Search results for the GEO ID: GSE21222  |
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|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM530601 | GPL570 |
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WIBR3 hESC (5%pO2)
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WIBR3 hESC (5%pO2)
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cell type: Human embryonic stem cells (hESC)
cell subtype: WIBR3 hESC (5%pO2)
|
Gene expression data of cell lineWIBR3 hESC (5%pO2)
|
| Sample_geo_accession | GSM530601
| | Sample_status | Public on Apr 22 2010
| | Sample_submission_date | Apr 06 2010
| | Sample_last_update_date | Aug 15 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | RNA was feshly extracted from MEF depleted different human embryonic stem cells grown at optimal confluency.
| | Sample_growth_protocol_ch1 | Naïve and conventional human ESCs and iPSCs were propagated as described in Hanna et al. PNAS 2010
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | 100 ng total RNA was used to prepare biotinylated aRNA (cRNA) according to the manufacturer’s protocol (Affymetrix 3’ IVT Express Kit). Briefly, total RNA undergoes T7 oligo(dT)-primed reverse transcription to synthesize first-strand cDNA containing a T7 promoter sequence. This cDNA is then converted into a double-stranded DNA template for transcription using DNA Polymerase and RNase H to simultaneously degrade the RNA and synthesize second strand cDNA. In vitro transcription synthesizes aRNA and incorporates a biotin-conjugated nucleotide. The aRNA is then purified to remove unincorporated NTPs, salts, enzymes, and inorganic phosphate. Fragmentation of the biotin-labeled aRNA prepares the sample for hybridization onto GeneChip 3’ expression arrays.
| | Sample_hyb_protocol | Samples were prepared for hybridization using 12.5 µg of biotinylated aRNA in a 1X hybridization cocktail according the Affymetrix hybridization manual. Additional hybridization cocktail components were provided in the Affymetrix GeneChip Hybridization, Wash and Stain Kit. GeneChip arrays (Human U133 2.0) were hybridized in a GeneChip Hybridization Oven at 45°C for 16 hours at 60 RPM. Washing was done using a GeneChip Fluidics Station 450 according to the manufacturer’s instructions, using the buffers provided in the Affymetrix GeneChip Hybridization, Wash and Stain Kit.
| | Sample_scan_protocol | Arrays were scanned on a GeneChip Scanner 3000 and images were extracted with Affymetrix GeneChip Command Console (AGCC), and analyzed using GeneChip Expression Console.
| | Sample_data_processing | The data were analyzed with Affy and limma package (MAS5)
| | Sample_platform_id | GPL570
| | Sample_contact_name | Albert,W,Cheng
| | Sample_contact_email | awcheng@mit.edu
| | Sample_contact_institute | Whitehead Institute
| | Sample_contact_address | Room 453, 9 Cambridge Center
| | Sample_contact_city | Cambridge
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02139
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM530nnn/GSM530601/suppl/GSM530601.CEL.gz
| | Sample_relation | Reanalyzed by: GSE49910
| | Sample_series_id | GSE21222
| | Sample_data_row_count | 54675
| | |
|
GSM530602 | GPL570 |
|
BGO1 hESC
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BGO1 hESC
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cell type: Human embryonic stem cells (hESC)
cell subtype: BGO1 hESC
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Gene expression data of cell lineBGO1 hESC
|
| Sample_geo_accession | GSM530602
| | Sample_status | Public on Apr 22 2010
| | Sample_submission_date | Apr 06 2010
| | Sample_last_update_date | Aug 15 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | RNA was feshly extracted from MEF depleted different human embryonic stem cells grown at optimal confluency.
| | Sample_growth_protocol_ch1 | Naïve and conventional human ESCs and iPSCs were propagated as described in Hanna et al. PNAS 2010
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | 100 ng total RNA was used to prepare biotinylated aRNA (cRNA) according to the manufacturer’s protocol (Affymetrix 3’ IVT Express Kit). Briefly, total RNA undergoes T7 oligo(dT)-primed reverse transcription to synthesize first-strand cDNA containing a T7 promoter sequence. This cDNA is then converted into a double-stranded DNA template for transcription using DNA Polymerase and RNase H to simultaneously degrade the RNA and synthesize second strand cDNA. In vitro transcription synthesizes aRNA and incorporates a biotin-conjugated nucleotide. The aRNA is then purified to remove unincorporated NTPs, salts, enzymes, and inorganic phosphate. Fragmentation of the biotin-labeled aRNA prepares the sample for hybridization onto GeneChip 3’ expression arrays.
| | Sample_hyb_protocol | Samples were prepared for hybridization using 12.5 µg of biotinylated aRNA in a 1X hybridization cocktail according the Affymetrix hybridization manual. Additional hybridization cocktail components were provided in the Affymetrix GeneChip Hybridization, Wash and Stain Kit. GeneChip arrays (Human U133 2.0) were hybridized in a GeneChip Hybridization Oven at 45°C for 16 hours at 60 RPM. Washing was done using a GeneChip Fluidics Station 450 according to the manufacturer’s instructions, using the buffers provided in the Affymetrix GeneChip Hybridization, Wash and Stain Kit.
| | Sample_scan_protocol | Arrays were scanned on a GeneChip Scanner 3000 and images were extracted with Affymetrix GeneChip Command Console (AGCC), and analyzed using GeneChip Expression Console.
| | Sample_data_processing | The data were analyzed with Affy and limma package (MAS5)
| | Sample_platform_id | GPL570
| | Sample_contact_name | Albert,W,Cheng
| | Sample_contact_email | awcheng@mit.edu
| | Sample_contact_institute | Whitehead Institute
| | Sample_contact_address | Room 453, 9 Cambridge Center
| | Sample_contact_city | Cambridge
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02139
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM530nnn/GSM530602/suppl/GSM530602.CEL.gz
| | Sample_relation | Reanalyzed by: GSE49910
| | Sample_series_id | GSE21222
| | Sample_data_row_count | 54675
| | |
|
GSM530603 | GPL570 |
|
WIBR2 hESC
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WIBR2 hESC
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cell type: Human embryonic stem cells (hESC)
cell subtype: WIBR2 hESC
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Gene expression data of cell lineWIBR2 hESC
|
| Sample_geo_accession | GSM530603
| | Sample_status | Public on Apr 22 2010
| | Sample_submission_date | Apr 06 2010
| | Sample_last_update_date | Aug 15 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | RNA was feshly extracted from MEF depleted different human embryonic stem cells grown at optimal confluency.
| | Sample_growth_protocol_ch1 | Naïve and conventional human ESCs and iPSCs were propagated as described in Hanna et al. PNAS 2010
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | 100 ng total RNA was used to prepare biotinylated aRNA (cRNA) according to the manufacturer’s protocol (Affymetrix 3’ IVT Express Kit). Briefly, total RNA undergoes T7 oligo(dT)-primed reverse transcription to synthesize first-strand cDNA containing a T7 promoter sequence. This cDNA is then converted into a double-stranded DNA template for transcription using DNA Polymerase and RNase H to simultaneously degrade the RNA and synthesize second strand cDNA. In vitro transcription synthesizes aRNA and incorporates a biotin-conjugated nucleotide. The aRNA is then purified to remove unincorporated NTPs, salts, enzymes, and inorganic phosphate. Fragmentation of the biotin-labeled aRNA prepares the sample for hybridization onto GeneChip 3’ expression arrays.
| | Sample_hyb_protocol | Samples were prepared for hybridization using 12.5 µg of biotinylated aRNA in a 1X hybridization cocktail according the Affymetrix hybridization manual. Additional hybridization cocktail components were provided in the Affymetrix GeneChip Hybridization, Wash and Stain Kit. GeneChip arrays (Human U133 2.0) were hybridized in a GeneChip Hybridization Oven at 45°C for 16 hours at 60 RPM. Washing was done using a GeneChip Fluidics Station 450 according to the manufacturer’s instructions, using the buffers provided in the Affymetrix GeneChip Hybridization, Wash and Stain Kit.
| | Sample_scan_protocol | Arrays were scanned on a GeneChip Scanner 3000 and images were extracted with Affymetrix GeneChip Command Console (AGCC), and analyzed using GeneChip Expression Console.
| | Sample_data_processing | The data were analyzed with Affy and limma package (MAS5)
| | Sample_platform_id | GPL570
| | Sample_contact_name | Albert,W,Cheng
| | Sample_contact_email | awcheng@mit.edu
| | Sample_contact_institute | Whitehead Institute
| | Sample_contact_address | Room 453, 9 Cambridge Center
| | Sample_contact_city | Cambridge
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02139
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM530nnn/GSM530603/suppl/GSM530603.CEL.gz
| | Sample_relation | Reanalyzed by: GSE49910
| | Sample_series_id | GSE21222
| | Sample_data_row_count | 54675
| | |
|
GSM530604 | GPL570 |
|
WIBR3
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WIBR3
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cell type: Human embryonic stem cells (hESC)
cell subtype: WIBR3
|
Gene expression data of cell lineWIBR3
|
| Sample_geo_accession | GSM530604
| | Sample_status | Public on Apr 22 2010
| | Sample_submission_date | Apr 06 2010
| | Sample_last_update_date | Aug 15 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | RNA was feshly extracted from MEF depleted different human embryonic stem cells grown at optimal confluency.
| | Sample_growth_protocol_ch1 | Naïve and conventional human ESCs and iPSCs were propagated as described in Hanna et al. PNAS 2010
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | 100 ng total RNA was used to prepare biotinylated aRNA (cRNA) according to the manufacturer’s protocol (Affymetrix 3’ IVT Express Kit). Briefly, total RNA undergoes T7 oligo(dT)-primed reverse transcription to synthesize first-strand cDNA containing a T7 promoter sequence. This cDNA is then converted into a double-stranded DNA template for transcription using DNA Polymerase and RNase H to simultaneously degrade the RNA and synthesize second strand cDNA. In vitro transcription synthesizes aRNA and incorporates a biotin-conjugated nucleotide. The aRNA is then purified to remove unincorporated NTPs, salts, enzymes, and inorganic phosphate. Fragmentation of the biotin-labeled aRNA prepares the sample for hybridization onto GeneChip 3’ expression arrays.
| | Sample_hyb_protocol | Samples were prepared for hybridization using 12.5 µg of biotinylated aRNA in a 1X hybridization cocktail according the Affymetrix hybridization manual. Additional hybridization cocktail components were provided in the Affymetrix GeneChip Hybridization, Wash and Stain Kit. GeneChip arrays (Human U133 2.0) were hybridized in a GeneChip Hybridization Oven at 45°C for 16 hours at 60 RPM. Washing was done using a GeneChip Fluidics Station 450 according to the manufacturer’s instructions, using the buffers provided in the Affymetrix GeneChip Hybridization, Wash and Stain Kit.
| | Sample_scan_protocol | Arrays were scanned on a GeneChip Scanner 3000 and images were extracted with Affymetrix GeneChip Command Console (AGCC), and analyzed using GeneChip Expression Console.
| | Sample_data_processing | The data were analyzed with Affy and limma package (MAS5)
| | Sample_platform_id | GPL570
| | Sample_contact_name | Albert,W,Cheng
| | Sample_contact_email | awcheng@mit.edu
| | Sample_contact_institute | Whitehead Institute
| | Sample_contact_address | Room 453, 9 Cambridge Center
| | Sample_contact_city | Cambridge
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02139
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM530nnn/GSM530604/suppl/GSM530604.CEL.gz
| | Sample_relation | Reanalyzed by: GSE49910
| | Sample_series_id | GSE21222
| | Sample_data_row_count | 54675
| | |
|
GSM530605 | GPL570 |
|
BGO1-Nanog transgenic hESC line
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BGO1-Nanog transgenic hESC line
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cell type: Human embryonic stem cells (hESC)
cell subtype: BGO1-Nanog transgenic hESC line
|
Gene expression data of cell lineBGO1-Nanog transgenic hESC line
|
| Sample_geo_accession | GSM530605
| | Sample_status | Public on Apr 22 2010
| | Sample_submission_date | Apr 06 2010
| | Sample_last_update_date | Aug 15 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | RNA was feshly extracted from MEF depleted different human embryonic stem cells grown at optimal confluency.
| | Sample_growth_protocol_ch1 | Naïve and conventional human ESCs and iPSCs were propagated as described in Hanna et al. PNAS 2010
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | 100 ng total RNA was used to prepare biotinylated aRNA (cRNA) according to the manufacturer’s protocol (Affymetrix 3’ IVT Express Kit). Briefly, total RNA undergoes T7 oligo(dT)-primed reverse transcription to synthesize first-strand cDNA containing a T7 promoter sequence. This cDNA is then converted into a double-stranded DNA template for transcription using DNA Polymerase and RNase H to simultaneously degrade the RNA and synthesize second strand cDNA. In vitro transcription synthesizes aRNA and incorporates a biotin-conjugated nucleotide. The aRNA is then purified to remove unincorporated NTPs, salts, enzymes, and inorganic phosphate. Fragmentation of the biotin-labeled aRNA prepares the sample for hybridization onto GeneChip 3’ expression arrays.
| | Sample_hyb_protocol | Samples were prepared for hybridization using 12.5 µg of biotinylated aRNA in a 1X hybridization cocktail according the Affymetrix hybridization manual. Additional hybridization cocktail components were provided in the Affymetrix GeneChip Hybridization, Wash and Stain Kit. GeneChip arrays (Human U133 2.0) were hybridized in a GeneChip Hybridization Oven at 45°C for 16 hours at 60 RPM. Washing was done using a GeneChip Fluidics Station 450 according to the manufacturer’s instructions, using the buffers provided in the Affymetrix GeneChip Hybridization, Wash and Stain Kit.
| | Sample_scan_protocol | Arrays were scanned on a GeneChip Scanner 3000 and images were extracted with Affymetrix GeneChip Command Console (AGCC), and analyzed using GeneChip Expression Console.
| | Sample_data_processing | The data were analyzed with Affy and limma package (MAS5)
| | Sample_platform_id | GPL570
| | Sample_contact_name | Albert,W,Cheng
| | Sample_contact_email | awcheng@mit.edu
| | Sample_contact_institute | Whitehead Institute
| | Sample_contact_address | Room 453, 9 Cambridge Center
| | Sample_contact_city | Cambridge
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02139
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM530nnn/GSM530605/suppl/GSM530605.CEL.gz
| | Sample_relation | Reanalyzed by: GSE49910
| | Sample_series_id | GSE21222
| | Sample_data_row_count | 54675
| | |
|
GSM530606 | GPL570 |
|
WIBR1 hESC
|
WIBR1 hESC
|
cell type: Human embryonic stem cells (hESC)
cell subtype: WIBR1 hESC
|
Gene expression data of cell lineWIBR1 hESC
|
| Sample_geo_accession | GSM530606
| | Sample_status | Public on Apr 22 2010
| | Sample_submission_date | Apr 06 2010
| | Sample_last_update_date | Aug 15 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | RNA was feshly extracted from MEF depleted different human embryonic stem cells grown at optimal confluency.
| | Sample_growth_protocol_ch1 | Naïve and conventional human ESCs and iPSCs were propagated as described in Hanna et al. PNAS 2010
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | 100 ng total RNA was used to prepare biotinylated aRNA (cRNA) according to the manufacturer’s protocol (Affymetrix 3’ IVT Express Kit). Briefly, total RNA undergoes T7 oligo(dT)-primed reverse transcription to synthesize first-strand cDNA containing a T7 promoter sequence. This cDNA is then converted into a double-stranded DNA template for transcription using DNA Polymerase and RNase H to simultaneously degrade the RNA and synthesize second strand cDNA. In vitro transcription synthesizes aRNA and incorporates a biotin-conjugated nucleotide. The aRNA is then purified to remove unincorporated NTPs, salts, enzymes, and inorganic phosphate. Fragmentation of the biotin-labeled aRNA prepares the sample for hybridization onto GeneChip 3’ expression arrays.
| | Sample_hyb_protocol | Samples were prepared for hybridization using 12.5 µg of biotinylated aRNA in a 1X hybridization cocktail according the Affymetrix hybridization manual. Additional hybridization cocktail components were provided in the Affymetrix GeneChip Hybridization, Wash and Stain Kit. GeneChip arrays (Human U133 2.0) were hybridized in a GeneChip Hybridization Oven at 45°C for 16 hours at 60 RPM. Washing was done using a GeneChip Fluidics Station 450 according to the manufacturer’s instructions, using the buffers provided in the Affymetrix GeneChip Hybridization, Wash and Stain Kit.
| | Sample_scan_protocol | Arrays were scanned on a GeneChip Scanner 3000 and images were extracted with Affymetrix GeneChip Command Console (AGCC), and analyzed using GeneChip Expression Console.
| | Sample_data_processing | The data were analyzed with Affy and limma package (MAS5)
| | Sample_platform_id | GPL570
| | Sample_contact_name | Albert,W,Cheng
| | Sample_contact_email | awcheng@mit.edu
| | Sample_contact_institute | Whitehead Institute
| | Sample_contact_address | Room 453, 9 Cambridge Center
| | Sample_contact_city | Cambridge
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02139
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM530nnn/GSM530606/suppl/GSM530606.CEL.gz
| | Sample_relation | Reanalyzed by: GSE49910
| | Sample_series_id | GSE21222
| | Sample_data_row_count | 54675
| | |
|
GSM530607 | GPL570 |
|
BGO1 hESC (mTESR)
|
BGO1 hESC (mTESR)
|
cell type: Human embryonic stem cells (hESC)
cell subtype: BGO1 hESC (mTESR)
|
Gene expression data of cell lineBGO1 hESC (mTESR)
|
| Sample_geo_accession | GSM530607
| | Sample_status | Public on Apr 22 2010
| | Sample_submission_date | Apr 06 2010
| | Sample_last_update_date | Aug 15 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | RNA was feshly extracted from MEF depleted different human embryonic stem cells grown at optimal confluency.
| | Sample_growth_protocol_ch1 | Naïve and conventional human ESCs and iPSCs were propagated as described in Hanna et al. PNAS 2010
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | 100 ng total RNA was used to prepare biotinylated aRNA (cRNA) according to the manufacturer’s protocol (Affymetrix 3’ IVT Express Kit). Briefly, total RNA undergoes T7 oligo(dT)-primed reverse transcription to synthesize first-strand cDNA containing a T7 promoter sequence. This cDNA is then converted into a double-stranded DNA template for transcription using DNA Polymerase and RNase H to simultaneously degrade the RNA and synthesize second strand cDNA. In vitro transcription synthesizes aRNA and incorporates a biotin-conjugated nucleotide. The aRNA is then purified to remove unincorporated NTPs, salts, enzymes, and inorganic phosphate. Fragmentation of the biotin-labeled aRNA prepares the sample for hybridization onto GeneChip 3’ expression arrays.
| | Sample_hyb_protocol | Samples were prepared for hybridization using 12.5 µg of biotinylated aRNA in a 1X hybridization cocktail according the Affymetrix hybridization manual. Additional hybridization cocktail components were provided in the Affymetrix GeneChip Hybridization, Wash and Stain Kit. GeneChip arrays (Human U133 2.0) were hybridized in a GeneChip Hybridization Oven at 45°C for 16 hours at 60 RPM. Washing was done using a GeneChip Fluidics Station 450 according to the manufacturer’s instructions, using the buffers provided in the Affymetrix GeneChip Hybridization, Wash and Stain Kit.
| | Sample_scan_protocol | Arrays were scanned on a GeneChip Scanner 3000 and images were extracted with Affymetrix GeneChip Command Console (AGCC), and analyzed using GeneChip Expression Console.
| | Sample_data_processing | The data were analyzed with Affy and limma package (MAS5)
| | Sample_platform_id | GPL570
| | Sample_contact_name | Albert,W,Cheng
| | Sample_contact_email | awcheng@mit.edu
| | Sample_contact_institute | Whitehead Institute
| | Sample_contact_address | Room 453, 9 Cambridge Center
| | Sample_contact_city | Cambridge
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02139
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM530nnn/GSM530607/suppl/GSM530607.CEL.gz
| | Sample_relation | Reanalyzed by: GSE49910
| | Sample_series_id | GSE21222
| | Sample_data_row_count | 54675
| | |
|
GSM530608 | GPL570 |
|
C1 hiPSC (exposed to PD/CH/FK/Lif for 48 hours)
|
C1 hiPSC (exposed to PD/CH/FK/Lif for 48 hours)
|
cell type: Human embryonic stem cells (hESC)
cell subtype: C1 hiPSC (exposed to PD/CH/FK/Lif for 48 hours)
|
Gene expression data of cell lineC1 hiPSC (exposed to PD/CH/FK/Lif for 48 hours)
|
| Sample_geo_accession | GSM530608
| | Sample_status | Public on Apr 22 2010
| | Sample_submission_date | Apr 06 2010
| | Sample_last_update_date | Apr 22 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | RNA was feshly extracted from MEF depleted different human embryonic stem cells grown at optimal confluency.
| | Sample_growth_protocol_ch1 | Naïve and conventional human ESCs and iPSCs were propagated as described in Hanna et al. PNAS 2010
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | 100 ng total RNA was used to prepare biotinylated aRNA (cRNA) according to the manufacturer’s protocol (Affymetrix 3’ IVT Express Kit). Briefly, total RNA undergoes T7 oligo(dT)-primed reverse transcription to synthesize first-strand cDNA containing a T7 promoter sequence. This cDNA is then converted into a double-stranded DNA template for transcription using DNA Polymerase and RNase H to simultaneously degrade the RNA and synthesize second strand cDNA. In vitro transcription synthesizes aRNA and incorporates a biotin-conjugated nucleotide. The aRNA is then purified to remove unincorporated NTPs, salts, enzymes, and inorganic phosphate. Fragmentation of the biotin-labeled aRNA prepares the sample for hybridization onto GeneChip 3’ expression arrays.
| | Sample_hyb_protocol | Samples were prepared for hybridization using 12.5 µg of biotinylated aRNA in a 1X hybridization cocktail according the Affymetrix hybridization manual. Additional hybridization cocktail components were provided in the Affymetrix GeneChip Hybridization, Wash and Stain Kit. GeneChip arrays (Human U133 2.0) were hybridized in a GeneChip Hybridization Oven at 45°C for 16 hours at 60 RPM. Washing was done using a GeneChip Fluidics Station 450 according to the manufacturer’s instructions, using the buffers provided in the Affymetrix GeneChip Hybridization, Wash and Stain Kit.
| | Sample_scan_protocol | Arrays were scanned on a GeneChip Scanner 3000 and images were extracted with Affymetrix GeneChip Command Console (AGCC), and analyzed using GeneChip Expression Console.
| | Sample_data_processing | The data were analyzed with Affy and limma package (MAS5)
| | Sample_platform_id | GPL570
| | Sample_contact_name | Albert,W,Cheng
| | Sample_contact_email | awcheng@mit.edu
| | Sample_contact_institute | Whitehead Institute
| | Sample_contact_address | Room 453, 9 Cambridge Center
| | Sample_contact_city | Cambridge
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02139
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM530nnn/GSM530608/suppl/GSM530608.CEL.gz
| | Sample_series_id | GSE21222
| | Sample_data_row_count | 54675
| | |
|
GSM530609 | GPL570 |
|
C1 hiPSC
|
C1 hiPSC
|
cell type: Human embryonic stem cells (hESC)
cell subtype: C1 hiPSC
|
Gene expression data of cell lineC1 hiPSC
|
| Sample_geo_accession | GSM530609
| | Sample_status | Public on Apr 22 2010
| | Sample_submission_date | Apr 06 2010
| | Sample_last_update_date | Apr 22 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | RNA was feshly extracted from MEF depleted different human embryonic stem cells grown at optimal confluency.
| | Sample_growth_protocol_ch1 | Naïve and conventional human ESCs and iPSCs were propagated as described in Hanna et al. PNAS 2010
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | 100 ng total RNA was used to prepare biotinylated aRNA (cRNA) according to the manufacturer’s protocol (Affymetrix 3’ IVT Express Kit). Briefly, total RNA undergoes T7 oligo(dT)-primed reverse transcription to synthesize first-strand cDNA containing a T7 promoter sequence. This cDNA is then converted into a double-stranded DNA template for transcription using DNA Polymerase and RNase H to simultaneously degrade the RNA and synthesize second strand cDNA. In vitro transcription synthesizes aRNA and incorporates a biotin-conjugated nucleotide. The aRNA is then purified to remove unincorporated NTPs, salts, enzymes, and inorganic phosphate. Fragmentation of the biotin-labeled aRNA prepares the sample for hybridization onto GeneChip 3’ expression arrays.
| | Sample_hyb_protocol | Samples were prepared for hybridization using 12.5 µg of biotinylated aRNA in a 1X hybridization cocktail according the Affymetrix hybridization manual. Additional hybridization cocktail components were provided in the Affymetrix GeneChip Hybridization, Wash and Stain Kit. GeneChip arrays (Human U133 2.0) were hybridized in a GeneChip Hybridization Oven at 45°C for 16 hours at 60 RPM. Washing was done using a GeneChip Fluidics Station 450 according to the manufacturer’s instructions, using the buffers provided in the Affymetrix GeneChip Hybridization, Wash and Stain Kit.
| | Sample_scan_protocol | Arrays were scanned on a GeneChip Scanner 3000 and images were extracted with Affymetrix GeneChip Command Console (AGCC), and analyzed using GeneChip Expression Console.
| | Sample_data_processing | The data were analyzed with Affy and limma package (MAS5)
| | Sample_platform_id | GPL570
| | Sample_contact_name | Albert,W,Cheng
| | Sample_contact_email | awcheng@mit.edu
| | Sample_contact_institute | Whitehead Institute
| | Sample_contact_address | Room 453, 9 Cambridge Center
| | Sample_contact_city | Cambridge
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02139
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM530nnn/GSM530609/suppl/GSM530609.CEL.gz
| | Sample_series_id | GSE21222
| | Sample_data_row_count | 54675
| | |
|
GSM530610 | GPL570 |
|
pri-C1.2 hiPSC
|
pri-C1.2 hiPSC
|
cell type: Human embryonic stem cells (hESC)
cell subtype: pri-C1.2 hiPSC
|
Gene expression data of cell line pri-C1.2 hiPSC
|
| Sample_geo_accession | GSM530610
| | Sample_status | Public on Apr 22 2010
| | Sample_submission_date | Apr 06 2010
| | Sample_last_update_date | Jun 14 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | RNA was feshly extracted from MEF depleted different human embryonic stem cells grown at optimal confluency.
| | Sample_growth_protocol_ch1 | Naïve and conventional human ESCs and iPSCs were propagated as described in Hanna et al. PNAS 2010
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | 100 ng total RNA was used to prepare biotinylated aRNA (cRNA) according to the manufacturer’s protocol (Affymetrix 3’ IVT Express Kit). Briefly, total RNA undergoes T7 oligo(dT)-primed reverse transcription to synthesize first-strand cDNA containing a T7 promoter sequence. This cDNA is then converted into a double-stranded DNA template for transcription using DNA Polymerase and RNase H to simultaneously degrade the RNA and synthesize second strand cDNA. In vitro transcription synthesizes aRNA and incorporates a biotin-conjugated nucleotide. The aRNA is then purified to remove unincorporated NTPs, salts, enzymes, and inorganic phosphate. Fragmentation of the biotin-labeled aRNA prepares the sample for hybridization onto GeneChip 3’ expression arrays.
| | Sample_hyb_protocol | Samples were prepared for hybridization using 12.5 µg of biotinylated aRNA in a 1X hybridization cocktail according the Affymetrix hybridization manual. Additional hybridization cocktail components were provided in the Affymetrix GeneChip Hybridization, Wash and Stain Kit. GeneChip arrays (Human U133 2.0) were hybridized in a GeneChip Hybridization Oven at 45°C for 16 hours at 60 RPM. Washing was done using a GeneChip Fluidics Station 450 according to the manufacturer’s instructions, using the buffers provided in the Affymetrix GeneChip Hybridization, Wash and Stain Kit.
| | Sample_scan_protocol | Arrays were scanned on a GeneChip Scanner 3000 and images were extracted with Affymetrix GeneChip Command Console (AGCC), and analyzed using GeneChip Expression Console.
| | Sample_data_processing | The data were analyzed with Affy and limma package (MAS5)
| | Sample_platform_id | GPL570
| | Sample_contact_name | Albert,W,Cheng
| | Sample_contact_email | awcheng@mit.edu
| | Sample_contact_institute | Whitehead Institute
| | Sample_contact_address | Room 453, 9 Cambridge Center
| | Sample_contact_city | Cambridge
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02139
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM530nnn/GSM530610/suppl/GSM530610.CEL.gz
| | Sample_series_id | GSE21222
| | Sample_data_row_count | 54675
| | |
|
GSM530611 | GPL570 |
|
WIBR3 hESC
|
WIBR3 hESC
|
cell type: Human embryonic stem cells (hESC)
cell subtype: WIBR3 hESC
|
Gene expression data of cell lineWIBR3 hESC
|
| Sample_geo_accession | GSM530611
| | Sample_status | Public on Apr 22 2010
| | Sample_submission_date | Apr 06 2010
| | Sample_last_update_date | Aug 15 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | RNA was feshly extracted from MEF depleted different human embryonic stem cells grown at optimal confluency.
| | Sample_growth_protocol_ch1 | Naïve and conventional human ESCs and iPSCs were propagated as described in Hanna et al. PNAS 2010
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | 100 ng total RNA was used to prepare biotinylated aRNA (cRNA) according to the manufacturer’s protocol (Affymetrix 3’ IVT Express Kit). Briefly, total RNA undergoes T7 oligo(dT)-primed reverse transcription to synthesize first-strand cDNA containing a T7 promoter sequence. This cDNA is then converted into a double-stranded DNA template for transcription using DNA Polymerase and RNase H to simultaneously degrade the RNA and synthesize second strand cDNA. In vitro transcription synthesizes aRNA and incorporates a biotin-conjugated nucleotide. The aRNA is then purified to remove unincorporated NTPs, salts, enzymes, and inorganic phosphate. Fragmentation of the biotin-labeled aRNA prepares the sample for hybridization onto GeneChip 3’ expression arrays.
| | Sample_hyb_protocol | Samples were prepared for hybridization using 12.5 µg of biotinylated aRNA in a 1X hybridization cocktail according the Affymetrix hybridization manual. Additional hybridization cocktail components were provided in the Affymetrix GeneChip Hybridization, Wash and Stain Kit. GeneChip arrays (Human U133 2.0) were hybridized in a GeneChip Hybridization Oven at 45°C for 16 hours at 60 RPM. Washing was done using a GeneChip Fluidics Station 450 according to the manufacturer’s instructions, using the buffers provided in the Affymetrix GeneChip Hybridization, Wash and Stain Kit.
| | Sample_scan_protocol | Arrays were scanned on a GeneChip Scanner 3000 and images were extracted with Affymetrix GeneChip Command Console (AGCC), and analyzed using GeneChip Expression Console.
| | Sample_data_processing | The data were analyzed with Affy and limma package (MAS5)
| | Sample_platform_id | GPL570
| | Sample_contact_name | Albert,W,Cheng
| | Sample_contact_email | awcheng@mit.edu
| | Sample_contact_institute | Whitehead Institute
| | Sample_contact_address | Room 453, 9 Cambridge Center
| | Sample_contact_city | Cambridge
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02139
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM530nnn/GSM530611/suppl/GSM530611.CEL.gz
| | Sample_relation | Reanalyzed by: GSE49910
| | Sample_series_id | GSE21222
| | Sample_data_row_count | 54675
| | |
|
GSM530612 | GPL570 |
|
pri-WIBR3.1 hESC
|
pri-WIBR3.1 hESC
|
cell type: Human embryonic stem cells (hESC)
cell subtype: pri-WIBR3.1 hESC
|
Gene expression data of cell linepri-WIBR3.1 hESC
|
| Sample_geo_accession | GSM530612
| | Sample_status | Public on Apr 22 2010
| | Sample_submission_date | Apr 06 2010
| | Sample_last_update_date | Apr 22 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | RNA was feshly extracted from MEF depleted different human embryonic stem cells grown at optimal confluency.
| | Sample_growth_protocol_ch1 | Naïve and conventional human ESCs and iPSCs were propagated as described in Hanna et al. PNAS 2010
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | 100 ng total RNA was used to prepare biotinylated aRNA (cRNA) according to the manufacturer’s protocol (Affymetrix 3’ IVT Express Kit). Briefly, total RNA undergoes T7 oligo(dT)-primed reverse transcription to synthesize first-strand cDNA containing a T7 promoter sequence. This cDNA is then converted into a double-stranded DNA template for transcription using DNA Polymerase and RNase H to simultaneously degrade the RNA and synthesize second strand cDNA. In vitro transcription synthesizes aRNA and incorporates a biotin-conjugated nucleotide. The aRNA is then purified to remove unincorporated NTPs, salts, enzymes, and inorganic phosphate. Fragmentation of the biotin-labeled aRNA prepares the sample for hybridization onto GeneChip 3’ expression arrays.
| | Sample_hyb_protocol | Samples were prepared for hybridization using 12.5 µg of biotinylated aRNA in a 1X hybridization cocktail according the Affymetrix hybridization manual. Additional hybridization cocktail components were provided in the Affymetrix GeneChip Hybridization, Wash and Stain Kit. GeneChip arrays (Human U133 2.0) were hybridized in a GeneChip Hybridization Oven at 45°C for 16 hours at 60 RPM. Washing was done using a GeneChip Fluidics Station 450 according to the manufacturer’s instructions, using the buffers provided in the Affymetrix GeneChip Hybridization, Wash and Stain Kit.
| | Sample_scan_protocol | Arrays were scanned on a GeneChip Scanner 3000 and images were extracted with Affymetrix GeneChip Command Console (AGCC), and analyzed using GeneChip Expression Console.
| | Sample_data_processing | The data were analyzed with Affy and limma package (MAS5)
| | Sample_platform_id | GPL570
| | Sample_contact_name | Albert,W,Cheng
| | Sample_contact_email | awcheng@mit.edu
| | Sample_contact_institute | Whitehead Institute
| | Sample_contact_address | Room 453, 9 Cambridge Center
| | Sample_contact_city | Cambridge
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02139
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM530nnn/GSM530612/suppl/GSM530612.CEL.gz
| | Sample_series_id | GSE21222
| | Sample_data_row_count | 54675
| | |
|
GSM530613 | GPL570 |
|
naïve-C1.2 hiPSC
|
naïve-C1.2 hiPSC
|
cell type: Human embryonic stem cells (hESC)
cell subtype: naïve-C1.2 hiPSC
|
Gene expression data of cell linenaïve-C1.2 hiPSC
|
| Sample_geo_accession | GSM530613
| | Sample_status | Public on Apr 22 2010
| | Sample_submission_date | Apr 06 2010
| | Sample_last_update_date | Apr 22 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | RNA was feshly extracted from MEF depleted different human embryonic stem cells grown at optimal confluency.
| | Sample_growth_protocol_ch1 | Naïve and conventional human ESCs and iPSCs were propagated as described in Hanna et al. PNAS 2010
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | 100 ng total RNA was used to prepare biotinylated aRNA (cRNA) according to the manufacturer’s protocol (Affymetrix 3’ IVT Express Kit). Briefly, total RNA undergoes T7 oligo(dT)-primed reverse transcription to synthesize first-strand cDNA containing a T7 promoter sequence. This cDNA is then converted into a double-stranded DNA template for transcription using DNA Polymerase and RNase H to simultaneously degrade the RNA and synthesize second strand cDNA. In vitro transcription synthesizes aRNA and incorporates a biotin-conjugated nucleotide. The aRNA is then purified to remove unincorporated NTPs, salts, enzymes, and inorganic phosphate. Fragmentation of the biotin-labeled aRNA prepares the sample for hybridization onto GeneChip 3’ expression arrays.
| | Sample_hyb_protocol | Samples were prepared for hybridization using 12.5 µg of biotinylated aRNA in a 1X hybridization cocktail according the Affymetrix hybridization manual. Additional hybridization cocktail components were provided in the Affymetrix GeneChip Hybridization, Wash and Stain Kit. GeneChip arrays (Human U133 2.0) were hybridized in a GeneChip Hybridization Oven at 45°C for 16 hours at 60 RPM. Washing was done using a GeneChip Fluidics Station 450 according to the manufacturer’s instructions, using the buffers provided in the Affymetrix GeneChip Hybridization, Wash and Stain Kit.
| | Sample_scan_protocol | Arrays were scanned on a GeneChip Scanner 3000 and images were extracted with Affymetrix GeneChip Command Console (AGCC), and analyzed using GeneChip Expression Console.
| | Sample_data_processing | The data were analyzed with Affy and limma package (MAS5)
| | Sample_platform_id | GPL570
| | Sample_contact_name | Albert,W,Cheng
| | Sample_contact_email | awcheng@mit.edu
| | Sample_contact_institute | Whitehead Institute
| | Sample_contact_address | Room 453, 9 Cambridge Center
| | Sample_contact_city | Cambridge
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02139
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM530nnn/GSM530613/suppl/GSM530613.CEL.gz
| | Sample_series_id | GSE21222
| | Sample_data_row_count | 54675
| | |
|
GSM530614 | GPL570 |
|
naïve-C1.10 hiPSC
|
naïve-C1.10 hiPSC
|
cell type: Human embryonic stem cells (hESC)
cell subtype: naïve-C1.10 hiPSC
|
Gene expression data of cell linenaïve-C1.10 hiPSC
|
| Sample_geo_accession | GSM530614
| | Sample_status | Public on Apr 22 2010
| | Sample_submission_date | Apr 06 2010
| | Sample_last_update_date | Apr 22 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | RNA was feshly extracted from MEF depleted different human embryonic stem cells grown at optimal confluency.
| | Sample_growth_protocol_ch1 | Naïve and conventional human ESCs and iPSCs were propagated as described in Hanna et al. PNAS 2010
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | 100 ng total RNA was used to prepare biotinylated aRNA (cRNA) according to the manufacturer’s protocol (Affymetrix 3’ IVT Express Kit). Briefly, total RNA undergoes T7 oligo(dT)-primed reverse transcription to synthesize first-strand cDNA containing a T7 promoter sequence. This cDNA is then converted into a double-stranded DNA template for transcription using DNA Polymerase and RNase H to simultaneously degrade the RNA and synthesize second strand cDNA. In vitro transcription synthesizes aRNA and incorporates a biotin-conjugated nucleotide. The aRNA is then purified to remove unincorporated NTPs, salts, enzymes, and inorganic phosphate. Fragmentation of the biotin-labeled aRNA prepares the sample for hybridization onto GeneChip 3’ expression arrays.
| | Sample_hyb_protocol | Samples were prepared for hybridization using 12.5 µg of biotinylated aRNA in a 1X hybridization cocktail according the Affymetrix hybridization manual. Additional hybridization cocktail components were provided in the Affymetrix GeneChip Hybridization, Wash and Stain Kit. GeneChip arrays (Human U133 2.0) were hybridized in a GeneChip Hybridization Oven at 45°C for 16 hours at 60 RPM. Washing was done using a GeneChip Fluidics Station 450 according to the manufacturer’s instructions, using the buffers provided in the Affymetrix GeneChip Hybridization, Wash and Stain Kit.
| | Sample_scan_protocol | Arrays were scanned on a GeneChip Scanner 3000 and images were extracted with Affymetrix GeneChip Command Console (AGCC), and analyzed using GeneChip Expression Console.
| | Sample_data_processing | The data were analyzed with Affy and limma package (MAS5)
| | Sample_platform_id | GPL570
| | Sample_contact_name | Albert,W,Cheng
| | Sample_contact_email | awcheng@mit.edu
| | Sample_contact_institute | Whitehead Institute
| | Sample_contact_address | Room 453, 9 Cambridge Center
| | Sample_contact_city | Cambridge
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02139
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM530nnn/GSM530614/suppl/GSM530614.CEL.gz
| | Sample_series_id | GSE21222
| | Sample_data_row_count | 54675
| | |
|
GSM530615 | GPL570 |
|
naïve-WIBR3.1 hESC
|
naïve-WIBR3.1 hESC
|
cell type: Human embryonic stem cells (hESC)
cell subtype: naïve-WIBR3.1 hESC
|
Gene expression data of cell linenaïve-WIBR3.1 hESC
|
| Sample_geo_accession | GSM530615
| | Sample_status | Public on Apr 22 2010
| | Sample_submission_date | Apr 06 2010
| | Sample_last_update_date | Apr 22 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | RNA was feshly extracted from MEF depleted different human embryonic stem cells grown at optimal confluency.
| | Sample_growth_protocol_ch1 | Naïve and conventional human ESCs and iPSCs were propagated as described in Hanna et al. PNAS 2010
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | 100 ng total RNA was used to prepare biotinylated aRNA (cRNA) according to the manufacturer’s protocol (Affymetrix 3’ IVT Express Kit). Briefly, total RNA undergoes T7 oligo(dT)-primed reverse transcription to synthesize first-strand cDNA containing a T7 promoter sequence. This cDNA is then converted into a double-stranded DNA template for transcription using DNA Polymerase and RNase H to simultaneously degrade the RNA and synthesize second strand cDNA. In vitro transcription synthesizes aRNA and incorporates a biotin-conjugated nucleotide. The aRNA is then purified to remove unincorporated NTPs, salts, enzymes, and inorganic phosphate. Fragmentation of the biotin-labeled aRNA prepares the sample for hybridization onto GeneChip 3’ expression arrays.
| | Sample_hyb_protocol | Samples were prepared for hybridization using 12.5 µg of biotinylated aRNA in a 1X hybridization cocktail according the Affymetrix hybridization manual. Additional hybridization cocktail components were provided in the Affymetrix GeneChip Hybridization, Wash and Stain Kit. GeneChip arrays (Human U133 2.0) were hybridized in a GeneChip Hybridization Oven at 45°C for 16 hours at 60 RPM. Washing was done using a GeneChip Fluidics Station 450 according to the manufacturer’s instructions, using the buffers provided in the Affymetrix GeneChip Hybridization, Wash and Stain Kit.
| | Sample_scan_protocol | Arrays were scanned on a GeneChip Scanner 3000 and images were extracted with Affymetrix GeneChip Command Console (AGCC), and analyzed using GeneChip Expression Console.
| | Sample_data_processing | The data were analyzed with Affy and limma package (MAS5)
| | Sample_platform_id | GPL570
| | Sample_contact_name | Albert,W,Cheng
| | Sample_contact_email | awcheng@mit.edu
| | Sample_contact_institute | Whitehead Institute
| | Sample_contact_address | Room 453, 9 Cambridge Center
| | Sample_contact_city | Cambridge
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02139
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM530nnn/GSM530615/suppl/GSM530615.CEL.gz
| | Sample_series_id | GSE21222
| | Sample_data_row_count | 54675
| | |
|
GSM530616 | GPL570 |
|
naïve-WIBR3.2 hESC
|
naïve-WIBR3.2 hESC
|
cell type: Human embryonic stem cells (hESC)
cell subtype: naïve-WIBR3.2 hESC
|
Gene expression data of cell linenaïve-WIBR3.2 hESC
|
| Sample_geo_accession | GSM530616
| | Sample_status | Public on Apr 22 2010
| | Sample_submission_date | Apr 06 2010
| | Sample_last_update_date | Apr 22 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | RNA was feshly extracted from MEF depleted different human embryonic stem cells grown at optimal confluency.
| | Sample_growth_protocol_ch1 | Naïve and conventional human ESCs and iPSCs were propagated as described in Hanna et al. PNAS 2010
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | 100 ng total RNA was used to prepare biotinylated aRNA (cRNA) according to the manufacturer’s protocol (Affymetrix 3’ IVT Express Kit). Briefly, total RNA undergoes T7 oligo(dT)-primed reverse transcription to synthesize first-strand cDNA containing a T7 promoter sequence. This cDNA is then converted into a double-stranded DNA template for transcription using DNA Polymerase and RNase H to simultaneously degrade the RNA and synthesize second strand cDNA. In vitro transcription synthesizes aRNA and incorporates a biotin-conjugated nucleotide. The aRNA is then purified to remove unincorporated NTPs, salts, enzymes, and inorganic phosphate. Fragmentation of the biotin-labeled aRNA prepares the sample for hybridization onto GeneChip 3’ expression arrays.
| | Sample_hyb_protocol | Samples were prepared for hybridization using 12.5 µg of biotinylated aRNA in a 1X hybridization cocktail according the Affymetrix hybridization manual. Additional hybridization cocktail components were provided in the Affymetrix GeneChip Hybridization, Wash and Stain Kit. GeneChip arrays (Human U133 2.0) were hybridized in a GeneChip Hybridization Oven at 45°C for 16 hours at 60 RPM. Washing was done using a GeneChip Fluidics Station 450 according to the manufacturer’s instructions, using the buffers provided in the Affymetrix GeneChip Hybridization, Wash and Stain Kit.
| | Sample_scan_protocol | Arrays were scanned on a GeneChip Scanner 3000 and images were extracted with Affymetrix GeneChip Command Console (AGCC), and analyzed using GeneChip Expression Console.
| | Sample_data_processing | The data were analyzed with Affy and limma package (MAS5)
| | Sample_platform_id | GPL570
| | Sample_contact_name | Albert,W,Cheng
| | Sample_contact_email | awcheng@mit.edu
| | Sample_contact_institute | Whitehead Institute
| | Sample_contact_address | Room 453, 9 Cambridge Center
| | Sample_contact_city | Cambridge
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02139
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM530nnn/GSM530616/suppl/GSM530616.CEL.gz
| | Sample_series_id | GSE21222
| | Sample_data_row_count | 54675
| | |
|
GSM530617 | GPL570 |
|
naïve-WIBR3.3 hESC
|
naïve-WIBR3.3 hESC
|
cell type: Human embryonic stem cells (hESC)
cell subtype: naïve-WIBR3.3 hESC
|
Gene expression data of cell linenaïve-WIBR3.3 hESC
|
| Sample_geo_accession | GSM530617
| | Sample_status | Public on Apr 22 2010
| | Sample_submission_date | Apr 06 2010
| | Sample_last_update_date | Apr 22 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | RNA was feshly extracted from MEF depleted different human embryonic stem cells grown at optimal confluency.
| | Sample_growth_protocol_ch1 | Naïve and conventional human ESCs and iPSCs were propagated as described in Hanna et al. PNAS 2010
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | 100 ng total RNA was used to prepare biotinylated aRNA (cRNA) according to the manufacturer’s protocol (Affymetrix 3’ IVT Express Kit). Briefly, total RNA undergoes T7 oligo(dT)-primed reverse transcription to synthesize first-strand cDNA containing a T7 promoter sequence. This cDNA is then converted into a double-stranded DNA template for transcription using DNA Polymerase and RNase H to simultaneously degrade the RNA and synthesize second strand cDNA. In vitro transcription synthesizes aRNA and incorporates a biotin-conjugated nucleotide. The aRNA is then purified to remove unincorporated NTPs, salts, enzymes, and inorganic phosphate. Fragmentation of the biotin-labeled aRNA prepares the sample for hybridization onto GeneChip 3’ expression arrays.
| | Sample_hyb_protocol | Samples were prepared for hybridization using 12.5 µg of biotinylated aRNA in a 1X hybridization cocktail according the Affymetrix hybridization manual. Additional hybridization cocktail components were provided in the Affymetrix GeneChip Hybridization, Wash and Stain Kit. GeneChip arrays (Human U133 2.0) were hybridized in a GeneChip Hybridization Oven at 45°C for 16 hours at 60 RPM. Washing was done using a GeneChip Fluidics Station 450 according to the manufacturer’s instructions, using the buffers provided in the Affymetrix GeneChip Hybridization, Wash and Stain Kit.
| | Sample_scan_protocol | Arrays were scanned on a GeneChip Scanner 3000 and images were extracted with Affymetrix GeneChip Command Console (AGCC), and analyzed using GeneChip Expression Console.
| | Sample_data_processing | The data were analyzed with Affy and limma package (MAS5)
| | Sample_platform_id | GPL570
| | Sample_contact_name | Albert,W,Cheng
| | Sample_contact_email | awcheng@mit.edu
| | Sample_contact_institute | Whitehead Institute
| | Sample_contact_address | Room 453, 9 Cambridge Center
| | Sample_contact_city | Cambridge
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02139
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM530nnn/GSM530617/suppl/GSM530617.CEL.gz
| | Sample_series_id | GSE21222
| | Sample_data_row_count | 54675
| | |
|
GSM530618 | GPL570 |
|
naïve-WIBR3.5 hESC
|
naïve-WIBR3.5 hESC
|
cell type: Human embryonic stem cells (hESC)
cell subtype: naïve-WIBR3.5 hESC
|
Gene expression data of cell linenaïve-WIBR3.5 hESC
|
| Sample_geo_accession | GSM530618
| | Sample_status | Public on Apr 22 2010
| | Sample_submission_date | Apr 06 2010
| | Sample_last_update_date | Apr 22 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | RNA was feshly extracted from MEF depleted different human embryonic stem cells grown at optimal confluency.
| | Sample_growth_protocol_ch1 | Naïve and conventional human ESCs and iPSCs were propagated as described in Hanna et al. PNAS 2010
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | 100 ng total RNA was used to prepare biotinylated aRNA (cRNA) according to the manufacturer’s protocol (Affymetrix 3’ IVT Express Kit). Briefly, total RNA undergoes T7 oligo(dT)-primed reverse transcription to synthesize first-strand cDNA containing a T7 promoter sequence. This cDNA is then converted into a double-stranded DNA template for transcription using DNA Polymerase and RNase H to simultaneously degrade the RNA and synthesize second strand cDNA. In vitro transcription synthesizes aRNA and incorporates a biotin-conjugated nucleotide. The aRNA is then purified to remove unincorporated NTPs, salts, enzymes, and inorganic phosphate. Fragmentation of the biotin-labeled aRNA prepares the sample for hybridization onto GeneChip 3’ expression arrays.
| | Sample_hyb_protocol | Samples were prepared for hybridization using 12.5 µg of biotinylated aRNA in a 1X hybridization cocktail according the Affymetrix hybridization manual. Additional hybridization cocktail components were provided in the Affymetrix GeneChip Hybridization, Wash and Stain Kit. GeneChip arrays (Human U133 2.0) were hybridized in a GeneChip Hybridization Oven at 45°C for 16 hours at 60 RPM. Washing was done using a GeneChip Fluidics Station 450 according to the manufacturer’s instructions, using the buffers provided in the Affymetrix GeneChip Hybridization, Wash and Stain Kit.
| | Sample_scan_protocol | Arrays were scanned on a GeneChip Scanner 3000 and images were extracted with Affymetrix GeneChip Command Console (AGCC), and analyzed using GeneChip Expression Console.
| | Sample_data_processing | The data were analyzed with Affy and limma package (MAS5)
| | Sample_platform_id | GPL570
| | Sample_contact_name | Albert,W,Cheng
| | Sample_contact_email | awcheng@mit.edu
| | Sample_contact_institute | Whitehead Institute
| | Sample_contact_address | Room 453, 9 Cambridge Center
| | Sample_contact_city | Cambridge
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02139
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM530nnn/GSM530618/suppl/GSM530618.CEL.gz
| | Sample_series_id | GSE21222
| | Sample_data_row_count | 54675
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