Result

Search results for the GEO ID: GSE30147

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Description

Characteristics

GSM746613

GPL1355

Rosiglitazone treated, 9 week_old, biological rep1

Rosiglitazone treated ZDF rat islets at 9 weeks of age

strain: Zucker Diabetic Fatty Rat gender: male age: 9 weeks tissue: pancreatic islets

Gene expression data from Rosiglitazone treated (weeks 5-9) ZDF rat at 9 weeks of age.

Sample_geo_accession	GSM746613
Sample_status	Public on Jun 21 2013
Sample_submission_date	Jun 22 2011
Sample_last_update_date	Jun 21 2013
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Rattus norvegicus
Sample_taxid_ch1	10116
Sample_treatment_protocol_ch1	Five-week old ZDF (fa/fa) animals (n=24) were purchased from Charles River Laboratories (Wilmington, MA). Following 48 hours of acclimation, animals were randomized into one of three groups: rosiglitazone treated (RT), rosiglitazone withdrawal (RW), or untreated controls (UC) and sacrificed at either 9, 11, 13, or 15 weeks of age. All animals were fed the Purina 5008 diet. Rosiglitazone was administered in the diet as powdered Avandia tablets (3mg rosiglitazone/kg body weight).
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Total RNA was isolated from 20-30 mg of islets using the RNEasy kit according to the manufacturer’s instructions (Qiagen, Valencia, CA). Equal amounts of RNA from each of 3 replicates were reverse transcribed to cDNA after the purity and concentration of RNA samples were determined from OD260/280 readings using a dual beam UV spectrophotometer and RNA integrity was determined by capillary electrophoresis using the RNA 6000 Nano Lab-on-a-Chip kit and the Bioanalyzer 2100 (Agilent Technologies).
Sample_label_ch1	biotin
Sample_label_protocol_ch1	cRNA was synthesized and labeled with biotinylated UTP and CTP by in vitro transcription using the T7 promoter-coupled double stranded cDNA as template and the Bioarray™ HighYield™ RNA Transcript Labeling Kit (ENZO Diagnostics Inc.).
Sample_hyb_protocol	Labeled cRNA (15.0 ug) was fragmented by Magnesium ion-mediated hydrolysis and hybridized for 16hr at 45oC to Affymetrix GeneChip Rat Genome 230 2.0 arrays, which contain probes for over 31,000 transcripts representing approximately 28,700 annotated rat genes and expressed sequence tags (ESTs) (Affymetrix, Santa Clara, CA). Arrays were washed and stained using a Fluidics Station 450 (Affymetrix). The arrays were stained with phycoerythrein-conjugated streptavidin (Invitrogen, Carlsbad, CA).
Sample_scan_protocol	Fluorescence intensities were determined using a GCS 3000 7G high-resolution confocal laser scanner (Affymetrix). The scanned images were analyzed using programs resident in AGCC and Expression Console (Affymetrix). Quality control metrics for cRNA integrity, sample loading, and variations in staining were determined by MAS 5.0 statistical algorithms.
Sample_data_processing	Signal values were generated by the RMA method and Detection p-values were generated by MAS 5.0. Probe sets exhibiting significant differential expression were identified using GeneMaths XT (Applied Maths, Austin TX), based on the following criteria: 1) MAS5.0 detection p-values ≤ 0.05 for all samples in at least one experimental group, 2) ANOVA p-value ≤ 0.05, 3) Absolute Signal log ratio ≥ 1.0 and independent t-test p-value ≤ 0.05 for at least one pair wise comparison versus the control group. Unsupervised hierarchical clustering and heat map generation were performed in GeneMaths XT following row mean centering of log2 transformed RMA signal values; probe set clustering was performed by the Unweighted Pair Group Method using Arithmetic averages (UPGMA) using Pearson correlation as the similarity metric. Gene annotation, gene ontology information and biochemical pathway information were obtained from the Database for Annotation, Visualization and Integrated Discovery (DAVID) v6.7 from the National Institute of Allergy and Infectious Diseases (NIAID), at the National Institutes of Health (NIH).
Sample_platform_id	GPL1355
Sample_contact_name	Cyrus,Farrokh,Khambatta
Sample_contact_laboratory	Hellerstein
Sample_contact_department	Nutritional Sciences
Sample_contact_institute	University of California at Berkeley
Sample_contact_address	309 Morgan Hall
Sample_contact_city	Berkeley
Sample_contact_state	CA
Sample_contact_zip/postal_code	94720
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM746nnn/GSM746613/suppl/GSM746613_MX0001-230_2.CEL.gz
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM746nnn/GSM746613/suppl/GSM746613_MX0001-230_2.rma.chp.gz
Sample_series_id	GSE30147
Sample_data_row_count	31099

GSM746614

GPL1355

Rosiglitazone treated, 9 week_old, biological rep2

Rosiglitazone treated ZDF rat islets at 9 weeks of age

strain: Zucker Diabetic Fatty Rat gender: male age: 9 weeks tissue: pancreatic islets

Gene expression data from Rosiglitazone treated (weeks 5-9) ZDF rat at 9 weeks of age.

Sample_geo_accession	GSM746614
Sample_status	Public on Jun 21 2013
Sample_submission_date	Jun 22 2011
Sample_last_update_date	Jun 21 2013
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Rattus norvegicus
Sample_taxid_ch1	10116
Sample_treatment_protocol_ch1	Five-week old ZDF (fa/fa) animals (n=24) were purchased from Charles River Laboratories (Wilmington, MA). Following 48 hours of acclimation, animals were randomized into one of three groups: rosiglitazone treated (RT), rosiglitazone withdrawal (RW), or untreated controls (UC) and sacrificed at either 9, 11, 13, or 15 weeks of age. All animals were fed the Purina 5008 diet. Rosiglitazone was administered in the diet as powdered Avandia tablets (3mg rosiglitazone/kg body weight).
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Total RNA was isolated from 20-30 mg of islets using the RNEasy kit according to the manufacturer’s instructions (Qiagen, Valencia, CA). Equal amounts of RNA from each of 3 replicates were reverse transcribed to cDNA after the purity and concentration of RNA samples were determined from OD260/280 readings using a dual beam UV spectrophotometer and RNA integrity was determined by capillary electrophoresis using the RNA 6000 Nano Lab-on-a-Chip kit and the Bioanalyzer 2100 (Agilent Technologies).
Sample_label_ch1	biotin
Sample_label_protocol_ch1	cRNA was synthesized and labeled with biotinylated UTP and CTP by in vitro transcription using the T7 promoter-coupled double stranded cDNA as template and the Bioarray™ HighYield™ RNA Transcript Labeling Kit (ENZO Diagnostics Inc.).
Sample_hyb_protocol	Labeled cRNA (15.0 ug) was fragmented by Magnesium ion-mediated hydrolysis and hybridized for 16hr at 45oC to Affymetrix GeneChip Rat Genome 230 2.0 arrays, which contain probes for over 31,000 transcripts representing approximately 28,700 annotated rat genes and expressed sequence tags (ESTs) (Affymetrix, Santa Clara, CA). Arrays were washed and stained using a Fluidics Station 450 (Affymetrix). The arrays were stained with phycoerythrein-conjugated streptavidin (Invitrogen, Carlsbad, CA).
Sample_scan_protocol	Fluorescence intensities were determined using a GCS 3000 7G high-resolution confocal laser scanner (Affymetrix). The scanned images were analyzed using programs resident in AGCC and Expression Console (Affymetrix). Quality control metrics for cRNA integrity, sample loading, and variations in staining were determined by MAS 5.0 statistical algorithms.
Sample_data_processing	Signal values were generated by the RMA method and Detection p-values were generated by MAS 5.0. Probe sets exhibiting significant differential expression were identified using GeneMaths XT (Applied Maths, Austin TX), based on the following criteria: 1) MAS5.0 detection p-values ≤ 0.05 for all samples in at least one experimental group, 2) ANOVA p-value ≤ 0.05, 3) Absolute Signal log ratio ≥ 1.0 and independent t-test p-value ≤ 0.05 for at least one pair wise comparison versus the control group. Unsupervised hierarchical clustering and heat map generation were performed in GeneMaths XT following row mean centering of log2 transformed RMA signal values; probe set clustering was performed by the Unweighted Pair Group Method using Arithmetic averages (UPGMA) using Pearson correlation as the similarity metric. Gene annotation, gene ontology information and biochemical pathway information were obtained from the Database for Annotation, Visualization and Integrated Discovery (DAVID) v6.7 from the National Institute of Allergy and Infectious Diseases (NIAID), at the National Institutes of Health (NIH).
Sample_platform_id	GPL1355
Sample_contact_name	Cyrus,Farrokh,Khambatta
Sample_contact_laboratory	Hellerstein
Sample_contact_department	Nutritional Sciences
Sample_contact_institute	University of California at Berkeley
Sample_contact_address	309 Morgan Hall
Sample_contact_city	Berkeley
Sample_contact_state	CA
Sample_contact_zip/postal_code	94720
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM746nnn/GSM746614/suppl/GSM746614_MX0002-230_2.CEL.gz
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM746nnn/GSM746614/suppl/GSM746614_MX0002-230_2.rma.chp.gz
Sample_series_id	GSE30147
Sample_data_row_count	31099

GSM746615

GPL1355

Rosiglitazone treated, 9 week_old, biological rep3

Rosiglitazone treated ZDF rat islets at 9 weeks of age

strain: Zucker Diabetic Fatty Rat gender: male age: 9 weeks tissue: pancreatic islets

Gene expression data from Rosiglitazone treated (weeks 5-9) ZDF rat at 9 weeks of age.

Sample_geo_accession	GSM746615
Sample_status	Public on Jun 21 2013
Sample_submission_date	Jun 22 2011
Sample_last_update_date	Jun 21 2013
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Rattus norvegicus
Sample_taxid_ch1	10116
Sample_treatment_protocol_ch1	Five-week old ZDF (fa/fa) animals (n=24) were purchased from Charles River Laboratories (Wilmington, MA). Following 48 hours of acclimation, animals were randomized into one of three groups: rosiglitazone treated (RT), rosiglitazone withdrawal (RW), or untreated controls (UC) and sacrificed at either 9, 11, 13, or 15 weeks of age. All animals were fed the Purina 5008 diet. Rosiglitazone was administered in the diet as powdered Avandia tablets (3mg rosiglitazone/kg body weight).
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Total RNA was isolated from 20-30 mg of islets using the RNEasy kit according to the manufacturer’s instructions (Qiagen, Valencia, CA). Equal amounts of RNA from each of 3 replicates were reverse transcribed to cDNA after the purity and concentration of RNA samples were determined from OD260/280 readings using a dual beam UV spectrophotometer and RNA integrity was determined by capillary electrophoresis using the RNA 6000 Nano Lab-on-a-Chip kit and the Bioanalyzer 2100 (Agilent Technologies).
Sample_label_ch1	biotin
Sample_label_protocol_ch1	cRNA was synthesized and labeled with biotinylated UTP and CTP by in vitro transcription using the T7 promoter-coupled double stranded cDNA as template and the Bioarray™ HighYield™ RNA Transcript Labeling Kit (ENZO Diagnostics Inc.).
Sample_hyb_protocol	Labeled cRNA (15.0 ug) was fragmented by Magnesium ion-mediated hydrolysis and hybridized for 16hr at 45oC to Affymetrix GeneChip Rat Genome 230 2.0 arrays, which contain probes for over 31,000 transcripts representing approximately 28,700 annotated rat genes and expressed sequence tags (ESTs) (Affymetrix, Santa Clara, CA). Arrays were washed and stained using a Fluidics Station 450 (Affymetrix). The arrays were stained with phycoerythrein-conjugated streptavidin (Invitrogen, Carlsbad, CA).
Sample_scan_protocol	Fluorescence intensities were determined using a GCS 3000 7G high-resolution confocal laser scanner (Affymetrix). The scanned images were analyzed using programs resident in AGCC and Expression Console (Affymetrix). Quality control metrics for cRNA integrity, sample loading, and variations in staining were determined by MAS 5.0 statistical algorithms.
Sample_data_processing	Signal values were generated by the RMA method and Detection p-values were generated by MAS 5.0. Probe sets exhibiting significant differential expression were identified using GeneMaths XT (Applied Maths, Austin TX), based on the following criteria: 1) MAS5.0 detection p-values ≤ 0.05 for all samples in at least one experimental group, 2) ANOVA p-value ≤ 0.05, 3) Absolute Signal log ratio ≥ 1.0 and independent t-test p-value ≤ 0.05 for at least one pair wise comparison versus the control group. Unsupervised hierarchical clustering and heat map generation were performed in GeneMaths XT following row mean centering of log2 transformed RMA signal values; probe set clustering was performed by the Unweighted Pair Group Method using Arithmetic averages (UPGMA) using Pearson correlation as the similarity metric. Gene annotation, gene ontology information and biochemical pathway information were obtained from the Database for Annotation, Visualization and Integrated Discovery (DAVID) v6.7 from the National Institute of Allergy and Infectious Diseases (NIAID), at the National Institutes of Health (NIH).
Sample_platform_id	GPL1355
Sample_contact_name	Cyrus,Farrokh,Khambatta
Sample_contact_laboratory	Hellerstein
Sample_contact_department	Nutritional Sciences
Sample_contact_institute	University of California at Berkeley
Sample_contact_address	309 Morgan Hall
Sample_contact_city	Berkeley
Sample_contact_state	CA
Sample_contact_zip/postal_code	94720
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM746nnn/GSM746615/suppl/GSM746615_MX0003-230_2.CEL.gz
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM746nnn/GSM746615/suppl/GSM746615_MX0003-230_2.rma.chp.gz
Sample_series_id	GSE30147
Sample_data_row_count	31099

GSM746616

GPL1355

Rosiglitazone 2 week withdrawal, 11 week_old, biological rep1

Rosiglitazone withdrawal ZDF rat islets at 11 weeks of age

strain: Zucker Diabetic Fatty Rat gender: male age: 11 weeks tissue: pancreatic islets

Gene expression data from Rosiglitazone treated (weeks 5-9) then withdrawal (weeks 9-11) ZDF rat at 11 weeks of age.

Sample_geo_accession	GSM746616
Sample_status	Public on Jun 21 2013
Sample_submission_date	Jun 22 2011
Sample_last_update_date	Jun 21 2013
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Rattus norvegicus
Sample_taxid_ch1	10116
Sample_treatment_protocol_ch1	Five-week old ZDF (fa/fa) animals (n=24) were purchased from Charles River Laboratories (Wilmington, MA). Following 48 hours of acclimation, animals were randomized into one of three groups: rosiglitazone treated (RT), rosiglitazone withdrawal (RW), or untreated controls (UC) and sacrificed at either 9, 11, 13, or 15 weeks of age. All animals were fed the Purina 5008 diet. Rosiglitazone was administered in the diet as powdered Avandia tablets (3mg rosiglitazone/kg body weight).
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Total RNA was isolated from 20-30 mg of islets using the RNEasy kit according to the manufacturer’s instructions (Qiagen, Valencia, CA). Equal amounts of RNA from each of 3 replicates were reverse transcribed to cDNA after the purity and concentration of RNA samples were determined from OD260/280 readings using a dual beam UV spectrophotometer and RNA integrity was determined by capillary electrophoresis using the RNA 6000 Nano Lab-on-a-Chip kit and the Bioanalyzer 2100 (Agilent Technologies).
Sample_label_ch1	biotin
Sample_label_protocol_ch1	cRNA was synthesized and labeled with biotinylated UTP and CTP by in vitro transcription using the T7 promoter-coupled double stranded cDNA as template and the Bioarray™ HighYield™ RNA Transcript Labeling Kit (ENZO Diagnostics Inc.).
Sample_hyb_protocol	Labeled cRNA (15.0 ug) was fragmented by Magnesium ion-mediated hydrolysis and hybridized for 16hr at 45oC to Affymetrix GeneChip Rat Genome 230 2.0 arrays, which contain probes for over 31,000 transcripts representing approximately 28,700 annotated rat genes and expressed sequence tags (ESTs) (Affymetrix, Santa Clara, CA). Arrays were washed and stained using a Fluidics Station 450 (Affymetrix). The arrays were stained with phycoerythrein-conjugated streptavidin (Invitrogen, Carlsbad, CA).
Sample_scan_protocol	Fluorescence intensities were determined using a GCS 3000 7G high-resolution confocal laser scanner (Affymetrix). The scanned images were analyzed using programs resident in AGCC and Expression Console (Affymetrix). Quality control metrics for cRNA integrity, sample loading, and variations in staining were determined by MAS 5.0 statistical algorithms.
Sample_data_processing	Signal values were generated by the RMA method and Detection p-values were generated by MAS 5.0. Probe sets exhibiting significant differential expression were identified using GeneMaths XT (Applied Maths, Austin TX), based on the following criteria: 1) MAS5.0 detection p-values ≤ 0.05 for all samples in at least one experimental group, 2) ANOVA p-value ≤ 0.05, 3) Absolute Signal log ratio ≥ 1.0 and independent t-test p-value ≤ 0.05 for at least one pair wise comparison versus the control group. Unsupervised hierarchical clustering and heat map generation were performed in GeneMaths XT following row mean centering of log2 transformed RMA signal values; probe set clustering was performed by the Unweighted Pair Group Method using Arithmetic averages (UPGMA) using Pearson correlation as the similarity metric. Gene annotation, gene ontology information and biochemical pathway information were obtained from the Database for Annotation, Visualization and Integrated Discovery (DAVID) v6.7 from the National Institute of Allergy and Infectious Diseases (NIAID), at the National Institutes of Health (NIH).
Sample_platform_id	GPL1355
Sample_contact_name	Cyrus,Farrokh,Khambatta
Sample_contact_laboratory	Hellerstein
Sample_contact_department	Nutritional Sciences
Sample_contact_institute	University of California at Berkeley
Sample_contact_address	309 Morgan Hall
Sample_contact_city	Berkeley
Sample_contact_state	CA
Sample_contact_zip/postal_code	94720
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM746nnn/GSM746616/suppl/GSM746616_MX0012-230_2.CEL.gz
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM746nnn/GSM746616/suppl/GSM746616_MX0012-230_2.rma.chp.gz
Sample_series_id	GSE30147
Sample_data_row_count	31099

GSM746617

GPL1355

Rosiglitazone 2 week withdrawal, 11 week_old, biological rep2

Rosiglitazone withdrawal ZDF rat islets at 11 weeks of age

strain: Zucker Diabetic Fatty Rat gender: male age: 11 weeks tissue: pancreatic islets

Gene expression data from Rosiglitazone treated (weeks 5-9) then withdrawal (weeks 9-11) ZDF rat at 11 weeks of age.

Sample_geo_accession	GSM746617
Sample_status	Public on Jun 21 2013
Sample_submission_date	Jun 22 2011
Sample_last_update_date	Jun 21 2013
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Rattus norvegicus
Sample_taxid_ch1	10116
Sample_treatment_protocol_ch1	Five-week old ZDF (fa/fa) animals (n=24) were purchased from Charles River Laboratories (Wilmington, MA). Following 48 hours of acclimation, animals were randomized into one of three groups: rosiglitazone treated (RT), rosiglitazone withdrawal (RW), or untreated controls (UC) and sacrificed at either 9, 11, 13, or 15 weeks of age. All animals were fed the Purina 5008 diet. Rosiglitazone was administered in the diet as powdered Avandia tablets (3mg rosiglitazone/kg body weight).
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Total RNA was isolated from 20-30 mg of islets using the RNEasy kit according to the manufacturer’s instructions (Qiagen, Valencia, CA). Equal amounts of RNA from each of 3 replicates were reverse transcribed to cDNA after the purity and concentration of RNA samples were determined from OD260/280 readings using a dual beam UV spectrophotometer and RNA integrity was determined by capillary electrophoresis using the RNA 6000 Nano Lab-on-a-Chip kit and the Bioanalyzer 2100 (Agilent Technologies).
Sample_label_ch1	biotin
Sample_label_protocol_ch1	cRNA was synthesized and labeled with biotinylated UTP and CTP by in vitro transcription using the T7 promoter-coupled double stranded cDNA as template and the Bioarray™ HighYield™ RNA Transcript Labeling Kit (ENZO Diagnostics Inc.).
Sample_hyb_protocol	Labeled cRNA (15.0 ug) was fragmented by Magnesium ion-mediated hydrolysis and hybridized for 16hr at 45oC to Affymetrix GeneChip Rat Genome 230 2.0 arrays, which contain probes for over 31,000 transcripts representing approximately 28,700 annotated rat genes and expressed sequence tags (ESTs) (Affymetrix, Santa Clara, CA). Arrays were washed and stained using a Fluidics Station 450 (Affymetrix). The arrays were stained with phycoerythrein-conjugated streptavidin (Invitrogen, Carlsbad, CA).
Sample_scan_protocol	Fluorescence intensities were determined using a GCS 3000 7G high-resolution confocal laser scanner (Affymetrix). The scanned images were analyzed using programs resident in AGCC and Expression Console (Affymetrix). Quality control metrics for cRNA integrity, sample loading, and variations in staining were determined by MAS 5.0 statistical algorithms.
Sample_data_processing	Signal values were generated by the RMA method and Detection p-values were generated by MAS 5.0. Probe sets exhibiting significant differential expression were identified using GeneMaths XT (Applied Maths, Austin TX), based on the following criteria: 1) MAS5.0 detection p-values ≤ 0.05 for all samples in at least one experimental group, 2) ANOVA p-value ≤ 0.05, 3) Absolute Signal log ratio ≥ 1.0 and independent t-test p-value ≤ 0.05 for at least one pair wise comparison versus the control group. Unsupervised hierarchical clustering and heat map generation were performed in GeneMaths XT following row mean centering of log2 transformed RMA signal values; probe set clustering was performed by the Unweighted Pair Group Method using Arithmetic averages (UPGMA) using Pearson correlation as the similarity metric. Gene annotation, gene ontology information and biochemical pathway information were obtained from the Database for Annotation, Visualization and Integrated Discovery (DAVID) v6.7 from the National Institute of Allergy and Infectious Diseases (NIAID), at the National Institutes of Health (NIH).
Sample_platform_id	GPL1355
Sample_contact_name	Cyrus,Farrokh,Khambatta
Sample_contact_laboratory	Hellerstein
Sample_contact_department	Nutritional Sciences
Sample_contact_institute	University of California at Berkeley
Sample_contact_address	309 Morgan Hall
Sample_contact_city	Berkeley
Sample_contact_state	CA
Sample_contact_zip/postal_code	94720
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM746nnn/GSM746617/suppl/GSM746617_MX0013-230_2.CEL.gz
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM746nnn/GSM746617/suppl/GSM746617_MX0013-230_2.rma.chp.gz
Sample_series_id	GSE30147
Sample_data_row_count	31099

GSM746618

GPL1355

Rosiglitazone 2 week withdrawal, 11 week_old, biological rep3

Rosiglitazone withdrawal ZDF rat islets at 11 weeks of age

strain: Zucker Diabetic Fatty Rat gender: male age: 11 weeks tissue: pancreatic islets

Gene expression data from Rosiglitazone treated (weeks 5-9) then withdrawal (weeks 9-11) ZDF rat at 11 weeks of age.

Sample_geo_accession	GSM746618
Sample_status	Public on Jun 21 2013
Sample_submission_date	Jun 22 2011
Sample_last_update_date	Jun 21 2013
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Rattus norvegicus
Sample_taxid_ch1	10116
Sample_treatment_protocol_ch1	Five-week old ZDF (fa/fa) animals (n=24) were purchased from Charles River Laboratories (Wilmington, MA). Following 48 hours of acclimation, animals were randomized into one of three groups: rosiglitazone treated (RT), rosiglitazone withdrawal (RW), or untreated controls (UC) and sacrificed at either 9, 11, 13, or 15 weeks of age. All animals were fed the Purina 5008 diet. Rosiglitazone was administered in the diet as powdered Avandia tablets (3mg rosiglitazone/kg body weight).
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Total RNA was isolated from 20-30 mg of islets using the RNEasy kit according to the manufacturer’s instructions (Qiagen, Valencia, CA). Equal amounts of RNA from each of 3 replicates were reverse transcribed to cDNA after the purity and concentration of RNA samples were determined from OD260/280 readings using a dual beam UV spectrophotometer and RNA integrity was determined by capillary electrophoresis using the RNA 6000 Nano Lab-on-a-Chip kit and the Bioanalyzer 2100 (Agilent Technologies).
Sample_label_ch1	biotin
Sample_label_protocol_ch1	cRNA was synthesized and labeled with biotinylated UTP and CTP by in vitro transcription using the T7 promoter-coupled double stranded cDNA as template and the Bioarray™ HighYield™ RNA Transcript Labeling Kit (ENZO Diagnostics Inc.).
Sample_hyb_protocol	Labeled cRNA (15.0 ug) was fragmented by Magnesium ion-mediated hydrolysis and hybridized for 16hr at 45oC to Affymetrix GeneChip Rat Genome 230 2.0 arrays, which contain probes for over 31,000 transcripts representing approximately 28,700 annotated rat genes and expressed sequence tags (ESTs) (Affymetrix, Santa Clara, CA). Arrays were washed and stained using a Fluidics Station 450 (Affymetrix). The arrays were stained with phycoerythrein-conjugated streptavidin (Invitrogen, Carlsbad, CA).
Sample_scan_protocol	Fluorescence intensities were determined using a GCS 3000 7G high-resolution confocal laser scanner (Affymetrix). The scanned images were analyzed using programs resident in AGCC and Expression Console (Affymetrix). Quality control metrics for cRNA integrity, sample loading, and variations in staining were determined by MAS 5.0 statistical algorithms.
Sample_data_processing	Signal values were generated by the RMA method and Detection p-values were generated by MAS 5.0. Probe sets exhibiting significant differential expression were identified using GeneMaths XT (Applied Maths, Austin TX), based on the following criteria: 1) MAS5.0 detection p-values ≤ 0.05 for all samples in at least one experimental group, 2) ANOVA p-value ≤ 0.05, 3) Absolute Signal log ratio ≥ 1.0 and independent t-test p-value ≤ 0.05 for at least one pair wise comparison versus the control group. Unsupervised hierarchical clustering and heat map generation were performed in GeneMaths XT following row mean centering of log2 transformed RMA signal values; probe set clustering was performed by the Unweighted Pair Group Method using Arithmetic averages (UPGMA) using Pearson correlation as the similarity metric. Gene annotation, gene ontology information and biochemical pathway information were obtained from the Database for Annotation, Visualization and Integrated Discovery (DAVID) v6.7 from the National Institute of Allergy and Infectious Diseases (NIAID), at the National Institutes of Health (NIH).
Sample_platform_id	GPL1355
Sample_contact_name	Cyrus,Farrokh,Khambatta
Sample_contact_laboratory	Hellerstein
Sample_contact_department	Nutritional Sciences
Sample_contact_institute	University of California at Berkeley
Sample_contact_address	309 Morgan Hall
Sample_contact_city	Berkeley
Sample_contact_state	CA
Sample_contact_zip/postal_code	94720
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM746nnn/GSM746618/suppl/GSM746618_MX0014-230_2.CEL.gz
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM746nnn/GSM746618/suppl/GSM746618_MX0014-230_2.rma.chp.gz
Sample_series_id	GSE30147
Sample_data_row_count	31099

GSM746619

GPL1355

Untreated control, 13 week_old, biological rep1

Untreated control ZDF rat islets at 13 weeks of age

strain: Zucker Diabetic Fatty Rat gender: male age: 13 weeks tissue: pancreatic islets

Gene expression data from untreated ZDF rat at 13 weeks of age.

Sample_geo_accession	GSM746619
Sample_status	Public on Jun 21 2013
Sample_submission_date	Jun 22 2011
Sample_last_update_date	Jun 21 2013
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Rattus norvegicus
Sample_taxid_ch1	10116
Sample_treatment_protocol_ch1	Five-week old ZDF (fa/fa) animals (n=24) were purchased from Charles River Laboratories (Wilmington, MA). Following 48 hours of acclimation, animals were randomized into one of three groups: rosiglitazone treated (RT), rosiglitazone withdrawal (RW), or untreated controls (UC) and sacrificed at either 9, 11, 13, or 15 weeks of age. All animals were fed the Purina 5008 diet. Rosiglitazone was administered in the diet as powdered Avandia tablets (3mg rosiglitazone/kg body weight).
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Total RNA was isolated from 20-30 mg of islets using the RNEasy kit according to the manufacturer’s instructions (Qiagen, Valencia, CA). Equal amounts of RNA from each of 3 replicates were reverse transcribed to cDNA after the purity and concentration of RNA samples were determined from OD260/280 readings using a dual beam UV spectrophotometer and RNA integrity was determined by capillary electrophoresis using the RNA 6000 Nano Lab-on-a-Chip kit and the Bioanalyzer 2100 (Agilent Technologies).
Sample_label_ch1	biotin
Sample_label_protocol_ch1	cRNA was synthesized and labeled with biotinylated UTP and CTP by in vitro transcription using the T7 promoter-coupled double stranded cDNA as template and the Bioarray™ HighYield™ RNA Transcript Labeling Kit (ENZO Diagnostics Inc.).
Sample_hyb_protocol	Labeled cRNA (15.0 ug) was fragmented by Magnesium ion-mediated hydrolysis and hybridized for 16hr at 45oC to Affymetrix GeneChip Rat Genome 230 2.0 arrays, which contain probes for over 31,000 transcripts representing approximately 28,700 annotated rat genes and expressed sequence tags (ESTs) (Affymetrix, Santa Clara, CA). Arrays were washed and stained using a Fluidics Station 450 (Affymetrix). The arrays were stained with phycoerythrein-conjugated streptavidin (Invitrogen, Carlsbad, CA).
Sample_scan_protocol	Fluorescence intensities were determined using a GCS 3000 7G high-resolution confocal laser scanner (Affymetrix). The scanned images were analyzed using programs resident in AGCC and Expression Console (Affymetrix). Quality control metrics for cRNA integrity, sample loading, and variations in staining were determined by MAS 5.0 statistical algorithms.
Sample_data_processing	Signal values were generated by the RMA method and Detection p-values were generated by MAS 5.0. Probe sets exhibiting significant differential expression were identified using GeneMaths XT (Applied Maths, Austin TX), based on the following criteria: 1) MAS5.0 detection p-values ≤ 0.05 for all samples in at least one experimental group, 2) ANOVA p-value ≤ 0.05, 3) Absolute Signal log ratio ≥ 1.0 and independent t-test p-value ≤ 0.05 for at least one pair wise comparison versus the control group. Unsupervised hierarchical clustering and heat map generation were performed in GeneMaths XT following row mean centering of log2 transformed RMA signal values; probe set clustering was performed by the Unweighted Pair Group Method using Arithmetic averages (UPGMA) using Pearson correlation as the similarity metric. Gene annotation, gene ontology information and biochemical pathway information were obtained from the Database for Annotation, Visualization and Integrated Discovery (DAVID) v6.7 from the National Institute of Allergy and Infectious Diseases (NIAID), at the National Institutes of Health (NIH).
Sample_platform_id	GPL1355
Sample_contact_name	Cyrus,Farrokh,Khambatta
Sample_contact_laboratory	Hellerstein
Sample_contact_department	Nutritional Sciences
Sample_contact_institute	University of California at Berkeley
Sample_contact_address	309 Morgan Hall
Sample_contact_city	Berkeley
Sample_contact_state	CA
Sample_contact_zip/postal_code	94720
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM746nnn/GSM746619/suppl/GSM746619_MX0016-230_2.CEL.gz
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM746nnn/GSM746619/suppl/GSM746619_MX0016-230_2.rma.chp.gz
Sample_series_id	GSE30147
Sample_data_row_count	31099

GSM746620

GPL1355

Untreated control, 13 week_old, biological rep2

Untreated control ZDF rat islets at 13 weeks of age

strain: Zucker Diabetic Fatty Rat gender: male age: 13 weeks tissue: pancreatic islets

Gene expression data from untreated ZDF rat at 13 weeks of age.

Sample_geo_accession	GSM746620
Sample_status	Public on Jun 21 2013
Sample_submission_date	Jun 22 2011
Sample_last_update_date	Jun 21 2013
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Rattus norvegicus
Sample_taxid_ch1	10116
Sample_treatment_protocol_ch1	Five-week old ZDF (fa/fa) animals (n=24) were purchased from Charles River Laboratories (Wilmington, MA). Following 48 hours of acclimation, animals were randomized into one of three groups: rosiglitazone treated (RT), rosiglitazone withdrawal (RW), or untreated controls (UC) and sacrificed at either 9, 11, 13, or 15 weeks of age. All animals were fed the Purina 5008 diet. Rosiglitazone was administered in the diet as powdered Avandia tablets (3mg rosiglitazone/kg body weight).
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Total RNA was isolated from 20-30 mg of islets using the RNEasy kit according to the manufacturer’s instructions (Qiagen, Valencia, CA). Equal amounts of RNA from each of 3 replicates were reverse transcribed to cDNA after the purity and concentration of RNA samples were determined from OD260/280 readings using a dual beam UV spectrophotometer and RNA integrity was determined by capillary electrophoresis using the RNA 6000 Nano Lab-on-a-Chip kit and the Bioanalyzer 2100 (Agilent Technologies).
Sample_label_ch1	biotin
Sample_label_protocol_ch1	cRNA was synthesized and labeled with biotinylated UTP and CTP by in vitro transcription using the T7 promoter-coupled double stranded cDNA as template and the Bioarray™ HighYield™ RNA Transcript Labeling Kit (ENZO Diagnostics Inc.).
Sample_hyb_protocol	Labeled cRNA (15.0 ug) was fragmented by Magnesium ion-mediated hydrolysis and hybridized for 16hr at 45oC to Affymetrix GeneChip Rat Genome 230 2.0 arrays, which contain probes for over 31,000 transcripts representing approximately 28,700 annotated rat genes and expressed sequence tags (ESTs) (Affymetrix, Santa Clara, CA). Arrays were washed and stained using a Fluidics Station 450 (Affymetrix). The arrays were stained with phycoerythrein-conjugated streptavidin (Invitrogen, Carlsbad, CA).
Sample_scan_protocol	Fluorescence intensities were determined using a GCS 3000 7G high-resolution confocal laser scanner (Affymetrix). The scanned images were analyzed using programs resident in AGCC and Expression Console (Affymetrix). Quality control metrics for cRNA integrity, sample loading, and variations in staining were determined by MAS 5.0 statistical algorithms.
Sample_data_processing	Signal values were generated by the RMA method and Detection p-values were generated by MAS 5.0. Probe sets exhibiting significant differential expression were identified using GeneMaths XT (Applied Maths, Austin TX), based on the following criteria: 1) MAS5.0 detection p-values ≤ 0.05 for all samples in at least one experimental group, 2) ANOVA p-value ≤ 0.05, 3) Absolute Signal log ratio ≥ 1.0 and independent t-test p-value ≤ 0.05 for at least one pair wise comparison versus the control group. Unsupervised hierarchical clustering and heat map generation were performed in GeneMaths XT following row mean centering of log2 transformed RMA signal values; probe set clustering was performed by the Unweighted Pair Group Method using Arithmetic averages (UPGMA) using Pearson correlation as the similarity metric. Gene annotation, gene ontology information and biochemical pathway information were obtained from the Database for Annotation, Visualization and Integrated Discovery (DAVID) v6.7 from the National Institute of Allergy and Infectious Diseases (NIAID), at the National Institutes of Health (NIH).
Sample_platform_id	GPL1355
Sample_contact_name	Cyrus,Farrokh,Khambatta
Sample_contact_laboratory	Hellerstein
Sample_contact_department	Nutritional Sciences
Sample_contact_institute	University of California at Berkeley
Sample_contact_address	309 Morgan Hall
Sample_contact_city	Berkeley
Sample_contact_state	CA
Sample_contact_zip/postal_code	94720
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM746nnn/GSM746620/suppl/GSM746620_MX0017-230_2.CEL.gz
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM746nnn/GSM746620/suppl/GSM746620_MX0017-230_2.rma.chp.gz
Sample_series_id	GSE30147
Sample_data_row_count	31099

GSM746621

GPL1355

Untreated control, 13 week_old, biological rep3

Untreated control ZDF rat islets at 13 weeks of age

strain: Zucker Diabetic Fatty Rat gender: male age: 13 weeks tissue: pancreatic islets

Gene expression data from untreated ZDF rat at 13 weeks of age.

Sample_geo_accession	GSM746621
Sample_status	Public on Jun 21 2013
Sample_submission_date	Jun 22 2011
Sample_last_update_date	Jun 21 2013
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Rattus norvegicus
Sample_taxid_ch1	10116
Sample_treatment_protocol_ch1	Five-week old ZDF (fa/fa) animals (n=24) were purchased from Charles River Laboratories (Wilmington, MA). Following 48 hours of acclimation, animals were randomized into one of three groups: rosiglitazone treated (RT), rosiglitazone withdrawal (RW), or untreated controls (UC) and sacrificed at either 9, 11, 13, or 15 weeks of age. All animals were fed the Purina 5008 diet. Rosiglitazone was administered in the diet as powdered Avandia tablets (3mg rosiglitazone/kg body weight).
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Total RNA was isolated from 20-30 mg of islets using the RNEasy kit according to the manufacturer’s instructions (Qiagen, Valencia, CA). Equal amounts of RNA from each of 3 replicates were reverse transcribed to cDNA after the purity and concentration of RNA samples were determined from OD260/280 readings using a dual beam UV spectrophotometer and RNA integrity was determined by capillary electrophoresis using the RNA 6000 Nano Lab-on-a-Chip kit and the Bioanalyzer 2100 (Agilent Technologies).
Sample_label_ch1	biotin
Sample_label_protocol_ch1	cRNA was synthesized and labeled with biotinylated UTP and CTP by in vitro transcription using the T7 promoter-coupled double stranded cDNA as template and the Bioarray™ HighYield™ RNA Transcript Labeling Kit (ENZO Diagnostics Inc.).
Sample_hyb_protocol	Labeled cRNA (15.0 ug) was fragmented by Magnesium ion-mediated hydrolysis and hybridized for 16hr at 45oC to Affymetrix GeneChip Rat Genome 230 2.0 arrays, which contain probes for over 31,000 transcripts representing approximately 28,700 annotated rat genes and expressed sequence tags (ESTs) (Affymetrix, Santa Clara, CA). Arrays were washed and stained using a Fluidics Station 450 (Affymetrix). The arrays were stained with phycoerythrein-conjugated streptavidin (Invitrogen, Carlsbad, CA).
Sample_scan_protocol	Fluorescence intensities were determined using a GCS 3000 7G high-resolution confocal laser scanner (Affymetrix). The scanned images were analyzed using programs resident in AGCC and Expression Console (Affymetrix). Quality control metrics for cRNA integrity, sample loading, and variations in staining were determined by MAS 5.0 statistical algorithms.
Sample_data_processing	Signal values were generated by the RMA method and Detection p-values were generated by MAS 5.0. Probe sets exhibiting significant differential expression were identified using GeneMaths XT (Applied Maths, Austin TX), based on the following criteria: 1) MAS5.0 detection p-values ≤ 0.05 for all samples in at least one experimental group, 2) ANOVA p-value ≤ 0.05, 3) Absolute Signal log ratio ≥ 1.0 and independent t-test p-value ≤ 0.05 for at least one pair wise comparison versus the control group. Unsupervised hierarchical clustering and heat map generation were performed in GeneMaths XT following row mean centering of log2 transformed RMA signal values; probe set clustering was performed by the Unweighted Pair Group Method using Arithmetic averages (UPGMA) using Pearson correlation as the similarity metric. Gene annotation, gene ontology information and biochemical pathway information were obtained from the Database for Annotation, Visualization and Integrated Discovery (DAVID) v6.7 from the National Institute of Allergy and Infectious Diseases (NIAID), at the National Institutes of Health (NIH).
Sample_platform_id	GPL1355
Sample_contact_name	Cyrus,Farrokh,Khambatta
Sample_contact_laboratory	Hellerstein
Sample_contact_department	Nutritional Sciences
Sample_contact_institute	University of California at Berkeley
Sample_contact_address	309 Morgan Hall
Sample_contact_city	Berkeley
Sample_contact_state	CA
Sample_contact_zip/postal_code	94720
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM746nnn/GSM746621/suppl/GSM746621_MX0018-230_2.CEL.gz
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM746nnn/GSM746621/suppl/GSM746621_MX0018-230_2.rma.chp.gz
Sample_series_id	GSE30147
Sample_data_row_count	31099

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