Search results for the GEO ID: GSE27395  |
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|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM499759 | GPL1261 |
|
Gsk-3a-/- ESCs Rep1
|
Total RNA from Gsk-3a-/- ESCs
|
genotype/variation: Gsk-3a-/-
cell type: embryonic stem cells
|
none
|
| Sample_geo_accession | GSM499759
| | Sample_status | Public on Sep 15 2011
| | Sample_submission_date | Jan 22 2010
| | Sample_last_update_date | Sep 15 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_growth_protocol_ch1 | Feeder-free wild-type, GSK-3a-/-, Gsk-3b-/-, and Gsk-3 DKO ESCs were grown on gelatin coated plates in high glucose DMEM (GIBCO) supplemented with 15% fetal bovine serum (Hyclone), 1X non-essential amino acids, 1X sodium pyruvate, 2mM L-glutamine, 1X penicillin/streptomycin (GIBCO), 55 mM 2-mercaptoethanol, and 1000 units/ml ESGRO (Millilpore). Media was replenished every other day.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Cells were collected by addition of 0.25% trypsin EDTA to PBS washed cells and incubated for 1 minute at 37C. Trypsin was inactivated by addition of twice the volume of ESC media. Cells were washed in PBS, and resuspended in TRIzol (Invitrogen), and RNA was isolated following the manufacturer's protocol. RNA was then further purified with the RNeasy RNA cleanup procedure (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | The Ovation™ Biotin RNA Amplification and Labeling System (NuGen Technologies, Inc., San Carlos, CA) was used to prepare amplified, biotin-labeled cDNA from total RNA for following manufacturer’s instructions. Briefly, first strand cDNA was synthesized from 25 ng of total RNA using a unique first strand DNA/RNA chimeric primer and reverse transcriptase. Following double strand cDNA generation, amplification of cDNA was achieved by utilizing an isothermal DNA amplification process that involves repeated SPIA™ DNA/RNA primer binding, DNA duplication, strand displacement and RNA cleavage. The amplified SPIA™ cDNA was purified and subjected to a two-step fragmentation and labeling process. The fragmented/biotinylated cDNA content was measured in a ND-1000 spectrophotometer and the quality was analyzed on an RNA 6000 Nano LabChip (Agilent) using Agilent Bioanalyzer 2100.
| | Sample_hyb_protocol | Following fragmentation, labeled cRNA was hybridized to the Mouse 430 2.0 array. Hybridization was allowed to continue for 16 hours at 45ºC followed by washing and staining of microarrays in a Fluidics Station 450 (Affymetrix Inc., USA).
| | Sample_scan_protocol | GeneChips were scanned in a GeneChip Scanner 3000 (Affymetrix Inc., USA)
| | Sample_data_processing | CEL files were generated from DAT files using GeneChip® Operating Software (GCOS) software (Affymetrix Inc., USA). The probe set signals were generated using the Background Adjustment Using Sequence Information (gcrma 2.14.1) Package in R version 2.8.0. Data was used to determine differential gene expression by pair-wise comparisons and statistical analysis was performed using both the Linear Models for Microarray Data (limma 2.16.5) and Multiple testing using SAM and Efron's empirical Bayes approaches (siggenes 1.16.0) packages. The genes that were altered two-fold either way with significance at either a 10% FDR or adjusted P value of <= 0.05 were sorted and used for further interpretation of the microarray data.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Christopher,,Phiel
| | Sample_contact_email | phiel.1@osu.edu
| | Sample_contact_institute | The Research Institute at Nationwide Children's Hospital
| | Sample_contact_address | 700 Children's Drive W432
| | Sample_contact_city | Columbus
| | Sample_contact_state | OH
| | Sample_contact_zip/postal_code | 43205
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM499nnn/GSM499759/suppl/GSM499759.CEL.gz
| | Sample_series_id | GSE27395
| | Sample_data_row_count | 45101
| | |
|
GSM499760 | GPL1261 |
|
Gsk-3a-/- ESCs Rep2
|
Total RNA from Gsk-3a-/- ESCs
|
genotype/variation: Gsk-3a-/-
cell type: embryonic stem cells
|
none
|
| Sample_geo_accession | GSM499760
| | Sample_status | Public on Sep 15 2011
| | Sample_submission_date | Jan 22 2010
| | Sample_last_update_date | Sep 15 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_growth_protocol_ch1 | Feeder-free wild-type, GSK-3a-/-, Gsk-3b-/-, and Gsk-3 DKO ESCs were grown on gelatin coated plates in high glucose DMEM (GIBCO) supplemented with 15% fetal bovine serum (Hyclone), 1X non-essential amino acids, 1X sodium pyruvate, 2mM L-glutamine, 1X penicillin/streptomycin (GIBCO), 55 mM 2-mercaptoethanol, and 1000 units/ml ESGRO (Millilpore). Media was replenished every other day.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Cells were collected by addition of 0.25% trypsin EDTA to PBS washed cells and incubated for 1 minute at 37C. Trypsin was inactivated by addition of twice the volume of ESC media. Cells were washed in PBS, and resuspended in TRIzol (Invitrogen), and RNA was isolated following the manufacturer's protocol. RNA was then further purified with the RNeasy RNA cleanup procedure (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | The Ovation™ Biotin RNA Amplification and Labeling System (NuGen Technologies, Inc., San Carlos, CA) was used to prepare amplified, biotin-labeled cDNA from total RNA for following manufacturer’s instructions. Briefly, first strand cDNA was synthesized from 25 ng of total RNA using a unique first strand DNA/RNA chimeric primer and reverse transcriptase. Following double strand cDNA generation, amplification of cDNA was achieved by utilizing an isothermal DNA amplification process that involves repeated SPIA™ DNA/RNA primer binding, DNA duplication, strand displacement and RNA cleavage. The amplified SPIA™ cDNA was purified and subjected to a two-step fragmentation and labeling process. The fragmented/biotinylated cDNA content was measured in a ND-1000 spectrophotometer and the quality was analyzed on an RNA 6000 Nano LabChip (Agilent) using Agilent Bioanalyzer 2100.
| | Sample_hyb_protocol | Following fragmentation, labeled cRNA was hybridized to the Mouse 430 2.0 array. Hybridization was allowed to continue for 16 hours at 45ºC followed by washing and staining of microarrays in a Fluidics Station 450 (Affymetrix Inc., USA).
| | Sample_scan_protocol | GeneChips were scanned in a GeneChip Scanner 3000 (Affymetrix Inc., USA)
| | Sample_data_processing | CEL files were generated from DAT files using GeneChip® Operating Software (GCOS) software (Affymetrix Inc., USA). The probe set signals were generated using the Background Adjustment Using Sequence Information (gcrma 2.14.1) Package in R version 2.8.0. Data was used to determine differential gene expression by pair-wise comparisons and statistical analysis was performed using both the Linear Models for Microarray Data (limma 2.16.5) and Multiple testing using SAM and Efron's empirical Bayes approaches (siggenes 1.16.0) packages. The genes that were altered two-fold either way with significance at either a 10% FDR or adjusted P value of <= 0.05 were sorted and used for further interpretation of the microarray data.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Christopher,,Phiel
| | Sample_contact_email | phiel.1@osu.edu
| | Sample_contact_institute | The Research Institute at Nationwide Children's Hospital
| | Sample_contact_address | 700 Children's Drive W432
| | Sample_contact_city | Columbus
| | Sample_contact_state | OH
| | Sample_contact_zip/postal_code | 43205
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM499nnn/GSM499760/suppl/GSM499760.CEL.gz
| | Sample_series_id | GSE27395
| | Sample_data_row_count | 45101
| | |
|
GSM499761 | GPL1261 |
|
Gsk-3a-/- ESCs Rep3
|
Total RNA from Gsk-3a-/- ESCs
|
genotype/variation: Gsk-3a-/-
cell type: embryonic stem cells
|
none
|
| Sample_geo_accession | GSM499761
| | Sample_status | Public on Sep 15 2011
| | Sample_submission_date | Jan 22 2010
| | Sample_last_update_date | Sep 15 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_growth_protocol_ch1 | Feeder-free wild-type, GSK-3a-/-, Gsk-3b-/-, and Gsk-3 DKO ESCs were grown on gelatin coated plates in high glucose DMEM (GIBCO) supplemented with 15% fetal bovine serum (Hyclone), 1X non-essential amino acids, 1X sodium pyruvate, 2mM L-glutamine, 1X penicillin/streptomycin (GIBCO), 55 mM 2-mercaptoethanol, and 1000 units/ml ESGRO (Millilpore). Media was replenished every other day.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Cells were collected by addition of 0.25% trypsin EDTA to PBS washed cells and incubated for 1 minute at 37C. Trypsin was inactivated by addition of twice the volume of ESC media. Cells were washed in PBS, and resuspended in TRIzol (Invitrogen), and RNA was isolated following the manufacturer's protocol. RNA was then further purified with the RNeasy RNA cleanup procedure (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | The Ovation™ Biotin RNA Amplification and Labeling System (NuGen Technologies, Inc., San Carlos, CA) was used to prepare amplified, biotin-labeled cDNA from total RNA for following manufacturer’s instructions. Briefly, first strand cDNA was synthesized from 25 ng of total RNA using a unique first strand DNA/RNA chimeric primer and reverse transcriptase. Following double strand cDNA generation, amplification of cDNA was achieved by utilizing an isothermal DNA amplification process that involves repeated SPIA™ DNA/RNA primer binding, DNA duplication, strand displacement and RNA cleavage. The amplified SPIA™ cDNA was purified and subjected to a two-step fragmentation and labeling process. The fragmented/biotinylated cDNA content was measured in a ND-1000 spectrophotometer and the quality was analyzed on an RNA 6000 Nano LabChip (Agilent) using Agilent Bioanalyzer 2100.
| | Sample_hyb_protocol | Following fragmentation, labeled cRNA was hybridized to the Mouse 430 2.0 array. Hybridization was allowed to continue for 16 hours at 45ºC followed by washing and staining of microarrays in a Fluidics Station 450 (Affymetrix Inc., USA).
| | Sample_scan_protocol | GeneChips were scanned in a GeneChip Scanner 3000 (Affymetrix Inc., USA)
| | Sample_data_processing | CEL files were generated from DAT files using GeneChip® Operating Software (GCOS) software (Affymetrix Inc., USA). The probe set signals were generated using the Background Adjustment Using Sequence Information (gcrma 2.14.1) Package in R version 2.8.0. Data was used to determine differential gene expression by pair-wise comparisons and statistical analysis was performed using both the Linear Models for Microarray Data (limma 2.16.5) and Multiple testing using SAM and Efron's empirical Bayes approaches (siggenes 1.16.0) packages. The genes that were altered two-fold either way with significance at either a 10% FDR or adjusted P value of <= 0.05 were sorted and used for further interpretation of the microarray data.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Christopher,,Phiel
| | Sample_contact_email | phiel.1@osu.edu
| | Sample_contact_institute | The Research Institute at Nationwide Children's Hospital
| | Sample_contact_address | 700 Children's Drive W432
| | Sample_contact_city | Columbus
| | Sample_contact_state | OH
| | Sample_contact_zip/postal_code | 43205
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM499nnn/GSM499761/suppl/GSM499761.CEL.gz
| | Sample_series_id | GSE27395
| | Sample_data_row_count | 45101
| | |
|
GSM499762 | GPL1261 |
|
Gsk-3b-/- ESCs Rep1
|
Total RNA from Gsk-3b-/- ESCs
|
genotype/variation: GSK-3b-/-
cell type: embryonic stem cells
|
none
|
| Sample_geo_accession | GSM499762
| | Sample_status | Public on Sep 15 2011
| | Sample_submission_date | Jan 22 2010
| | Sample_last_update_date | Sep 15 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_growth_protocol_ch1 | Feeder-free wild-type, GSK-3a-/-, Gsk-3b-/-, and Gsk-3 DKO ESCs were grown on gelatin coated plates in high glucose DMEM (GIBCO) supplemented with 15% fetal bovine serum (Hyclone), 1X non-essential amino acids, 1X sodium pyruvate, 2mM L-glutamine, 1X penicillin/streptomycin (GIBCO), 55 mM 2-mercaptoethanol, and 1000 units/ml ESGRO (Millilpore). Media was replenished every other day.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Cells were collected by addition of 0.25% trypsin EDTA to PBS washed cells and incubated for 1 minute at 37C. Trypsin was inactivated by addition of twice the volume of ESC media. Cells were washed in PBS, and resuspended in TRIzol (Invitrogen), and RNA was isolated following the manufacturer's protocol. RNA was then further purified with the RNeasy RNA cleanup procedure (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | The Ovation™ Biotin RNA Amplification and Labeling System (NuGen Technologies, Inc., San Carlos, CA) was used to prepare amplified, biotin-labeled cDNA from total RNA for following manufacturer’s instructions. Briefly, first strand cDNA was synthesized from 25 ng of total RNA using a unique first strand DNA/RNA chimeric primer and reverse transcriptase. Following double strand cDNA generation, amplification of cDNA was achieved by utilizing an isothermal DNA amplification process that involves repeated SPIA™ DNA/RNA primer binding, DNA duplication, strand displacement and RNA cleavage. The amplified SPIA™ cDNA was purified and subjected to a two-step fragmentation and labeling process. The fragmented/biotinylated cDNA content was measured in a ND-1000 spectrophotometer and the quality was analyzed on an RNA 6000 Nano LabChip (Agilent) using Agilent Bioanalyzer 2100.
| | Sample_hyb_protocol | Following fragmentation, labeled cRNA was hybridized to the Mouse 430 2.0 array. Hybridization was allowed to continue for 16 hours at 45ºC followed by washing and staining of microarrays in a Fluidics Station 450 (Affymetrix Inc., USA).
| | Sample_scan_protocol | GeneChips were scanned in a GeneChip Scanner 3000 (Affymetrix Inc., USA)
| | Sample_data_processing | CEL files were generated from DAT files using GeneChip® Operating Software (GCOS) software (Affymetrix Inc., USA). The probe set signals were generated using the Background Adjustment Using Sequence Information (gcrma 2.14.1) Package in R version 2.8.0. Data was used to determine differential gene expression by pair-wise comparisons and statistical analysis was performed using both the Linear Models for Microarray Data (limma 2.16.5) and Multiple testing using SAM and Efron's empirical Bayes approaches (siggenes 1.16.0) packages. The genes that were altered two-fold either way with significance at either a 10% FDR or adjusted P value of <= 0.05 were sorted and used for further interpretation of the microarray data.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Christopher,,Phiel
| | Sample_contact_email | phiel.1@osu.edu
| | Sample_contact_institute | The Research Institute at Nationwide Children's Hospital
| | Sample_contact_address | 700 Children's Drive W432
| | Sample_contact_city | Columbus
| | Sample_contact_state | OH
| | Sample_contact_zip/postal_code | 43205
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM499nnn/GSM499762/suppl/GSM499762.CEL.gz
| | Sample_series_id | GSE27395
| | Sample_data_row_count | 45101
| | |
|
GSM499763 | GPL1261 |
|
Gsk-3b-/- ESCs Rep2
|
Total RNA from Gsk-3b-/- ESCs
|
genotype/variation: GSK-3b-/-
cell type: embryonic stem cells
|
none
|
| Sample_geo_accession | GSM499763
| | Sample_status | Public on Sep 15 2011
| | Sample_submission_date | Jan 22 2010
| | Sample_last_update_date | Sep 15 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_growth_protocol_ch1 | Feeder-free wild-type, GSK-3a-/-, Gsk-3b-/-, and Gsk-3 DKO ESCs were grown on gelatin coated plates in high glucose DMEM (GIBCO) supplemented with 15% fetal bovine serum (Hyclone), 1X non-essential amino acids, 1X sodium pyruvate, 2mM L-glutamine, 1X penicillin/streptomycin (GIBCO), 55 mM 2-mercaptoethanol, and 1000 units/ml ESGRO (Millilpore). Media was replenished every other day.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Cells were collected by addition of 0.25% trypsin EDTA to PBS washed cells and incubated for 1 minute at 37C. Trypsin was inactivated by addition of twice the volume of ESC media. Cells were washed in PBS, and resuspended in TRIzol (Invitrogen), and RNA was isolated following the manufacturer's protocol. RNA was then further purified with the RNeasy RNA cleanup procedure (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | The Ovation™ Biotin RNA Amplification and Labeling System (NuGen Technologies, Inc., San Carlos, CA) was used to prepare amplified, biotin-labeled cDNA from total RNA for following manufacturer’s instructions. Briefly, first strand cDNA was synthesized from 25 ng of total RNA using a unique first strand DNA/RNA chimeric primer and reverse transcriptase. Following double strand cDNA generation, amplification of cDNA was achieved by utilizing an isothermal DNA amplification process that involves repeated SPIA™ DNA/RNA primer binding, DNA duplication, strand displacement and RNA cleavage. The amplified SPIA™ cDNA was purified and subjected to a two-step fragmentation and labeling process. The fragmented/biotinylated cDNA content was measured in a ND-1000 spectrophotometer and the quality was analyzed on an RNA 6000 Nano LabChip (Agilent) using Agilent Bioanalyzer 2100.
| | Sample_hyb_protocol | Following fragmentation, labeled cRNA was hybridized to the Mouse 430 2.0 array. Hybridization was allowed to continue for 16 hours at 45ºC followed by washing and staining of microarrays in a Fluidics Station 450 (Affymetrix Inc., USA).
| | Sample_scan_protocol | GeneChips were scanned in a GeneChip Scanner 3000 (Affymetrix Inc., USA)
| | Sample_data_processing | CEL files were generated from DAT files using GeneChip® Operating Software (GCOS) software (Affymetrix Inc., USA). The probe set signals were generated using the Background Adjustment Using Sequence Information (gcrma 2.14.1) Package in R version 2.8.0. Data was used to determine differential gene expression by pair-wise comparisons and statistical analysis was performed using both the Linear Models for Microarray Data (limma 2.16.5) and Multiple testing using SAM and Efron's empirical Bayes approaches (siggenes 1.16.0) packages. The genes that were altered two-fold either way with significance at either a 10% FDR or adjusted P value of <= 0.05 were sorted and used for further interpretation of the microarray data.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Christopher,,Phiel
| | Sample_contact_email | phiel.1@osu.edu
| | Sample_contact_institute | The Research Institute at Nationwide Children's Hospital
| | Sample_contact_address | 700 Children's Drive W432
| | Sample_contact_city | Columbus
| | Sample_contact_state | OH
| | Sample_contact_zip/postal_code | 43205
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM499nnn/GSM499763/suppl/GSM499763.CEL.gz
| | Sample_series_id | GSE27395
| | Sample_data_row_count | 45101
| | |
|
GSM499764 | GPL1261 |
|
Gsk-3b-/- ESCs Rep3
|
Total RNA from Gsk-3b-/- ESCs
|
genotype/variation: GSK-3b-/-
cell type: embryonic stem cells
|
none
|
| Sample_geo_accession | GSM499764
| | Sample_status | Public on Sep 15 2011
| | Sample_submission_date | Jan 22 2010
| | Sample_last_update_date | Sep 15 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_growth_protocol_ch1 | Feeder-free wild-type, GSK-3a-/-, Gsk-3b-/-, and Gsk-3 DKO ESCs were grown on gelatin coated plates in high glucose DMEM (GIBCO) supplemented with 15% fetal bovine serum (Hyclone), 1X non-essential amino acids, 1X sodium pyruvate, 2mM L-glutamine, 1X penicillin/streptomycin (GIBCO), 55 mM 2-mercaptoethanol, and 1000 units/ml ESGRO (Millilpore). Media was replenished every other day.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Cells were collected by addition of 0.25% trypsin EDTA to PBS washed cells and incubated for 1 minute at 37C. Trypsin was inactivated by addition of twice the volume of ESC media. Cells were washed in PBS, and resuspended in TRIzol (Invitrogen), and RNA was isolated following the manufacturer's protocol. RNA was then further purified with the RNeasy RNA cleanup procedure (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | The Ovation™ Biotin RNA Amplification and Labeling System (NuGen Technologies, Inc., San Carlos, CA) was used to prepare amplified, biotin-labeled cDNA from total RNA for following manufacturer’s instructions. Briefly, first strand cDNA was synthesized from 25 ng of total RNA using a unique first strand DNA/RNA chimeric primer and reverse transcriptase. Following double strand cDNA generation, amplification of cDNA was achieved by utilizing an isothermal DNA amplification process that involves repeated SPIA™ DNA/RNA primer binding, DNA duplication, strand displacement and RNA cleavage. The amplified SPIA™ cDNA was purified and subjected to a two-step fragmentation and labeling process. The fragmented/biotinylated cDNA content was measured in a ND-1000 spectrophotometer and the quality was analyzed on an RNA 6000 Nano LabChip (Agilent) using Agilent Bioanalyzer 2100.
| | Sample_hyb_protocol | Following fragmentation, labeled cRNA was hybridized to the Mouse 430 2.0 array. Hybridization was allowed to continue for 16 hours at 45ºC followed by washing and staining of microarrays in a Fluidics Station 450 (Affymetrix Inc., USA).
| | Sample_scan_protocol | GeneChips were scanned in a GeneChip Scanner 3000 (Affymetrix Inc., USA)
| | Sample_data_processing | CEL files were generated from DAT files using GeneChip® Operating Software (GCOS) software (Affymetrix Inc., USA). The probe set signals were generated using the Background Adjustment Using Sequence Information (gcrma 2.14.1) Package in R version 2.8.0. Data was used to determine differential gene expression by pair-wise comparisons and statistical analysis was performed using both the Linear Models for Microarray Data (limma 2.16.5) and Multiple testing using SAM and Efron's empirical Bayes approaches (siggenes 1.16.0) packages. The genes that were altered two-fold either way with significance at either a 10% FDR or adjusted P value of <= 0.05 were sorted and used for further interpretation of the microarray data.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Christopher,,Phiel
| | Sample_contact_email | phiel.1@osu.edu
| | Sample_contact_institute | The Research Institute at Nationwide Children's Hospital
| | Sample_contact_address | 700 Children's Drive W432
| | Sample_contact_city | Columbus
| | Sample_contact_state | OH
| | Sample_contact_zip/postal_code | 43205
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM499nnn/GSM499764/suppl/GSM499764.CEL.gz
| | Sample_series_id | GSE27395
| | Sample_data_row_count | 45101
| | |
|
GSM499765 | GPL1261 |
|
Gsk-3a-/-; Gsk-3b-/- ESCs Rep1
|
Total RNA from Gsk-3a-/-; Gsk-3b-/- ESCs
|
genotype/variation: Gsk-3a-/-; Gsk-3b-/-
cell type: embryonic stem cells
|
none
|
| Sample_geo_accession | GSM499765
| | Sample_status | Public on Jun 16 2011
| | Sample_submission_date | Jan 22 2010
| | Sample_last_update_date | Jun 16 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_growth_protocol_ch1 | Feeder-free wild-type, GSK-3a-/-, Gsk-3b-/-, and Gsk-3 DKO ESCs were grown on gelatin coated plates in high glucose DMEM (GIBCO) supplemented with 15% fetal bovine serum (Hyclone), 1X non-essential amino acids, 1X sodium pyruvate, 2mM L-glutamine, 1X penicillin/streptomycin (GIBCO), 55 mM 2-mercaptoethanol, and 1000 units/ml ESGRO (Millilpore). Media was replenished every other day.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Cells were collected by addition of 0.25% trypsin EDTA to PBS washed cells and incubated for 1 minute at 37C. Trypsin was inactivated by addition of twice the volume of ESC media. Cells were washed in PBS, and resuspended in TRIzol (Invitrogen), and RNA was isolated following the manufacturer's protocol. RNA was then further purified with the RNeasy RNA cleanup procedure (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | The Ovation™ Biotin RNA Amplification and Labeling System (NuGen Technologies, Inc., San Carlos, CA) was used to prepare amplified, biotin-labeled cDNA from total RNA for following manufacturer’s instructions. Briefly, first strand cDNA was synthesized from 25 ng of total RNA using a unique first strand DNA/RNA chimeric primer and reverse transcriptase. Following double strand cDNA generation, amplification of cDNA was achieved by utilizing an isothermal DNA amplification process that involves repeated SPIA™ DNA/RNA primer binding, DNA duplication, strand displacement and RNA cleavage. The amplified SPIA™ cDNA was purified and subjected to a two-step fragmentation and labeling process. The fragmented/biotinylated cDNA content was measured in a ND-1000 spectrophotometer and the quality was analyzed on an RNA 6000 Nano LabChip (Agilent) using Agilent Bioanalyzer 2100.
| | Sample_hyb_protocol | Following fragmentation, labeled cRNA was hybridized to the Mouse 430 2.0 array. Hybridization was allowed to continue for 16 hours at 45ºC followed by washing and staining of microarrays in a Fluidics Station 450 (Affymetrix Inc., USA).
| | Sample_scan_protocol | GeneChips were scanned in a GeneChip Scanner 3000 (Affymetrix Inc., USA)
| | Sample_data_processing | CEL files were generated from DAT files using GeneChip® Operating Software (GCOS) software (Affymetrix Inc., USA). The probe set signals were generated using the Background Adjustment Using Sequence Information (gcrma 2.14.1) Package in R version 2.8.0. Data was used to determine differential gene expression by pair-wise comparisons and statistical analysis was performed using both the Linear Models for Microarray Data (limma 2.16.5) and Multiple testing using SAM and Efron's empirical Bayes approaches (siggenes 1.16.0) packages. The genes that were altered two-fold either way with significance at either a 10% FDR or adjusted P value of <= 0.05 were sorted and used for further interpretation of the microarray data.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Christopher,,Phiel
| | Sample_contact_email | phiel.1@osu.edu
| | Sample_contact_institute | The Research Institute at Nationwide Children's Hospital
| | Sample_contact_address | 700 Children's Drive W432
| | Sample_contact_city | Columbus
| | Sample_contact_state | OH
| | Sample_contact_zip/postal_code | 43205
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM499nnn/GSM499765/suppl/GSM499765.CEL.gz
| | Sample_series_id | GSE20015
| | Sample_series_id | GSE27395
| | Sample_data_row_count | 45101
| | |
|
GSM499766 | GPL1261 |
|
Gsk-3a-/-; Gsk-3b-/- ESCs Rep2
|
Total RNA from Gsk-3a-/-; Gsk-3b-/- ESCs
|
genotype/variation: Gsk-3a-/-; Gsk-3b-/-
cell type: embryonic stem cells
|
none
|
| Sample_geo_accession | GSM499766
| | Sample_status | Public on Jun 16 2011
| | Sample_submission_date | Jan 22 2010
| | Sample_last_update_date | Jun 16 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_growth_protocol_ch1 | Feeder-free wild-type, GSK-3a-/-, Gsk-3b-/-, and Gsk-3 DKO ESCs were grown on gelatin coated plates in high glucose DMEM (GIBCO) supplemented with 15% fetal bovine serum (Hyclone), 1X non-essential amino acids, 1X sodium pyruvate, 2mM L-glutamine, 1X penicillin/streptomycin (GIBCO), 55 mM 2-mercaptoethanol, and 1000 units/ml ESGRO (Millilpore). Media was replenished every other day.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Cells were collected by addition of 0.25% trypsin EDTA to PBS washed cells and incubated for 1 minute at 37C. Trypsin was inactivated by addition of twice the volume of ESC media. Cells were washed in PBS, and resuspended in TRIzol (Invitrogen), and RNA was isolated following the manufacturer's protocol. RNA was then further purified with the RNeasy RNA cleanup procedure (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | The Ovation™ Biotin RNA Amplification and Labeling System (NuGen Technologies, Inc., San Carlos, CA) was used to prepare amplified, biotin-labeled cDNA from total RNA for following manufacturer’s instructions. Briefly, first strand cDNA was synthesized from 25 ng of total RNA using a unique first strand DNA/RNA chimeric primer and reverse transcriptase. Following double strand cDNA generation, amplification of cDNA was achieved by utilizing an isothermal DNA amplification process that involves repeated SPIA™ DNA/RNA primer binding, DNA duplication, strand displacement and RNA cleavage. The amplified SPIA™ cDNA was purified and subjected to a two-step fragmentation and labeling process. The fragmented/biotinylated cDNA content was measured in a ND-1000 spectrophotometer and the quality was analyzed on an RNA 6000 Nano LabChip (Agilent) using Agilent Bioanalyzer 2100.
| | Sample_hyb_protocol | Following fragmentation, labeled cRNA was hybridized to the Mouse 430 2.0 array. Hybridization was allowed to continue for 16 hours at 45ºC followed by washing and staining of microarrays in a Fluidics Station 450 (Affymetrix Inc., USA).
| | Sample_scan_protocol | GeneChips were scanned in a GeneChip Scanner 3000 (Affymetrix Inc., USA)
| | Sample_data_processing | CEL files were generated from DAT files using GeneChip® Operating Software (GCOS) software (Affymetrix Inc., USA). The probe set signals were generated using the Background Adjustment Using Sequence Information (gcrma 2.14.1) Package in R version 2.8.0. Data was used to determine differential gene expression by pair-wise comparisons and statistical analysis was performed using both the Linear Models for Microarray Data (limma 2.16.5) and Multiple testing using SAM and Efron's empirical Bayes approaches (siggenes 1.16.0) packages. The genes that were altered two-fold either way with significance at either a 10% FDR or adjusted P value of <= 0.05 were sorted and used for further interpretation of the microarray data.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Christopher,,Phiel
| | Sample_contact_email | phiel.1@osu.edu
| | Sample_contact_institute | The Research Institute at Nationwide Children's Hospital
| | Sample_contact_address | 700 Children's Drive W432
| | Sample_contact_city | Columbus
| | Sample_contact_state | OH
| | Sample_contact_zip/postal_code | 43205
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM499nnn/GSM499766/suppl/GSM499766.CEL.gz
| | Sample_series_id | GSE20015
| | Sample_series_id | GSE27395
| | Sample_data_row_count | 45101
| | |
|
GSM499767 | GPL1261 |
|
Gsk-3a-/-; Gsk-3b-/- ESCs Rep3
|
Total RNA from Gsk-3a-/-; Gsk-3b-/- ESCs
|
genotype/variation: Gsk-3a-/-; Gsk-3b-/-
cell type: embryonic stem cells
|
none
|
| Sample_geo_accession | GSM499767
| | Sample_status | Public on Jun 16 2011
| | Sample_submission_date | Jan 22 2010
| | Sample_last_update_date | Jun 16 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_growth_protocol_ch1 | Feeder-free wild-type, GSK-3a-/-, Gsk-3b-/-, and Gsk-3 DKO ESCs were grown on gelatin coated plates in high glucose DMEM (GIBCO) supplemented with 15% fetal bovine serum (Hyclone), 1X non-essential amino acids, 1X sodium pyruvate, 2mM L-glutamine, 1X penicillin/streptomycin (GIBCO), 55 mM 2-mercaptoethanol, and 1000 units/ml ESGRO (Millilpore). Media was replenished every other day.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Cells were collected by addition of 0.25% trypsin EDTA to PBS washed cells and incubated for 1 minute at 37C. Trypsin was inactivated by addition of twice the volume of ESC media. Cells were washed in PBS, and resuspended in TRIzol (Invitrogen), and RNA was isolated following the manufacturer's protocol. RNA was then further purified with the RNeasy RNA cleanup procedure (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | The Ovation™ Biotin RNA Amplification and Labeling System (NuGen Technologies, Inc., San Carlos, CA) was used to prepare amplified, biotin-labeled cDNA from total RNA for following manufacturer’s instructions. Briefly, first strand cDNA was synthesized from 25 ng of total RNA using a unique first strand DNA/RNA chimeric primer and reverse transcriptase. Following double strand cDNA generation, amplification of cDNA was achieved by utilizing an isothermal DNA amplification process that involves repeated SPIA™ DNA/RNA primer binding, DNA duplication, strand displacement and RNA cleavage. The amplified SPIA™ cDNA was purified and subjected to a two-step fragmentation and labeling process. The fragmented/biotinylated cDNA content was measured in a ND-1000 spectrophotometer and the quality was analyzed on an RNA 6000 Nano LabChip (Agilent) using Agilent Bioanalyzer 2100.
| | Sample_hyb_protocol | Following fragmentation, labeled cRNA was hybridized to the Mouse 430 2.0 array. Hybridization was allowed to continue for 16 hours at 45ºC followed by washing and staining of microarrays in a Fluidics Station 450 (Affymetrix Inc., USA).
| | Sample_scan_protocol | GeneChips were scanned in a GeneChip Scanner 3000 (Affymetrix Inc., USA)
| | Sample_data_processing | CEL files were generated from DAT files using GeneChip® Operating Software (GCOS) software (Affymetrix Inc., USA). The probe set signals were generated using the Background Adjustment Using Sequence Information (gcrma 2.14.1) Package in R version 2.8.0. Data was used to determine differential gene expression by pair-wise comparisons and statistical analysis was performed using both the Linear Models for Microarray Data (limma 2.16.5) and Multiple testing using SAM and Efron's empirical Bayes approaches (siggenes 1.16.0) packages. The genes that were altered two-fold either way with significance at either a 10% FDR or adjusted P value of <= 0.05 were sorted and used for further interpretation of the microarray data.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Christopher,,Phiel
| | Sample_contact_email | phiel.1@osu.edu
| | Sample_contact_institute | The Research Institute at Nationwide Children's Hospital
| | Sample_contact_address | 700 Children's Drive W432
| | Sample_contact_city | Columbus
| | Sample_contact_state | OH
| | Sample_contact_zip/postal_code | 43205
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM499nnn/GSM499767/suppl/GSM499767.CEL.gz
| | Sample_series_id | GSE20015
| | Sample_series_id | GSE27395
| | Sample_data_row_count | 45101
| | |
|
GSM499768 | GPL1261 |
|
Wild-type ESCs Rep1
|
Total RNA from WT ESCs
|
genotype/variation: Wild-type (E14K)
cell type: embryonic stem cells
|
none
|
| Sample_geo_accession | GSM499768
| | Sample_status | Public on Jun 16 2011
| | Sample_submission_date | Jan 22 2010
| | Sample_last_update_date | Jun 16 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_growth_protocol_ch1 | Feeder-free wild-type, GSK-3a-/-, Gsk-3b-/-, and Gsk-3 DKO ESCs were grown on gelatin coated plates in high glucose DMEM (GIBCO) supplemented with 15% fetal bovine serum (Hyclone), 1X non-essential amino acids, 1X sodium pyruvate, 2mM L-glutamine, 1X penicillin/streptomycin (GIBCO), 55 mM 2-mercaptoethanol, and 1000 units/ml ESGRO (Millilpore). Media was replenished every other day.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Cells were collected by addition of 0.25% trypsin EDTA to PBS washed cells and incubated for 1 minute at 37C. Trypsin was inactivated by addition of twice the volume of ESC media. Cells were washed in PBS, and resuspended in TRIzol (Invitrogen), and RNA was isolated following the manufacturer's protocol. RNA was then further purified with the RNeasy RNA cleanup procedure (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | The Ovation™ Biotin RNA Amplification and Labeling System (NuGen Technologies, Inc., San Carlos, CA) was used to prepare amplified, biotin-labeled cDNA from total RNA for following manufacturer’s instructions. Briefly, first strand cDNA was synthesized from 25 ng of total RNA using a unique first strand DNA/RNA chimeric primer and reverse transcriptase. Following double strand cDNA generation, amplification of cDNA was achieved by utilizing an isothermal DNA amplification process that involves repeated SPIA™ DNA/RNA primer binding, DNA duplication, strand displacement and RNA cleavage. The amplified SPIA™ cDNA was purified and subjected to a two-step fragmentation and labeling process. The fragmented/biotinylated cDNA content was measured in a ND-1000 spectrophotometer and the quality was analyzed on an RNA 6000 Nano LabChip (Agilent) using Agilent Bioanalyzer 2100.
| | Sample_hyb_protocol | Following fragmentation, labeled cRNA was hybridized to the Mouse 430 2.0 array. Hybridization was allowed to continue for 16 hours at 45ºC followed by washing and staining of microarrays in a Fluidics Station 450 (Affymetrix Inc., USA).
| | Sample_scan_protocol | GeneChips were scanned in a GeneChip Scanner 3000 (Affymetrix Inc., USA)
| | Sample_data_processing | CEL files were generated from DAT files using GeneChip® Operating Software (GCOS) software (Affymetrix Inc., USA). The probe set signals were generated using the Background Adjustment Using Sequence Information (gcrma 2.14.1) Package in R version 2.8.0. Data was used to determine differential gene expression by pair-wise comparisons and statistical analysis was performed using both the Linear Models for Microarray Data (limma 2.16.5) and Multiple testing using SAM and Efron's empirical Bayes approaches (siggenes 1.16.0) packages. The genes that were altered two-fold either way with significance at either a 10% FDR or adjusted P value of <= 0.05 were sorted and used for further interpretation of the microarray data.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Christopher,,Phiel
| | Sample_contact_email | phiel.1@osu.edu
| | Sample_contact_institute | The Research Institute at Nationwide Children's Hospital
| | Sample_contact_address | 700 Children's Drive W432
| | Sample_contact_city | Columbus
| | Sample_contact_state | OH
| | Sample_contact_zip/postal_code | 43205
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM499nnn/GSM499768/suppl/GSM499768.CEL.gz
| | Sample_series_id | GSE20015
| | Sample_series_id | GSE27395
| | Sample_data_row_count | 45101
| | |
|
GSM499769 | GPL1261 |
|
Wild-type ESCs Rep2
|
Total RNA from WT ESCs
|
genotype/variation: Wild-type (E14K)
cell type: embryonic stem cells
|
none
|
| Sample_geo_accession | GSM499769
| | Sample_status | Public on Jun 16 2011
| | Sample_submission_date | Jan 22 2010
| | Sample_last_update_date | Jun 16 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_growth_protocol_ch1 | Feeder-free wild-type, GSK-3a-/-, Gsk-3b-/-, and Gsk-3 DKO ESCs were grown on gelatin coated plates in high glucose DMEM (GIBCO) supplemented with 15% fetal bovine serum (Hyclone), 1X non-essential amino acids, 1X sodium pyruvate, 2mM L-glutamine, 1X penicillin/streptomycin (GIBCO), 55 mM 2-mercaptoethanol, and 1000 units/ml ESGRO (Millilpore). Media was replenished every other day.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Cells were collected by addition of 0.25% trypsin EDTA to PBS washed cells and incubated for 1 minute at 37C. Trypsin was inactivated by addition of twice the volume of ESC media. Cells were washed in PBS, and resuspended in TRIzol (Invitrogen), and RNA was isolated following the manufacturer's protocol. RNA was then further purified with the RNeasy RNA cleanup procedure (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | The Ovation™ Biotin RNA Amplification and Labeling System (NuGen Technologies, Inc., San Carlos, CA) was used to prepare amplified, biotin-labeled cDNA from total RNA for following manufacturer’s instructions. Briefly, first strand cDNA was synthesized from 25 ng of total RNA using a unique first strand DNA/RNA chimeric primer and reverse transcriptase. Following double strand cDNA generation, amplification of cDNA was achieved by utilizing an isothermal DNA amplification process that involves repeated SPIA™ DNA/RNA primer binding, DNA duplication, strand displacement and RNA cleavage. The amplified SPIA™ cDNA was purified and subjected to a two-step fragmentation and labeling process. The fragmented/biotinylated cDNA content was measured in a ND-1000 spectrophotometer and the quality was analyzed on an RNA 6000 Nano LabChip (Agilent) using Agilent Bioanalyzer 2100.
| | Sample_hyb_protocol | Following fragmentation, labeled cRNA was hybridized to the Mouse 430 2.0 array. Hybridization was allowed to continue for 16 hours at 45ºC followed by washing and staining of microarrays in a Fluidics Station 450 (Affymetrix Inc., USA).
| | Sample_scan_protocol | GeneChips were scanned in a GeneChip Scanner 3000 (Affymetrix Inc., USA)
| | Sample_data_processing | CEL files were generated from DAT files using GeneChip® Operating Software (GCOS) software (Affymetrix Inc., USA). The probe set signals were generated using the Background Adjustment Using Sequence Information (gcrma 2.14.1) Package in R version 2.8.0. Data was used to determine differential gene expression by pair-wise comparisons and statistical analysis was performed using both the Linear Models for Microarray Data (limma 2.16.5) and Multiple testing using SAM and Efron's empirical Bayes approaches (siggenes 1.16.0) packages. The genes that were altered two-fold either way with significance at either a 10% FDR or adjusted P value of <= 0.05 were sorted and used for further interpretation of the microarray data.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Christopher,,Phiel
| | Sample_contact_email | phiel.1@osu.edu
| | Sample_contact_institute | The Research Institute at Nationwide Children's Hospital
| | Sample_contact_address | 700 Children's Drive W432
| | Sample_contact_city | Columbus
| | Sample_contact_state | OH
| | Sample_contact_zip/postal_code | 43205
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM499nnn/GSM499769/suppl/GSM499769.CEL.gz
| | Sample_series_id | GSE20015
| | Sample_series_id | GSE27395
| | Sample_data_row_count | 45101
| | |
|
GSM499770 | GPL1261 |
|
Wild-type ESCs Rep3
|
Total RNA from WT ESCs
|
genotype/variation: Wild-type (E14K)
cell type: embryonic stem cells
|
none
|
| Sample_geo_accession | GSM499770
| | Sample_status | Public on Jun 16 2011
| | Sample_submission_date | Jan 22 2010
| | Sample_last_update_date | Jun 16 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_growth_protocol_ch1 | Feeder-free wild-type, GSK-3a-/-, Gsk-3b-/-, and Gsk-3 DKO ESCs were grown on gelatin coated plates in high glucose DMEM (GIBCO) supplemented with 15% fetal bovine serum (Hyclone), 1X non-essential amino acids, 1X sodium pyruvate, 2mM L-glutamine, 1X penicillin/streptomycin (GIBCO), 55 mM 2-mercaptoethanol, and 1000 units/ml ESGRO (Millilpore). Media was replenished every other day.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Cells were collected by addition of 0.25% trypsin EDTA to PBS washed cells and incubated for 1 minute at 37C. Trypsin was inactivated by addition of twice the volume of ESC media. Cells were washed in PBS, and resuspended in TRIzol (Invitrogen), and RNA was isolated following the manufacturer's protocol. RNA was then further purified with the RNeasy RNA cleanup procedure (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | The Ovation™ Biotin RNA Amplification and Labeling System (NuGen Technologies, Inc., San Carlos, CA) was used to prepare amplified, biotin-labeled cDNA from total RNA for following manufacturer’s instructions. Briefly, first strand cDNA was synthesized from 25 ng of total RNA using a unique first strand DNA/RNA chimeric primer and reverse transcriptase. Following double strand cDNA generation, amplification of cDNA was achieved by utilizing an isothermal DNA amplification process that involves repeated SPIA™ DNA/RNA primer binding, DNA duplication, strand displacement and RNA cleavage. The amplified SPIA™ cDNA was purified and subjected to a two-step fragmentation and labeling process. The fragmented/biotinylated cDNA content was measured in a ND-1000 spectrophotometer and the quality was analyzed on an RNA 6000 Nano LabChip (Agilent) using Agilent Bioanalyzer 2100.
| | Sample_hyb_protocol | Following fragmentation, labeled cRNA was hybridized to the Mouse 430 2.0 array. Hybridization was allowed to continue for 16 hours at 45ºC followed by washing and staining of microarrays in a Fluidics Station 450 (Affymetrix Inc., USA).
| | Sample_scan_protocol | GeneChips were scanned in a GeneChip Scanner 3000 (Affymetrix Inc., USA)
| | Sample_data_processing | CEL files were generated from DAT files using GeneChip® Operating Software (GCOS) software (Affymetrix Inc., USA). The probe set signals were generated using the Background Adjustment Using Sequence Information (gcrma 2.14.1) Package in R version 2.8.0. Data was used to determine differential gene expression by pair-wise comparisons and statistical analysis was performed using both the Linear Models for Microarray Data (limma 2.16.5) and Multiple testing using SAM and Efron's empirical Bayes approaches (siggenes 1.16.0) packages. The genes that were altered two-fold either way with significance at either a 10% FDR or adjusted P value of <= 0.05 were sorted and used for further interpretation of the microarray data.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Christopher,,Phiel
| | Sample_contact_email | phiel.1@osu.edu
| | Sample_contact_institute | The Research Institute at Nationwide Children's Hospital
| | Sample_contact_address | 700 Children's Drive W432
| | Sample_contact_city | Columbus
| | Sample_contact_state | OH
| | Sample_contact_zip/postal_code | 43205
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM499nnn/GSM499770/suppl/GSM499770.CEL.gz
| | Sample_series_id | GSE20015
| | Sample_series_id | GSE27395
| | Sample_data_row_count | 45101
| | |
|
| |
| |
Make groups for comparisons |
(2 groups will be compared at a time) |
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Enter the group name here: |
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