy specimens were collected at Aga Khan University & Hospital following institutional ethics committee guidelines, from 3-10-2005 to 10-9-2005
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated from frozen liver tissues using TRIzol reagent (Invitrogen, MD) and purified using affinity resin column (Rneasy Qiagen, Chatsworth, CA). Equal amounts of total RNA from 4 individuals with fibrosis stage 0 were pooled. The quality of RNA was checked using the Agilent 2100 Bioanalyzer (Agilent Technologies).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | 50ng of the isolated total RNA was converted to cDNA and amplified according to the manufacturer’s instructions for the Affymetrix GeneChipTM System (Santa Clara, CA) at the Microarray Facilities, Mayo Foundation General Clinic Research (Rochester, MN). Double stranded cDNA was then purified by phase lock gel (Eppendorf, Westbury, NY) with phenol/chloroform extraction. Purified cDNA was used as a template for an in vitro transcription reaction for the synthesis of biotinylated cRNA using RNA transcript labeling reagent (affymetrix, Inc., Santa Clara, CA).
| | Sample_hyb_protocol | The labeled cRNAs were then fragmented and hybridized onto the Affymetrix GeneChipTM arrays (Affymetrix HG U133 plus 2.0), according to manufacturer’s instructions. Briefly, appropriate amounts of fragmented cRNA and control oligonucleotide B2 were added to the hybridization buffer along with control cRNA (BioB, BioC, BioD), herring sperm DNA, and bovine serum albumin (BSA). The hybridization mixture was heated at 99o C for 5 min followed by incubation at 45o C for 5 min before injecting the sample into the GeneChipTM. Then the hybridization was done at 45oC for 16 h with mixing on a rotisserie at 60 rpm. After hybridization, the solution was removed and arrays were washed and stained with streptavidin-phycoerythrin (Molecular Probes, Eugene, OR).
| | Sample_hyb_protocol | The quality of the fragmented biotin-labeled cRNA in each experiment was evaluated by both gel electrophoresis and hybridization (fraction of the sample) onto test-3 microarray as a measure of quality control before hybridizing onto the Affymetrix Gene Expression Arrays.
| | Sample_scan_protocol | Probe arrays were scanned in the Affymetrix GeneChipTM system confocal scanner by using Affymetrix GeneChipTM Operating System v1.3 software. Chips were scaled to a value of 500 to allow array-to-array comparisons.
| | Sample_data_processing | The CEL files generated by Gene Chip Operating Software (GCOS) were uploaded to Genespring GX software. Gene expression measures were computed using the Robust Multi-chip average method (RMA) that includes background correction, probe-level quantile normalization and calculation of expression measures.
| | Sample_data_processing |
| | Sample_platform_id | GPL570
| | Sample_contact_name | Saira,,Sarfraz
| | Sample_contact_email | saira.sarfraz@aku.edu
| | Sample_contact_laboratory | Juma Research lab. BSL-2
| | Sample_contact_department | Biological & Biomedical Sciences
| | Sample_contact_institute | Aga Khan University
| | Sample_contact_address | Stadium road
| | Sample_contact_city | Karachi
| | Sample_contact_zip/postal_code | 74800
| | Sample_contact_country | Pakistan
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM182nnn/GSM182151/suppl/GSM182151.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM182nnn/GSM182151/suppl/GSM182151.CHP.gz
| | Sample_series_id | GSE7741
| | Sample_data_row_count | 54675
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