Search results for the GEO ID: GSE6721  |
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|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM154510 | GPL339 |
|
Liver cholesterol pool1 Affy
|
liver, high cholesterol diet
|
Strain: C57BL/6
Gender: male
Age: 9 - 12 weeks
Tissue: liver
Treatment: vehicle only (5% DMSO in corn oil)
Diet: 1% cholesterol diet
|
No additional data.
|
| Sample_geo_accession | GSM154510
| | Sample_status | Public on Nov 27 2007
| | Sample_submission_date | Jan 10 2007
| | Sample_last_update_date | Jan 30 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_biomaterial_provider_ch1 | Adrian Roth
| | Sample_treatment_protocol_ch1 | Animals were injected i.p. vehicle (5% DMSO in corn oil). After 10 h they were sacrificed.
| | Sample_growth_protocol_ch1 | Animals had free acess to food (standard laboratory chow) and drinking water. They were mantained in 12-hour light/12-hour dark cycle. Seven days prior treatment they were on 1% (w/w) cholesterol diet (Provimi Kliba SA, Kaiseraugst, CH).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated using TRIzol reagent (Invitrogen) according to the manufacturer protocol and purified by RNeasy Mini Kit (Qiagen). The total RNAs of two animals were pooled in equal amounts.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | All was done according to the Affymetrix recommendations. Briefly, double-stranded cDNA was synthesised using 10μg of total RNA with a (dT)24-T7 primer and amplified with T7 RNA polymerase in the presence of biotinylated nucleotides to cRNA.
| | Sample_hyb_protocol | After fragmentation, the cRNA was hybridised to the Gene Chips for 16 hours, followed by a standard amplification with biotin/streptavidin/phycoerythrin.
| | Sample_scan_protocol | Microarrays were scanned using a laser scanner (Affymetrix).
| | Sample_data_processing | Raw data were first normalized using log2-transformed expression measure summaries of the probe sets which were computed and normalized using the Robust Multichip Average (RMA) algorithm as described. After transformation to non-logarithmic data, the expression estimates were scaled to the average expression levels in the control group and transcript levels further analyzed using Gene Spring Software (Silicon Genetics, Redwood, USA).
| | Sample_platform_id | GPL339
| | Sample_contact_name | Peter,,Juvan
| | Sample_contact_phone | +386 1 543 7595
| | Sample_contact_laboratory | Center for Functional Genomics and Bio-Chips
| | Sample_contact_department | Institute of Biochemistry
| | Sample_contact_institute | Faculty of Medicine, University of Ljubljana
| | Sample_contact_address | Zaloska 4
| | Sample_contact_city | Ljubljana
| | Sample_contact_zip/postal_code | SI-1000
| | Sample_contact_country | Slovenia
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM154nnn/GSM154510/suppl/GSM154510.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM154nnn/GSM154510/suppl/GSM154510.EXP.gz
| | Sample_series_id | GSE6721
| | Sample_data_row_count | 22690
| | |
|
GSM154961 | GPL339 |
|
Liver cholesterol pool3 Affy
|
liver, high cholesterol diet
|
Strain: C57BL/6
Gender: male
Age: 9 - 12 weeks
Tissue: liver
Treatment: vehicle only (5% DMSO in corn oil)
Diet: 1% cholesterol diet
|
No additional data.
|
| Sample_geo_accession | GSM154961
| | Sample_status | Public on Nov 27 2007
| | Sample_submission_date | Jan 12 2007
| | Sample_last_update_date | Jan 30 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_biomaterial_provider_ch1 | Adrian Roth
| | Sample_treatment_protocol_ch1 | Animals were injected i.p. vehicle (5% DMSO in corn oil). After 10h they were sacrificed.
| | Sample_growth_protocol_ch1 | Animals had free acess to food (standard laboratory chow) and drinking water. They were mantained in 12-hour light/12-hour dark cycle. Seven days prior treatment they were on 1% (w/w) cholesterol diet (Provimi Kliba SA, Kaiseraugst, CH).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated using TRIzol reagent (Invitrogen) according to the manufacturer protocol and purified by RNeasy Mini Kit (Qiagen). The total RNAs of two animals were pooled in equal amounts.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | All was done according to the Affymetrix recommendations. Briefly, double-stranded cDNA was synthesised using 10mg of total RNA with a (dT)24-T7 primer and amplified with T7 RNA polymerase in the presence of biotinylated nucleotides to cRNA.
| | Sample_hyb_protocol | After fragmentation, the cRNA was hybridised to the Gene Chips for 16 hours, followed by a standard amplification with biotin/streptavidin/phycoerythrin.
| | Sample_scan_protocol | MIcroarrays were scanned using a laser scanner (Affymetrix).
| | Sample_data_processing | Raw data were normalized using the Robust Multichip Average (RMA) algorithm as described. After transformation to non-logarithmic data, the expression estimates were scaled to the average expression levels in the control group analyzed using GeneSpring software (Silicon Genetics, Redwood, USA).
| | Sample_platform_id | GPL339
| | Sample_contact_name | Peter,,Juvan
| | Sample_contact_phone | +386 1 543 7595
| | Sample_contact_laboratory | Center for Functional Genomics and Bio-Chips
| | Sample_contact_department | Institute of Biochemistry
| | Sample_contact_institute | Faculty of Medicine, University of Ljubljana
| | Sample_contact_address | Zaloska 4
| | Sample_contact_city | Ljubljana
| | Sample_contact_zip/postal_code | SI-1000
| | Sample_contact_country | Slovenia
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM154nnn/GSM154961/suppl/GSM154961.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM154nnn/GSM154961/suppl/GSM154961.EXP.gz
| | Sample_series_id | GSE6721
| | Sample_data_row_count | 22690
| | |
|
GSM154962 | GPL339 |
|
Liver cholesterol pool4 Affy
|
liver, high cholesterol diet
|
Strain: C57BL/6
Gender: male
Age: 9 - 12 weeks
Tissue: liver
Treatment: vehicle only (5% DMSO in corn oil)
Diet: 1% cholesterol diet
|
No additional data.
|
| Sample_geo_accession | GSM154962
| | Sample_status | Public on Nov 27 2007
| | Sample_submission_date | Jan 12 2007
| | Sample_last_update_date | Jan 30 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_biomaterial_provider_ch1 | Adrian Roth
| | Sample_treatment_protocol_ch1 | Animals were injected i.p. vehicle (5% DMSO in corn oil). After 10h they were sacrificed.
| | Sample_growth_protocol_ch1 | Animals had free acess to food (standard laboratory chow) and drinking water. They were mantained in 12-hour light/12-hour dark cycle. Seven days prior treatment they were on 1% (w/w) cholesterol diet (Provimi Kliba SA, Kaiseraugst, CH).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated using TRIzol reagent (Invitrogen) according to the manufacturer protocol and purified by RNeasy Mini Kit (Qiagen). The total RNAs of two animals were pooled in equal amounts.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | All was done according to the Affymetrix recommendations. Briefly, double-stranded cDNA was synthesised using 10mg of total RNA with a (dT)24-T7 primer and amplified with T7 RNA polymerase in the presence of biotinylated nucleotides to cRNA.
| | Sample_hyb_protocol | After fragmentation, the cRNA was hybridised to the Gene Chips for 16 hours, followed by a standard amplification with biotin/streptavidin/phycoerythrin.
| | Sample_scan_protocol | MIcroarrays were scanned using a laser scanner (Affymetrix).
| | Sample_data_processing | Raw data were normalized using the Robust Multichip Average (RMA) algorithm as described. After transformation to non-logarithmic data, the expression estimates were scaled to the average expression levels in the control group analyzed using GeneSpring software (Silicon Genetics, Redwood, USA).
| | Sample_platform_id | GPL339
| | Sample_contact_name | Peter,,Juvan
| | Sample_contact_phone | +386 1 543 7595
| | Sample_contact_laboratory | Center for Functional Genomics and Bio-Chips
| | Sample_contact_department | Institute of Biochemistry
| | Sample_contact_institute | Faculty of Medicine, University of Ljubljana
| | Sample_contact_address | Zaloska 4
| | Sample_contact_city | Ljubljana
| | Sample_contact_zip/postal_code | SI-1000
| | Sample_contact_country | Slovenia
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM154nnn/GSM154962/suppl/GSM154962.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM154nnn/GSM154962/suppl/GSM154962.EXP.gz
| | Sample_series_id | GSE6721
| | Sample_data_row_count | 22690
| | |
|
GSM154963 | GPL339 |
|
Liver cholesterol pool2 Affy
|
liver, high cholesterol diet
|
Strain: C57BL/6
Gender: male
Age: 9 - 12 weeks
Tissue: liver
Treatment: vehicle only (5% DMSO in corn oil)
Diet: 1% cholesterol diet
|
No additional data.
|
| Sample_geo_accession | GSM154963
| | Sample_status | Public on Nov 27 2007
| | Sample_submission_date | Jan 12 2007
| | Sample_last_update_date | Jan 30 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_biomaterial_provider_ch1 | Adrian Roth
| | Sample_treatment_protocol_ch1 | Animals were injected i.p. vehicle (5% DMSO in corn oil). After 10h they were sacrificed.
| | Sample_growth_protocol_ch1 | Animals had free acess to food (standard laboratory chow) and drinking water. They were mantained in 12-hour light/12-hour dark cycle. Seven days prior treatment they were on 1% (w/w) cholesterol diet (Provimi Kliba SA, Kaiseraugst, CH).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated using TRIzol reagent (Invitrogen) according to the manufacturer protocol and purified by RNeasy Mini Kit (Qiagen). The total RNAs of two animals were pooled in equal amounts.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | All was done according to the Affymetrix recommendations. Briefly, double-stranded cDNA was synthesised using 10mg of total RNA with a (dT)24-T7 primer and amplified with T7 RNA polymerase in the presence of biotinylated nucleotides to cRNA.
| | Sample_hyb_protocol | After fragmentation, the cRNA was hybridised to the Gene Chips for 16 hours, followed by a standard amplification with biotin/streptavidin/phycoerythrin.
| | Sample_scan_protocol | MIcroarrays were scanned using a laser scanner (Affymetrix).
| | Sample_data_processing | Raw data were normalized using the Robust Multichip Average (RMA) algorithm as described. After transformation to non-logarithmic data, the expression estimates were scaled to the average expression levels in the control group analyzed using GeneSpring software (Silicon Genetics, Redwood, USA).
| | Sample_platform_id | GPL339
| | Sample_contact_name | Peter,,Juvan
| | Sample_contact_phone | +386 1 543 7595
| | Sample_contact_laboratory | Center for Functional Genomics and Bio-Chips
| | Sample_contact_department | Institute of Biochemistry
| | Sample_contact_institute | Faculty of Medicine, University of Ljubljana
| | Sample_contact_address | Zaloska 4
| | Sample_contact_city | Ljubljana
| | Sample_contact_zip/postal_code | SI-1000
| | Sample_contact_country | Slovenia
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM154nnn/GSM154963/suppl/GSM154963.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM154nnn/GSM154963/suppl/GSM154963.EXP.gz
| | Sample_series_id | GSE6721
| | Sample_data_row_count | 22690
| | |
|
GSM154964 | GPL339 |
|
Liver phenobarbital pool1 Affy
|
liver, phenobarbital treated
|
Strain: C57BL/6
Gender: male
Age: 9 - 12 weeks
Tissue: liver
Treatment: 50 mg/kg of phenobarbital
|
No additional data.
|
| Sample_geo_accession | GSM154964
| | Sample_status | Public on Nov 27 2007
| | Sample_submission_date | Jan 12 2007
| | Sample_last_update_date | Jan 30 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_biomaterial_provider_ch1 | Adrian Roth
| | Sample_treatment_protocol_ch1 | Animals were injected i.p. 50 mg/kg of phenobarbital in vehicle (5% DMSO in corn oil). After 10h they were sacrificed.
| | Sample_growth_protocol_ch1 | Animals had free acess to food (standard laboratory chow) and drinking water. They were mantained in 12-hour light/12-hour dark cycle.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated using TRIzol reagent (Invitrogen) according to the manufacturer protocol and purified by RNeasy Mini Kit (Qiagen). The total RNAs of two animals were pooled in equal amounts.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | All was done according to the Affymetrix recommendations. Briefly, double-stranded cDNA was synthesised using 10mg of total RNA with a (dT)24-T7 primer and amplified with T7 RNA polymerase in the presence of biotinylated nucleotides to cRNA.
| | Sample_hyb_protocol | After fragmentation, the cRNA was hybridised to the Gene Chips for 16 hours, followed by a standard amplification with biotin/streptavidin/phycoerythrin.
| | Sample_scan_protocol | MIcroarrays were scanned using a laser scanner (Affymetrix).
| | Sample_data_processing | Raw data were normalized using the Robust Multichip Average (RMA) algorithm as described. After transformation to non-logarithmic data, the expression estimates were scaled to the average expression levels in the control group analyzed using GeneSpring software (Silicon Genetics, Redwood, USA).
| | Sample_platform_id | GPL339
| | Sample_contact_name | Peter,,Juvan
| | Sample_contact_phone | +386 1 543 7595
| | Sample_contact_laboratory | Center for Functional Genomics and Bio-Chips
| | Sample_contact_department | Institute of Biochemistry
| | Sample_contact_institute | Faculty of Medicine, University of Ljubljana
| | Sample_contact_address | Zaloska 4
| | Sample_contact_city | Ljubljana
| | Sample_contact_zip/postal_code | SI-1000
| | Sample_contact_country | Slovenia
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM154nnn/GSM154964/suppl/GSM154964.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM154nnn/GSM154964/suppl/GSM154964.EXP.gz
| | Sample_series_id | GSE6721
| | Sample_data_row_count | 22690
| | |
|
GSM154965 | GPL339 |
|
Liver phenobarbital pool3 Affy
|
liver, phenobarbital treated
|
Strain: C57BL/6
Gender: male
Age: 9 - 12 weeks
Tissue: liver
Treatment: 50 mg/kg of phenobarbital
|
No additional data.
|
| Sample_geo_accession | GSM154965
| | Sample_status | Public on Nov 27 2007
| | Sample_submission_date | Jan 12 2007
| | Sample_last_update_date | Jan 30 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_biomaterial_provider_ch1 | Adrian Roth
| | Sample_treatment_protocol_ch1 | Animals were injected i.p. 50 mg/kg of phenobarbital in vehicle (5% DMSO in corn oil). After 10h they were sacrificed.
| | Sample_growth_protocol_ch1 | Animals had free acess to food (standard laboratory chow) and drinking water. They were mantained in 12-hour light/12-hour dark cycle.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated using TRIzol reagent (Invitrogen) according to the manufacturer protocol and purified by RNeasy Mini Kit (Qiagen). The total RNAs of two animals were pooled in equal amounts.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | All was done according to the Affymetrix recommendations. Briefly, double-stranded cDNA was synthesised using 10mg of total RNA with a (dT)24-T7 primer and amplified with T7 RNA polymerase in the presence of biotinylated nucleotides to cRNA.
| | Sample_hyb_protocol | After fragmentation, the cRNA was hybridised to the Gene Chips for 16 hours, followed by a standard amplification with biotin/streptavidin/phycoerythrin.
| | Sample_scan_protocol | MIcroarrays were scanned using a laser scanner (Affymetrix).
| | Sample_data_processing | Raw data were normalized using the Robust Multichip Average (RMA) algorithm as described. After transformation to non-logarithmic data, the expression estimates were scaled to the average expression levels in the control group analyzed using GeneSpring software (Silicon Genetics, Redwood, USA).
| | Sample_platform_id | GPL339
| | Sample_contact_name | Peter,,Juvan
| | Sample_contact_phone | +386 1 543 7595
| | Sample_contact_laboratory | Center for Functional Genomics and Bio-Chips
| | Sample_contact_department | Institute of Biochemistry
| | Sample_contact_institute | Faculty of Medicine, University of Ljubljana
| | Sample_contact_address | Zaloska 4
| | Sample_contact_city | Ljubljana
| | Sample_contact_zip/postal_code | SI-1000
| | Sample_contact_country | Slovenia
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM154nnn/GSM154965/suppl/GSM154965.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM154nnn/GSM154965/suppl/GSM154965.EXP.gz
| | Sample_series_id | GSE6721
| | Sample_data_row_count | 22690
| | |
|
GSM154966 | GPL339 |
|
Liver phenobarbital pool4 Affy
|
liver, phenobarbital treated
|
Strain: C57BL/6
Gender: male
Age: 9 - 12 weeks
Tissue: liver
Treatment: 50 mg/kg of phenobarbital
|
No additional data.
|
| Sample_geo_accession | GSM154966
| | Sample_status | Public on Nov 27 2007
| | Sample_submission_date | Jan 12 2007
| | Sample_last_update_date | Jan 30 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_biomaterial_provider_ch1 | Adrian Roth
| | Sample_treatment_protocol_ch1 | Animals were injected i.p. 50 mg/kg of phenobarbital in vehicle (5% DMSO in corn oil). After 10h they were sacrificed.
| | Sample_growth_protocol_ch1 | Animals had free acess to food (standard laboratory chow) and drinking water. They were mantained in 12-hour light/12-hour dark cycle.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated using TRIzol reagent (Invitrogen) according to the manufacturer protocol and purified by RNeasy Mini Kit (Qiagen). The total RNAs of two animals were pooled in equal amounts.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | All was done according to the Affymetrix recommendations. Briefly, double-stranded cDNA was synthesised using 10mg of total RNA with a (dT)24-T7 primer and amplified with T7 RNA polymerase in the presence of biotinylated nucleotides to cRNA.
| | Sample_hyb_protocol | After fragmentation, the cRNA was hybridised to the Gene Chips for 16 hours, followed by a standard amplification with biotin/streptavidin/phycoerythrin.
| | Sample_scan_protocol | MIcroarrays were scanned using a laser scanner (Affymetrix).
| | Sample_data_processing | Raw data were normalized using the Robust Multichip Average (RMA) algorithm as described. After transformation to non-logarithmic data, the expression estimates were scaled to the average expression levels in the control group analyzed using GeneSpring software (Silicon Genetics, Redwood, USA).
| | Sample_platform_id | GPL339
| | Sample_contact_name | Peter,,Juvan
| | Sample_contact_phone | +386 1 543 7595
| | Sample_contact_laboratory | Center for Functional Genomics and Bio-Chips
| | Sample_contact_department | Institute of Biochemistry
| | Sample_contact_institute | Faculty of Medicine, University of Ljubljana
| | Sample_contact_address | Zaloska 4
| | Sample_contact_city | Ljubljana
| | Sample_contact_zip/postal_code | SI-1000
| | Sample_contact_country | Slovenia
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM154nnn/GSM154966/suppl/GSM154966.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM154nnn/GSM154966/suppl/GSM154966.EXP.gz
| | Sample_series_id | GSE6721
| | Sample_data_row_count | 22690
| | |
|
GSM154967 | GPL339 |
|
Liver phenobarbital pool2 Affy
|
liver, phenobarbital treated
|
Strain: C57BL/6
Gender: male
Age: 9 - 12 weeks
Tissue: liver
Treatment: 50 mg/kg of phenobarbital
|
No additional data.
|
| Sample_geo_accession | GSM154967
| | Sample_status | Public on Nov 27 2007
| | Sample_submission_date | Jan 12 2007
| | Sample_last_update_date | Jan 30 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_biomaterial_provider_ch1 | Adrian Roth
| | Sample_treatment_protocol_ch1 | Animals were injected i.p. 50 mg/kg of phenobarbital in vehicle (5% DMSO in corn oil). After 10h they were sacrificed.
| | Sample_growth_protocol_ch1 | Animals had free acess to food (standard laboratory chow) and drinking water. They were mantained in 12-hour light/12-hour dark cycle.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated using TRIzol reagent (Invitrogen) according to the manufacturer protocol and purified by RNeasy Mini Kit (Qiagen). The total RNAs of two animals were pooled in equal amounts.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | All was done according to the Affymetrix recommendations. Briefly, double-stranded cDNA was synthesised using 10mg of total RNA with a (dT)24-T7 primer and amplified with T7 RNA polymerase in the presence of biotinylated nucleotides to cRNA.
| | Sample_hyb_protocol | After fragmentation, the cRNA was hybridised to the Gene Chips for 16 hours, followed by a standard amplification with biotin/streptavidin/phycoerythrin.
| | Sample_scan_protocol | MIcroarrays were scanned using a laser scanner (Affymetrix).
| | Sample_data_processing | Raw data were normalized using the Robust Multichip Average (RMA) algorithm as described. After transformation to non-logarithmic data, the expression estimates were scaled to the average expression levels in the control group analyzed using GeneSpring software (Silicon Genetics, Redwood, USA).
| | Sample_platform_id | GPL339
| | Sample_contact_name | Peter,,Juvan
| | Sample_contact_phone | +386 1 543 7595
| | Sample_contact_laboratory | Center for Functional Genomics and Bio-Chips
| | Sample_contact_department | Institute of Biochemistry
| | Sample_contact_institute | Faculty of Medicine, University of Ljubljana
| | Sample_contact_address | Zaloska 4
| | Sample_contact_city | Ljubljana
| | Sample_contact_zip/postal_code | SI-1000
| | Sample_contact_country | Slovenia
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM154nnn/GSM154967/suppl/GSM154967.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM154nnn/GSM154967/suppl/GSM154967.EXP.gz
| | Sample_series_id | GSE6721
| | Sample_data_row_count | 22690
| | |
|
GSM154968 | GPL339 |
|
Liver control pool2 Affy
|
liver, untreated
|
Strain: C57BL/6
Gender: male
Age: 9 - 12 weeks
Tissue: liver
Treatment: vehicle only (5% DMSO in corn oil)
|
No additional data.
|
| Sample_geo_accession | GSM154968
| | Sample_status | Public on Nov 27 2007
| | Sample_submission_date | Jan 12 2007
| | Sample_last_update_date | Jan 30 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_biomaterial_provider_ch1 | Adrian Roth
| | Sample_treatment_protocol_ch1 | Animals were injected i.p. vehicle (5% DMSO in corn oil). After 10h they were sacrificed.
| | Sample_growth_protocol_ch1 | Animals had free acess to food (standard laboratory chow) and drinking water. They were mantained in 12-hour light/12-hour dark cycle.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated using TRIzol reagent (Invitrogen) according to the manufacturer protocol and purified by RNeasy Mini Kit (Qiagen). The total RNAs of two animals were pooled in equal amounts.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | All was done according to the Affymetrix recommendations. Briefly, double-stranded cDNA was synthesised using 10mg of total RNA with a (dT)24-T7 primer and amplified with T7 RNA polymerase in the presence of biotinylated nucleotides to cRNA.
| | Sample_hyb_protocol | After fragmentation, the cRNA was hybridised to the Gene Chips for 16 hours, followed by a standard amplification with biotin/streptavidin/phycoerythrin.
| | Sample_scan_protocol | MIcroarrays were scanned using a laser scanner (Affymetrix).
| | Sample_data_processing | Raw data were normalized using the Robust Multichip Average (RMA) algorithm as described. After transformation to non-logarithmic data, the expression estimates were scaled to the average expression levels in the control group analyzed using GeneSpring software (Silicon Genetics, Redwood, USA).
| | Sample_platform_id | GPL339
| | Sample_contact_name | Peter,,Juvan
| | Sample_contact_phone | +386 1 543 7595
| | Sample_contact_laboratory | Center for Functional Genomics and Bio-Chips
| | Sample_contact_department | Institute of Biochemistry
| | Sample_contact_institute | Faculty of Medicine, University of Ljubljana
| | Sample_contact_address | Zaloska 4
| | Sample_contact_city | Ljubljana
| | Sample_contact_zip/postal_code | SI-1000
| | Sample_contact_country | Slovenia
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM154nnn/GSM154968/suppl/GSM154968.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM154nnn/GSM154968/suppl/GSM154968.EXP.gz
| | Sample_series_id | GSE6721
| | Sample_data_row_count | 22690
| | |
|
GSM154969 | GPL339 |
|
Liver control pool4 Affy
|
liver, untreated
|
Strain: C57BL/6
Gender: male
Age: 9 - 12 weeks
Tissue: liver
Treatment: vehicle only (5% DMSO in corn oil)
|
No additional data.
|
| Sample_geo_accession | GSM154969
| | Sample_status | Public on Nov 27 2007
| | Sample_submission_date | Jan 12 2007
| | Sample_last_update_date | Jan 30 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_biomaterial_provider_ch1 | Adrian Roth
| | Sample_treatment_protocol_ch1 | Animals were injected i.p. vehicle (5% DMSO in corn oil). After 10h they were sacrificed.
| | Sample_growth_protocol_ch1 | Animals had free acess to food (standard laboratory chow) and drinking water. They were mantained in 12-hour light/12-hour dark cycle.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated using TRIzol reagent (Invitrogen) according to the manufacturer protocol and purified by RNeasy Mini Kit (Qiagen). The total RNAs of two animals were pooled in equal amounts.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | All was done according to the Affymetrix recommendations. Briefly, double-stranded cDNA was synthesised using 10mg of total RNA with a (dT)24-T7 primer and amplified with T7 RNA polymerase in the presence of biotinylated nucleotides to cRNA.
| | Sample_hyb_protocol | After fragmentation, the cRNA was hybridised to the Gene Chips for 16 hours, followed by a standard amplification with biotin/streptavidin/phycoerythrin.
| | Sample_scan_protocol | MIcroarrays were scanned using a laser scanner (Affymetrix).
| | Sample_data_processing | Raw data were normalized using the Robust Multichip Average (RMA) algorithm as described. After transformation to non-logarithmic data, the expression estimates were scaled to the average expression levels in the control group analyzed using GeneSpring software (Silicon Genetics, Redwood, USA).
| | Sample_platform_id | GPL339
| | Sample_contact_name | Peter,,Juvan
| | Sample_contact_phone | +386 1 543 7595
| | Sample_contact_laboratory | Center for Functional Genomics and Bio-Chips
| | Sample_contact_department | Institute of Biochemistry
| | Sample_contact_institute | Faculty of Medicine, University of Ljubljana
| | Sample_contact_address | Zaloska 4
| | Sample_contact_city | Ljubljana
| | Sample_contact_zip/postal_code | SI-1000
| | Sample_contact_country | Slovenia
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM154nnn/GSM154969/suppl/GSM154969.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM154nnn/GSM154969/suppl/GSM154969.EXP.gz
| | Sample_series_id | GSE6721
| | Sample_data_row_count | 22690
| | |
|
GSM154970 | GPL339 |
|
Liver control pool1 Affy
|
liver, untreated
|
Strain: C57BL/6
Gender: male
Age: 9 - 12 weeks
Tissue: liver
Treatment: vehicle only (5% DMSO in corn oil)
|
No additional data.
|
| Sample_geo_accession | GSM154970
| | Sample_status | Public on Nov 27 2007
| | Sample_submission_date | Jan 12 2007
| | Sample_last_update_date | Jan 30 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_biomaterial_provider_ch1 | Adrian Roth
| | Sample_treatment_protocol_ch1 | Animals were injected i.p. vehicle (5% DMSO in corn oil). After 10h they were sacrificed.
| | Sample_growth_protocol_ch1 | Animals had free acess to food (standard laboratory chow) and drinking water. They were mantained in 12-hour light/12-hour dark cycle.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated using TRIzol reagent (Invitrogen) according to the manufacturer protocol and purified by RNeasy Mini Kit (Qiagen). The total RNAs of two animals were pooled in equal amounts.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | All was done according to the Affymetrix recommendations. Briefly, double-stranded cDNA was synthesised using 10mg of total RNA with a (dT)24-T7 primer and amplified with T7 RNA polymerase in the presence of biotinylated nucleotides to cRNA.
| | Sample_hyb_protocol | After fragmentation, the cRNA was hybridised to the Gene Chips for 16 hours, followed by a standard amplification with biotin/streptavidin/phycoerythrin.
| | Sample_scan_protocol | MIcroarrays were scanned using a laser scanner (Affymetrix).
| | Sample_data_processing | Raw data were normalized using the Robust Multichip Average (RMA) algorithm as described. After transformation to non-logarithmic data, the expression estimates were scaled to the average expression levels in the control group analyzed using GeneSpring software (Silicon Genetics, Redwood, USA).
| | Sample_platform_id | GPL339
| | Sample_contact_name | Peter,,Juvan
| | Sample_contact_phone | +386 1 543 7595
| | Sample_contact_laboratory | Center for Functional Genomics and Bio-Chips
| | Sample_contact_department | Institute of Biochemistry
| | Sample_contact_institute | Faculty of Medicine, University of Ljubljana
| | Sample_contact_address | Zaloska 4
| | Sample_contact_city | Ljubljana
| | Sample_contact_zip/postal_code | SI-1000
| | Sample_contact_country | Slovenia
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM154nnn/GSM154970/suppl/GSM154970.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM154nnn/GSM154970/suppl/GSM154970.EXP.gz
| | Sample_series_id | GSE6721
| | Sample_data_row_count | 22690
| | |
|
GSM154971 | GPL339 |
|
Liver control pool3 Affy
|
liver, untreated
|
Strain: C57BL/6
Gender: male
Age: 9 - 12 weeks
Tissue: liver
Treatment: vehicle only (5% DMSO in corn oil)
|
No additional data.
|
| Sample_geo_accession | GSM154971
| | Sample_status | Public on Nov 27 2007
| | Sample_submission_date | Jan 12 2007
| | Sample_last_update_date | Jan 30 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_biomaterial_provider_ch1 | Adrian Roth
| | Sample_treatment_protocol_ch1 | Animals were injected i.p. vehicle (5% DMSO in corn oil). After 10h they were sacrificed.
| | Sample_growth_protocol_ch1 | Animals had free acess to food (standard laboratory chow) and drinking water. They were mantained in 12-hour light/12-hour dark cycle.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated using TRIzol reagent (Invitrogen) according to the manufacturer protocol and purified by RNeasy Mini Kit (Qiagen). The total RNAs of two animals were pooled in equal amounts.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | All was done according to the Affymetrix recommendations. Briefly, double-stranded cDNA was synthesised using 10mg of total RNA with a (dT)24-T7 primer and amplified with T7 RNA polymerase in the presence of biotinylated nucleotides to cRNA.
| | Sample_hyb_protocol | After fragmentation, the cRNA was hybridised to the Gene Chips for 16 hours, followed by a standard amplification with biotin/streptavidin/phycoerythrin.
| | Sample_scan_protocol | MIcroarrays were scanned using a laser scanner (Affymetrix).
| | Sample_data_processing | Raw data were normalized using the Robust Multichip Average (RMA) algorithm as described. After transformation to non-logarithmic data, the expression estimates were scaled to the average expression levels in the control group analyzed using GeneSpring software (Silicon Genetics, Redwood, USA).
| | Sample_platform_id | GPL339
| | Sample_contact_name | Peter,,Juvan
| | Sample_contact_phone | +386 1 543 7595
| | Sample_contact_laboratory | Center for Functional Genomics and Bio-Chips
| | Sample_contact_department | Institute of Biochemistry
| | Sample_contact_institute | Faculty of Medicine, University of Ljubljana
| | Sample_contact_address | Zaloska 4
| | Sample_contact_city | Ljubljana
| | Sample_contact_zip/postal_code | SI-1000
| | Sample_contact_country | Slovenia
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM154nnn/GSM154971/suppl/GSM154971.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM154nnn/GSM154971/suppl/GSM154971.EXP.gz
| | Sample_series_id | GSE6721
| | Sample_data_row_count | 22690
| | |
|
| |
| |
Make groups for comparisons |
(2 groups will be compared at a time) |
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| Select GSMs and click on "Add groups" |
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