Search results for the GEO ID: GSE23983  |
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|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM590763 | GPL1355 |
|
Control, replicate 1
|
Liver, control
|
strain: Sprague-Dawley
gender: male
tissue: liver
treatment: control
|
|
| Sample_geo_accession | GSM590763
| | Sample_status | Public on Sep 01 2012
| | Sample_submission_date | Sep 06 2010
| | Sample_last_update_date | Sep 01 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Liver samples were removed from the storage in liquid nitrogen and homogenized using the TissueLyser (Qiagen, Hilden, Germany). Total RNA was extracted with the RNeasy®Plus Mini Kit (Qiagen, Hilden, Germany). RNA quality and quantity were assessed by spectrophotometric measurements (Nanodrop 1000, NanoDrop Technologies, USA) and potential RNA degradation was measured with RNA StdSens Analysis Kit and Experion (Experion™ Electrophoresis Station, Bio-Rad Laboratories, Hercules, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | The microarray experiments were performed at the Swegene Centre for Integrative Biology at Lund University (SCIBLU). In short, 5µg total RNA was processed following the GeneChip® Expression 3′-Amplification Reagents One-cycle cDNA synthesis kit instructions (Affymetrix Inc, Santa Clara, CA, USA) to produce double-stranded cDNA. This was used as a template to generate biotin-targeted cRNA following the manufacturer’s specifications.
| | Sample_hyb_protocol | Fifteen micrograms of the biotin-labeled cRNA were fragmented to strands between 35 and 200 bases in length, 10 micrograms of which were hybridized onto the GeneChip® Rat Genome 230 2.0 Array overnight in the GeneChip® Hybridisation 6400 oven using standard procedures. The arrays were washed and then stained in a GeneChip® Fluidics Station 450.
| | Sample_scan_protocol | Scanning was carried out with the GeneChip® Scanner 3000 and image analysis was performed using GeneChip® Operating Software.
| | Sample_data_processing | The microarray data was analyzed in the statistical language R 2.8.1 using the Bioconductor package. Preprocessing was performed using robust multi-array average from the rma package.
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Erik,,Kristiansson
| | Sample_contact_email | erik.kristiansson@zool.gu.se
| | Sample_contact_department | Department of Zoology
| | Sample_contact_institute | University of Gothenburg
| | Sample_contact_address | Box 463
| | Sample_contact_city | Göteborg
| | Sample_contact_zip/postal_code | 405 30
| | Sample_contact_country | Sweden
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM590nnn/GSM590763/suppl/GSM590763.cel.gz
| | Sample_series_id | GSE23983
| | Sample_data_row_count | 31099
| | |
|
GSM590764 | GPL1355 |
|
Exposed, replicate 1
|
Liver, exposed
|
strain: Sprague-Dawley
gender: male
tissue: liver
treatment: exposed
|
|
| Sample_geo_accession | GSM590764
| | Sample_status | Public on Sep 01 2012
| | Sample_submission_date | Sep 06 2010
| | Sample_last_update_date | Sep 01 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Liver samples were removed from the storage in liquid nitrogen and homogenized using the TissueLyser (Qiagen, Hilden, Germany). Total RNA was extracted with the RNeasy®Plus Mini Kit (Qiagen, Hilden, Germany). RNA quality and quantity were assessed by spectrophotometric measurements (Nanodrop 1000, NanoDrop Technologies, USA) and potential RNA degradation was measured with RNA StdSens Analysis Kit and Experion (Experion™ Electrophoresis Station, Bio-Rad Laboratories, Hercules, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | The microarray experiments were performed at the Swegene Centre for Integrative Biology at Lund University (SCIBLU). In short, 5µg total RNA was processed following the GeneChip® Expression 3′-Amplification Reagents One-cycle cDNA synthesis kit instructions (Affymetrix Inc, Santa Clara, CA, USA) to produce double-stranded cDNA. This was used as a template to generate biotin-targeted cRNA following the manufacturer’s specifications.
| | Sample_hyb_protocol | Fifteen micrograms of the biotin-labeled cRNA were fragmented to strands between 35 and 200 bases in length, 10 micrograms of which were hybridized onto the GeneChip® Rat Genome 230 2.0 Array overnight in the GeneChip® Hybridisation 6400 oven using standard procedures. The arrays were washed and then stained in a GeneChip® Fluidics Station 450.
| | Sample_scan_protocol | Scanning was carried out with the GeneChip® Scanner 3000 and image analysis was performed using GeneChip® Operating Software.
| | Sample_data_processing | The microarray data was analyzed in the statistical language R 2.8.1 using the Bioconductor package. Preprocessing was performed using robust multi-array average from the rma package.
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Erik,,Kristiansson
| | Sample_contact_email | erik.kristiansson@zool.gu.se
| | Sample_contact_department | Department of Zoology
| | Sample_contact_institute | University of Gothenburg
| | Sample_contact_address | Box 463
| | Sample_contact_city | Göteborg
| | Sample_contact_zip/postal_code | 405 30
| | Sample_contact_country | Sweden
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM590nnn/GSM590764/suppl/GSM590764.cel.gz
| | Sample_series_id | GSE23983
| | Sample_data_row_count | 31099
| | |
|
GSM590765 | GPL1355 |
|
Control, replicate 2
|
Liver, control
|
strain: Sprague-Dawley
gender: male
tissue: liver
treatment: control
|
|
| Sample_geo_accession | GSM590765
| | Sample_status | Public on Sep 01 2012
| | Sample_submission_date | Sep 06 2010
| | Sample_last_update_date | Sep 01 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Liver samples were removed from the storage in liquid nitrogen and homogenized using the TissueLyser (Qiagen, Hilden, Germany). Total RNA was extracted with the RNeasy®Plus Mini Kit (Qiagen, Hilden, Germany). RNA quality and quantity were assessed by spectrophotometric measurements (Nanodrop 1000, NanoDrop Technologies, USA) and potential RNA degradation was measured with RNA StdSens Analysis Kit and Experion (Experion™ Electrophoresis Station, Bio-Rad Laboratories, Hercules, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | The microarray experiments were performed at the Swegene Centre for Integrative Biology at Lund University (SCIBLU). In short, 5µg total RNA was processed following the GeneChip® Expression 3′-Amplification Reagents One-cycle cDNA synthesis kit instructions (Affymetrix Inc, Santa Clara, CA, USA) to produce double-stranded cDNA. This was used as a template to generate biotin-targeted cRNA following the manufacturer’s specifications.
| | Sample_hyb_protocol | Fifteen micrograms of the biotin-labeled cRNA were fragmented to strands between 35 and 200 bases in length, 10 micrograms of which were hybridized onto the GeneChip® Rat Genome 230 2.0 Array overnight in the GeneChip® Hybridisation 6400 oven using standard procedures. The arrays were washed and then stained in a GeneChip® Fluidics Station 450.
| | Sample_scan_protocol | Scanning was carried out with the GeneChip® Scanner 3000 and image analysis was performed using GeneChip® Operating Software.
| | Sample_data_processing | The microarray data was analyzed in the statistical language R 2.8.1 using the Bioconductor package. Preprocessing was performed using robust multi-array average from the rma package.
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Erik,,Kristiansson
| | Sample_contact_email | erik.kristiansson@zool.gu.se
| | Sample_contact_department | Department of Zoology
| | Sample_contact_institute | University of Gothenburg
| | Sample_contact_address | Box 463
| | Sample_contact_city | Göteborg
| | Sample_contact_zip/postal_code | 405 30
| | Sample_contact_country | Sweden
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM590nnn/GSM590765/suppl/GSM590765.cel.gz
| | Sample_series_id | GSE23983
| | Sample_data_row_count | 31099
| | |
|
GSM590769 | GPL1355 |
|
Exposed, replicate 2
|
Liver, exposed
|
strain: Sprague-Dawley
gender: male
tissue: liver
treatment: exposed
|
|
| Sample_geo_accession | GSM590769
| | Sample_status | Public on Sep 01 2012
| | Sample_submission_date | Sep 07 2010
| | Sample_last_update_date | Sep 01 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Liver samples were removed from the storage in liquid nitrogen and homogenized using the TissueLyser (Qiagen, Hilden, Germany). Total RNA was extracted with the RNeasy®Plus Mini Kit (Qiagen, Hilden, Germany). RNA quality and quantity were assessed by spectrophotometric measurements (Nanodrop 1000, NanoDrop Technologies, USA) and potential RNA degradation was measured with RNA StdSens Analysis Kit and Experion (Experion™ Electrophoresis Station, Bio-Rad Laboratories, Hercules, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | The microarray experiments were performed at the Swegene Centre for Integrative Biology at Lund University (SCIBLU). In short, 5µg total RNA was processed following the GeneChip® Expression 3′-Amplification Reagents One-cycle cDNA synthesis kit instructions (Affymetrix Inc, Santa Clara, CA, USA) to produce double-stranded cDNA. This was used as a template to generate biotin-targeted cRNA following the manufacturer’s specifications.
| | Sample_hyb_protocol | Fifteen micrograms of the biotin-labeled cRNA were fragmented to strands between 35 and 200 bases in length, 10 micrograms of which were hybridized onto the GeneChip® Rat Genome 230 2.0 Array overnight in the GeneChip® Hybridisation 6400 oven using standard procedures. The arrays were washed and then stained in a GeneChip® Fluidics Station 450.
| | Sample_scan_protocol | Scanning was carried out with the GeneChip® Scanner 3000 and image analysis was performed using GeneChip® Operating Software.
| | Sample_data_processing | The microarray data was analyzed in the statistical language R 2.8.1 using the Bioconductor package. Preprocessing was performed using robust multi-array average from the rma package.
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Erik,,Kristiansson
| | Sample_contact_email | erik.kristiansson@zool.gu.se
| | Sample_contact_department | Department of Zoology
| | Sample_contact_institute | University of Gothenburg
| | Sample_contact_address | Box 463
| | Sample_contact_city | Göteborg
| | Sample_contact_zip/postal_code | 405 30
| | Sample_contact_country | Sweden
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM590nnn/GSM590769/suppl/GSM590769.cel.gz
| | Sample_series_id | GSE23983
| | Sample_data_row_count | 31099
| | |
|
GSM590771 | GPL1355 |
|
Control, replicate 3
|
Liver, control
|
strain: Sprague-Dawley
gender: male
tissue: liver
treatment: control
|
|
| Sample_geo_accession | GSM590771
| | Sample_status | Public on Sep 01 2012
| | Sample_submission_date | Sep 07 2010
| | Sample_last_update_date | Sep 01 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Liver samples were removed from the storage in liquid nitrogen and homogenized using the TissueLyser (Qiagen, Hilden, Germany). Total RNA was extracted with the RNeasy®Plus Mini Kit (Qiagen, Hilden, Germany). RNA quality and quantity were assessed by spectrophotometric measurements (Nanodrop 1000, NanoDrop Technologies, USA) and potential RNA degradation was measured with RNA StdSens Analysis Kit and Experion (Experion™ Electrophoresis Station, Bio-Rad Laboratories, Hercules, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | The microarray experiments were performed at the Swegene Centre for Integrative Biology at Lund University (SCIBLU). In short, 5µg total RNA was processed following the GeneChip® Expression 3′-Amplification Reagents One-cycle cDNA synthesis kit instructions (Affymetrix Inc, Santa Clara, CA, USA) to produce double-stranded cDNA. This was used as a template to generate biotin-targeted cRNA following the manufacturer’s specifications.
| | Sample_hyb_protocol | Fifteen micrograms of the biotin-labeled cRNA were fragmented to strands between 35 and 200 bases in length, 10 micrograms of which were hybridized onto the GeneChip® Rat Genome 230 2.0 Array overnight in the GeneChip® Hybridisation 6400 oven using standard procedures. The arrays were washed and then stained in a GeneChip® Fluidics Station 450.
| | Sample_scan_protocol | Scanning was carried out with the GeneChip® Scanner 3000 and image analysis was performed using GeneChip® Operating Software.
| | Sample_data_processing | The microarray data was analyzed in the statistical language R 2.8.1 using the Bioconductor package. Preprocessing was performed using robust multi-array average from the rma package.
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Erik,,Kristiansson
| | Sample_contact_email | erik.kristiansson@zool.gu.se
| | Sample_contact_department | Department of Zoology
| | Sample_contact_institute | University of Gothenburg
| | Sample_contact_address | Box 463
| | Sample_contact_city | Göteborg
| | Sample_contact_zip/postal_code | 405 30
| | Sample_contact_country | Sweden
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM590nnn/GSM590771/suppl/GSM590771.cel.gz
| | Sample_series_id | GSE23983
| | Sample_data_row_count | 31099
| | |
|
GSM590772 | GPL1355 |
|
Exposed, replicate 3
|
Liver, exposed
|
strain: Sprague-Dawley
gender: male
tissue: liver
treatment: exposed
|
|
| Sample_geo_accession | GSM590772
| | Sample_status | Public on Sep 01 2012
| | Sample_submission_date | Sep 07 2010
| | Sample_last_update_date | Sep 01 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Liver samples were removed from the storage in liquid nitrogen and homogenized using the TissueLyser (Qiagen, Hilden, Germany). Total RNA was extracted with the RNeasy®Plus Mini Kit (Qiagen, Hilden, Germany). RNA quality and quantity were assessed by spectrophotometric measurements (Nanodrop 1000, NanoDrop Technologies, USA) and potential RNA degradation was measured with RNA StdSens Analysis Kit and Experion (Experion™ Electrophoresis Station, Bio-Rad Laboratories, Hercules, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | The microarray experiments were performed at the Swegene Centre for Integrative Biology at Lund University (SCIBLU). In short, 5µg total RNA was processed following the GeneChip® Expression 3′-Amplification Reagents One-cycle cDNA synthesis kit instructions (Affymetrix Inc, Santa Clara, CA, USA) to produce double-stranded cDNA. This was used as a template to generate biotin-targeted cRNA following the manufacturer’s specifications.
| | Sample_hyb_protocol | Fifteen micrograms of the biotin-labeled cRNA were fragmented to strands between 35 and 200 bases in length, 10 micrograms of which were hybridized onto the GeneChip® Rat Genome 230 2.0 Array overnight in the GeneChip® Hybridisation 6400 oven using standard procedures. The arrays were washed and then stained in a GeneChip® Fluidics Station 450.
| | Sample_scan_protocol | Scanning was carried out with the GeneChip® Scanner 3000 and image analysis was performed using GeneChip® Operating Software.
| | Sample_data_processing | The microarray data was analyzed in the statistical language R 2.8.1 using the Bioconductor package. Preprocessing was performed using robust multi-array average from the rma package.
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Erik,,Kristiansson
| | Sample_contact_email | erik.kristiansson@zool.gu.se
| | Sample_contact_department | Department of Zoology
| | Sample_contact_institute | University of Gothenburg
| | Sample_contact_address | Box 463
| | Sample_contact_city | Göteborg
| | Sample_contact_zip/postal_code | 405 30
| | Sample_contact_country | Sweden
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM590nnn/GSM590772/suppl/GSM590772.cel.gz
| | Sample_series_id | GSE23983
| | Sample_data_row_count | 31099
| | |
|
GSM590773 | GPL1355 |
|
Control, replicate 4
|
Liver, control
|
strain: Sprague-Dawley
gender: male
tissue: liver
treatment: control
|
|
| Sample_geo_accession | GSM590773
| | Sample_status | Public on Sep 01 2012
| | Sample_submission_date | Sep 07 2010
| | Sample_last_update_date | Sep 01 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Liver samples were removed from the storage in liquid nitrogen and homogenized using the TissueLyser (Qiagen, Hilden, Germany). Total RNA was extracted with the RNeasy®Plus Mini Kit (Qiagen, Hilden, Germany). RNA quality and quantity were assessed by spectrophotometric measurements (Nanodrop 1000, NanoDrop Technologies, USA) and potential RNA degradation was measured with RNA StdSens Analysis Kit and Experion (Experion™ Electrophoresis Station, Bio-Rad Laboratories, Hercules, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | The microarray experiments were performed at the Swegene Centre for Integrative Biology at Lund University (SCIBLU). In short, 5µg total RNA was processed following the GeneChip® Expression 3′-Amplification Reagents One-cycle cDNA synthesis kit instructions (Affymetrix Inc, Santa Clara, CA, USA) to produce double-stranded cDNA. This was used as a template to generate biotin-targeted cRNA following the manufacturer’s specifications.
| | Sample_hyb_protocol | Fifteen micrograms of the biotin-labeled cRNA were fragmented to strands between 35 and 200 bases in length, 10 micrograms of which were hybridized onto the GeneChip® Rat Genome 230 2.0 Array overnight in the GeneChip® Hybridisation 6400 oven using standard procedures. The arrays were washed and then stained in a GeneChip® Fluidics Station 450.
| | Sample_scan_protocol | Scanning was carried out with the GeneChip® Scanner 3000 and image analysis was performed using GeneChip® Operating Software.
| | Sample_data_processing | The microarray data was analyzed in the statistical language R 2.8.1 using the Bioconductor package. Preprocessing was performed using robust multi-array average from the rma package.
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Erik,,Kristiansson
| | Sample_contact_email | erik.kristiansson@zool.gu.se
| | Sample_contact_department | Department of Zoology
| | Sample_contact_institute | University of Gothenburg
| | Sample_contact_address | Box 463
| | Sample_contact_city | Göteborg
| | Sample_contact_zip/postal_code | 405 30
| | Sample_contact_country | Sweden
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM590nnn/GSM590773/suppl/GSM590773.cel.gz
| | Sample_series_id | GSE23983
| | Sample_data_row_count | 31099
| | |
|
GSM590774 | GPL1355 |
|
Exposed, replicate 4
|
Liver, exposed
|
strain: Sprague-Dawley
gender: male
tissue: liver
treatment: exposed
|
|
| Sample_geo_accession | GSM590774
| | Sample_status | Public on Sep 01 2012
| | Sample_submission_date | Sep 07 2010
| | Sample_last_update_date | Sep 01 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Liver samples were removed from the storage in liquid nitrogen and homogenized using the TissueLyser (Qiagen, Hilden, Germany). Total RNA was extracted with the RNeasy®Plus Mini Kit (Qiagen, Hilden, Germany). RNA quality and quantity were assessed by spectrophotometric measurements (Nanodrop 1000, NanoDrop Technologies, USA) and potential RNA degradation was measured with RNA StdSens Analysis Kit and Experion (Experion™ Electrophoresis Station, Bio-Rad Laboratories, Hercules, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | The microarray experiments were performed at the Swegene Centre for Integrative Biology at Lund University (SCIBLU). In short, 5µg total RNA was processed following the GeneChip® Expression 3′-Amplification Reagents One-cycle cDNA synthesis kit instructions (Affymetrix Inc, Santa Clara, CA, USA) to produce double-stranded cDNA. This was used as a template to generate biotin-targeted cRNA following the manufacturer’s specifications.
| | Sample_hyb_protocol | Fifteen micrograms of the biotin-labeled cRNA were fragmented to strands between 35 and 200 bases in length, 10 micrograms of which were hybridized onto the GeneChip® Rat Genome 230 2.0 Array overnight in the GeneChip® Hybridisation 6400 oven using standard procedures. The arrays were washed and then stained in a GeneChip® Fluidics Station 450.
| | Sample_scan_protocol | Scanning was carried out with the GeneChip® Scanner 3000 and image analysis was performed using GeneChip® Operating Software.
| | Sample_data_processing | The microarray data was analyzed in the statistical language R 2.8.1 using the Bioconductor package. Preprocessing was performed using robust multi-array average from the rma package.
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Erik,,Kristiansson
| | Sample_contact_email | erik.kristiansson@zool.gu.se
| | Sample_contact_department | Department of Zoology
| | Sample_contact_institute | University of Gothenburg
| | Sample_contact_address | Box 463
| | Sample_contact_city | Göteborg
| | Sample_contact_zip/postal_code | 405 30
| | Sample_contact_country | Sweden
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM590nnn/GSM590774/suppl/GSM590774.cel.gz
| | Sample_series_id | GSE23983
| | Sample_data_row_count | 31099
| | |
|
GSM590775 | GPL1355 |
|
Control, replicate 5
|
Liver, control
|
strain: Sprague-Dawley
gender: male
tissue: liver
treatment: control
|
|
| Sample_geo_accession | GSM590775
| | Sample_status | Public on Sep 01 2012
| | Sample_submission_date | Sep 07 2010
| | Sample_last_update_date | Sep 01 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Liver samples were removed from the storage in liquid nitrogen and homogenized using the TissueLyser (Qiagen, Hilden, Germany). Total RNA was extracted with the RNeasy®Plus Mini Kit (Qiagen, Hilden, Germany). RNA quality and quantity were assessed by spectrophotometric measurements (Nanodrop 1000, NanoDrop Technologies, USA) and potential RNA degradation was measured with RNA StdSens Analysis Kit and Experion (Experion™ Electrophoresis Station, Bio-Rad Laboratories, Hercules, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | The microarray experiments were performed at the Swegene Centre for Integrative Biology at Lund University (SCIBLU). In short, 5µg total RNA was processed following the GeneChip® Expression 3′-Amplification Reagents One-cycle cDNA synthesis kit instructions (Affymetrix Inc, Santa Clara, CA, USA) to produce double-stranded cDNA. This was used as a template to generate biotin-targeted cRNA following the manufacturer’s specifications.
| | Sample_hyb_protocol | Fifteen micrograms of the biotin-labeled cRNA were fragmented to strands between 35 and 200 bases in length, 10 micrograms of which were hybridized onto the GeneChip® Rat Genome 230 2.0 Array overnight in the GeneChip® Hybridisation 6400 oven using standard procedures. The arrays were washed and then stained in a GeneChip® Fluidics Station 450.
| | Sample_scan_protocol | Scanning was carried out with the GeneChip® Scanner 3000 and image analysis was performed using GeneChip® Operating Software.
| | Sample_data_processing | The microarray data was analyzed in the statistical language R 2.8.1 using the Bioconductor package. Preprocessing was performed using robust multi-array average from the rma package.
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Erik,,Kristiansson
| | Sample_contact_email | erik.kristiansson@zool.gu.se
| | Sample_contact_department | Department of Zoology
| | Sample_contact_institute | University of Gothenburg
| | Sample_contact_address | Box 463
| | Sample_contact_city | Göteborg
| | Sample_contact_zip/postal_code | 405 30
| | Sample_contact_country | Sweden
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM590nnn/GSM590775/suppl/GSM590775.cel.gz
| | Sample_series_id | GSE23983
| | Sample_data_row_count | 31099
| | |
|
GSM590776 | GPL1355 |
|
Exposed, replicate 5
|
Liver, exposed
|
strain: Sprague-Dawley
gender: male
tissue: liver
treatment: exposed
|
|
| Sample_geo_accession | GSM590776
| | Sample_status | Public on Sep 01 2012
| | Sample_submission_date | Sep 07 2010
| | Sample_last_update_date | Sep 01 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Liver samples were removed from the storage in liquid nitrogen and homogenized using the TissueLyser (Qiagen, Hilden, Germany). Total RNA was extracted with the RNeasy®Plus Mini Kit (Qiagen, Hilden, Germany). RNA quality and quantity were assessed by spectrophotometric measurements (Nanodrop 1000, NanoDrop Technologies, USA) and potential RNA degradation was measured with RNA StdSens Analysis Kit and Experion (Experion™ Electrophoresis Station, Bio-Rad Laboratories, Hercules, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | The microarray experiments were performed at the Swegene Centre for Integrative Biology at Lund University (SCIBLU). In short, 5µg total RNA was processed following the GeneChip® Expression 3′-Amplification Reagents One-cycle cDNA synthesis kit instructions (Affymetrix Inc, Santa Clara, CA, USA) to produce double-stranded cDNA. This was used as a template to generate biotin-targeted cRNA following the manufacturer’s specifications.
| | Sample_hyb_protocol | Fifteen micrograms of the biotin-labeled cRNA were fragmented to strands between 35 and 200 bases in length, 10 micrograms of which were hybridized onto the GeneChip® Rat Genome 230 2.0 Array overnight in the GeneChip® Hybridisation 6400 oven using standard procedures. The arrays were washed and then stained in a GeneChip® Fluidics Station 450.
| | Sample_scan_protocol | Scanning was carried out with the GeneChip® Scanner 3000 and image analysis was performed using GeneChip® Operating Software.
| | Sample_data_processing | The microarray data was analyzed in the statistical language R 2.8.1 using the Bioconductor package. Preprocessing was performed using robust multi-array average from the rma package.
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Erik,,Kristiansson
| | Sample_contact_email | erik.kristiansson@zool.gu.se
| | Sample_contact_department | Department of Zoology
| | Sample_contact_institute | University of Gothenburg
| | Sample_contact_address | Box 463
| | Sample_contact_city | Göteborg
| | Sample_contact_zip/postal_code | 405 30
| | Sample_contact_country | Sweden
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM590nnn/GSM590776/suppl/GSM590776.cel.gz
| | Sample_series_id | GSE23983
| | Sample_data_row_count | 31099
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Make groups for comparisons |
(2 groups will be compared at a time) |
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| Select GSMs and click on "Add groups" |
Enter the group name here: |
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