Result

Search results for the GEO ID: GSE6929

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Title

Source name

Description

Characteristics

GSM159830

GPL1355

Liver vehicle rep1

cirrhotic liver, vehicle treatment

Strain:Wistar, Gender: male, Tissue: cirrhotic liver, Induction of cirrhosis: CCl4

Sample_geo_accession	GSM159830
Sample_status	Public on Oct 18 2007
Sample_submission_date	Jan 31 2007
Sample_last_update_date	Oct 18 2007
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Rattus norvegicus
Sample_taxid_ch1	10116
Sample_treatment_protocol_ch1	Cirrhosis was induced by inhalation of CCl4 administered twice weekly. Control and cirrhotic rats were fed ad libitum with standard feed and water containing Phenobarbital (0.3 g/L) as drinking fluid .
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Total RNA was extracted from frozen liver with Trizol reagent (Life Technologies, Rockville, MD). The extracted total RNA was purified with the RNeasy kit (Qiagen).
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Twenty µg of total RNA was used to synthesize double-strand cDNA with SuperScript II reverse transcriptase (Life Technologies) and a T7-(dT)24 primer (Metabion, Germany). Then, biotinylated cRNA was synthesized from the double-stranded cDNA using the RNA Transcript Labeling kit (Enzo Life Sciences) and was purified and fragmented.
Sample_hyb_protocol	The fragmented cRNA was hybridized to the oligonucleotide microarray, which was washed and stained with streptavidin-phycoerythrin as described in the Affymetrix GeneChip Expression Analysis Manual (Affymetrix, Santa Clara, CA)
Sample_scan_protocol	Scanning was performed with an Agilent Microarray Scanner (Agilent Technologies)
Sample_data_processing	GeneChip analysis was performed with libraries from the Bioconductor project. The starting point for all the analysis was the CEL files generated by the Affymetrix software. Each CEL file contains data on the intensity at each probe on the GeneChip. To import CEL file data into the Bioconductor system, we used the ReadAffy function of the “affy” package. Next, we used the RMA approximation for background adjustment, normalization, and summarization using the median polish algorithm . The RMA measures were computed using the RMA function from the affy package.
Sample_platform_id	GPL1355
Sample_contact_name	Manuel,,Morales-Ruiz
Sample_contact_email	morales@clinic.ub.es
Sample_contact_phone	34932275400 (2667)
Sample_contact_department	Biochemistry and Molecular Genetics
Sample_contact_institute	Hospital Clinic
Sample_contact_address	Villarroel 170
Sample_contact_city	Barcelona
Sample_contact_zip/postal_code	08036
Sample_contact_country	Spain
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM159nnn/GSM159830/suppl/GSM159830.CEL.gz
Sample_series_id	GSE6929
Sample_data_row_count	31099

GSM159831

GPL1355

Liver antiangiogenic-treatment rep2

cirrhotic liver, antiangiogenic treatment

Strain:Wistar, Gender: male, Tissue: cirrhotic liver, Induction of cirrhosis: CCl4

Sample_geo_accession	GSM159831
Sample_status	Public on Oct 18 2007
Sample_submission_date	Jan 31 2007
Sample_last_update_date	Oct 18 2007
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Rattus norvegicus
Sample_taxid_ch1	10116
Sample_treatment_protocol_ch1	Cirrhosis was induced by inhalation of CCl4 administered twice weekly. Control and cirrhotic rats were fed ad libitum with standard feed and water containing Phenobarbital (0.3 g/L) as drinking fluid .
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Total RNA was extracted from frozen liver with Trizol reagent (Life Technologies, Rockville, MD). The extracted total RNA was purified with the RNeasy kit (Qiagen).
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Twenty µg of total RNA was used to synthesize double-strand cDNA with SuperScript II reverse transcriptase (Life Technologies) and a T7-(dT)24 primer (Metabion, Germany). Then, biotinylated cRNA was synthesized from the double-stranded cDNA using the RNA Transcript Labeling kit (Enzo Life Sciences) and was purified and fragmented.
Sample_hyb_protocol	The fragmented cRNA was hybridized to the oligonucleotide microarray, which was washed and stained with streptavidin-phycoerythrin as described in the Affymetrix GeneChip Expression Analysis Manual (Affymetrix, Santa Clara, CA)
Sample_scan_protocol	Scanning was performed with an Agilent Microarray Scanner (Agilent Technologies)
Sample_data_processing	GeneChip analysis was performed with libraries from the Bioconductor project. The starting point for all the analysis was the CEL files generated by the Affymetrix software. Each CEL file contains data on the intensity at each probe on the GeneChip. To import CEL file data into the Bioconductor system, we used the ReadAffy function of the “affy” package. Next, we used the RMA approximation for background adjustment, normalization, and summarization using the median polish algorithm . The RMA measures were computed using the RMA function from the affy package.
Sample_platform_id	GPL1355
Sample_contact_name	Manuel,,Morales-Ruiz
Sample_contact_email	morales@clinic.ub.es
Sample_contact_phone	34932275400 (2667)
Sample_contact_department	Biochemistry and Molecular Genetics
Sample_contact_institute	Hospital Clinic
Sample_contact_address	Villarroel 170
Sample_contact_city	Barcelona
Sample_contact_zip/postal_code	08036
Sample_contact_country	Spain
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM159nnn/GSM159831/suppl/GSM159831.CEL.gz
Sample_series_id	GSE6929
Sample_data_row_count	31099

GSM159832

GPL1355

Liver antiangiogenic-treatment rep1

cirrhotic liver, antiangiogenic treatment

Strain:Wistar, Gender: male, Tissue: cirrhotic liver, Induction of cirrhosis: CCl4

Sample_geo_accession	GSM159832
Sample_status	Public on Oct 18 2007
Sample_submission_date	Jan 31 2007
Sample_last_update_date	Oct 18 2007
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Rattus norvegicus
Sample_taxid_ch1	10116
Sample_treatment_protocol_ch1	Cirrhosis was induced by inhalation of CCl4 administered twice weekly. Control and cirrhotic rats were fed ad libitum with standard feed and water containing Phenobarbital (0.3 g/L) as drinking fluid .
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Total RNA was extracted from frozen liver with Trizol reagent (Life Technologies, Rockville, MD). The extracted total RNA was purified with the RNeasy kit (Qiagen).
Sample_label_ch1	Biotin
Sample_label_protocol_ch1	Twenty µg of total RNA was used to synthesize double-strand cDNA with SuperScript II reverse transcriptase (Life Technologies) and a T7-(dT)24 primer (Metabion, Germany). Then, biotinylated cRNA was synthesized from the double-stranded cDNA using the RNA Transcript Labeling kit (Enzo Life Sciences) and was purified and fragmented.
Sample_hyb_protocol	The fragmented cRNA was hybridized to the oligonucleotide microarray, which was washed and stained with streptavidin-phycoerythrin as described in the Affymetrix GeneChip Expression Analysis Manual (Affymetrix, Santa Clara, CA)
Sample_scan_protocol	Scanning was performed with an Agilent Microarray Scanner (Agilent Technologies)
Sample_data_processing	GeneChip analysis was performed with libraries from the Bioconductor project. The starting point for all the analysis was the CEL files generated by the Affymetrix software. Each CEL file contains data on the intensity at each probe on the GeneChip. To import CEL file data into the Bioconductor system, we used the ReadAffy function of the “affy” package. Next, we used the RMA approximation for background adjustment, normalization, and summarization using the median polish algorithm . The RMA measures were computed using the RMA function from the affy package.
Sample_platform_id	GPL1355
Sample_contact_name	Manuel,,Morales-Ruiz
Sample_contact_email	morales@clinic.ub.es
Sample_contact_phone	34932275400 (2667)
Sample_contact_department	Biochemistry and Molecular Genetics
Sample_contact_institute	Hospital Clinic
Sample_contact_address	Villarroel 170
Sample_contact_city	Barcelona
Sample_contact_zip/postal_code	08036
Sample_contact_country	Spain
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM159nnn/GSM159832/suppl/GSM159832.CEL.gz
Sample_series_id	GSE6929
Sample_data_row_count	31099

GSM159833

GPL1355

Liver vehicle rep2

cirrhotic liver, vehicle treatment

Strain:Wistar, Gender: male, Tissue: cirrhotic liver, Induction of cirrhosis: CCl4

Sample_geo_accession	GSM159833
Sample_status	Public on Oct 18 2007
Sample_submission_date	Feb 01 2007
Sample_last_update_date	Oct 18 2007
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Rattus norvegicus
Sample_taxid_ch1	10116
Sample_treatment_protocol_ch1	Cirrhosis was induced by inhalation of CCl4 administered twice weekly. Control and cirrhotic rats were fed ad libitum with standard feed and water containing Phenobarbital (0.3 g/L) as drinking fluid
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Total RNA was extracted from frozen liver with Trizol reagent (Life Technologies, Rockville, MD). The extracted total RNA was purified with the RNeasy kit (Qiagen).
Sample_label_ch1	Biotin
Sample_label_protocol_ch1	Twenty µg of total RNA was used to synthesize double-strand cDNA with SuperScript II reverse transcriptase (Life Technologies) and a T7-(dT)24 primer (Metabion, Germany). Then, biotinylated cRNA was synthesized from the double-stranded cDNA using the RNA Transcript Labeling kit (Enzo Life Sciences) and was purified and fragmented.
Sample_hyb_protocol	The fragmented cRNA was hybridized to the oligonucleotide microarray, which was washed and stained with streptavidin-phycoerythrin as described in the Affymetrix GeneChip Expression Analysis Manual (Affymetrix, Santa Clara, CA)
Sample_scan_protocol	Scanning was performed with an Agilent Microarray Scanner (Agilent Technologies)
Sample_data_processing	GeneChip analysis was performed with libraries from the Bioconductor project. The starting point for all the analysis was the CEL files generated by the Affymetrix software. Each CEL file contains data on the intensity at each probe on the GeneChip. To import CEL file data into the Bioconductor system, we used the ReadAffy function of the “affy” package. Next, we used the RMA approximation for background adjustment, normalization, and summarization using the median polish algorithm . The RMA measures were computed using the RMA function from the affy package.
Sample_platform_id	GPL1355
Sample_contact_name	Manuel,,Morales-Ruiz
Sample_contact_email	morales@clinic.ub.es
Sample_contact_phone	34932275400 (2667)
Sample_contact_department	Biochemistry and Molecular Genetics
Sample_contact_institute	Hospital Clinic
Sample_contact_address	Villarroel 170
Sample_contact_city	Barcelona
Sample_contact_zip/postal_code	08036
Sample_contact_country	Spain
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM159nnn/GSM159833/suppl/GSM159833.CEL.gz
Sample_series_id	GSE6929
Sample_data_row_count	31099

GSM159834

GPL1355

Liver vehicle rep3

cirrhotic liver, vehicle treatment

Strain:Wistar, Gender: male, Tissue: cirrhotic liver, Induction of cirrhosis: CCl4

Sample_geo_accession	GSM159834
Sample_status	Public on Oct 18 2007
Sample_submission_date	Feb 01 2007
Sample_last_update_date	Oct 18 2007
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Rattus norvegicus
Sample_taxid_ch1	10116
Sample_treatment_protocol_ch1	Cirrhosis was induced by inhalation of CCl4 administered twice weekly. Control and cirrhotic rats were fed ad libitum with standard feed and water containing Phenobarbital (0.3 g/L) as drinking fluid
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Total RNA was extracted from frozen liver with Trizol reagent (Life Technologies, Rockville, MD). The extracted total RNA was purified with the RNeasy kit (Qiagen).
Sample_label_ch1	Biotin
Sample_label_protocol_ch1	Twenty µg of total RNA was used to synthesize double-strand cDNA with SuperScript II reverse transcriptase (Life Technologies) and a T7-(dT)24 primer (Metabion, Germany). Then, biotinylated cRNA was synthesized from the double-stranded cDNA using the RNA Transcript Labeling kit (Enzo Life Sciences) and was purified and fragmented.
Sample_hyb_protocol	The fragmented cRNA was hybridized to the oligonucleotide microarray, which was washed and stained with streptavidin-phycoerythrin as described in the Affymetrix GeneChip Expression Analysis Manual (Affymetrix, Santa Clara, CA)
Sample_scan_protocol	Scanning was performed with an Agilent Microarray Scanner (Agilent Technologies)
Sample_data_processing	GeneChip analysis was performed with libraries from the Bioconductor project. The starting point for all the analysis was the CEL files generated by the Affymetrix software. Each CEL file contains data on the intensity at each probe on the GeneChip. To import CEL file data into the Bioconductor system, we used the ReadAffy function of the “affy” package. Next, we used the RMA approximation for background adjustment, normalization, and summarization using the median polish algorithm . The RMA measures were computed using the RMA function from the affy package.
Sample_platform_id	GPL1355
Sample_contact_name	Manuel,,Morales-Ruiz
Sample_contact_email	morales@clinic.ub.es
Sample_contact_phone	34932275400 (2667)
Sample_contact_department	Biochemistry and Molecular Genetics
Sample_contact_institute	Hospital Clinic
Sample_contact_address	Villarroel 170
Sample_contact_city	Barcelona
Sample_contact_zip/postal_code	08036
Sample_contact_country	Spain
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM159nnn/GSM159834/suppl/GSM159834.CEL.gz
Sample_series_id	GSE6929
Sample_data_row_count	31099

GSM159835

GPL1355

Liver vehicle rep4

cirrhotic liver, vehicle treatment

Strain:Wistar, Gender: male, Tissue: cirrhotic liver, Induction of cirrhosis: CCl4

Sample_geo_accession	GSM159835
Sample_status	Public on Oct 18 2007
Sample_submission_date	Feb 01 2007
Sample_last_update_date	Oct 18 2007
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Rattus norvegicus
Sample_taxid_ch1	10116
Sample_treatment_protocol_ch1	Cirrhosis was induced by inhalation of CCl4 administered twice weekly. Control and cirrhotic rats were fed ad libitum with standard feed and water containing Phenobarbital (0.3 g/L) as drinking fluid
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Total RNA was extracted from frozen liver with Trizol reagent (Life Technologies, Rockville, MD). The extracted total RNA was purified with the RNeasy kit (Qiagen).
Sample_label_ch1	Biotin
Sample_label_protocol_ch1	Twenty µg of total RNA was used to synthesize double-strand cDNA with SuperScript II reverse transcriptase (Life Technologies) and a T7-(dT)24 primer (Metabion, Germany). Then, biotinylated cRNA was synthesized from the double-stranded cDNA using the RNA Transcript Labeling kit (Enzo Life Sciences) and was purified and fragmented.
Sample_hyb_protocol	The fragmented cRNA was hybridized to the oligonucleotide microarray, which was washed and stained with streptavidin-phycoerythrin as described in the Affymetrix GeneChip Expression Analysis Manual (Affymetrix, Santa Clara, CA)
Sample_scan_protocol	Scanning was performed with an Agilent Microarray Scanner (Agilent Technologies)
Sample_data_processing	GeneChip analysis was performed with libraries from the Bioconductor project. The starting point for all the analysis was the CEL files generated by the Affymetrix software. Each CEL file contains data on the intensity at each probe on the GeneChip. To import CEL file data into the Bioconductor system, we used the ReadAffy function of the “affy” package. Next, we used the RMA approximation for background adjustment, normalization, and summarization using the median polish algorithm . The RMA measures were computed using the RMA function from the affy package.
Sample_platform_id	GPL1355
Sample_contact_name	Manuel,,Morales-Ruiz
Sample_contact_email	morales@clinic.ub.es
Sample_contact_phone	34932275400 (2667)
Sample_contact_department	Biochemistry and Molecular Genetics
Sample_contact_institute	Hospital Clinic
Sample_contact_address	Villarroel 170
Sample_contact_city	Barcelona
Sample_contact_zip/postal_code	08036
Sample_contact_country	Spain
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM159nnn/GSM159835/suppl/GSM159835.CEL.gz
Sample_series_id	GSE6929
Sample_data_row_count	31099

GSM159837

GPL1355

Liver antiangiogenic-treatment rep3

cirrhotic liver, antiangiogenic treatment

Strain:Wistar, Gender: male, Tissue: cirrhotic liver, Induction of cirrhosis: CCl4

Sample_geo_accession	GSM159837
Sample_status	Public on Oct 18 2007
Sample_submission_date	Feb 01 2007
Sample_last_update_date	Oct 18 2007
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Rattus norvegicus
Sample_taxid_ch1	10116
Sample_treatment_protocol_ch1	Cirrhosis was induced by inhalation of CCl4 administered twice weekly. Control and cirrhotic rats were fed ad libitum with standard feed and water containing Phenobarbital (0.3 g/L) as drinking fluid
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Total RNA was extracted from frozen liver with Trizol reagent (Life Technologies, Rockville, MD). The extracted total RNA was purified with the RNeasy kit (Qiagen).
Sample_label_ch1	Biotin
Sample_label_protocol_ch1	Twenty µg of total RNA was used to synthesize double-strand cDNA with SuperScript II reverse transcriptase (Life Technologies) and a T7-(dT)24 primer (Metabion, Germany). Then, biotinylated cRNA was synthesized from the double-stranded cDNA using the RNA Transcript Labeling kit (Enzo Life Sciences) and was purified and fragmented.
Sample_hyb_protocol	The fragmented cRNA was hybridized to the oligonucleotide microarray, which was washed and stained with streptavidin-phycoerythrin as described in the Affymetrix GeneChip Expression Analysis Manual (Affymetrix, Santa Clara, CA)
Sample_scan_protocol	Scanning was performed with an Agilent Microarray Scanner (Agilent Technologies)
Sample_data_processing	GeneChip analysis was performed with libraries from the Bioconductor project. The starting point for all the analysis was the CEL files generated by the Affymetrix software. Each CEL file contains data on the intensity at each probe on the GeneChip. To import CEL file data into the Bioconductor system, we used the ReadAffy function of the “affy” package. Next, we used the RMA approximation for background adjustment, normalization, and summarization using the median polish algorithm . The RMA measures were computed using the RMA function from the affy package.
Sample_platform_id	GPL1355
Sample_contact_name	Manuel,,Morales-Ruiz
Sample_contact_email	morales@clinic.ub.es
Sample_contact_phone	34932275400 (2667)
Sample_contact_department	Biochemistry and Molecular Genetics
Sample_contact_institute	Hospital Clinic
Sample_contact_address	Villarroel 170
Sample_contact_city	Barcelona
Sample_contact_zip/postal_code	08036
Sample_contact_country	Spain
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM159nnn/GSM159837/suppl/GSM159837.CEL.gz
Sample_series_id	GSE6929
Sample_data_row_count	31099

GSM159838

GPL1355

Liver antiangiogenic-treatment rep4

cirrhotic liver, antiangiogenic treatment

Strain:Wistar, Gender: male, Tissue: cirrhotic liver, Induction of cirrhosis: CCl4

Sample_geo_accession	GSM159838
Sample_status	Public on Oct 18 2007
Sample_submission_date	Feb 01 2007
Sample_last_update_date	Oct 18 2007
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Rattus norvegicus
Sample_taxid_ch1	10116
Sample_treatment_protocol_ch1	Cirrhosis was induced by inhalation of CCl4 administered twice weekly. Control and cirrhotic rats were fed ad libitum with standard feed and water containing Phenobarbital (0.3 g/L) as drinking fluid
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Total RNA was extracted from frozen liver with Trizol reagent (Life Technologies, Rockville, MD). The extracted total RNA was purified with the RNeasy kit (Qiagen).
Sample_label_ch1	Biotin
Sample_label_protocol_ch1	Twenty µg of total RNA was used to synthesize double-strand cDNA with SuperScript II reverse transcriptase (Life Technologies) and a T7-(dT)24 primer (Metabion, Germany). Then, biotinylated cRNA was synthesized from the double-stranded cDNA using the RNA Transcript Labeling kit (Enzo Life Sciences) and was purified and fragmented.
Sample_hyb_protocol	The fragmented cRNA was hybridized to the oligonucleotide microarray, which was washed and stained with streptavidin-phycoerythrin as described in the Affymetrix GeneChip Expression Analysis Manual (Affymetrix, Santa Clara, CA)
Sample_scan_protocol	Scanning was performed with an Agilent Microarray Scanner (Agilent Technologies)
Sample_data_processing	GeneChip analysis was performed with libraries from the Bioconductor project. The starting point for all the analysis was the CEL files generated by the Affymetrix software. Each CEL file contains data on the intensity at each probe on the GeneChip. To import CEL file data into the Bioconductor system, we used the ReadAffy function of the “affy” package. Next, we used the RMA approximation for background adjustment, normalization, and summarization using the median polish algorithm . The RMA measures were computed using the RMA function from the affy package.
Sample_platform_id	GPL1355
Sample_contact_name	Manuel,,Morales-Ruiz
Sample_contact_email	morales@clinic.ub.es
Sample_contact_phone	34932275400 (2667)
Sample_contact_department	Biochemistry and Molecular Genetics
Sample_contact_institute	Hospital Clinic
Sample_contact_address	Villarroel 170
Sample_contact_city	Barcelona
Sample_contact_zip/postal_code	08036
Sample_contact_country	Spain
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM159nnn/GSM159838/suppl/GSM159838.CEL.gz
Sample_series_id	GSE6929
Sample_data_row_count	31099

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