Search results for the GEO ID: GSE39770  |
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|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM978927 | GPL1261 |
|
siNonTarget replicate1
|
siNonTarget
|
cell line: NG4
cell type: embryonic stem cells
transfection: siNonTarget
|
48hrs post siRNA transfection
|
| Sample_geo_accession | GSM978927
| | Sample_status | Public on Aug 01 2012
| | Sample_submission_date | Jul 31 2012
| | Sample_last_update_date | Aug 01 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_biomaterial_provider_ch1 | NG4 derived in the lab of Ihor Lemischka
| | Sample_treatment_protocol_ch1 | Embryonic stem cells were reverse transfected with siRNA, and differentiated for 48hrs in conditions with retinoic acid, 48 hrs post transfection cells were isloated for RNA extraction and hybridization on Affymetrix microarrays
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Qiagen RNEasy Plus mini Kit was used to extract total cellular RNA according to the manufacturer's protocol, and the RNA was amplified and converted into cDNA using the Ovation Amplification v2 and Biotin cDNA Biotin systems
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | 5 ng total RNA was amplified by Nugen Ovation RNA amplification system V2 and the resulting cDNA biotin-labeled using the FL-Ovation™ cDNA Biotin Module V2
| | Sample_hyb_protocol | 3.75 mcg of biotin-labeled cDNA were hybridized for 16 hrs onto the GeneChip Mouse Genome 430 2.0 Arrays (Affymetrix)
| | Sample_scan_protocol | Affymetrix 7G GeneArray scanner
| | Sample_data_processing | Feature intensity was extracted by GeneChip Operating System as CEL files. The probe-level analysis of the CEL files was performed by the RMA algorithm using dChip program. No further adjustments were made to the data in the table.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Shannon ,,Buckley
| | Sample_contact_institute | NYU School of Medicine
| | Sample_contact_address | 550 First Ave MSB 504
| | Sample_contact_city | New York
| | Sample_contact_state | NY
| | Sample_contact_zip/postal_code | 10022
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM978nnn/GSM978927/suppl/GSM978927_Shannon_1_120810.CEL.gz
| | Sample_series_id | GSE39770
| | Sample_series_id | GSE39772
| | Sample_data_row_count | 45101
| | |
|
GSM978928 | GPL1261 |
|
siNonTarget replicate2
|
siNonTarget
|
cell line: NG4
cell type: embryonic stem cells
transfection: siNonTarget
|
48hrs post siRNA transfection
|
| Sample_geo_accession | GSM978928
| | Sample_status | Public on Aug 01 2012
| | Sample_submission_date | Jul 31 2012
| | Sample_last_update_date | Aug 01 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_biomaterial_provider_ch1 | NG4 derived in the lab of Ihor Lemischka
| | Sample_treatment_protocol_ch1 | Embryonic stem cells were reverse transfected with siRNA, and differentiated for 48hrs in conditions with retinoic acid, 48 hrs post transfection cells were isloated for RNA extraction and hybridization on Affymetrix microarrays
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Qiagen RNEasy Plus mini Kit was used to extract total cellular RNA according to the manufacturer's protocol, and the RNA was amplified and converted into cDNA using the Ovation Amplification v2 and Biotin cDNA Biotin systems
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | 5 ng total RNA was amplified by Nugen Ovation RNA amplification system V2 and the resulting cDNA biotin-labeled using the FL-Ovation™ cDNA Biotin Module V2
| | Sample_hyb_protocol | 3.75 mcg of biotin-labeled cDNA were hybridized for 16 hrs onto the GeneChip Mouse Genome 430 2.0 Arrays (Affymetrix)
| | Sample_scan_protocol | Affymetrix 7G GeneArray scanner
| | Sample_data_processing | Feature intensity was extracted by GeneChip Operating System as CEL files. The probe-level analysis of the CEL files was performed by the RMA algorithm using dChip program. No further adjustments were made to the data in the table.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Shannon ,,Buckley
| | Sample_contact_institute | NYU School of Medicine
| | Sample_contact_address | 550 First Ave MSB 504
| | Sample_contact_city | New York
| | Sample_contact_state | NY
| | Sample_contact_zip/postal_code | 10022
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM978nnn/GSM978928/suppl/GSM978928_Shannon_2_120810.CEL.gz
| | Sample_series_id | GSE39770
| | Sample_series_id | GSE39772
| | Sample_data_row_count | 45101
| | |
|
GSM978929 | GPL1261 |
|
siSox17 replicate1
|
siSox17
|
cell line: NG4
cell type: embryonic stem cells
transfection: siSox17
|
48hrs post siRNA transfection
|
| Sample_geo_accession | GSM978929
| | Sample_status | Public on Aug 01 2012
| | Sample_submission_date | Jul 31 2012
| | Sample_last_update_date | Aug 01 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_biomaterial_provider_ch1 | NG4 derived in the lab of Ihor Lemischka
| | Sample_treatment_protocol_ch1 | Embryonic stem cells were reverse transfected with siRNA, and differentiated for 48hrs in conditions with retinoic acid, 48 hrs post transfection cells were isloated for RNA extraction and hybridization on Affymetrix microarrays
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Qiagen RNEasy Plus mini Kit was used to extract total cellular RNA according to the manufacturer's protocol, and the RNA was amplified and converted into cDNA using the Ovation Amplification v2 and Biotin cDNA Biotin systems
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | 5 ng total RNA was amplified by Nugen Ovation RNA amplification system V2 and the resulting cDNA biotin-labeled using the FL-Ovation™ cDNA Biotin Module V2
| | Sample_hyb_protocol | 3.75 mcg of biotin-labeled cDNA were hybridized for 16 hrs onto the GeneChip Mouse Genome 430 2.0 Arrays (Affymetrix)
| | Sample_scan_protocol | Affymetrix 7G GeneArray scanner
| | Sample_data_processing | Feature intensity was extracted by GeneChip Operating System as CEL files. The probe-level analysis of the CEL files was performed by the RMA algorithm using dChip program. No further adjustments were made to the data in the table.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Shannon ,,Buckley
| | Sample_contact_institute | NYU School of Medicine
| | Sample_contact_address | 550 First Ave MSB 504
| | Sample_contact_city | New York
| | Sample_contact_state | NY
| | Sample_contact_zip/postal_code | 10022
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM978nnn/GSM978929/suppl/GSM978929_Shannon_3_120810.CEL.gz
| | Sample_series_id | GSE39770
| | Sample_series_id | GSE39772
| | Sample_data_row_count | 45101
| | |
|
GSM978930 | GPL1261 |
|
siSox17 replicate2
|
siSox17
|
cell line: NG4
cell type: embryonic stem cells
transfection: siSox17
|
48hrs post siRNA transfection
|
| Sample_geo_accession | GSM978930
| | Sample_status | Public on Aug 01 2012
| | Sample_submission_date | Jul 31 2012
| | Sample_last_update_date | Aug 01 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_biomaterial_provider_ch1 | NG4 derived in the lab of Ihor Lemischka
| | Sample_treatment_protocol_ch1 | Embryonic stem cells were reverse transfected with siRNA, and differentiated for 48hrs in conditions with retinoic acid, 48 hrs post transfection cells were isloated for RNA extraction and hybridization on Affymetrix microarrays
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Qiagen RNEasy Plus mini Kit was used to extract total cellular RNA according to the manufacturer's protocol, and the RNA was amplified and converted into cDNA using the Ovation Amplification v2 and Biotin cDNA Biotin systems
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | 5 ng total RNA was amplified by Nugen Ovation RNA amplification system V2 and the resulting cDNA biotin-labeled using the FL-Ovation™ cDNA Biotin Module V2
| | Sample_hyb_protocol | 3.75 mcg of biotin-labeled cDNA were hybridized for 16 hrs onto the GeneChip Mouse Genome 430 2.0 Arrays (Affymetrix)
| | Sample_scan_protocol | Affymetrix 7G GeneArray scanner
| | Sample_data_processing | Feature intensity was extracted by GeneChip Operating System as CEL files. The probe-level analysis of the CEL files was performed by the RMA algorithm using dChip program. No further adjustments were made to the data in the table.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Shannon ,,Buckley
| | Sample_contact_institute | NYU School of Medicine
| | Sample_contact_address | 550 First Ave MSB 504
| | Sample_contact_city | New York
| | Sample_contact_state | NY
| | Sample_contact_zip/postal_code | 10022
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM978nnn/GSM978930/suppl/GSM978930_Shannon_4_120810.CEL.gz
| | Sample_series_id | GSE39770
| | Sample_series_id | GSE39772
| | Sample_data_row_count | 45101
| | |
|
GSM978931 | GPL1261 |
|
siFbxw7 replicate1
|
siFbxw7
|
cell line: NG4
cell type: embryonic stem cells
transfection: siFbxw7
|
48hrs post siRNA transfection
|
| Sample_geo_accession | GSM978931
| | Sample_status | Public on Aug 01 2012
| | Sample_submission_date | Jul 31 2012
| | Sample_last_update_date | Aug 01 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_biomaterial_provider_ch1 | NG4 derived in the lab of Ihor Lemischka
| | Sample_treatment_protocol_ch1 | Embryonic stem cells were reverse transfected with siRNA, and differentiated for 48hrs in conditions with retinoic acid, 48 hrs post transfection cells were isloated for RNA extraction and hybridization on Affymetrix microarrays
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Qiagen RNEasy Plus mini Kit was used to extract total cellular RNA according to the manufacturer's protocol, and the RNA was amplified and converted into cDNA using the Ovation Amplification v2 and Biotin cDNA Biotin systems
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | 5 ng total RNA was amplified by Nugen Ovation RNA amplification system V2 and the resulting cDNA biotin-labeled using the FL-Ovation™ cDNA Biotin Module V2
| | Sample_hyb_protocol | 3.75 mcg of biotin-labeled cDNA were hybridized for 16 hrs onto the GeneChip Mouse Genome 430 2.0 Arrays (Affymetrix)
| | Sample_scan_protocol | Affymetrix 7G GeneArray scanner
| | Sample_data_processing | Feature intensity was extracted by GeneChip Operating System as CEL files. The probe-level analysis of the CEL files was performed by the RMA algorithm using dChip program. No further adjustments were made to the data in the table.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Shannon ,,Buckley
| | Sample_contact_institute | NYU School of Medicine
| | Sample_contact_address | 550 First Ave MSB 504
| | Sample_contact_city | New York
| | Sample_contact_state | NY
| | Sample_contact_zip/postal_code | 10022
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM978nnn/GSM978931/suppl/GSM978931_Shannon_5_120810.CEL.gz
| | Sample_series_id | GSE39770
| | Sample_series_id | GSE39772
| | Sample_data_row_count | 45101
| | |
|
GSM978932 | GPL1261 |
|
siFbxw7 replicate2
|
siFbxw7
|
cell line: NG4
cell type: embryonic stem cells
transfection: siFbxw7
|
48hrs post siRNA transfection
|
| Sample_geo_accession | GSM978932
| | Sample_status | Public on Aug 01 2012
| | Sample_submission_date | Jul 31 2012
| | Sample_last_update_date | Aug 01 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_biomaterial_provider_ch1 | NG4 derived in the lab of Ihor Lemischka
| | Sample_treatment_protocol_ch1 | Embryonic stem cells were reverse transfected with siRNA, and differentiated for 48hrs in conditions with retinoic acid, 48 hrs post transfection cells were isloated for RNA extraction and hybridization on Affymetrix microarrays
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Qiagen RNEasy Plus mini Kit was used to extract total cellular RNA according to the manufacturer's protocol, and the RNA was amplified and converted into cDNA using the Ovation Amplification v2 and Biotin cDNA Biotin systems
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | 5 ng total RNA was amplified by Nugen Ovation RNA amplification system V2 and the resulting cDNA biotin-labeled using the FL-Ovation™ cDNA Biotin Module V2
| | Sample_hyb_protocol | 3.75 mcg of biotin-labeled cDNA were hybridized for 16 hrs onto the GeneChip Mouse Genome 430 2.0 Arrays (Affymetrix)
| | Sample_scan_protocol | Affymetrix 7G GeneArray scanner
| | Sample_data_processing | Feature intensity was extracted by GeneChip Operating System as CEL files. The probe-level analysis of the CEL files was performed by the RMA algorithm using dChip program. No further adjustments were made to the data in the table.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Shannon ,,Buckley
| | Sample_contact_institute | NYU School of Medicine
| | Sample_contact_address | 550 First Ave MSB 504
| | Sample_contact_city | New York
| | Sample_contact_state | NY
| | Sample_contact_zip/postal_code | 10022
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM978nnn/GSM978932/suppl/GSM978932_Shannon_6_120810.CEL.gz
| | Sample_series_id | GSE39770
| | Sample_series_id | GSE39772
| | Sample_data_row_count | 45101
| | |
|
GSM978933 | GPL1261 |
|
siSocs3 replicate1
|
siSocs3
|
cell line: NG4
cell type: embryonic stem cells
transfection: siSocs3
|
48hrs post siRNA transfection
|
| Sample_geo_accession | GSM978933
| | Sample_status | Public on Aug 01 2012
| | Sample_submission_date | Jul 31 2012
| | Sample_last_update_date | Aug 01 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_biomaterial_provider_ch1 | NG4 derived in the lab of Ihor Lemischka
| | Sample_treatment_protocol_ch1 | Embryonic stem cells were reverse transfected with siRNA, and differentiated for 48hrs in conditions with retinoic acid, 48 hrs post transfection cells were isloated for RNA extraction and hybridization on Affymetrix microarrays
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Qiagen RNEasy Plus mini Kit was used to extract total cellular RNA according to the manufacturer's protocol, and the RNA was amplified and converted into cDNA using the Ovation Amplification v2 and Biotin cDNA Biotin systems
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | 5 ng total RNA was amplified by Nugen Ovation RNA amplification system V2 and the resulting cDNA biotin-labeled using the FL-Ovation™ cDNA Biotin Module V2
| | Sample_hyb_protocol | 3.75 mcg of biotin-labeled cDNA were hybridized for 16 hrs onto the GeneChip Mouse Genome 430 2.0 Arrays (Affymetrix)
| | Sample_scan_protocol | Affymetrix 7G GeneArray scanner
| | Sample_data_processing | Feature intensity was extracted by GeneChip Operating System as CEL files. The probe-level analysis of the CEL files was performed by the RMA algorithm using dChip program. No further adjustments were made to the data in the table.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Shannon ,,Buckley
| | Sample_contact_institute | NYU School of Medicine
| | Sample_contact_address | 550 First Ave MSB 504
| | Sample_contact_city | New York
| | Sample_contact_state | NY
| | Sample_contact_zip/postal_code | 10022
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM978nnn/GSM978933/suppl/GSM978933_Shannon_7_120810.CEL.gz
| | Sample_series_id | GSE39770
| | Sample_series_id | GSE39772
| | Sample_data_row_count | 45101
| | |
|
GSM978934 | GPL1261 |
|
siSocs3 replicate2
|
siSocs3
|
cell line: NG4
cell type: embryonic stem cells
transfection: siSocs3
|
48hrs post siRNA transfection
|
| Sample_geo_accession | GSM978934
| | Sample_status | Public on Aug 01 2012
| | Sample_submission_date | Jul 31 2012
| | Sample_last_update_date | Aug 01 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_biomaterial_provider_ch1 | NG4 derived in the lab of Ihor Lemischka
| | Sample_treatment_protocol_ch1 | Embryonic stem cells were reverse transfected with siRNA, and differentiated for 48hrs in conditions with retinoic acid, 48 hrs post transfection cells were isloated for RNA extraction and hybridization on Affymetrix microarrays
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Qiagen RNEasy Plus mini Kit was used to extract total cellular RNA according to the manufacturer's protocol, and the RNA was amplified and converted into cDNA using the Ovation Amplification v2 and Biotin cDNA Biotin systems
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | 5 ng total RNA was amplified by Nugen Ovation RNA amplification system V2 and the resulting cDNA biotin-labeled using the FL-Ovation™ cDNA Biotin Module V2
| | Sample_hyb_protocol | 3.75 mcg of biotin-labeled cDNA were hybridized for 16 hrs onto the GeneChip Mouse Genome 430 2.0 Arrays (Affymetrix)
| | Sample_scan_protocol | Affymetrix 7G GeneArray scanner
| | Sample_data_processing | Feature intensity was extracted by GeneChip Operating System as CEL files. The probe-level analysis of the CEL files was performed by the RMA algorithm using dChip program. No further adjustments were made to the data in the table.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Shannon ,,Buckley
| | Sample_contact_institute | NYU School of Medicine
| | Sample_contact_address | 550 First Ave MSB 504
| | Sample_contact_city | New York
| | Sample_contact_state | NY
| | Sample_contact_zip/postal_code | 10022
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM978nnn/GSM978934/suppl/GSM978934_Shannon_8_120810.CEL.gz
| | Sample_series_id | GSE39770
| | Sample_series_id | GSE39772
| | Sample_data_row_count | 45101
| | |
|
GSM978935 | GPL1261 |
|
siRnf31 replicate1
|
siRnf31
|
cell line: NG4
cell type: embryonic stem cells
transfection: siRnf31
|
48hrs post siRNA transfection
|
| Sample_geo_accession | GSM978935
| | Sample_status | Public on Aug 01 2012
| | Sample_submission_date | Jul 31 2012
| | Sample_last_update_date | Aug 01 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_biomaterial_provider_ch1 | NG4 derived in the lab of Ihor Lemischka
| | Sample_treatment_protocol_ch1 | Embryonic stem cells were reverse transfected with siRNA, and differentiated for 48hrs in conditions with retinoic acid, 48 hrs post transfection cells were isloated for RNA extraction and hybridization on Affymetrix microarrays
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Qiagen RNEasy Plus mini Kit was used to extract total cellular RNA according to the manufacturer's protocol, and the RNA was amplified and converted into cDNA using the Ovation Amplification v2 and Biotin cDNA Biotin systems
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | 5 ng total RNA was amplified by Nugen Ovation RNA amplification system V2 and the resulting cDNA biotin-labeled using the FL-Ovation™ cDNA Biotin Module V2
| | Sample_hyb_protocol | 3.75 mcg of biotin-labeled cDNA were hybridized for 16 hrs onto the GeneChip Mouse Genome 430 2.0 Arrays (Affymetrix)
| | Sample_scan_protocol | Affymetrix 7G GeneArray scanner
| | Sample_data_processing | Feature intensity was extracted by GeneChip Operating System as CEL files. The probe-level analysis of the CEL files was performed by the RMA algorithm using dChip program. No further adjustments were made to the data in the table.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Shannon ,,Buckley
| | Sample_contact_institute | NYU School of Medicine
| | Sample_contact_address | 550 First Ave MSB 504
| | Sample_contact_city | New York
| | Sample_contact_state | NY
| | Sample_contact_zip/postal_code | 10022
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM978nnn/GSM978935/suppl/GSM978935_Shannon_9_120810.CEL.gz
| | Sample_series_id | GSE39770
| | Sample_series_id | GSE39772
| | Sample_data_row_count | 45101
| | |
|
GSM978936 | GPL1261 |
|
siRnf31 replicate2
|
siRnf31
|
cell line: NG4
cell type: embryonic stem cells
transfection: siRnf31
|
48hrs post siRNA transfection
|
| Sample_geo_accession | GSM978936
| | Sample_status | Public on Aug 01 2012
| | Sample_submission_date | Jul 31 2012
| | Sample_last_update_date | Aug 01 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_biomaterial_provider_ch1 | NG4 derived in the lab of Ihor Lemischka
| | Sample_treatment_protocol_ch1 | Embryonic stem cells were reverse transfected with siRNA, and differentiated for 48hrs in conditions with retinoic acid, 48 hrs post transfection cells were isloated for RNA extraction and hybridization on Affymetrix microarrays
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Qiagen RNEasy Plus mini Kit was used to extract total cellular RNA according to the manufacturer's protocol, and the RNA was amplified and converted into cDNA using the Ovation Amplification v2 and Biotin cDNA Biotin systems
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | 5 ng total RNA was amplified by Nugen Ovation RNA amplification system V2 and the resulting cDNA biotin-labeled using the FL-Ovation™ cDNA Biotin Module V2
| | Sample_hyb_protocol | 3.75 mcg of biotin-labeled cDNA were hybridized for 16 hrs onto the GeneChip Mouse Genome 430 2.0 Arrays (Affymetrix)
| | Sample_scan_protocol | Affymetrix 7G GeneArray scanner
| | Sample_data_processing | Feature intensity was extracted by GeneChip Operating System as CEL files. The probe-level analysis of the CEL files was performed by the RMA algorithm using dChip program. No further adjustments were made to the data in the table.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Shannon ,,Buckley
| | Sample_contact_institute | NYU School of Medicine
| | Sample_contact_address | 550 First Ave MSB 504
| | Sample_contact_city | New York
| | Sample_contact_state | NY
| | Sample_contact_zip/postal_code | 10022
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM978nnn/GSM978936/suppl/GSM978936_Shannon_10_120810.CEL.gz
| | Sample_series_id | GSE39770
| | Sample_series_id | GSE39772
| | Sample_data_row_count | 45101
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