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Search results for the GEO ID: GSE11941

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Description

Characteristics

GSM301599

GPL570

Human Hepatocytes_Trovafloxacin, Donor_1

Primary human hepatocytes

Human hepatocytes isolated from specimens obtained from patients undergoing hepatic resections sex: male; age: 63; reason for liver resection: liver metastasis, kidney carcinoma

no additional information

Sample_geo_accession	GSM301599
Sample_status	Public on Oct 01 2008
Sample_submission_date	Jun 30 2008
Sample_last_update_date	Jun 30 2008
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Homo sapiens
Sample_taxid_ch1	9606
Sample_treatment_protocol_ch1	Prior to exposure, cells were allowed to recover from the isolation procedure for 4 to 5 days. Cells were harvested after treatment with 100 µg/ml of trovafloxacin and after 72 hours of treatment.
Sample_growth_protocol_ch1	Primary hepatocytes were cultured enclosed between two layers of collagen. One ml collagen solution containing 1.1 mg/ml collagen was used for coating one 60-mm Petri dish (Greiner, Frickenhausen, Germany). The pH of the collagen was adjusted to 7.4 using a 10x DMEM concentrate (Biochrom, Berlin, Germany). The 2 x 106 hepatocytes per dish were seeded. Two hours after seeding and attachment of the cells, culture medium was removed along with nonadherent cells. After 24-48 h in culture, the medium was aspirated and a second layer of collagen was pipetted on top of the cells. After gelation of this second layer, culture medium was added. Culture medium (2 ml) was changed daily. The total volume of cell culture supernatant was 4 ml, including the hydrated collagen matrix volume of 2 ml.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Total RNA was isolated from the hepatocytes using RNeasy total RNA isolation kit (QIAGEN). A second cleanup of isolated RNA was done using RNeasy Mini Kit (Qiagen). RNA was checked for quantity, purity and integrity of the 18S and 28S ribosomal bands by capillary electrophoresis using NanoDrop ND-1000 and Agilent 2100 Bioanalyzer.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	One to 15 µg of total RNA were used as starting material to prepare cDNA. Synthesis of double-stranded cDNA was performed using a GeneChip® one-cycle cDNA Kit (Affymetrix). The cleanup of double-stranded cDNA was done using a GeneChip® Sample Cleanup module (Affymetrix). Depending on the starting amount of total RNA, 12 (1 to 8 µg total RNA) or 6 µl (8 to 15 µg total RNA) of cDNA solution were used for in-vitro transcription. The in-vitro transcription was conducted with a GeneChip® IVT Labeling Kit (Affymetrix). The total amount of the reaction product was purified with a GeneChip® Sample Cleanup module (Affymetrix). Purified cRNA was quantified and checked for quality using NanoDrop ND-1000 and Agilent 2100 Bioanalyzer. Purified cRNA was cleaved into fragments of 35-200 bases by metal-induced hydrolysis. The degree of fragmentation and the length distribution of the fragmented biotinylated cRNA was checked by capillary electrophoresis using Agilent 2100 Bioanalyzer.
Sample_hyb_protocol	Ten µg of biotinylated fragmented cRNA were hybridized onto the GeneChip® Array according to the manufacturer's recommendation. In case that the yield of biotinylated cRNA was less than 10 µg, the in-vitro transcription was repeated using the same cDNA as template as had been used in the failed reaction. In case there was no sufficient cDNA left, a new cDNA synthesis was initiated. The hybridization was performed for 16 hours at 60 rpm and 45 °C in a GeneChip® Hybridization Oven 640 (Affymetrix). Washing and staining of the arrays was done on a Gene Chip® Fluidics Station 400 (Affymetrix) according to the manufacturer's recommendation. The antibody signal amplification, washing and staining protocol (Affymetrix) was used to stain the arrays with streptavidin R-phycoerythrin (SAPE; Invitrogen, USA). To amplify staining, SAPE solution was added twice with a biotinylated anti-streptavidin antibody (Vector Laboratories, CA) staining step in between.
Sample_scan_protocol	The arrays were scanned using a GeneChip® Scanner 3000. Scanned image files were visually inspected for artifacts and then analyzed, each image being scaled to the same target value for comparison between chips. The GeneChip® Operating Software (GCOS) was used to control the fluidics station and the scanner, to capture probe array data and to analyze hybridization intensity data. Default parameters provided in the Affymetrix data analysis software package were applied for analysis.
Sample_data_processing	Affymetrix .CEL files were uploaded into our database ArrayTrack, which is a toxicogenomics software for microarray data management and analysis. Significant gene lists were prepared in ArrayTrack by using the Welch t-test, applying the following criteria: p-values < 0.05, mean channel intensities > 100, abs fold-change > 2.5.
Sample_platform_id	GPL570
Sample_contact_name	Jürgen,,Borlak
Sample_contact_email	borlak@item.fraunhofer.de
Sample_contact_phone	+49-511 5350-520
Sample_contact_fax	+49-511 5350-573
Sample_contact_institute	Fraunhofer Institut
Sample_contact_address	Nikolai-Fuchs-Strasse 1
Sample_contact_city	Hannover
Sample_contact_zip/postal_code	30625
Sample_contact_country	Germany
Sample_contact_web_link	http://www.item.fraunhofer.de
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM301nnn/GSM301599/suppl/GSM301599.CEL.gz
Sample_series_id	GSE11941
Sample_series_id	GSE11942
Sample_data_row_count	54675

GSM301600

GPL570

Human Hepatocytes_Trovafloxacin, Donor_2

Primary human hepatocytes

Human hepatocytes isolated from specimens obtained from patients undergoing hepatic resections sex: female; age: 60; reason for liver resection: liver metastasis, mamma carcinoma

no additional information

Sample_geo_accession	GSM301600
Sample_status	Public on Oct 01 2008
Sample_submission_date	Jun 30 2008
Sample_last_update_date	Jun 30 2008
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Homo sapiens
Sample_taxid_ch1	9606
Sample_treatment_protocol_ch1	Prior to exposure, cells were allowed to recover from the isolation procedure for 4 to 5 days. Cells were harvested after treatment with 100 µg/ml of trovafloxacin and after 72 hours of treatment.
Sample_growth_protocol_ch1	Primary hepatocytes were cultured enclosed between two layers of collagen. One ml collagen solution containing 1.1 mg/ml collagen was used for coating one 60-mm Petri dish (Greiner, Frickenhausen, Germany). The pH of the collagen was adjusted to 7.4 using a 10x DMEM concentrate (Biochrom, Berlin, Germany). The 2 x 106 hepatocytes per dish were seeded. Two hours after seeding and attachment of the cells, culture medium was removed along with nonadherent cells. After 24-48 h in culture, the medium was aspirated and a second layer of collagen was pipetted on top of the cells. After gelation of this second layer, culture medium was added. Culture medium (2 ml) was changed daily. The total volume of cell culture supernatant was 4 ml, including the hydrated collagen matrix volume of 2 ml.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Total RNA was isolated from the hepatocytes using RNeasy total RNA isolation kit (QIAGEN). A second cleanup of isolated RNA was done using RNeasy Mini Kit (Qiagen). RNA was checked for quantity, purity and integrity of the 18S and 28S ribosomal bands by capillary electrophoresis using NanoDrop ND-1000 and Agilent 2100 Bioanalyzer.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	One to 15 µg of total RNA were used as starting material to prepare cDNA. Synthesis of double-stranded cDNA was performed using a GeneChip® one-cycle cDNA Kit (Affymetrix). The cleanup of double-stranded cDNA was done using a GeneChip® Sample Cleanup module (Affymetrix). Depending on the starting amount of total RNA, 12 (1 to 8 µg total RNA) or 6 µl (8 to 15 µg total RNA) of cDNA solution were used for in-vitro transcription. The in-vitro transcription was conducted with a GeneChip® IVT Labeling Kit (Affymetrix). The total amount of the reaction product was purified with a GeneChip® Sample Cleanup module (Affymetrix). Purified cRNA was quantified and checked for quality using NanoDrop ND-1000 and Agilent 2100 Bioanalyzer. Purified cRNA was cleaved into fragments of 35-200 bases by metal-induced hydrolysis. The degree of fragmentation and the length distribution of the fragmented biotinylated cRNA was checked by capillary electrophoresis using Agilent 2100 Bioanalyzer.
Sample_hyb_protocol	Ten µg of biotinylated fragmented cRNA were hybridized onto the GeneChip® Array according to the manufacturer's recommendation. In case that the yield of biotinylated cRNA was less than 10 µg, the in-vitro transcription was repeated using the same cDNA as template as had been used in the failed reaction. In case there was no sufficient cDNA left, a new cDNA synthesis was initiated. The hybridization was performed for 16 hours at 60 rpm and 45 °C in a GeneChip® Hybridization Oven 640 (Affymetrix). Washing and staining of the arrays was done on a Gene Chip® Fluidics Station 400 (Affymetrix) according to the manufacturer's recommendation. The antibody signal amplification, washing and staining protocol (Affymetrix) was used to stain the arrays with streptavidin R-phycoerythrin (SAPE; Invitrogen, USA). To amplify staining, SAPE solution was added twice with a biotinylated anti-streptavidin antibody (Vector Laboratories, CA) staining step in between.
Sample_scan_protocol	The arrays were scanned using a GeneChip® Scanner 3000. Scanned image files were visually inspected for artifacts and then analyzed, each image being scaled to the same target value for comparison between chips. The GeneChip® Operating Software (GCOS) was used to control the fluidics station and the scanner, to capture probe array data and to analyze hybridization intensity data. Default parameters provided in the Affymetrix data analysis software package were applied for analysis.
Sample_data_processing	Affymetrix .CEL files were uploaded into our database ArrayTrack, which is a toxicogenomics software for microarray data management and analysis. Significant gene lists were prepared in ArrayTrack by using the Welch t-test, applying the following criteria: p-values < 0.05, mean channel intensities > 100, abs fold-change > 2.5.
Sample_platform_id	GPL570
Sample_contact_name	Jürgen,,Borlak
Sample_contact_email	borlak@item.fraunhofer.de
Sample_contact_phone	+49-511 5350-520
Sample_contact_fax	+49-511 5350-573
Sample_contact_institute	Fraunhofer Institut
Sample_contact_address	Nikolai-Fuchs-Strasse 1
Sample_contact_city	Hannover
Sample_contact_zip/postal_code	30625
Sample_contact_country	Germany
Sample_contact_web_link	http://www.item.fraunhofer.de
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM301nnn/GSM301600/suppl/GSM301600.CEL.gz
Sample_series_id	GSE11941
Sample_series_id	GSE11942
Sample_data_row_count	54675

GSM301601

GPL570

Human Hepatocytes_Trovafloxacin, Donor_3

Primary human hepatocytes

Human hepatocytes isolated from specimens obtained from patients undergoing hepatic resections sex: female; age: 43; reason for liver resection: liver adenoma

no additional information

Sample_geo_accession	GSM301601
Sample_status	Public on Oct 01 2008
Sample_submission_date	Jun 30 2008
Sample_last_update_date	Jun 30 2008
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Homo sapiens
Sample_taxid_ch1	9606
Sample_treatment_protocol_ch1	Prior to exposure, cells were allowed to recover from the isolation procedure for 4 to 5 days. Cells were harvested after treatment with 100 µg/ml of trovafloxacin and after 72 hours of treatment.
Sample_growth_protocol_ch1	Primary hepatocytes were cultured enclosed between two layers of collagen. One ml collagen solution containing 1.1 mg/ml collagen was used for coating one 60-mm Petri dish (Greiner, Frickenhausen, Germany). The pH of the collagen was adjusted to 7.4 using a 10x DMEM concentrate (Biochrom, Berlin, Germany). The 2 x 106 hepatocytes per dish were seeded. Two hours after seeding and attachment of the cells, culture medium was removed along with nonadherent cells. After 24-48 h in culture, the medium was aspirated and a second layer of collagen was pipetted on top of the cells. After gelation of this second layer, culture medium was added. Culture medium (2 ml) was changed daily. The total volume of cell culture supernatant was 4 ml, including the hydrated collagen matrix volume of 2 ml.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Total RNA was isolated from the hepatocytes using RNeasy total RNA isolation kit (QIAGEN). A second cleanup of isolated RNA was done using RNeasy Mini Kit (Qiagen). RNA was checked for quantity, purity and integrity of the 18S and 28S ribosomal bands by capillary electrophoresis using NanoDrop ND-1000 and Agilent 2100 Bioanalyzer.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	One to 15 µg of total RNA were used as starting material to prepare cDNA. Synthesis of double-stranded cDNA was performed using a GeneChip® one-cycle cDNA Kit (Affymetrix). The cleanup of double-stranded cDNA was done using a GeneChip® Sample Cleanup module (Affymetrix). Depending on the starting amount of total RNA, 12 (1 to 8 µg total RNA) or 6 µl (8 to 15 µg total RNA) of cDNA solution were used for in-vitro transcription. The in-vitro transcription was conducted with a GeneChip® IVT Labeling Kit (Affymetrix). The total amount of the reaction product was purified with a GeneChip® Sample Cleanup module (Affymetrix). Purified cRNA was quantified and checked for quality using NanoDrop ND-1000 and Agilent 2100 Bioanalyzer. Purified cRNA was cleaved into fragments of 35-200 bases by metal-induced hydrolysis. The degree of fragmentation and the length distribution of the fragmented biotinylated cRNA was checked by capillary electrophoresis using Agilent 2100 Bioanalyzer.
Sample_hyb_protocol	Ten µg of biotinylated fragmented cRNA were hybridized onto the GeneChip® Array according to the manufacturer's recommendation. In case that the yield of biotinylated cRNA was less than 10 µg, the in-vitro transcription was repeated using the same cDNA as template as had been used in the failed reaction. In case there was no sufficient cDNA left, a new cDNA synthesis was initiated. The hybridization was performed for 16 hours at 60 rpm and 45 °C in a GeneChip® Hybridization Oven 640 (Affymetrix). Washing and staining of the arrays was done on a Gene Chip® Fluidics Station 400 (Affymetrix) according to the manufacturer's recommendation. The antibody signal amplification, washing and staining protocol (Affymetrix) was used to stain the arrays with streptavidin R-phycoerythrin (SAPE; Invitrogen, USA). To amplify staining, SAPE solution was added twice with a biotinylated anti-streptavidin antibody (Vector Laboratories, CA) staining step in between.
Sample_scan_protocol	The arrays were scanned using a GeneChip® Scanner 3000. Scanned image files were visually inspected for artifacts and then analyzed, each image being scaled to the same target value for comparison between chips. The GeneChip® Operating Software (GCOS) was used to control the fluidics station and the scanner, to capture probe array data and to analyze hybridization intensity data. Default parameters provided in the Affymetrix data analysis software package were applied for analysis.
Sample_data_processing	Affymetrix .CEL files were uploaded into our database ArrayTrack, which is a toxicogenomics software for microarray data management and analysis. Significant gene lists were prepared in ArrayTrack by using the Welch t-test, applying the following criteria: p-values < 0.05, mean channel intensities > 100, abs fold-change > 2.5.
Sample_platform_id	GPL570
Sample_contact_name	Jürgen,,Borlak
Sample_contact_email	borlak@item.fraunhofer.de
Sample_contact_phone	+49-511 5350-520
Sample_contact_fax	+49-511 5350-573
Sample_contact_institute	Fraunhofer Institut
Sample_contact_address	Nikolai-Fuchs-Strasse 1
Sample_contact_city	Hannover
Sample_contact_zip/postal_code	30625
Sample_contact_country	Germany
Sample_contact_web_link	http://www.item.fraunhofer.de
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM301nnn/GSM301601/suppl/GSM301601.CEL.gz
Sample_series_id	GSE11941
Sample_series_id	GSE11942
Sample_data_row_count	54675

GSM301602

GPL570

Human Hepatocytes_Trovafloxacin, Donor_4

Primary human hepatocytes

Human hepatocytes isolated from specimens obtained from patients undergoing hepatic resections sex: male; age: 65; reason for liver resection: colorectal liver metastasis

no additional information

Sample_geo_accession	GSM301602
Sample_status	Public on Oct 01 2008
Sample_submission_date	Jun 30 2008
Sample_last_update_date	Jun 30 2008
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Homo sapiens
Sample_taxid_ch1	9606
Sample_treatment_protocol_ch1	Prior to exposure, cells were allowed to recover from the isolation procedure for 4 to 5 days. Cells were harvested after treatment with 100 µg/ml of trovafloxacin and after 72 hours of treatment.
Sample_growth_protocol_ch1	Primary hepatocytes were cultured enclosed between two layers of collagen. One ml collagen solution containing 1.1 mg/ml collagen was used for coating one 60-mm Petri dish (Greiner, Frickenhausen, Germany). The pH of the collagen was adjusted to 7.4 using a 10x DMEM concentrate (Biochrom, Berlin, Germany). The 2 x 106 hepatocytes per dish were seeded. Two hours after seeding and attachment of the cells, culture medium was removed along with nonadherent cells. After 24-48 h in culture, the medium was aspirated and a second layer of collagen was pipetted on top of the cells. After gelation of this second layer, culture medium was added. Culture medium (2 ml) was changed daily. The total volume of cell culture supernatant was 4 ml, including the hydrated collagen matrix volume of 2 ml.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Total RNA was isolated from the hepatocytes using RNeasy total RNA isolation kit (QIAGEN). A second cleanup of isolated RNA was done using RNeasy Mini Kit (Qiagen). RNA was checked for quantity, purity and integrity of the 18S and 28S ribosomal bands by capillary electrophoresis using NanoDrop ND-1000 and Agilent 2100 Bioanalyzer.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	One to 15 µg of total RNA were used as starting material to prepare cDNA. Synthesis of double-stranded cDNA was performed using a GeneChip® one-cycle cDNA Kit (Affymetrix). The cleanup of double-stranded cDNA was done using a GeneChip® Sample Cleanup module (Affymetrix). Depending on the starting amount of total RNA, 12 (1 to 8 µg total RNA) or 6 µl (8 to 15 µg total RNA) of cDNA solution were used for in-vitro transcription. The in-vitro transcription was conducted with a GeneChip® IVT Labeling Kit (Affymetrix). The total amount of the reaction product was purified with a GeneChip® Sample Cleanup module (Affymetrix). Purified cRNA was quantified and checked for quality using NanoDrop ND-1000 and Agilent 2100 Bioanalyzer. Purified cRNA was cleaved into fragments of 35-200 bases by metal-induced hydrolysis. The degree of fragmentation and the length distribution of the fragmented biotinylated cRNA was checked by capillary electrophoresis using Agilent 2100 Bioanalyzer.
Sample_hyb_protocol	Ten µg of biotinylated fragmented cRNA were hybridized onto the GeneChip® Array according to the manufacturer's recommendation. In case that the yield of biotinylated cRNA was less than 10 µg, the in-vitro transcription was repeated using the same cDNA as template as had been used in the failed reaction. In case there was no sufficient cDNA left, a new cDNA synthesis was initiated. The hybridization was performed for 16 hours at 60 rpm and 45 °C in a GeneChip® Hybridization Oven 640 (Affymetrix). Washing and staining of the arrays was done on a Gene Chip® Fluidics Station 400 (Affymetrix) according to the manufacturer's recommendation. The antibody signal amplification, washing and staining protocol (Affymetrix) was used to stain the arrays with streptavidin R-phycoerythrin (SAPE; Invitrogen, USA). To amplify staining, SAPE solution was added twice with a biotinylated anti-streptavidin antibody (Vector Laboratories, CA) staining step in between.
Sample_scan_protocol	The arrays were scanned using a GeneChip® Scanner 3000. Scanned image files were visually inspected for artifacts and then analyzed, each image being scaled to the same target value for comparison between chips. The GeneChip® Operating Software (GCOS) was used to control the fluidics station and the scanner, to capture probe array data and to analyze hybridization intensity data. Default parameters provided in the Affymetrix data analysis software package were applied for analysis.
Sample_data_processing	Affymetrix .CEL files were uploaded into our database ArrayTrack, which is a toxicogenomics software for microarray data management and analysis. Significant gene lists were prepared in ArrayTrack by using the Welch t-test, applying the following criteria: p-values < 0.05, mean channel intensities > 100, abs fold-change > 2.5.
Sample_platform_id	GPL570
Sample_contact_name	Jürgen,,Borlak
Sample_contact_email	borlak@item.fraunhofer.de
Sample_contact_phone	+49-511 5350-520
Sample_contact_fax	+49-511 5350-573
Sample_contact_institute	Fraunhofer Institut
Sample_contact_address	Nikolai-Fuchs-Strasse 1
Sample_contact_city	Hannover
Sample_contact_zip/postal_code	30625
Sample_contact_country	Germany
Sample_contact_web_link	http://www.item.fraunhofer.de
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM301nnn/GSM301602/suppl/GSM301602.CEL.gz
Sample_series_id	GSE11941
Sample_series_id	GSE11942
Sample_data_row_count	54675

GSM301603

GPL570

Human Hepatocytes_Control, Donor_1

Primary human hepatocytes

Human hepatocytes isolated from specimens obtained from patients undergoing hepatic resections sex: male; age: 63; reason for liver resection: liver metastasis, kidney carcinoma

no additional information

Sample_geo_accession	GSM301603
Sample_status	Public on Oct 01 2008
Sample_submission_date	Jun 30 2008
Sample_last_update_date	Jun 30 2008
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Homo sapiens
Sample_taxid_ch1	9606
Sample_treatment_protocol_ch1	Prior to exposure, cells were allowed to recover from the isolation procedure for 4 to 5 days. Cells were harvested after treatment with 100 µg/ml of trovafloxacin and after 72 hours of treatment.
Sample_growth_protocol_ch1	Primary hepatocytes were cultured enclosed between two layers of collagen. One ml collagen solution containing 1.1 mg/ml collagen was used for coating one 60-mm Petri dish (Greiner, Frickenhausen, Germany). The pH of the collagen was adjusted to 7.4 using a 10x DMEM concentrate (Biochrom, Berlin, Germany). The 2 x 106 hepatocytes per dish were seeded. Two hours after seeding and attachment of the cells, culture medium was removed along with nonadherent cells. After 24-48 h in culture, the medium was aspirated and a second layer of collagen was pipetted on top of the cells. After gelation of this second layer, culture medium was added. Culture medium (2 ml) was changed daily. The total volume of cell culture supernatant was 4 ml, including the hydrated collagen matrix volume of 2 ml.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Total RNA was isolated from the hepatocytes using RNeasy total RNA isolation kit (QIAGEN). A second cleanup of isolated RNA was done using RNeasy Mini Kit (Qiagen). RNA was checked for quantity, purity and integrity of the 18S and 28S ribosomal bands by capillary electrophoresis using NanoDrop ND-1000 and Agilent 2100 Bioanalyzer.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	One to 15 µg of total RNA were used as starting material to prepare cDNA. Synthesis of double-stranded cDNA was performed using a GeneChip® one-cycle cDNA Kit (Affymetrix). The cleanup of double-stranded cDNA was done using a GeneChip® Sample Cleanup module (Affymetrix). Depending on the starting amount of total RNA, 12 (1 to 8 µg total RNA) or 6 µl (8 to 15 µg total RNA) of cDNA solution were used for in-vitro transcription. The in-vitro transcription was conducted with a GeneChip® IVT Labeling Kit (Affymetrix). The total amount of the reaction product was purified with a GeneChip® Sample Cleanup module (Affymetrix). Purified cRNA was quantified and checked for quality using NanoDrop ND-1000 and Agilent 2100 Bioanalyzer. Purified cRNA was cleaved into fragments of 35-200 bases by metal-induced hydrolysis. The degree of fragmentation and the length distribution of the fragmented biotinylated cRNA was checked by capillary electrophoresis using Agilent 2100 Bioanalyzer.
Sample_hyb_protocol	Ten µg of biotinylated fragmented cRNA were hybridized onto the GeneChip® Array according to the manufacturer's recommendation. In case that the yield of biotinylated cRNA was less than 10 µg, the in-vitro transcription was repeated using the same cDNA as template as had been used in the failed reaction. In case there was no sufficient cDNA left, a new cDNA synthesis was initiated. The hybridization was performed for 16 hours at 60 rpm and 45 °C in a GeneChip® Hybridization Oven 640 (Affymetrix). Washing and staining of the arrays was done on a Gene Chip® Fluidics Station 400 (Affymetrix) according to the manufacturer's recommendation. The antibody signal amplification, washing and staining protocol (Affymetrix) was used to stain the arrays with streptavidin R-phycoerythrin (SAPE; Invitrogen, USA). To amplify staining, SAPE solution was added twice with a biotinylated anti-streptavidin antibody (Vector Laboratories, CA) staining step in between.
Sample_scan_protocol	The arrays were scanned using a GeneChip® Scanner 3000. Scanned image files were visually inspected for artifacts and then analyzed, each image being scaled to the same target value for comparison between chips. The GeneChip® Operating Software (GCOS) was used to control the fluidics station and the scanner, to capture probe array data and to analyze hybridization intensity data. Default parameters provided in the Affymetrix data analysis software package were applied for analysis.
Sample_data_processing	Affymetrix .CEL files were uploaded into our database ArrayTrack, which is a toxicogenomics software for microarray data management and analysis. Significant gene lists were prepared in ArrayTrack by using the Welch t-test, applying the following criteria: p-values < 0.05, mean channel intensities > 100, abs fold-change > 2.5.
Sample_platform_id	GPL570
Sample_contact_name	Jürgen,,Borlak
Sample_contact_email	borlak@item.fraunhofer.de
Sample_contact_phone	+49-511 5350-520
Sample_contact_fax	+49-511 5350-573
Sample_contact_institute	Fraunhofer Institut
Sample_contact_address	Nikolai-Fuchs-Strasse 1
Sample_contact_city	Hannover
Sample_contact_zip/postal_code	30625
Sample_contact_country	Germany
Sample_contact_web_link	http://www.item.fraunhofer.de
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM301nnn/GSM301603/suppl/GSM301603.CEL.gz
Sample_series_id	GSE11941
Sample_series_id	GSE11942
Sample_data_row_count	54675

GSM301604

GPL570

Human Hepatocytes_Control, Donor_2

Primary human hepatocytes

Human hepatocytes isolated from specimens obtained from patients undergoing hepatic resections sex: female; age: 60; reason for liver resection: liver metastasis, mamma carcinoma

no additional information

Sample_geo_accession	GSM301604
Sample_status	Public on Oct 01 2008
Sample_submission_date	Jun 30 2008
Sample_last_update_date	Jun 30 2008
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Homo sapiens
Sample_taxid_ch1	9606
Sample_treatment_protocol_ch1	Prior to exposure, cells were allowed to recover from the isolation procedure for 4 to 5 days. Cells were harvested after treatment with 100 µg/ml of trovafloxacin and after 72 hours of treatment.
Sample_growth_protocol_ch1	Primary hepatocytes were cultured enclosed between two layers of collagen. One ml collagen solution containing 1.1 mg/ml collagen was used for coating one 60-mm Petri dish (Greiner, Frickenhausen, Germany). The pH of the collagen was adjusted to 7.4 using a 10x DMEM concentrate (Biochrom, Berlin, Germany). The 2 x 106 hepatocytes per dish were seeded. Two hours after seeding and attachment of the cells, culture medium was removed along with nonadherent cells. After 24-48 h in culture, the medium was aspirated and a second layer of collagen was pipetted on top of the cells. After gelation of this second layer, culture medium was added. Culture medium (2 ml) was changed daily. The total volume of cell culture supernatant was 4 ml, including the hydrated collagen matrix volume of 2 ml.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Total RNA was isolated from the hepatocytes using RNeasy total RNA isolation kit (QIAGEN). A second cleanup of isolated RNA was done using RNeasy Mini Kit (Qiagen). RNA was checked for quantity, purity and integrity of the 18S and 28S ribosomal bands by capillary electrophoresis using NanoDrop ND-1000 and Agilent 2100 Bioanalyzer.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	One to 15 µg of total RNA were used as starting material to prepare cDNA. Synthesis of double-stranded cDNA was performed using a GeneChip® one-cycle cDNA Kit (Affymetrix). The cleanup of double-stranded cDNA was done using a GeneChip® Sample Cleanup module (Affymetrix). Depending on the starting amount of total RNA, 12 (1 to 8 µg total RNA) or 6 µl (8 to 15 µg total RNA) of cDNA solution were used for in-vitro transcription. The in-vitro transcription was conducted with a GeneChip® IVT Labeling Kit (Affymetrix). The total amount of the reaction product was purified with a GeneChip® Sample Cleanup module (Affymetrix). Purified cRNA was quantified and checked for quality using NanoDrop ND-1000 and Agilent 2100 Bioanalyzer. Purified cRNA was cleaved into fragments of 35-200 bases by metal-induced hydrolysis. The degree of fragmentation and the length distribution of the fragmented biotinylated cRNA was checked by capillary electrophoresis using Agilent 2100 Bioanalyzer.
Sample_hyb_protocol	Ten µg of biotinylated fragmented cRNA were hybridized onto the GeneChip® Array according to the manufacturer's recommendation. In case that the yield of biotinylated cRNA was less than 10 µg, the in-vitro transcription was repeated using the same cDNA as template as had been used in the failed reaction. In case there was no sufficient cDNA left, a new cDNA synthesis was initiated. The hybridization was performed for 16 hours at 60 rpm and 45 °C in a GeneChip® Hybridization Oven 640 (Affymetrix). Washing and staining of the arrays was done on a Gene Chip® Fluidics Station 400 (Affymetrix) according to the manufacturer's recommendation. The antibody signal amplification, washing and staining protocol (Affymetrix) was used to stain the arrays with streptavidin R-phycoerythrin (SAPE; Invitrogen, USA). To amplify staining, SAPE solution was added twice with a biotinylated anti-streptavidin antibody (Vector Laboratories, CA) staining step in between.
Sample_scan_protocol	The arrays were scanned using a GeneChip® Scanner 3000. Scanned image files were visually inspected for artifacts and then analyzed, each image being scaled to the same target value for comparison between chips. The GeneChip® Operating Software (GCOS) was used to control the fluidics station and the scanner, to capture probe array data and to analyze hybridization intensity data. Default parameters provided in the Affymetrix data analysis software package were applied for analysis.
Sample_data_processing	Affymetrix .CEL files were uploaded into our database ArrayTrack, which is a toxicogenomics software for microarray data management and analysis. Significant gene lists were prepared in ArrayTrack by using the Welch t-test, applying the following criteria: p-values < 0.05, mean channel intensities > 100, abs fold-change > 2.5.
Sample_platform_id	GPL570
Sample_contact_name	Jürgen,,Borlak
Sample_contact_email	borlak@item.fraunhofer.de
Sample_contact_phone	+49-511 5350-520
Sample_contact_fax	+49-511 5350-573
Sample_contact_institute	Fraunhofer Institut
Sample_contact_address	Nikolai-Fuchs-Strasse 1
Sample_contact_city	Hannover
Sample_contact_zip/postal_code	30625
Sample_contact_country	Germany
Sample_contact_web_link	http://www.item.fraunhofer.de
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM301nnn/GSM301604/suppl/GSM301604.CEL.gz
Sample_series_id	GSE11941
Sample_series_id	GSE11942
Sample_data_row_count	54675

GSM301605

GPL570

Human Hepatocytes_Control, Donor_3

Primary human hepatocytes

Human hepatocytes isolated from specimens obtained from patients undergoing hepatic resections sex: female; age: 43; reason for liver resection: liver adenoma

no additional information

Sample_geo_accession	GSM301605
Sample_status	Public on Oct 01 2008
Sample_submission_date	Jun 30 2008
Sample_last_update_date	Jun 30 2008
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Homo sapiens
Sample_taxid_ch1	9606
Sample_treatment_protocol_ch1	Prior to exposure, cells were allowed to recover from the isolation procedure for 4 to 5 days. Cells were harvested after treatment with 100 µg/ml of trovafloxacin and after 72 hours of treatment.
Sample_growth_protocol_ch1	Primary hepatocytes were cultured enclosed between two layers of collagen. One ml collagen solution containing 1.1 mg/ml collagen was used for coating one 60-mm Petri dish (Greiner, Frickenhausen, Germany). The pH of the collagen was adjusted to 7.4 using a 10x DMEM concentrate (Biochrom, Berlin, Germany). The 2 x 106 hepatocytes per dish were seeded. Two hours after seeding and attachment of the cells, culture medium was removed along with nonadherent cells. After 24-48 h in culture, the medium was aspirated and a second layer of collagen was pipetted on top of the cells. After gelation of this second layer, culture medium was added. Culture medium (2 ml) was changed daily. The total volume of cell culture supernatant was 4 ml, including the hydrated collagen matrix volume of 2 ml.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Total RNA was isolated from the hepatocytes using RNeasy total RNA isolation kit (QIAGEN). A second cleanup of isolated RNA was done using RNeasy Mini Kit (Qiagen). RNA was checked for quantity, purity and integrity of the 18S and 28S ribosomal bands by capillary electrophoresis using NanoDrop ND-1000 and Agilent 2100 Bioanalyzer.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	One to 15 µg of total RNA were used as starting material to prepare cDNA. Synthesis of double-stranded cDNA was performed using a GeneChip® one-cycle cDNA Kit (Affymetrix). The cleanup of double-stranded cDNA was done using a GeneChip® Sample Cleanup module (Affymetrix). Depending on the starting amount of total RNA, 12 (1 to 8 µg total RNA) or 6 µl (8 to 15 µg total RNA) of cDNA solution were used for in-vitro transcription. The in-vitro transcription was conducted with a GeneChip® IVT Labeling Kit (Affymetrix). The total amount of the reaction product was purified with a GeneChip® Sample Cleanup module (Affymetrix). Purified cRNA was quantified and checked for quality using NanoDrop ND-1000 and Agilent 2100 Bioanalyzer. Purified cRNA was cleaved into fragments of 35-200 bases by metal-induced hydrolysis. The degree of fragmentation and the length distribution of the fragmented biotinylated cRNA was checked by capillary electrophoresis using Agilent 2100 Bioanalyzer.
Sample_hyb_protocol	Ten µg of biotinylated fragmented cRNA were hybridized onto the GeneChip® Array according to the manufacturer's recommendation. In case that the yield of biotinylated cRNA was less than 10 µg, the in-vitro transcription was repeated using the same cDNA as template as had been used in the failed reaction. In case there was no sufficient cDNA left, a new cDNA synthesis was initiated. The hybridization was performed for 16 hours at 60 rpm and 45 °C in a GeneChip® Hybridization Oven 640 (Affymetrix). Washing and staining of the arrays was done on a Gene Chip® Fluidics Station 400 (Affymetrix) according to the manufacturer's recommendation. The antibody signal amplification, washing and staining protocol (Affymetrix) was used to stain the arrays with streptavidin R-phycoerythrin (SAPE; Invitrogen, USA). To amplify staining, SAPE solution was added twice with a biotinylated anti-streptavidin antibody (Vector Laboratories, CA) staining step in between.
Sample_scan_protocol	The arrays were scanned using a GeneChip® Scanner 3000. Scanned image files were visually inspected for artifacts and then analyzed, each image being scaled to the same target value for comparison between chips. The GeneChip® Operating Software (GCOS) was used to control the fluidics station and the scanner, to capture probe array data and to analyze hybridization intensity data. Default parameters provided in the Affymetrix data analysis software package were applied for analysis.
Sample_data_processing	Affymetrix .CEL files were uploaded into our database ArrayTrack, which is a toxicogenomics software for microarray data management and analysis. Significant gene lists were prepared in ArrayTrack by using the Welch t-test, applying the following criteria: p-values < 0.05, mean channel intensities > 100, abs fold-change > 2.5.
Sample_platform_id	GPL570
Sample_contact_name	Jürgen,,Borlak
Sample_contact_email	borlak@item.fraunhofer.de
Sample_contact_phone	+49-511 5350-520
Sample_contact_fax	+49-511 5350-573
Sample_contact_institute	Fraunhofer Institut
Sample_contact_address	Nikolai-Fuchs-Strasse 1
Sample_contact_city	Hannover
Sample_contact_zip/postal_code	30625
Sample_contact_country	Germany
Sample_contact_web_link	http://www.item.fraunhofer.de
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM301nnn/GSM301605/suppl/GSM301605.CEL.gz
Sample_series_id	GSE11941
Sample_series_id	GSE11942
Sample_data_row_count	54675

GSM301606

GPL570

Human Hepatocytes_Control, Donor_4

Primary human hepatocytes

Human hepatocytes isolated from specimens obtained from patients undergoing hepatic resections sex: male; age: 65; reason for liver resection: colorectal liver metastasis

no additional information

Sample_geo_accession	GSM301606
Sample_status	Public on Oct 01 2008
Sample_submission_date	Jun 30 2008
Sample_last_update_date	Jun 30 2008
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Homo sapiens
Sample_taxid_ch1	9606
Sample_treatment_protocol_ch1	Prior to exposure, cells were allowed to recover from the isolation procedure for 4 to 5 days. Cells were harvested after treatment with 100 µg/ml of trovafloxacin and after 72 hours of treatment.
Sample_growth_protocol_ch1	Primary hepatocytes were cultured enclosed between two layers of collagen. One ml collagen solution containing 1.1 mg/ml collagen was used for coating one 60-mm Petri dish (Greiner, Frickenhausen, Germany). The pH of the collagen was adjusted to 7.4 using a 10x DMEM concentrate (Biochrom, Berlin, Germany). The 2 x 106 hepatocytes per dish were seeded. Two hours after seeding and attachment of the cells, culture medium was removed along with nonadherent cells. After 24-48 h in culture, the medium was aspirated and a second layer of collagen was pipetted on top of the cells. After gelation of this second layer, culture medium was added. Culture medium (2 ml) was changed daily. The total volume of cell culture supernatant was 4 ml, including the hydrated collagen matrix volume of 2 ml.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Total RNA was isolated from the hepatocytes using RNeasy total RNA isolation kit (QIAGEN). A second cleanup of isolated RNA was done using RNeasy Mini Kit (Qiagen). RNA was checked for quantity, purity and integrity of the 18S and 28S ribosomal bands by capillary electrophoresis using NanoDrop ND-1000 and Agilent 2100 Bioanalyzer.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	One to 15 µg of total RNA were used as starting material to prepare cDNA. Synthesis of double-stranded cDNA was performed using a GeneChip® one-cycle cDNA Kit (Affymetrix). The cleanup of double-stranded cDNA was done using a GeneChip® Sample Cleanup module (Affymetrix). Depending on the starting amount of total RNA, 12 (1 to 8 µg total RNA) or 6 µl (8 to 15 µg total RNA) of cDNA solution were used for in-vitro transcription. The in-vitro transcription was conducted with a GeneChip® IVT Labeling Kit (Affymetrix). The total amount of the reaction product was purified with a GeneChip® Sample Cleanup module (Affymetrix). Purified cRNA was quantified and checked for quality using NanoDrop ND-1000 and Agilent 2100 Bioanalyzer. Purified cRNA was cleaved into fragments of 35-200 bases by metal-induced hydrolysis. The degree of fragmentation and the length distribution of the fragmented biotinylated cRNA was checked by capillary electrophoresis using Agilent 2100 Bioanalyzer.
Sample_hyb_protocol	Ten µg of biotinylated fragmented cRNA were hybridized onto the GeneChip® Array according to the manufacturer's recommendation. In case that the yield of biotinylated cRNA was less than 10 µg, the in-vitro transcription was repeated using the same cDNA as template as had been used in the failed reaction. In case there was no sufficient cDNA left, a new cDNA synthesis was initiated. The hybridization was performed for 16 hours at 60 rpm and 45 °C in a GeneChip® Hybridization Oven 640 (Affymetrix). Washing and staining of the arrays was done on a Gene Chip® Fluidics Station 400 (Affymetrix) according to the manufacturer's recommendation. The antibody signal amplification, washing and staining protocol (Affymetrix) was used to stain the arrays with streptavidin R-phycoerythrin (SAPE; Invitrogen, USA). To amplify staining, SAPE solution was added twice with a biotinylated anti-streptavidin antibody (Vector Laboratories, CA) staining step in between.
Sample_scan_protocol	The arrays were scanned using a GeneChip® Scanner 3000. Scanned image files were visually inspected for artifacts and then analyzed, each image being scaled to the same target value for comparison between chips. The GeneChip® Operating Software (GCOS) was used to control the fluidics station and the scanner, to capture probe array data and to analyze hybridization intensity data. Default parameters provided in the Affymetrix data analysis software package were applied for analysis.
Sample_data_processing	Affymetrix .CEL files were uploaded into our database ArrayTrack, which is a toxicogenomics software for microarray data management and analysis. Significant gene lists were prepared in ArrayTrack by using the Welch t-test, applying the following criteria: p-values < 0.05, mean channel intensities > 100, abs fold-change > 2.5.
Sample_platform_id	GPL570
Sample_contact_name	Jürgen,,Borlak
Sample_contact_email	borlak@item.fraunhofer.de
Sample_contact_phone	+49-511 5350-520
Sample_contact_fax	+49-511 5350-573
Sample_contact_institute	Fraunhofer Institut
Sample_contact_address	Nikolai-Fuchs-Strasse 1
Sample_contact_city	Hannover
Sample_contact_zip/postal_code	30625
Sample_contact_country	Germany
Sample_contact_web_link	http://www.item.fraunhofer.de
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM301nnn/GSM301606/suppl/GSM301606.CEL.gz
Sample_series_id	GSE11941
Sample_series_id	GSE11942
Sample_data_row_count	54675

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