Search results for the GEO ID: GSE22009  |
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|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM547137 | GPL1261 |
|
liver_gp130delta(hepa)_CLP_rep1
|
liver from liver-specific Gp130 knockout [Gp130delta(hepa)] mice, 12 hrs after cecal ligation and puncture
|
tissue: liver
genotype/variation: liver-specific Gp130 knockout mice [Gp130delta(hepa)]
treatment: 12 hrs after cecal ligation and puncture
gender: male
age: 8-12 weeks
|
liver from liver-specific Gp130 knockout [Gp130delta(hepa)] mice, 12 hrs after cecal ligation and puncture, replicate 1
|
| Sample_geo_accession | GSM547137
| | Sample_status | Public on May 27 2010
| | Sample_submission_date | May 26 2010
| | Sample_last_update_date | May 27 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | Livers were dissected from control or liver-specific Gp130 knockout mice that were subjected to either cecal ligation and puncture for 12 hrs, or no prior treatment. Liver RNA samples from 3 mice per experimental group were used for microarray analysis.
| | Sample_growth_protocol_ch1 | Male control [gp130f/f] and liver-specific Gp130 knockout [gp130delta(hepa)] mice, aged 8-12 weeks were maintained on standard laboratory chow. Generation of the mice strains has been described in Klein et al. (J Clin Invest. 2005;115(4):860-869; PubMed ID 15761498). Polymicrobial sepsis was induced by cecal ligation and puncture (CLP). Briefly, mice were anesthetized, the cecum was ligated and punctured twice with a 20 Gauge needle. Twelve hours after CLP mice were sacrificed and livers were removed. For control treatment mice were sacrified without any prior treatment.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was prepared from mouse livers using TRIzol reagent and whereafter purified total RNA was isolated using Qiagen RNEasy columns. RNA integrity was checked on chip analysis (Agilent 2100 bioanalyzer, Agilent Technologies, Amsterdam, the Netherlands) according to the manufacturer's instructions. RNA was judged as suitable for array hybridization only if samples exhibited intact bands corresponding to the 18S and 28S ribosomal RNA subunits, and displayed no chromosomal peaks or RNA degradation products (RNA Integrity Number > 8.0).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | The Affymetrix GeneChip RNA One cycle Amplification Kit was used to prepare labelled cRNA from 5 μg of total RNA. The protocol was conducted using the reagents provided by Affymetrix in the One-Cycle cDNA synthesis kit (P/N 900431), One-Cycle IVT labelling kit (P/N 90449) and GeneChip Sample Cleanup Module (P/N 900371). A detailed description can be found in the Genechip Expression Analysis Technical Manual, section 2 (Eukaryotic Sample and Array Processing), chapter 1 (Eukaryotic Target Preparation) (P/N 701025, revision 6).
| | Sample_hyb_protocol | Hybridisation of 10ug cRNA was done overnight for 16 hours at 45ºC in a Hybridisation Oven 640 (Affymetrix). The protocol is conducted as described in the Genechip Expression Analysis Technical Manual, section 2 (Eukaryotic Sample and Array Processing), chapter 2 (Eukaryotic Target Hybridization) (P/N 701027, revision 5).
| | Sample_scan_protocol | Arrays were scanned on an Affymetrix 3000 7G scanner, as described in the Genechip Expression Analysis Technical Manual, section 2 (Eukaryotic Sample and Array Processing), chapter 2 (Eukaryotic Arrays: Washing, Staining and Scanning (P/N 701028, revision 5).
| | Sample_data_processing | Expression estimates were calculated using GCRMA (v2.20.0) in Bioconductor, applying the emperical Bayes (EB) model for background estimation.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Guido,,Hooiveld
| | Sample_contact_email | guido.hooiveld@wur.nl
| | Sample_contact_laboratory | Nutrition, Metabolism & Genomics Group
| | Sample_contact_department | Div. Human Nutrition
| | Sample_contact_institute | Wageningen University
| | Sample_contact_address | Bomenweg 2
| | Sample_contact_city | Wageningen
| | Sample_contact_zip/postal_code | NL-6703HD
| | Sample_contact_country | Netherlands
| | Sample_contact_web_link | http://nutrigene.4t.com
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM547nnn/GSM547137/suppl/GSM547137.CEL.gz
| | Sample_series_id | GSE22009
| | Sample_data_row_count | 45101
| | |
|
GSM547138 | GPL1261 |
|
liver_gp130delta(hepa)_CLP_rep2
|
liver from liver-specific Gp130 knockout [Gp130delta(hepa)] mice, 12 hrs after cecal ligation and puncture
|
tissue: liver
genotype/variation: liver-specific Gp130 knockout mice [Gp130delta(hepa)]
treatment: 12 hrs after cecal ligation and puncture
gender: male
age: 8-12 weeks
|
liver from liver-specific Gp130 knockout [Gp130delta(hepa)] mice, 12 hrs after cecal ligation and puncture, replicate 2
|
| Sample_geo_accession | GSM547138
| | Sample_status | Public on May 27 2010
| | Sample_submission_date | May 26 2010
| | Sample_last_update_date | May 27 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | Livers were dissected from control or liver-specific Gp130 knockout mice that were subjected to either cecal ligation and puncture for 12 hrs, or no prior treatment. Liver RNA samples from 3 mice per experimental group were used for microarray analysis.
| | Sample_growth_protocol_ch1 | Male control [gp130f/f] and liver-specific Gp130 knockout [gp130delta(hepa)] mice, aged 8-12 weeks were maintained on standard laboratory chow. Generation of the mice strains has been described in Klein et al. (J Clin Invest. 2005;115(4):860-869; PubMed ID 15761498). Polymicrobial sepsis was induced by cecal ligation and puncture (CLP). Briefly, mice were anesthetized, the cecum was ligated and punctured twice with a 20 Gauge needle. Twelve hours after CLP mice were sacrificed and livers were removed. For control treatment mice were sacrified without any prior treatment.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was prepared from mouse livers using TRIzol reagent and whereafter purified total RNA was isolated using Qiagen RNEasy columns. RNA integrity was checked on chip analysis (Agilent 2100 bioanalyzer, Agilent Technologies, Amsterdam, the Netherlands) according to the manufacturer's instructions. RNA was judged as suitable for array hybridization only if samples exhibited intact bands corresponding to the 18S and 28S ribosomal RNA subunits, and displayed no chromosomal peaks or RNA degradation products (RNA Integrity Number > 8.0).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | The Affymetrix GeneChip RNA One cycle Amplification Kit was used to prepare labelled cRNA from 5 μg of total RNA. The protocol was conducted using the reagents provided by Affymetrix in the One-Cycle cDNA synthesis kit (P/N 900431), One-Cycle IVT labelling kit (P/N 90449) and GeneChip Sample Cleanup Module (P/N 900371). A detailed description can be found in the Genechip Expression Analysis Technical Manual, section 2 (Eukaryotic Sample and Array Processing), chapter 1 (Eukaryotic Target Preparation) (P/N 701025, revision 6).
| | Sample_hyb_protocol | Hybridisation of 10ug cRNA was done overnight for 16 hours at 45ºC in a Hybridisation Oven 640 (Affymetrix). The protocol is conducted as described in the Genechip Expression Analysis Technical Manual, section 2 (Eukaryotic Sample and Array Processing), chapter 2 (Eukaryotic Target Hybridization) (P/N 701027, revision 5).
| | Sample_scan_protocol | Arrays were scanned on an Affymetrix 3000 7G scanner, as described in the Genechip Expression Analysis Technical Manual, section 2 (Eukaryotic Sample and Array Processing), chapter 2 (Eukaryotic Arrays: Washing, Staining and Scanning (P/N 701028, revision 5).
| | Sample_data_processing | Expression estimates were calculated using GCRMA (v2.20.0) in Bioconductor, applying the emperical Bayes (EB) model for background estimation.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Guido,,Hooiveld
| | Sample_contact_email | guido.hooiveld@wur.nl
| | Sample_contact_laboratory | Nutrition, Metabolism & Genomics Group
| | Sample_contact_department | Div. Human Nutrition
| | Sample_contact_institute | Wageningen University
| | Sample_contact_address | Bomenweg 2
| | Sample_contact_city | Wageningen
| | Sample_contact_zip/postal_code | NL-6703HD
| | Sample_contact_country | Netherlands
| | Sample_contact_web_link | http://nutrigene.4t.com
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM547nnn/GSM547138/suppl/GSM547138.CEL.gz
| | Sample_series_id | GSE22009
| | Sample_data_row_count | 45101
| | |
|
GSM547139 | GPL1261 |
|
liver_gp130delta(hepa)_CLP_rep3
|
liver from liver-specific Gp130 knockout [Gp130delta(hepa)] mice, 12 hrs after cecal ligation and puncture
|
tissue: liver
genotype/variation: liver-specific Gp130 knockout mice [Gp130delta(hepa)]
treatment: 12 hrs after cecal ligation and puncture
gender: male
age: 8-12 weeks
|
liver from liver-specific Gp130 knockout [Gp130delta(hepa)] mice, 12 hrs after cecal ligation and puncture, replicate 3
|
| Sample_geo_accession | GSM547139
| | Sample_status | Public on May 27 2010
| | Sample_submission_date | May 26 2010
| | Sample_last_update_date | May 27 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | Livers were dissected from control or liver-specific Gp130 knockout mice that were subjected to either cecal ligation and puncture for 12 hrs, or no prior treatment. Liver RNA samples from 3 mice per experimental group were used for microarray analysis.
| | Sample_growth_protocol_ch1 | Male control [gp130f/f] and liver-specific Gp130 knockout [gp130delta(hepa)] mice, aged 8-12 weeks were maintained on standard laboratory chow. Generation of the mice strains has been described in Klein et al. (J Clin Invest. 2005;115(4):860-869; PubMed ID 15761498). Polymicrobial sepsis was induced by cecal ligation and puncture (CLP). Briefly, mice were anesthetized, the cecum was ligated and punctured twice with a 20 Gauge needle. Twelve hours after CLP mice were sacrificed and livers were removed. For control treatment mice were sacrified without any prior treatment.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was prepared from mouse livers using TRIzol reagent and whereafter purified total RNA was isolated using Qiagen RNEasy columns. RNA integrity was checked on chip analysis (Agilent 2100 bioanalyzer, Agilent Technologies, Amsterdam, the Netherlands) according to the manufacturer's instructions. RNA was judged as suitable for array hybridization only if samples exhibited intact bands corresponding to the 18S and 28S ribosomal RNA subunits, and displayed no chromosomal peaks or RNA degradation products (RNA Integrity Number > 8.0).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | The Affymetrix GeneChip RNA One cycle Amplification Kit was used to prepare labelled cRNA from 5 μg of total RNA. The protocol was conducted using the reagents provided by Affymetrix in the One-Cycle cDNA synthesis kit (P/N 900431), One-Cycle IVT labelling kit (P/N 90449) and GeneChip Sample Cleanup Module (P/N 900371). A detailed description can be found in the Genechip Expression Analysis Technical Manual, section 2 (Eukaryotic Sample and Array Processing), chapter 1 (Eukaryotic Target Preparation) (P/N 701025, revision 6).
| | Sample_hyb_protocol | Hybridisation of 10ug cRNA was done overnight for 16 hours at 45ºC in a Hybridisation Oven 640 (Affymetrix). The protocol is conducted as described in the Genechip Expression Analysis Technical Manual, section 2 (Eukaryotic Sample and Array Processing), chapter 2 (Eukaryotic Target Hybridization) (P/N 701027, revision 5).
| | Sample_scan_protocol | Arrays were scanned on an Affymetrix 3000 7G scanner, as described in the Genechip Expression Analysis Technical Manual, section 2 (Eukaryotic Sample and Array Processing), chapter 2 (Eukaryotic Arrays: Washing, Staining and Scanning (P/N 701028, revision 5).
| | Sample_data_processing | Expression estimates were calculated using GCRMA (v2.20.0) in Bioconductor, applying the emperical Bayes (EB) model for background estimation.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Guido,,Hooiveld
| | Sample_contact_email | guido.hooiveld@wur.nl
| | Sample_contact_laboratory | Nutrition, Metabolism & Genomics Group
| | Sample_contact_department | Div. Human Nutrition
| | Sample_contact_institute | Wageningen University
| | Sample_contact_address | Bomenweg 2
| | Sample_contact_city | Wageningen
| | Sample_contact_zip/postal_code | NL-6703HD
| | Sample_contact_country | Netherlands
| | Sample_contact_web_link | http://nutrigene.4t.com
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM547nnn/GSM547139/suppl/GSM547139.CEL.gz
| | Sample_series_id | GSE22009
| | Sample_data_row_count | 45101
| | |
|
GSM547140 | GPL1261 |
|
liver_WT_CLP_rep1
|
liver from control (Gp130f/f ) mice, 12 hrs after cecal ligation and puncture
|
tissue: liver
genotype/variation: control mice [Gp130f/f]
treatment: 12 hrs after cecal ligation and puncture
gender: male
age: 8-12 weeks
|
liver from control (Gp130f/f ) mice, 12 hrs after cecal ligation and puncture, replicate 1
|
| Sample_geo_accession | GSM547140
| | Sample_status | Public on May 27 2010
| | Sample_submission_date | May 26 2010
| | Sample_last_update_date | May 27 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | Livers were dissected from control or liver-specific Gp130 knockout mice that were subjected to either cecal ligation and puncture for 12 hrs, or no prior treatment. Liver RNA samples from 3 mice per experimental group were used for microarray analysis.
| | Sample_growth_protocol_ch1 | Male control [gp130f/f] and liver-specific Gp130 knockout [gp130delta(hepa)] mice, aged 8-12 weeks were maintained on standard laboratory chow. Generation of the mice strains has been described in Klein et al. (J Clin Invest. 2005;115(4):860-869; PubMed ID 15761498). Polymicrobial sepsis was induced by cecal ligation and puncture (CLP). Briefly, mice were anesthetized, the cecum was ligated and punctured twice with a 20 Gauge needle. Twelve hours after CLP mice were sacrificed and livers were removed. For control treatment mice were sacrified without any prior treatment.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was prepared from mouse livers using TRIzol reagent and whereafter purified total RNA was isolated using Qiagen RNEasy columns. RNA integrity was checked on chip analysis (Agilent 2100 bioanalyzer, Agilent Technologies, Amsterdam, the Netherlands) according to the manufacturer's instructions. RNA was judged as suitable for array hybridization only if samples exhibited intact bands corresponding to the 18S and 28S ribosomal RNA subunits, and displayed no chromosomal peaks or RNA degradation products (RNA Integrity Number > 8.0).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | The Affymetrix GeneChip RNA One cycle Amplification Kit was used to prepare labelled cRNA from 5 μg of total RNA. The protocol was conducted using the reagents provided by Affymetrix in the One-Cycle cDNA synthesis kit (P/N 900431), One-Cycle IVT labelling kit (P/N 90449) and GeneChip Sample Cleanup Module (P/N 900371). A detailed description can be found in the Genechip Expression Analysis Technical Manual, section 2 (Eukaryotic Sample and Array Processing), chapter 1 (Eukaryotic Target Preparation) (P/N 701025, revision 6).
| | Sample_hyb_protocol | Hybridisation of 10ug cRNA was done overnight for 16 hours at 45ºC in a Hybridisation Oven 640 (Affymetrix). The protocol is conducted as described in the Genechip Expression Analysis Technical Manual, section 2 (Eukaryotic Sample and Array Processing), chapter 2 (Eukaryotic Target Hybridization) (P/N 701027, revision 5).
| | Sample_scan_protocol | Arrays were scanned on an Affymetrix 3000 7G scanner, as described in the Genechip Expression Analysis Technical Manual, section 2 (Eukaryotic Sample and Array Processing), chapter 2 (Eukaryotic Arrays: Washing, Staining and Scanning (P/N 701028, revision 5).
| | Sample_data_processing | Expression estimates were calculated using GCRMA (v2.20.0) in Bioconductor, applying the emperical Bayes (EB) model for background estimation.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Guido,,Hooiveld
| | Sample_contact_email | guido.hooiveld@wur.nl
| | Sample_contact_laboratory | Nutrition, Metabolism & Genomics Group
| | Sample_contact_department | Div. Human Nutrition
| | Sample_contact_institute | Wageningen University
| | Sample_contact_address | Bomenweg 2
| | Sample_contact_city | Wageningen
| | Sample_contact_zip/postal_code | NL-6703HD
| | Sample_contact_country | Netherlands
| | Sample_contact_web_link | http://nutrigene.4t.com
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM547nnn/GSM547140/suppl/GSM547140.CEL.gz
| | Sample_series_id | GSE22009
| | Sample_data_row_count | 45101
| | |
|
GSM547141 | GPL1261 |
|
liver_WT_CLP_rep2
|
liver from control (Gp130f/f ) mice, 12 hrs after cecal ligation and puncture
|
tissue: liver
genotype/variation: control mice [Gp130f/f]
treatment: 12 hrs after cecal ligation and puncture
gender: male
age: 8-12 weeks
|
liver from control (Gp130f/f ) mice, 12 hrs after cecal ligation and puncture, replicate 2
|
| Sample_geo_accession | GSM547141
| | Sample_status | Public on May 27 2010
| | Sample_submission_date | May 26 2010
| | Sample_last_update_date | May 27 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | Livers were dissected from control or liver-specific Gp130 knockout mice that were subjected to either cecal ligation and puncture for 12 hrs, or no prior treatment. Liver RNA samples from 3 mice per experimental group were used for microarray analysis.
| | Sample_growth_protocol_ch1 | Male control [gp130f/f] and liver-specific Gp130 knockout [gp130delta(hepa)] mice, aged 8-12 weeks were maintained on standard laboratory chow. Generation of the mice strains has been described in Klein et al. (J Clin Invest. 2005;115(4):860-869; PubMed ID 15761498). Polymicrobial sepsis was induced by cecal ligation and puncture (CLP). Briefly, mice were anesthetized, the cecum was ligated and punctured twice with a 20 Gauge needle. Twelve hours after CLP mice were sacrificed and livers were removed. For control treatment mice were sacrified without any prior treatment.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was prepared from mouse livers using TRIzol reagent and whereafter purified total RNA was isolated using Qiagen RNEasy columns. RNA integrity was checked on chip analysis (Agilent 2100 bioanalyzer, Agilent Technologies, Amsterdam, the Netherlands) according to the manufacturer's instructions. RNA was judged as suitable for array hybridization only if samples exhibited intact bands corresponding to the 18S and 28S ribosomal RNA subunits, and displayed no chromosomal peaks or RNA degradation products (RNA Integrity Number > 8.0).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | The Affymetrix GeneChip RNA One cycle Amplification Kit was used to prepare labelled cRNA from 5 μg of total RNA. The protocol was conducted using the reagents provided by Affymetrix in the One-Cycle cDNA synthesis kit (P/N 900431), One-Cycle IVT labelling kit (P/N 90449) and GeneChip Sample Cleanup Module (P/N 900371). A detailed description can be found in the Genechip Expression Analysis Technical Manual, section 2 (Eukaryotic Sample and Array Processing), chapter 1 (Eukaryotic Target Preparation) (P/N 701025, revision 6).
| | Sample_hyb_protocol | Hybridisation of 10ug cRNA was done overnight for 16 hours at 45ºC in a Hybridisation Oven 640 (Affymetrix). The protocol is conducted as described in the Genechip Expression Analysis Technical Manual, section 2 (Eukaryotic Sample and Array Processing), chapter 2 (Eukaryotic Target Hybridization) (P/N 701027, revision 5).
| | Sample_scan_protocol | Arrays were scanned on an Affymetrix 3000 7G scanner, as described in the Genechip Expression Analysis Technical Manual, section 2 (Eukaryotic Sample and Array Processing), chapter 2 (Eukaryotic Arrays: Washing, Staining and Scanning (P/N 701028, revision 5).
| | Sample_data_processing | Expression estimates were calculated using GCRMA (v2.20.0) in Bioconductor, applying the emperical Bayes (EB) model for background estimation.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Guido,,Hooiveld
| | Sample_contact_email | guido.hooiveld@wur.nl
| | Sample_contact_laboratory | Nutrition, Metabolism & Genomics Group
| | Sample_contact_department | Div. Human Nutrition
| | Sample_contact_institute | Wageningen University
| | Sample_contact_address | Bomenweg 2
| | Sample_contact_city | Wageningen
| | Sample_contact_zip/postal_code | NL-6703HD
| | Sample_contact_country | Netherlands
| | Sample_contact_web_link | http://nutrigene.4t.com
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM547nnn/GSM547141/suppl/GSM547141.CEL.gz
| | Sample_series_id | GSE22009
| | Sample_data_row_count | 45101
| | |
|
GSM547142 | GPL1261 |
|
liver_WT_CLP_rep3
|
liver from control (Gp130f/f ) mice, 12 hrs after cecal ligation and puncture
|
tissue: liver
genotype/variation: control mice [Gp130f/f]
treatment: 12 hrs after cecal ligation and puncture
gender: male
age: 8-12 weeks
|
liver from control (Gp130f/f ) mice, 12 hrs after cecal ligation and puncture, replicate 3
|
| Sample_geo_accession | GSM547142
| | Sample_status | Public on May 27 2010
| | Sample_submission_date | May 26 2010
| | Sample_last_update_date | May 27 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | Livers were dissected from control or liver-specific Gp130 knockout mice that were subjected to either cecal ligation and puncture for 12 hrs, or no prior treatment. Liver RNA samples from 3 mice per experimental group were used for microarray analysis.
| | Sample_growth_protocol_ch1 | Male control [gp130f/f] and liver-specific Gp130 knockout [gp130delta(hepa)] mice, aged 8-12 weeks were maintained on standard laboratory chow. Generation of the mice strains has been described in Klein et al. (J Clin Invest. 2005;115(4):860-869; PubMed ID 15761498). Polymicrobial sepsis was induced by cecal ligation and puncture (CLP). Briefly, mice were anesthetized, the cecum was ligated and punctured twice with a 20 Gauge needle. Twelve hours after CLP mice were sacrificed and livers were removed. For control treatment mice were sacrified without any prior treatment.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was prepared from mouse livers using TRIzol reagent and whereafter purified total RNA was isolated using Qiagen RNEasy columns. RNA integrity was checked on chip analysis (Agilent 2100 bioanalyzer, Agilent Technologies, Amsterdam, the Netherlands) according to the manufacturer's instructions. RNA was judged as suitable for array hybridization only if samples exhibited intact bands corresponding to the 18S and 28S ribosomal RNA subunits, and displayed no chromosomal peaks or RNA degradation products (RNA Integrity Number > 8.0).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | The Affymetrix GeneChip RNA One cycle Amplification Kit was used to prepare labelled cRNA from 5 μg of total RNA. The protocol was conducted using the reagents provided by Affymetrix in the One-Cycle cDNA synthesis kit (P/N 900431), One-Cycle IVT labelling kit (P/N 90449) and GeneChip Sample Cleanup Module (P/N 900371). A detailed description can be found in the Genechip Expression Analysis Technical Manual, section 2 (Eukaryotic Sample and Array Processing), chapter 1 (Eukaryotic Target Preparation) (P/N 701025, revision 6).
| | Sample_hyb_protocol | Hybridisation of 10ug cRNA was done overnight for 16 hours at 45ºC in a Hybridisation Oven 640 (Affymetrix). The protocol is conducted as described in the Genechip Expression Analysis Technical Manual, section 2 (Eukaryotic Sample and Array Processing), chapter 2 (Eukaryotic Target Hybridization) (P/N 701027, revision 5).
| | Sample_scan_protocol | Arrays were scanned on an Affymetrix 3000 7G scanner, as described in the Genechip Expression Analysis Technical Manual, section 2 (Eukaryotic Sample and Array Processing), chapter 2 (Eukaryotic Arrays: Washing, Staining and Scanning (P/N 701028, revision 5).
| | Sample_data_processing | Expression estimates were calculated using GCRMA (v2.20.0) in Bioconductor, applying the emperical Bayes (EB) model for background estimation.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Guido,,Hooiveld
| | Sample_contact_email | guido.hooiveld@wur.nl
| | Sample_contact_laboratory | Nutrition, Metabolism & Genomics Group
| | Sample_contact_department | Div. Human Nutrition
| | Sample_contact_institute | Wageningen University
| | Sample_contact_address | Bomenweg 2
| | Sample_contact_city | Wageningen
| | Sample_contact_zip/postal_code | NL-6703HD
| | Sample_contact_country | Netherlands
| | Sample_contact_web_link | http://nutrigene.4t.com
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM547nnn/GSM547142/suppl/GSM547142.CEL.gz
| | Sample_series_id | GSE22009
| | Sample_data_row_count | 45101
| | |
|
GSM547143 | GPL1261 |
|
liver_gp130delta(hepa)_control_rep1
|
liver from liver-specific Gp130 knockout [Gp130delta(hepa)] mice, no prior treatment
|
tissue: liver
genotype/variation: liver-specific Gp130 knockout mice [Gp130delta(hepa)]
treatment: no previous treatment
gender: male
age: 8-12 weeks
|
liver from liver-specific Gp130 knockout [Gp130delta(hepa)] mice, no prior treatment, replicate 1
|
| Sample_geo_accession | GSM547143
| | Sample_status | Public on May 27 2010
| | Sample_submission_date | May 26 2010
| | Sample_last_update_date | May 27 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | Livers were dissected from control or liver-specific Gp130 knockout mice that were subjected to either cecal ligation and puncture for 12 hrs, or no prior treatment. Liver RNA samples from 3 mice per experimental group were used for microarray analysis.
| | Sample_growth_protocol_ch1 | Male control [gp130f/f] and liver-specific Gp130 knockout [gp130delta(hepa)] mice, aged 8-12 weeks were maintained on standard laboratory chow. Generation of the mice strains has been described in Klein et al. (J Clin Invest. 2005;115(4):860-869; PubMed ID 15761498). Polymicrobial sepsis was induced by cecal ligation and puncture (CLP). Briefly, mice were anesthetized, the cecum was ligated and punctured twice with a 20 Gauge needle. Twelve hours after CLP mice were sacrificed and livers were removed. For control treatment mice were sacrified without any prior treatment.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was prepared from mouse livers using TRIzol reagent and whereafter purified total RNA was isolated using Qiagen RNEasy columns. RNA integrity was checked on chip analysis (Agilent 2100 bioanalyzer, Agilent Technologies, Amsterdam, the Netherlands) according to the manufacturer's instructions. RNA was judged as suitable for array hybridization only if samples exhibited intact bands corresponding to the 18S and 28S ribosomal RNA subunits, and displayed no chromosomal peaks or RNA degradation products (RNA Integrity Number > 8.0).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | The Affymetrix GeneChip RNA One cycle Amplification Kit was used to prepare labelled cRNA from 5 μg of total RNA. The protocol was conducted using the reagents provided by Affymetrix in the One-Cycle cDNA synthesis kit (P/N 900431), One-Cycle IVT labelling kit (P/N 90449) and GeneChip Sample Cleanup Module (P/N 900371). A detailed description can be found in the Genechip Expression Analysis Technical Manual, section 2 (Eukaryotic Sample and Array Processing), chapter 1 (Eukaryotic Target Preparation) (P/N 701025, revision 6).
| | Sample_hyb_protocol | Hybridisation of 10ug cRNA was done overnight for 16 hours at 45ºC in a Hybridisation Oven 640 (Affymetrix). The protocol is conducted as described in the Genechip Expression Analysis Technical Manual, section 2 (Eukaryotic Sample and Array Processing), chapter 2 (Eukaryotic Target Hybridization) (P/N 701027, revision 5).
| | Sample_scan_protocol | Arrays were scanned on an Affymetrix 3000 7G scanner, as described in the Genechip Expression Analysis Technical Manual, section 2 (Eukaryotic Sample and Array Processing), chapter 2 (Eukaryotic Arrays: Washing, Staining and Scanning (P/N 701028, revision 5).
| | Sample_data_processing | Expression estimates were calculated using GCRMA (v2.20.0) in Bioconductor, applying the emperical Bayes (EB) model for background estimation.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Guido,,Hooiveld
| | Sample_contact_email | guido.hooiveld@wur.nl
| | Sample_contact_laboratory | Nutrition, Metabolism & Genomics Group
| | Sample_contact_department | Div. Human Nutrition
| | Sample_contact_institute | Wageningen University
| | Sample_contact_address | Bomenweg 2
| | Sample_contact_city | Wageningen
| | Sample_contact_zip/postal_code | NL-6703HD
| | Sample_contact_country | Netherlands
| | Sample_contact_web_link | http://nutrigene.4t.com
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM547nnn/GSM547143/suppl/GSM547143.CEL.gz
| | Sample_series_id | GSE22009
| | Sample_data_row_count | 45101
| | |
|
GSM547144 | GPL1261 |
|
liver_gp130delta(hepa)_control_rep2
|
liver from liver-specific Gp130 knockout [Gp130delta(hepa)] mice, no prior treatment
|
tissue: liver
genotype/variation: liver-specific Gp130 knockout mice [Gp130delta(hepa)]
treatment: no previous treatment
gender: male
age: 8-12 weeks
|
liver from liver-specific Gp130 knockout [Gp130delta(hepa)] mice, no prior treatment, replicate 2
|
| Sample_geo_accession | GSM547144
| | Sample_status | Public on May 27 2010
| | Sample_submission_date | May 26 2010
| | Sample_last_update_date | May 27 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | Livers were dissected from control or liver-specific Gp130 knockout mice that were subjected to either cecal ligation and puncture for 12 hrs, or no prior treatment. Liver RNA samples from 3 mice per experimental group were used for microarray analysis.
| | Sample_growth_protocol_ch1 | Male control [gp130f/f] and liver-specific Gp130 knockout [gp130delta(hepa)] mice, aged 8-12 weeks were maintained on standard laboratory chow. Generation of the mice strains has been described in Klein et al. (J Clin Invest. 2005;115(4):860-869; PubMed ID 15761498). Polymicrobial sepsis was induced by cecal ligation and puncture (CLP). Briefly, mice were anesthetized, the cecum was ligated and punctured twice with a 20 Gauge needle. Twelve hours after CLP mice were sacrificed and livers were removed. For control treatment mice were sacrified without any prior treatment.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was prepared from mouse livers using TRIzol reagent and whereafter purified total RNA was isolated using Qiagen RNEasy columns. RNA integrity was checked on chip analysis (Agilent 2100 bioanalyzer, Agilent Technologies, Amsterdam, the Netherlands) according to the manufacturer's instructions. RNA was judged as suitable for array hybridization only if samples exhibited intact bands corresponding to the 18S and 28S ribosomal RNA subunits, and displayed no chromosomal peaks or RNA degradation products (RNA Integrity Number > 8.0).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | The Affymetrix GeneChip RNA One cycle Amplification Kit was used to prepare labelled cRNA from 5 μg of total RNA. The protocol was conducted using the reagents provided by Affymetrix in the One-Cycle cDNA synthesis kit (P/N 900431), One-Cycle IVT labelling kit (P/N 90449) and GeneChip Sample Cleanup Module (P/N 900371). A detailed description can be found in the Genechip Expression Analysis Technical Manual, section 2 (Eukaryotic Sample and Array Processing), chapter 1 (Eukaryotic Target Preparation) (P/N 701025, revision 6).
| | Sample_hyb_protocol | Hybridisation of 10ug cRNA was done overnight for 16 hours at 45ºC in a Hybridisation Oven 640 (Affymetrix). The protocol is conducted as described in the Genechip Expression Analysis Technical Manual, section 2 (Eukaryotic Sample and Array Processing), chapter 2 (Eukaryotic Target Hybridization) (P/N 701027, revision 5).
| | Sample_scan_protocol | Arrays were scanned on an Affymetrix 3000 7G scanner, as described in the Genechip Expression Analysis Technical Manual, section 2 (Eukaryotic Sample and Array Processing), chapter 2 (Eukaryotic Arrays: Washing, Staining and Scanning (P/N 701028, revision 5).
| | Sample_data_processing | Expression estimates were calculated using GCRMA (v2.20.0) in Bioconductor, applying the emperical Bayes (EB) model for background estimation.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Guido,,Hooiveld
| | Sample_contact_email | guido.hooiveld@wur.nl
| | Sample_contact_laboratory | Nutrition, Metabolism & Genomics Group
| | Sample_contact_department | Div. Human Nutrition
| | Sample_contact_institute | Wageningen University
| | Sample_contact_address | Bomenweg 2
| | Sample_contact_city | Wageningen
| | Sample_contact_zip/postal_code | NL-6703HD
| | Sample_contact_country | Netherlands
| | Sample_contact_web_link | http://nutrigene.4t.com
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM547nnn/GSM547144/suppl/GSM547144.CEL.gz
| | Sample_series_id | GSE22009
| | Sample_data_row_count | 45101
| | |
|
GSM547145 | GPL1261 |
|
liver_gp130delta(hepa)_control_rep3
|
liver from liver-specific Gp130 knockout [Gp130delta(hepa)] mice, no prior treatment
|
tissue: liver
genotype/variation: liver-specific Gp130 knockout mice [Gp130delta(hepa)]
treatment: no previous treatment
gender: male
age: 8-12 weeks
|
liver from liver-specific Gp130 knockout [Gp130delta(hepa)] mice, no prior treatment, replicate 3
|
| Sample_geo_accession | GSM547145
| | Sample_status | Public on May 27 2010
| | Sample_submission_date | May 26 2010
| | Sample_last_update_date | May 27 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | Livers were dissected from control or liver-specific Gp130 knockout mice that were subjected to either cecal ligation and puncture for 12 hrs, or no prior treatment. Liver RNA samples from 3 mice per experimental group were used for microarray analysis.
| | Sample_growth_protocol_ch1 | Male control [gp130f/f] and liver-specific Gp130 knockout [gp130delta(hepa)] mice, aged 8-12 weeks were maintained on standard laboratory chow. Generation of the mice strains has been described in Klein et al. (J Clin Invest. 2005;115(4):860-869; PubMed ID 15761498). Polymicrobial sepsis was induced by cecal ligation and puncture (CLP). Briefly, mice were anesthetized, the cecum was ligated and punctured twice with a 20 Gauge needle. Twelve hours after CLP mice were sacrificed and livers were removed. For control treatment mice were sacrified without any prior treatment.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was prepared from mouse livers using TRIzol reagent and whereafter purified total RNA was isolated using Qiagen RNEasy columns. RNA integrity was checked on chip analysis (Agilent 2100 bioanalyzer, Agilent Technologies, Amsterdam, the Netherlands) according to the manufacturer's instructions. RNA was judged as suitable for array hybridization only if samples exhibited intact bands corresponding to the 18S and 28S ribosomal RNA subunits, and displayed no chromosomal peaks or RNA degradation products (RNA Integrity Number > 8.0).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | The Affymetrix GeneChip RNA One cycle Amplification Kit was used to prepare labelled cRNA from 5 μg of total RNA. The protocol was conducted using the reagents provided by Affymetrix in the One-Cycle cDNA synthesis kit (P/N 900431), One-Cycle IVT labelling kit (P/N 90449) and GeneChip Sample Cleanup Module (P/N 900371). A detailed description can be found in the Genechip Expression Analysis Technical Manual, section 2 (Eukaryotic Sample and Array Processing), chapter 1 (Eukaryotic Target Preparation) (P/N 701025, revision 6).
| | Sample_hyb_protocol | Hybridisation of 10ug cRNA was done overnight for 16 hours at 45ºC in a Hybridisation Oven 640 (Affymetrix). The protocol is conducted as described in the Genechip Expression Analysis Technical Manual, section 2 (Eukaryotic Sample and Array Processing), chapter 2 (Eukaryotic Target Hybridization) (P/N 701027, revision 5).
| | Sample_scan_protocol | Arrays were scanned on an Affymetrix 3000 7G scanner, as described in the Genechip Expression Analysis Technical Manual, section 2 (Eukaryotic Sample and Array Processing), chapter 2 (Eukaryotic Arrays: Washing, Staining and Scanning (P/N 701028, revision 5).
| | Sample_data_processing | Expression estimates were calculated using GCRMA (v2.20.0) in Bioconductor, applying the emperical Bayes (EB) model for background estimation.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Guido,,Hooiveld
| | Sample_contact_email | guido.hooiveld@wur.nl
| | Sample_contact_laboratory | Nutrition, Metabolism & Genomics Group
| | Sample_contact_department | Div. Human Nutrition
| | Sample_contact_institute | Wageningen University
| | Sample_contact_address | Bomenweg 2
| | Sample_contact_city | Wageningen
| | Sample_contact_zip/postal_code | NL-6703HD
| | Sample_contact_country | Netherlands
| | Sample_contact_web_link | http://nutrigene.4t.com
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM547nnn/GSM547145/suppl/GSM547145.CEL.gz
| | Sample_series_id | GSE22009
| | Sample_data_row_count | 45101
| | |
|
GSM547146 | GPL1261 |
|
liver_WT_control_rep1
|
liver from control (Gp130f/f ) mice, no prior treatment
|
tissue: liver
genotype/variation: control mice [Gp130f/f]
treatment: no previous treatment
gender: male
age: 8-12 weeks
|
liver from control (Gp130f/f ) mice, no prior treatment, replicate 1
|
| Sample_geo_accession | GSM547146
| | Sample_status | Public on May 27 2010
| | Sample_submission_date | May 26 2010
| | Sample_last_update_date | May 27 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | Livers were dissected from control or liver-specific Gp130 knockout mice that were subjected to either cecal ligation and puncture for 12 hrs, or no prior treatment. Liver RNA samples from 3 mice per experimental group were used for microarray analysis.
| | Sample_growth_protocol_ch1 | Male control [gp130f/f] and liver-specific Gp130 knockout [gp130delta(hepa)] mice, aged 8-12 weeks were maintained on standard laboratory chow. Generation of the mice strains has been described in Klein et al. (J Clin Invest. 2005;115(4):860-869; PubMed ID 15761498). Polymicrobial sepsis was induced by cecal ligation and puncture (CLP). Briefly, mice were anesthetized, the cecum was ligated and punctured twice with a 20 Gauge needle. Twelve hours after CLP mice were sacrificed and livers were removed. For control treatment mice were sacrified without any prior treatment.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was prepared from mouse livers using TRIzol reagent and whereafter purified total RNA was isolated using Qiagen RNEasy columns. RNA integrity was checked on chip analysis (Agilent 2100 bioanalyzer, Agilent Technologies, Amsterdam, the Netherlands) according to the manufacturer's instructions. RNA was judged as suitable for array hybridization only if samples exhibited intact bands corresponding to the 18S and 28S ribosomal RNA subunits, and displayed no chromosomal peaks or RNA degradation products (RNA Integrity Number > 8.0).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | The Affymetrix GeneChip RNA One cycle Amplification Kit was used to prepare labelled cRNA from 5 μg of total RNA. The protocol was conducted using the reagents provided by Affymetrix in the One-Cycle cDNA synthesis kit (P/N 900431), One-Cycle IVT labelling kit (P/N 90449) and GeneChip Sample Cleanup Module (P/N 900371). A detailed description can be found in the Genechip Expression Analysis Technical Manual, section 2 (Eukaryotic Sample and Array Processing), chapter 1 (Eukaryotic Target Preparation) (P/N 701025, revision 6).
| | Sample_hyb_protocol | Hybridisation of 10ug cRNA was done overnight for 16 hours at 45ºC in a Hybridisation Oven 640 (Affymetrix). The protocol is conducted as described in the Genechip Expression Analysis Technical Manual, section 2 (Eukaryotic Sample and Array Processing), chapter 2 (Eukaryotic Target Hybridization) (P/N 701027, revision 5).
| | Sample_scan_protocol | Arrays were scanned on an Affymetrix 3000 7G scanner, as described in the Genechip Expression Analysis Technical Manual, section 2 (Eukaryotic Sample and Array Processing), chapter 2 (Eukaryotic Arrays: Washing, Staining and Scanning (P/N 701028, revision 5).
| | Sample_data_processing | Expression estimates were calculated using GCRMA (v2.20.0) in Bioconductor, applying the emperical Bayes (EB) model for background estimation.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Guido,,Hooiveld
| | Sample_contact_email | guido.hooiveld@wur.nl
| | Sample_contact_laboratory | Nutrition, Metabolism & Genomics Group
| | Sample_contact_department | Div. Human Nutrition
| | Sample_contact_institute | Wageningen University
| | Sample_contact_address | Bomenweg 2
| | Sample_contact_city | Wageningen
| | Sample_contact_zip/postal_code | NL-6703HD
| | Sample_contact_country | Netherlands
| | Sample_contact_web_link | http://nutrigene.4t.com
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM547nnn/GSM547146/suppl/GSM547146.CEL.gz
| | Sample_series_id | GSE22009
| | Sample_data_row_count | 45101
| | |
|
GSM547147 | GPL1261 |
|
liver_WT_control_rep2
|
liver from control (Gp130f/f ) mice, no prior treatment
|
tissue: liver
genotype/variation: control mice [Gp130f/f]
treatment: no previous treatment
gender: male
age: 8-12 weeks
|
liver from control (Gp130f/f ) mice, no prior treatment, replicate 2
|
| Sample_geo_accession | GSM547147
| | Sample_status | Public on May 27 2010
| | Sample_submission_date | May 26 2010
| | Sample_last_update_date | May 27 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | Livers were dissected from control or liver-specific Gp130 knockout mice that were subjected to either cecal ligation and puncture for 12 hrs, or no prior treatment. Liver RNA samples from 3 mice per experimental group were used for microarray analysis.
| | Sample_growth_protocol_ch1 | Male control [gp130f/f] and liver-specific Gp130 knockout [gp130delta(hepa)] mice, aged 8-12 weeks were maintained on standard laboratory chow. Generation of the mice strains has been described in Klein et al. (J Clin Invest. 2005;115(4):860-869; PubMed ID 15761498). Polymicrobial sepsis was induced by cecal ligation and puncture (CLP). Briefly, mice were anesthetized, the cecum was ligated and punctured twice with a 20 Gauge needle. Twelve hours after CLP mice were sacrificed and livers were removed. For control treatment mice were sacrified without any prior treatment.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was prepared from mouse livers using TRIzol reagent and whereafter purified total RNA was isolated using Qiagen RNEasy columns. RNA integrity was checked on chip analysis (Agilent 2100 bioanalyzer, Agilent Technologies, Amsterdam, the Netherlands) according to the manufacturer's instructions. RNA was judged as suitable for array hybridization only if samples exhibited intact bands corresponding to the 18S and 28S ribosomal RNA subunits, and displayed no chromosomal peaks or RNA degradation products (RNA Integrity Number > 8.0).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | The Affymetrix GeneChip RNA One cycle Amplification Kit was used to prepare labelled cRNA from 5 μg of total RNA. The protocol was conducted using the reagents provided by Affymetrix in the One-Cycle cDNA synthesis kit (P/N 900431), One-Cycle IVT labelling kit (P/N 90449) and GeneChip Sample Cleanup Module (P/N 900371). A detailed description can be found in the Genechip Expression Analysis Technical Manual, section 2 (Eukaryotic Sample and Array Processing), chapter 1 (Eukaryotic Target Preparation) (P/N 701025, revision 6).
| | Sample_hyb_protocol | Hybridisation of 10ug cRNA was done overnight for 16 hours at 45ºC in a Hybridisation Oven 640 (Affymetrix). The protocol is conducted as described in the Genechip Expression Analysis Technical Manual, section 2 (Eukaryotic Sample and Array Processing), chapter 2 (Eukaryotic Target Hybridization) (P/N 701027, revision 5).
| | Sample_scan_protocol | Arrays were scanned on an Affymetrix 3000 7G scanner, as described in the Genechip Expression Analysis Technical Manual, section 2 (Eukaryotic Sample and Array Processing), chapter 2 (Eukaryotic Arrays: Washing, Staining and Scanning (P/N 701028, revision 5).
| | Sample_data_processing | Expression estimates were calculated using GCRMA (v2.20.0) in Bioconductor, applying the emperical Bayes (EB) model for background estimation.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Guido,,Hooiveld
| | Sample_contact_email | guido.hooiveld@wur.nl
| | Sample_contact_laboratory | Nutrition, Metabolism & Genomics Group
| | Sample_contact_department | Div. Human Nutrition
| | Sample_contact_institute | Wageningen University
| | Sample_contact_address | Bomenweg 2
| | Sample_contact_city | Wageningen
| | Sample_contact_zip/postal_code | NL-6703HD
| | Sample_contact_country | Netherlands
| | Sample_contact_web_link | http://nutrigene.4t.com
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM547nnn/GSM547147/suppl/GSM547147.CEL.gz
| | Sample_series_id | GSE22009
| | Sample_data_row_count | 45101
| | |
|
GSM547148 | GPL1261 |
|
liver_WT_control_rep3
|
liver from control (Gp130f/f ) mice, no prior treatment
|
tissue: liver
genotype/variation: control mice [Gp130f/f]
treatment: no previous treatment
gender: male
age: 8-12 weeks
|
liver from control (Gp130f/f ) mice, no prior treatment, replicate 3
|
| Sample_geo_accession | GSM547148
| | Sample_status | Public on May 27 2010
| | Sample_submission_date | May 26 2010
| | Sample_last_update_date | May 27 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | Livers were dissected from control or liver-specific Gp130 knockout mice that were subjected to either cecal ligation and puncture for 12 hrs, or no prior treatment. Liver RNA samples from 3 mice per experimental group were used for microarray analysis.
| | Sample_growth_protocol_ch1 | Male control [gp130f/f] and liver-specific Gp130 knockout [gp130delta(hepa)] mice, aged 8-12 weeks were maintained on standard laboratory chow. Generation of the mice strains has been described in Klein et al. (J Clin Invest. 2005;115(4):860-869; PubMed ID 15761498). Polymicrobial sepsis was induced by cecal ligation and puncture (CLP). Briefly, mice were anesthetized, the cecum was ligated and punctured twice with a 20 Gauge needle. Twelve hours after CLP mice were sacrificed and livers were removed. For control treatment mice were sacrified without any prior treatment.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was prepared from mouse livers using TRIzol reagent and whereafter purified total RNA was isolated using Qiagen RNEasy columns. RNA integrity was checked on chip analysis (Agilent 2100 bioanalyzer, Agilent Technologies, Amsterdam, the Netherlands) according to the manufacturer's instructions. RNA was judged as suitable for array hybridization only if samples exhibited intact bands corresponding to the 18S and 28S ribosomal RNA subunits, and displayed no chromosomal peaks or RNA degradation products (RNA Integrity Number > 8.0).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | The Affymetrix GeneChip RNA One cycle Amplification Kit was used to prepare labelled cRNA from 5 μg of total RNA. The protocol was conducted using the reagents provided by Affymetrix in the One-Cycle cDNA synthesis kit (P/N 900431), One-Cycle IVT labelling kit (P/N 90449) and GeneChip Sample Cleanup Module (P/N 900371). A detailed description can be found in the Genechip Expression Analysis Technical Manual, section 2 (Eukaryotic Sample and Array Processing), chapter 1 (Eukaryotic Target Preparation) (P/N 701025, revision 6).
| | Sample_hyb_protocol | Hybridisation of 10ug cRNA was done overnight for 16 hours at 45ºC in a Hybridisation Oven 640 (Affymetrix). The protocol is conducted as described in the Genechip Expression Analysis Technical Manual, section 2 (Eukaryotic Sample and Array Processing), chapter 2 (Eukaryotic Target Hybridization) (P/N 701027, revision 5).
| | Sample_scan_protocol | Arrays were scanned on an Affymetrix 3000 7G scanner, as described in the Genechip Expression Analysis Technical Manual, section 2 (Eukaryotic Sample and Array Processing), chapter 2 (Eukaryotic Arrays: Washing, Staining and Scanning (P/N 701028, revision 5).
| | Sample_data_processing | Expression estimates were calculated using GCRMA (v2.20.0) in Bioconductor, applying the emperical Bayes (EB) model for background estimation.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Guido,,Hooiveld
| | Sample_contact_email | guido.hooiveld@wur.nl
| | Sample_contact_laboratory | Nutrition, Metabolism & Genomics Group
| | Sample_contact_department | Div. Human Nutrition
| | Sample_contact_institute | Wageningen University
| | Sample_contact_address | Bomenweg 2
| | Sample_contact_city | Wageningen
| | Sample_contact_zip/postal_code | NL-6703HD
| | Sample_contact_country | Netherlands
| | Sample_contact_web_link | http://nutrigene.4t.com
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM547nnn/GSM547148/suppl/GSM547148.CEL.gz
| | Sample_series_id | GSE22009
| | Sample_data_row_count | 45101
| | |
|
| |
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