Result

Search results for the GEO ID: GSE11484

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Title

Source name

Description

Characteristics

GSM289098

GPL1261

mouse_islets_ctrl_01

Pancreatic islets, control, 01

disease model: Conditional beta cell specific KO mouse model using RIP2-Cre and Vhlh(fl/fl citation(s): Herrera PL 2000 and Haase VH et al. 2001 gender: male age: 26 weeks genotype/variation: control

mouse_islets_ctrl_01

Sample_geo_accession	GSM289098
Sample_status	Public on Nov 15 2008
Sample_submission_date	May 16 2008
Sample_last_update_date	Mar 21 2011
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Stratagene MicroRNA kit
Sample_label_ch1	biotin
Sample_label_protocol_ch1	The quality of the isolated RNA was determined with a NanoDrop ND 1000 (NanoDrop Technologies, Delaware, USA) and a Bioanalyzer 2100 (Agilent, Waldbronn, Germany). Only those samples with a 260 nm/280 nm ratio between 1.8–2.1 and a 28S/18S ratio within 1.5–2 were further processed. Total RNA samples (30 ng) were reverse-transcribed into double-stranded cDNA with Two-Cycle cDNA Synthesis Kit (Affymetrix Inc., P/N 900494, Santa Clara, CA). The double-stranded cDNA was purified using a Sample Cleanup Module (Affymetrix Inc., P/N 900371, Santa Clara, CA). The purified double-stranded cDNA were in vitro transcribed in presence of biotin-labeled nucleotides using a IVT Labeling Kit (Affymetrix Inc., P/N 900449, Santa Clara, CA). The biotinylated cRNA was purified using a Sample Cleanup Module (Affymetrix Inc., P/N 900371, Santa Clara, CA) and its quality and quantity was determined using NanoDrop ND 1000 and Bioanalyzer 2100.
Sample_hyb_protocol	Biotin-labeled cRNA samples (15 µg) were fragmented randomly to 35–200 bp at 94°C in Fragmentation Buffer (Affymetrix Inc., P/N 900371, Santa Clara, CA) and were mixed in 300 µl of hybridization buffer containing a hybridization Control cRNA and Control Oligo B2 control (Affymetrix Inc., P/N 900454, Santa Clara, CA), 0.1 mg/ml herring sperm DNA and 0.5 mg/ml acetylated bovine serum albumin in 2-(4-morpholino)-ethane sulfonic acid (MES) buffer, pH 6.7, before hybridization to GeneChip® Mouse Genome 430 2.0 arrays for 16 h at 45°C. Arrays were then washed using an Affymetrix Fluidics Station 450 EukGE-WS2v5_450 protocol.
Sample_scan_protocol	An Affymetrix GeneChip Scanner 3000 (Affymetrix Inc., Santa Clara, CA) was used to measure the fluorescent intensity emitted by the labeled target.
Sample_data_processing	Data processing was performed using the Affymetrix GCOS 1.4 software (Affymetrix Inc., Santa Clara, CA). After hybridization and scanning, probe cell intensities were calculated and summarized for the respective probe sets by means of the MAS5 algorithm (Hubbell et al 2002). To compare the expression values of the genes from chip to chip, global scaling was performed, which resulted in the normalization of the trimmed mean of each chip to a target intensity (TGT value) of 500 as detailed in the statistical algorithms description document of Affymetrix (2002). Quality control measures were considered before performing the statistical analysis. These included adequate scaling factors (between 1 and 3 for all samples) and appropriate numbers of present calls calculated by application of a signed-rank call algorithm (Liu et al., 2002). The efficiency of the labeling reaction and the hybridization performance was controlled with the following parameters: Present calls and optimal 3' /5' hybridization ratios (around 1) for the housekeeping genes, for the poly A spike in controls and the prokaryotic control.
Sample_platform_id	GPL1261
Sample_contact_name	Jens,,Zehetner
Sample_contact_email	jens.zehetner@cell.biol.ethz.ch
Sample_contact_laboratory	HPM
Sample_contact_department	Cell Biology
Sample_contact_institute	ETH Zurich
Sample_contact_address	Schafmattstrasse 18
Sample_contact_city	Zurich
Sample_contact_state	Zurich
Sample_contact_zip/postal_code	8093
Sample_contact_country	Switzerland
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM289nnn/GSM289098/suppl/GSM289098.CEL.gz
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM289nnn/GSM289098/suppl/GSM289098.CHP.gz
Sample_series_id	GSE11484
Sample_data_row_count	45101

GSM289160

GPL1261

mouse_islets_ctrl_02

Pancreatic islets, control, 02

disease model: Conditional beta cell specific KO mouse model using RIP2-Cre and Vhlh(fl/fl citation(s): Herrera PL 2000 and Haase VH et al. 2001 gender: female age: 20 weeks genotype/variation: control

mouse_islets_ctrl_02

Sample_geo_accession	GSM289160
Sample_status	Public on Nov 15 2008
Sample_submission_date	May 16 2008
Sample_last_update_date	Mar 21 2011
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Stratagene MicroRNA kit
Sample_label_ch1	biotin
Sample_label_protocol_ch1	The quality of the isolated RNA was determined with a NanoDrop ND 1000 (NanoDrop Technologies, Delaware, USA) and a Bioanalyzer 2100 (Agilent, Waldbronn, Germany). Only those samples with a 260 nm/280 nm ratio between 1.8–2.1 and a 28S/18S ratio within 1.5–2 were further processed. Total RNA samples (30 ng) were reverse-transcribed into double-stranded cDNA with Two-Cycle cDNA Synthesis Kit (Affymetrix Inc., P/N 900494, Santa Clara, CA). The double-stranded cDNA was purified using a Sample Cleanup Module (Affymetrix Inc., P/N 900371, Santa Clara, CA). The purified double-stranded cDNA were in vitro transcribed in presence of biotin-labeled nucleotides using a IVT Labeling Kit (Affymetrix Inc., P/N 900449, Santa Clara, CA). The biotinylated cRNA was purified using a Sample Cleanup Module (Affymetrix Inc., P/N 900371, Santa Clara, CA) and its quality and quantity was determined using NanoDrop ND 1000 and Bioanalyzer 2100.
Sample_hyb_protocol	Biotin-labeled cRNA samples (15 µg) were fragmented randomly to 35–200 bp at 94°C in Fragmentation Buffer (Affymetrix Inc., P/N 900371, Santa Clara, CA) and were mixed in 300 µl of hybridization buffer containing a hybridization Control cRNA and Control Oligo B2 control (Affymetrix Inc., P/N 900454, Santa Clara, CA), 0.1 mg/ml herring sperm DNA and 0.5 mg/ml acetylated bovine serum albumin in 2-(4-morpholino)-ethane sulfonic acid (MES) buffer, pH 6.7, before hybridization to GeneChip® Mouse Genome 430 2.0 arrays for 16 h at 45°C. Arrays were then washed using an Affymetrix Fluidics Station 450 EukGE-WS2v5_450 protocol.
Sample_scan_protocol	An Affymetrix GeneChip Scanner 3000 (Affymetrix Inc., Santa Clara, CA) was used to measure the fluorescent intensity emitted by the labeled target.
Sample_data_processing	Data processing was performed using the Affymetrix GCOS 1.4 software (Affymetrix Inc., Santa Clara, CA). After hybridization and scanning, probe cell intensities were calculated and summarized for the respective probe sets by means of the MAS5 algorithm (Hubbell et al 2002). To compare the expression values of the genes from chip to chip, global scaling was performed, which resulted in the normalization of the trimmed mean of each chip to a target intensity (TGT value) of 500 as detailed in the statistical algorithms description document of Affymetrix (2002). Quality control measures were considered before performing the statistical analysis. These included adequate scaling factors (between 1 and 3 for all samples) and appropriate numbers of present calls calculated by application of a signed-rank call algorithm (Liu et al., 2002). The efficiency of the labeling reaction and the hybridization performance was controlled with the following parameters: Present calls and optimal 3' /5' hybridization ratios (around 1) for the housekeeping genes, for the poly A spike in controls and the prokaryotic control.
Sample_platform_id	GPL1261
Sample_contact_name	Jens,,Zehetner
Sample_contact_email	jens.zehetner@cell.biol.ethz.ch
Sample_contact_laboratory	HPM
Sample_contact_department	Cell Biology
Sample_contact_institute	ETH Zurich
Sample_contact_address	Schafmattstrasse 18
Sample_contact_city	Zurich
Sample_contact_state	Zurich
Sample_contact_zip/postal_code	8093
Sample_contact_country	Switzerland
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM289nnn/GSM289160/suppl/GSM289160.CEL.gz
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM289nnn/GSM289160/suppl/GSM289160.CHP.gz
Sample_series_id	GSE11484
Sample_data_row_count	45101

GSM289161

GPL1261

mouse_islets_ctrl_03

Pancreatic islets, control, 03

disease model: Conditional beta cell specific KO mouse model using RIP2-Cre and Vhlh(fl/fl citation(s): Herrera PL 2000 and Haase VH et al. 2001 gender: male age: 18 weeks genotype/variation: control

mouse_islets_ctrl_03

Sample_geo_accession	GSM289161
Sample_status	Public on Nov 15 2008
Sample_submission_date	May 16 2008
Sample_last_update_date	Mar 21 2011
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Stratagene MicroRNA kit
Sample_label_ch1	biotin
Sample_label_protocol_ch1	The quality of the isolated RNA was determined with a NanoDrop ND 1000 (NanoDrop Technologies, Delaware, USA) and a Bioanalyzer 2100 (Agilent, Waldbronn, Germany). Only those samples with a 260 nm/280 nm ratio between 1.8–2.1 and a 28S/18S ratio within 1.5–2 were further processed. Total RNA samples (30 ng) were reverse-transcribed into double-stranded cDNA with Two-Cycle cDNA Synthesis Kit (Affymetrix Inc., P/N 900494, Santa Clara, CA). The double-stranded cDNA was purified using a Sample Cleanup Module (Affymetrix Inc., P/N 900371, Santa Clara, CA). The purified double-stranded cDNA were in vitro transcribed in presence of biotin-labeled nucleotides using a IVT Labeling Kit (Affymetrix Inc., P/N 900449, Santa Clara, CA). The biotinylated cRNA was purified using a Sample Cleanup Module (Affymetrix Inc., P/N 900371, Santa Clara, CA) and its quality and quantity was determined using NanoDrop ND 1000 and Bioanalyzer 2100.
Sample_hyb_protocol	Biotin-labeled cRNA samples (15 µg) were fragmented randomly to 35–200 bp at 94°C in Fragmentation Buffer (Affymetrix Inc., P/N 900371, Santa Clara, CA) and were mixed in 300 µl of hybridization buffer containing a hybridization Control cRNA and Control Oligo B2 control (Affymetrix Inc., P/N 900454, Santa Clara, CA), 0.1 mg/ml herring sperm DNA and 0.5 mg/ml acetylated bovine serum albumin in 2-(4-morpholino)-ethane sulfonic acid (MES) buffer, pH 6.7, before hybridization to GeneChip® Mouse Genome 430 2.0 arrays for 16 h at 45°C. Arrays were then washed using an Affymetrix Fluidics Station 450 EukGE-WS2v5_450 protocol.
Sample_scan_protocol	An Affymetrix GeneChip Scanner 3000 (Affymetrix Inc., Santa Clara, CA) was used to measure the fluorescent intensity emitted by the labeled target.
Sample_data_processing	Data processing was performed using the Affymetrix GCOS 1.4 software (Affymetrix Inc., Santa Clara, CA). After hybridization and scanning, probe cell intensities were calculated and summarized for the respective probe sets by means of the MAS5 algorithm (Hubbell et al 2002). To compare the expression values of the genes from chip to chip, global scaling was performed, which resulted in the normalization of the trimmed mean of each chip to a target intensity (TGT value) of 500 as detailed in the statistical algorithms description document of Affymetrix (2002). Quality control measures were considered before performing the statistical analysis. These included adequate scaling factors (between 1 and 3 for all samples) and appropriate numbers of present calls calculated by application of a signed-rank call algorithm (Liu et al., 2002). The efficiency of the labeling reaction and the hybridization performance was controlled with the following parameters: Present calls and optimal 3' /5' hybridization ratios (around 1) for the housekeeping genes, for the poly A spike in controls and the prokaryotic control.
Sample_platform_id	GPL1261
Sample_contact_name	Jens,,Zehetner
Sample_contact_email	jens.zehetner@cell.biol.ethz.ch
Sample_contact_laboratory	HPM
Sample_contact_department	Cell Biology
Sample_contact_institute	ETH Zurich
Sample_contact_address	Schafmattstrasse 18
Sample_contact_city	Zurich
Sample_contact_state	Zurich
Sample_contact_zip/postal_code	8093
Sample_contact_country	Switzerland
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM289nnn/GSM289161/suppl/GSM289161.CEL.gz
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM289nnn/GSM289161/suppl/GSM289161.CHP.gz
Sample_series_id	GSE11484
Sample_data_row_count	45101

GSM289162

GPL1261

mouse_islets_VhlhKO_01

Pancreatic islets, VhlhKO, 01

disease model: Conditional beta cell specific KO mouse model using RIP2-Cre and Vhlh(fl/fl citation(s): Herrera PL 2000 and Haase VH et al. 2001 gender: male age: 26 weeks genotype/variation: VhlhKO

mouse_islets_VhlhKO_01

Sample_geo_accession	GSM289162
Sample_status	Public on Nov 15 2008
Sample_submission_date	May 16 2008
Sample_last_update_date	Mar 21 2011
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Stratagene MicroRNA kit
Sample_label_ch1	biotin
Sample_label_protocol_ch1	The quality of the isolated RNA was determined with a NanoDrop ND 1000 (NanoDrop Technologies, Delaware, USA) and a Bioanalyzer 2100 (Agilent, Waldbronn, Germany). Only those samples with a 260 nm/280 nm ratio between 1.8–2.1 and a 28S/18S ratio within 1.5–2 were further processed. Total RNA samples (30 ng) were reverse-transcribed into double-stranded cDNA with Two-Cycle cDNA Synthesis Kit (Affymetrix Inc., P/N 900494, Santa Clara, CA). The double-stranded cDNA was purified using a Sample Cleanup Module (Affymetrix Inc., P/N 900371, Santa Clara, CA). The purified double-stranded cDNA were in vitro transcribed in presence of biotin-labeled nucleotides using a IVT Labeling Kit (Affymetrix Inc., P/N 900449, Santa Clara, CA). The biotinylated cRNA was purified using a Sample Cleanup Module (Affymetrix Inc., P/N 900371, Santa Clara, CA) and its quality and quantity was determined using NanoDrop ND 1000 and Bioanalyzer 2100.
Sample_hyb_protocol	Biotin-labeled cRNA samples (15 µg) were fragmented randomly to 35–200 bp at 94°C in Fragmentation Buffer (Affymetrix Inc., P/N 900371, Santa Clara, CA) and were mixed in 300 µl of hybridization buffer containing a hybridization Control cRNA and Control Oligo B2 control (Affymetrix Inc., P/N 900454, Santa Clara, CA), 0.1 mg/ml herring sperm DNA and 0.5 mg/ml acetylated bovine serum albumin in 2-(4-morpholino)-ethane sulfonic acid (MES) buffer, pH 6.7, before hybridization to GeneChip® Mouse Genome 430 2.0 arrays for 16 h at 45°C. Arrays were then washed using an Affymetrix Fluidics Station 450 EukGE-WS2v5_450 protocol.
Sample_scan_protocol	An Affymetrix GeneChip Scanner 3000 (Affymetrix Inc., Santa Clara, CA) was used to measure the fluorescent intensity emitted by the labeled target.
Sample_data_processing	Data processing was performed using the Affymetrix GCOS 1.4 software (Affymetrix Inc., Santa Clara, CA). After hybridization and scanning, probe cell intensities were calculated and summarized for the respective probe sets by means of the MAS5 algorithm (Hubbell et al 2002). To compare the expression values of the genes from chip to chip, global scaling was performed, which resulted in the normalization of the trimmed mean of each chip to a target intensity (TGT value) of 500 as detailed in the statistical algorithms description document of Affymetrix (2002). Quality control measures were considered before performing the statistical analysis. These included adequate scaling factors (between 1 and 3 for all samples) and appropriate numbers of present calls calculated by application of a signed-rank call algorithm (Liu et al., 2002). The efficiency of the labeling reaction and the hybridization performance was controlled with the following parameters: Present calls and optimal 3' /5' hybridization ratios (around 1) for the housekeeping genes, for the poly A spike in controls and the prokaryotic control.
Sample_platform_id	GPL1261
Sample_contact_name	Jens,,Zehetner
Sample_contact_email	jens.zehetner@cell.biol.ethz.ch
Sample_contact_laboratory	HPM
Sample_contact_department	Cell Biology
Sample_contact_institute	ETH Zurich
Sample_contact_address	Schafmattstrasse 18
Sample_contact_city	Zurich
Sample_contact_state	Zurich
Sample_contact_zip/postal_code	8093
Sample_contact_country	Switzerland
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM289nnn/GSM289162/suppl/GSM289162.CEL.gz
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM289nnn/GSM289162/suppl/GSM289162.CHP.gz
Sample_series_id	GSE11484
Sample_data_row_count	45101

GSM289163

GPL1261

mouse_islets_VhlhKO_02

Pancreatic islets, VhlhKO, 02

mouse_islets_VhlhKO_02

Sample_geo_accession	GSM289163
Sample_status	Public on Nov 15 2008
Sample_submission_date	May 16 2008
Sample_last_update_date	Mar 21 2011
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Stratagene MicroRNA kit
Sample_label_ch1	biotin
Sample_label_protocol_ch1	The quality of the isolated RNA was determined with a NanoDrop ND 1000 (NanoDrop Technologies, Delaware, USA) and a Bioanalyzer 2100 (Agilent, Waldbronn, Germany). Only those samples with a 260 nm/280 nm ratio between 1.8–2.1 and a 28S/18S ratio within 1.5–2 were further processed. Total RNA samples (30 ng) were reverse-transcribed into double-stranded cDNA with Two-Cycle cDNA Synthesis Kit (Affymetrix Inc., P/N 900494, Santa Clara, CA). The double-stranded cDNA was purified using a Sample Cleanup Module (Affymetrix Inc., P/N 900371, Santa Clara, CA). The purified double-stranded cDNA were in vitro transcribed in presence of biotin-labeled nucleotides using a IVT Labeling Kit (Affymetrix Inc., P/N 900449, Santa Clara, CA). The biotinylated cRNA was purified using a Sample Cleanup Module (Affymetrix Inc., P/N 900371, Santa Clara, CA) and its quality and quantity was determined using NanoDrop ND 1000 and Bioanalyzer 2100.
Sample_hyb_protocol	Biotin-labeled cRNA samples (15 µg) were fragmented randomly to 35–200 bp at 94°C in Fragmentation Buffer (Affymetrix Inc., P/N 900371, Santa Clara, CA) and were mixed in 300 µl of hybridization buffer containing a hybridization Control cRNA and Control Oligo B2 control (Affymetrix Inc., P/N 900454, Santa Clara, CA), 0.1 mg/ml herring sperm DNA and 0.5 mg/ml acetylated bovine serum albumin in 2-(4-morpholino)-ethane sulfonic acid (MES) buffer, pH 6.7, before hybridization to GeneChip® Mouse Genome 430 2.0 arrays for 16 h at 45°C. Arrays were then washed using an Affymetrix Fluidics Station 450 EukGE-WS2v5_450 protocol.
Sample_scan_protocol	An Affymetrix GeneChip Scanner 3000 (Affymetrix Inc., Santa Clara, CA) was used to measure the fluorescent intensity emitted by the labeled target.
Sample_data_processing	Data processing was performed using the Affymetrix GCOS 1.4 software (Affymetrix Inc., Santa Clara, CA). After hybridization and scanning, probe cell intensities were calculated and summarized for the respective probe sets by means of the MAS5 algorithm (Hubbell et al 2002). To compare the expression values of the genes from chip to chip, global scaling was performed, which resulted in the normalization of the trimmed mean of each chip to a target intensity (TGT value) of 500 as detailed in the statistical algorithms description document of Affymetrix (2002). Quality control measures were considered before performing the statistical analysis. These included adequate scaling factors (between 1 and 3 for all samples) and appropriate numbers of present calls calculated by application of a signed-rank call algorithm (Liu et al., 2002). The efficiency of the labeling reaction and the hybridization performance was controlled with the following parameters: Present calls and optimal 3' /5' hybridization ratios (around 1) for the housekeeping genes, for the poly A spike in controls and the prokaryotic control.
Sample_platform_id	GPL1261
Sample_contact_name	Jens,,Zehetner
Sample_contact_email	jens.zehetner@cell.biol.ethz.ch
Sample_contact_laboratory	HPM
Sample_contact_department	Cell Biology
Sample_contact_institute	ETH Zurich
Sample_contact_address	Schafmattstrasse 18
Sample_contact_city	Zurich
Sample_contact_state	Zurich
Sample_contact_zip/postal_code	8093
Sample_contact_country	Switzerland
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM289nnn/GSM289163/suppl/GSM289163.CEL.gz
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM289nnn/GSM289163/suppl/GSM289163.CHP.gz
Sample_series_id	GSE11484
Sample_data_row_count	45101

GSM289164

GPL1261

mouse_islets_VhlhKO_03

Pancreatic islets, VhlhKO, 03

disease model: Conditional beta cell specific KO mouse model using RIP2-Cre and Vhlh(fl/fl citation(s): Herrera PL 2000 and Haase VH et al. 2001 gender: male age: 18 weeks genotype/variation: VhlhKO

mouse_islets_VhlhKO_03

Sample_geo_accession	GSM289164
Sample_status	Public on Nov 15 2008
Sample_submission_date	May 16 2008
Sample_last_update_date	Mar 21 2011
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Stratagene MicroRNA kit
Sample_label_ch1	biotin
Sample_label_protocol_ch1	The quality of the isolated RNA was determined with a NanoDrop ND 1000 (NanoDrop Technologies, Delaware, USA) and a Bioanalyzer 2100 (Agilent, Waldbronn, Germany). Only those samples with a 260 nm/280 nm ratio between 1.8–2.1 and a 28S/18S ratio within 1.5–2 were further processed. Total RNA samples (30 ng) were reverse-transcribed into double-stranded cDNA with Two-Cycle cDNA Synthesis Kit (Affymetrix Inc., P/N 900494, Santa Clara, CA). The double-stranded cDNA was purified using a Sample Cleanup Module (Affymetrix Inc., P/N 900371, Santa Clara, CA). The purified double-stranded cDNA were in vitro transcribed in presence of biotin-labeled nucleotides using a IVT Labeling Kit (Affymetrix Inc., P/N 900449, Santa Clara, CA). The biotinylated cRNA was purified using a Sample Cleanup Module (Affymetrix Inc., P/N 900371, Santa Clara, CA) and its quality and quantity was determined using NanoDrop ND 1000 and Bioanalyzer 2100.
Sample_hyb_protocol	Biotin-labeled cRNA samples (15 µg) were fragmented randomly to 35–200 bp at 94°C in Fragmentation Buffer (Affymetrix Inc., P/N 900371, Santa Clara, CA) and were mixed in 300 µl of hybridization buffer containing a hybridization Control cRNA and Control Oligo B2 control (Affymetrix Inc., P/N 900454, Santa Clara, CA), 0.1 mg/ml herring sperm DNA and 0.5 mg/ml acetylated bovine serum albumin in 2-(4-morpholino)-ethane sulfonic acid (MES) buffer, pH 6.7, before hybridization to GeneChip® Mouse Genome 430 2.0 arrays for 16 h at 45°C. Arrays were then washed using an Affymetrix Fluidics Station 450 EukGE-WS2v5_450 protocol.
Sample_scan_protocol	An Affymetrix GeneChip Scanner 3000 (Affymetrix Inc., Santa Clara, CA) was used to measure the fluorescent intensity emitted by the labeled target.
Sample_data_processing	Data processing was performed using the Affymetrix GCOS 1.4 software (Affymetrix Inc., Santa Clara, CA). After hybridization and scanning, probe cell intensities were calculated and summarized for the respective probe sets by means of the MAS5 algorithm (Hubbell et al 2002). To compare the expression values of the genes from chip to chip, global scaling was performed, which resulted in the normalization of the trimmed mean of each chip to a target intensity (TGT value) of 500 as detailed in the statistical algorithms description document of Affymetrix (2002). Quality control measures were considered before performing the statistical analysis. These included adequate scaling factors (between 1 and 3 for all samples) and appropriate numbers of present calls calculated by application of a signed-rank call algorithm (Liu et al., 2002). The efficiency of the labeling reaction and the hybridization performance was controlled with the following parameters: Present calls and optimal 3' /5' hybridization ratios (around 1) for the housekeeping genes, for the poly A spike in controls and the prokaryotic control.
Sample_platform_id	GPL1261
Sample_contact_name	Jens,,Zehetner
Sample_contact_email	jens.zehetner@cell.biol.ethz.ch
Sample_contact_laboratory	HPM
Sample_contact_department	Cell Biology
Sample_contact_institute	ETH Zurich
Sample_contact_address	Schafmattstrasse 18
Sample_contact_city	Zurich
Sample_contact_state	Zurich
Sample_contact_zip/postal_code	8093
Sample_contact_country	Switzerland
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM289nnn/GSM289164/suppl/GSM289164.CEL.gz
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM289nnn/GSM289164/suppl/GSM289164.CHP.gz
Sample_series_id	GSE11484
Sample_data_row_count	45101

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