Search results for the GEO ID: GSE23402  |
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|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM574058 | GPL570 |
|
FIBROBLAST_GM_rep1_081006_7
|
human fibroblast line GM
|
cell line: human fibroblast line GM
|
Gene expression data from human fibroblast line GM
|
| Sample_geo_accession | GSM574058
| | Sample_status | Public on Aug 09 2010
| | Sample_submission_date | Aug 03 2010
| | Sample_last_update_date | Sep 15 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | Coriell Cell Repositories http://ccr.coriell.org/Sections/Search/Search.aspx?PgId=165&q=GM01660
| | Sample_growth_protocol_ch1 | All primary human fibroblasts cells described in this paper (PDB-AG20442 and GM-M01660) were purchased from the Coriell Cell Repository (Camden, NJ). Fibroblasts were cultured in fibroblast medium (Dulbecco's modified Eagle's medium [DMEM] supplemented with 15% fetal bovine serum [FBS; Hyclone], 1 mM glutamine [Invitrogen], 1% nonessential amino acids [Invitrogen], and penicillin/streptomycin [Invitrogen]).
| | Sample_growth_protocol_ch1 | hiPS cell lines iPS A1, iPS C1, iPS4, iPS A6 (Hockemeyer et al. 2009); hiPS cell lines iPS PDB2lox-17, iPS PDB2lox-21, iPS PDB2lox-5, iPS PDB2lox-22, iPS PDB1lox-17puro-5, iPS PDB1lox-17puro-10, iPS PDB1lox-17puro-33, iPS PDB1lox-21puro-20, iPS PDB1lox-21puro-26, and iPS PDB1lox-21puro-28 (Soldner et al. 2009); hES cell lines BG01 and BG03 (National Institutes of Health code: BG01 and BG03; BresaGen, Inc., Athens, GA); hES cell lines WIBR1, WIBR2, WIBR3, and WIBR7 (Lengner et al., 2010; Whitehead Institute Center for Human Stem Cell Research) and hES cell line H9 (NIH Code:WA09, Wisconsin Alumni Research Foundation, Madison, WI) were maintained on mitomycin C-inactivated mouse embryonic fibroblast (MEF) feeder layers in hESC medium (DMEM/F12 [Invitrogen] supplemented with 15% FBS [Hyclone], 5% KnockOut Serum Replacement [Invitrogen], 1 mM glutamine [Invitrogen], 1% nonessential amino acids [Invitrogen], 0.1 mM β-mercaptoethanol [Sigma], and 4 ng/ml FGF2 [R&D Systems]). Cultures were passaged every 5 to 7 days either manually or enzymatically with collagenase type IV (Invitrogen; 1.5 mg/ml). hiPS cell lines were passaged 15-25 times prior to ChIP-Seq and gene expression analysis.
| | Sample_molecule_ch1 | polyA RNA
| | Sample_extract_protocol_ch1 | RNA was isolated from hES and hiPS cells, which were mechanically separated from feeder cells, with the RNeasy Mini Kit (QIAGEN).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | 5 µg total RNA was used to prepare biotinylated cRNA according to the manufacturer’s protocol (Affymetrix One Cycle cDNA Synthesis Kit). Briefly, this method involves SuperScript II-directed reverse transcription using a T7-Oligo-dT promoter primer to create first strand cDNA. RNase H-mediated second strand cDNA synthesis is followed by T7 RNA Polymerase directed in vitro transcription, which incorporates a biotinylated nucleotide during cRNA amplification.
| | Sample_hyb_protocol | Samples were prepared for hybridization using 15 µg biotinylated cRNA in a 1X hybridization cocktail with additional hybridization cocktail components provided in the GeneChip Hybridization, Wash and Stain Kit (Affymetrix). GeneChip arrays (Human U133 Plus 2.0) were hybridized in a GeneChip Hybridization Oven at 45 degrees C for 16 hours at 60 RPM. Washing was performed 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 using default settings.
| | Sample_data_processing | Images were extracted and analyzed using the default settings of GeneChip Operating Software v1.4.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Garrett,M,Frampton
| | Sample_contact_email | frampton@mit.edu
| | Sample_contact_laboratory | Richard Young
| | Sample_contact_department | Biology
| | Sample_contact_institute | Whitehead Instute - MIT
| | Sample_contact_address | 9 Cambridge Center
| | Sample_contact_city | Cambridge
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02142
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM574nnn/GSM574058/suppl/GSM574058.CEL.gz
| | Sample_series_id | GSE22499
| | Sample_series_id | GSE23402
| | Sample_data_row_count | 54675
| | |
|
GSM574059 | GPL570 |
|
FIBROBLAST_GM_rep2_081006_8
|
human fibroblast line GM
|
cell line: human fibroblast line GM
|
Gene expression data from human fibroblast line GM
|
| Sample_geo_accession | GSM574059
| | Sample_status | Public on Aug 09 2010
| | Sample_submission_date | Aug 03 2010
| | Sample_last_update_date | Sep 15 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | Coriell Cell Repositories http://ccr.coriell.org/Sections/Search/Search.aspx?PgId=165&q=GM01660
| | Sample_growth_protocol_ch1 | All primary human fibroblasts cells described in this paper (PDB-AG20442 and GM-M01660) were purchased from the Coriell Cell Repository (Camden, NJ). Fibroblasts were cultured in fibroblast medium (Dulbecco's modified Eagle's medium [DMEM] supplemented with 15% fetal bovine serum [FBS; Hyclone], 1 mM glutamine [Invitrogen], 1% nonessential amino acids [Invitrogen], and penicillin/streptomycin [Invitrogen]).
| | Sample_growth_protocol_ch1 | hiPS cell lines iPS A1, iPS C1, iPS4, iPS A6 (Hockemeyer et al. 2009); hiPS cell lines iPS PDB2lox-17, iPS PDB2lox-21, iPS PDB2lox-5, iPS PDB2lox-22, iPS PDB1lox-17puro-5, iPS PDB1lox-17puro-10, iPS PDB1lox-17puro-33, iPS PDB1lox-21puro-20, iPS PDB1lox-21puro-26, and iPS PDB1lox-21puro-28 (Soldner et al. 2009); hES cell lines BG01 and BG03 (National Institutes of Health code: BG01 and BG03; BresaGen, Inc., Athens, GA); hES cell lines WIBR1, WIBR2, WIBR3, and WIBR7 (Lengner et al., 2010; Whitehead Institute Center for Human Stem Cell Research) and hES cell line H9 (NIH Code:WA09, Wisconsin Alumni Research Foundation, Madison, WI) were maintained on mitomycin C-inactivated mouse embryonic fibroblast (MEF) feeder layers in hESC medium (DMEM/F12 [Invitrogen] supplemented with 15% FBS [Hyclone], 5% KnockOut Serum Replacement [Invitrogen], 1 mM glutamine [Invitrogen], 1% nonessential amino acids [Invitrogen], 0.1 mM β-mercaptoethanol [Sigma], and 4 ng/ml FGF2 [R&D Systems]). Cultures were passaged every 5 to 7 days either manually or enzymatically with collagenase type IV (Invitrogen; 1.5 mg/ml). hiPS cell lines were passaged 15-25 times prior to ChIP-Seq and gene expression analysis.
| | Sample_molecule_ch1 | polyA RNA
| | Sample_extract_protocol_ch1 | RNA was isolated from hES and hiPS cells, which were mechanically separated from feeder cells, with the RNeasy Mini Kit (QIAGEN).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | 5 µg total RNA was used to prepare biotinylated cRNA according to the manufacturer’s protocol (Affymetrix One Cycle cDNA Synthesis Kit). Briefly, this method involves SuperScript II-directed reverse transcription using a T7-Oligo-dT promoter primer to create first strand cDNA. RNase H-mediated second strand cDNA synthesis is followed by T7 RNA Polymerase directed in vitro transcription, which incorporates a biotinylated nucleotide during cRNA amplification.
| | Sample_hyb_protocol | Samples were prepared for hybridization using 15 µg biotinylated cRNA in a 1X hybridization cocktail with additional hybridization cocktail components provided in the GeneChip Hybridization, Wash and Stain Kit (Affymetrix). GeneChip arrays (Human U133 Plus 2.0) were hybridized in a GeneChip Hybridization Oven at 45 degrees C for 16 hours at 60 RPM. Washing was performed 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 using default settings.
| | Sample_data_processing | Images were extracted and analyzed using the default settings of GeneChip Operating Software v1.4.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Garrett,M,Frampton
| | Sample_contact_email | frampton@mit.edu
| | Sample_contact_laboratory | Richard Young
| | Sample_contact_department | Biology
| | Sample_contact_institute | Whitehead Instute - MIT
| | Sample_contact_address | 9 Cambridge Center
| | Sample_contact_city | Cambridge
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02142
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM574nnn/GSM574059/suppl/GSM574059.CEL.gz
| | Sample_series_id | GSE22499
| | Sample_series_id | GSE23402
| | Sample_data_row_count | 54675
| | |
|
GSM574060 | GPL570 |
|
FIBROBLAST_PDB_rep1_120208_3
|
human fibroblast line PDB
|
cell line: human fibroblast line PDB
|
Gene expression data from human fibroblast line PDB
|
| Sample_geo_accession | GSM574060
| | Sample_status | Public on Aug 09 2010
| | Sample_submission_date | Aug 03 2010
| | Sample_last_update_date | Sep 15 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | Coriell Cell Repositories http://ccr.coriell.org/Sections/Search/Search.aspx?PgId=165&q=AG20442
| | Sample_growth_protocol_ch1 | All primary human fibroblasts cells described in this paper (PDB-AG20442 and GM-M01660) were purchased from the Coriell Cell Repository (Camden, NJ). Fibroblasts were cultured in fibroblast medium (Dulbecco's modified Eagle's medium [DMEM] supplemented with 15% fetal bovine serum [FBS; Hyclone], 1 mM glutamine [Invitrogen], 1% nonessential amino acids [Invitrogen], and penicillin/streptomycin [Invitrogen]).
| | Sample_growth_protocol_ch1 | hiPS cell lines iPS A1, iPS C1, iPS4, iPS A6 (Hockemeyer et al. 2009); hiPS cell lines iPS PDB2lox-17, iPS PDB2lox-21, iPS PDB2lox-5, iPS PDB2lox-22, iPS PDB1lox-17puro-5, iPS PDB1lox-17puro-10, iPS PDB1lox-17puro-33, iPS PDB1lox-21puro-20, iPS PDB1lox-21puro-26, and iPS PDB1lox-21puro-28 (Soldner et al. 2009); hES cell lines BG01 and BG03 (National Institutes of Health code: BG01 and BG03; BresaGen, Inc., Athens, GA); hES cell lines WIBR1, WIBR2, WIBR3, and WIBR7 (Lengner et al., 2010; Whitehead Institute Center for Human Stem Cell Research) and hES cell line H9 (NIH Code:WA09, Wisconsin Alumni Research Foundation, Madison, WI) were maintained on mitomycin C-inactivated mouse embryonic fibroblast (MEF) feeder layers in hESC medium (DMEM/F12 [Invitrogen] supplemented with 15% FBS [Hyclone], 5% KnockOut Serum Replacement [Invitrogen], 1 mM glutamine [Invitrogen], 1% nonessential amino acids [Invitrogen], 0.1 mM β-mercaptoethanol [Sigma], and 4 ng/ml FGF2 [R&D Systems]). Cultures were passaged every 5 to 7 days either manually or enzymatically with collagenase type IV (Invitrogen; 1.5 mg/ml). hiPS cell lines were passaged 15-25 times prior to ChIP-Seq and gene expression analysis.
| | Sample_molecule_ch1 | polyA RNA
| | Sample_extract_protocol_ch1 | RNA was isolated from hES and hiPS cells, which were mechanically separated from feeder cells, with the RNeasy Mini Kit (QIAGEN).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | 5 µg total RNA was used to prepare biotinylated cRNA according to the manufacturer’s protocol (Affymetrix One Cycle cDNA Synthesis Kit). Briefly, this method involves SuperScript II-directed reverse transcription using a T7-Oligo-dT promoter primer to create first strand cDNA. RNase H-mediated second strand cDNA synthesis is followed by T7 RNA Polymerase directed in vitro transcription, which incorporates a biotinylated nucleotide during cRNA amplification.
| | Sample_hyb_protocol | Samples were prepared for hybridization using 15 µg biotinylated cRNA in a 1X hybridization cocktail with additional hybridization cocktail components provided in the GeneChip Hybridization, Wash and Stain Kit (Affymetrix). GeneChip arrays (Human U133 Plus 2.0) were hybridized in a GeneChip Hybridization Oven at 45 degrees C for 16 hours at 60 RPM. Washing was performed 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 using default settings.
| | Sample_data_processing | Images were extracted and analyzed using the default settings of GeneChip Operating Software v1.4.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Garrett,M,Frampton
| | Sample_contact_email | frampton@mit.edu
| | Sample_contact_laboratory | Richard Young
| | Sample_contact_department | Biology
| | Sample_contact_institute | Whitehead Instute - MIT
| | Sample_contact_address | 9 Cambridge Center
| | Sample_contact_city | Cambridge
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02142
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM574nnn/GSM574060/suppl/GSM574060.CEL.gz
| | Sample_series_id | GSE22499
| | Sample_series_id | GSE23402
| | Sample_data_row_count | 54675
| | |
|
GSM574061 | GPL570 |
|
hES_BG01_rep1_081006_9
|
hES line BG01
|
cell line: hES line BG01
|
Gene expression data from hES line BG01
|
| Sample_geo_accession | GSM574061
| | Sample_status | Public on Aug 09 2010
| | Sample_submission_date | Aug 03 2010
| | Sample_last_update_date | Sep 15 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | All primary human fibroblasts cells described in this paper (PDB-AG20442 and GM-M01660) were purchased from the Coriell Cell Repository (Camden, NJ). Fibroblasts were cultured in fibroblast medium (Dulbecco's modified Eagle's medium [DMEM] supplemented with 15% fetal bovine serum [FBS; Hyclone], 1 mM glutamine [Invitrogen], 1% nonessential amino acids [Invitrogen], and penicillin/streptomycin [Invitrogen]).
| | Sample_growth_protocol_ch1 | hiPS cell lines iPS A1, iPS C1, iPS4, iPS A6 (Hockemeyer et al. 2009); hiPS cell lines iPS PDB2lox-17, iPS PDB2lox-21, iPS PDB2lox-5, iPS PDB2lox-22, iPS PDB1lox-17puro-5, iPS PDB1lox-17puro-10, iPS PDB1lox-17puro-33, iPS PDB1lox-21puro-20, iPS PDB1lox-21puro-26, and iPS PDB1lox-21puro-28 (Soldner et al. 2009); hES cell lines BG01 and BG03 (National Institutes of Health code: BG01 and BG03; BresaGen, Inc., Athens, GA); hES cell lines WIBR1, WIBR2, WIBR3, and WIBR7 (Lengner et al., 2010; Whitehead Institute Center for Human Stem Cell Research) and hES cell line H9 (NIH Code:WA09, Wisconsin Alumni Research Foundation, Madison, WI) were maintained on mitomycin C-inactivated mouse embryonic fibroblast (MEF) feeder layers in hESC medium (DMEM/F12 [Invitrogen] supplemented with 15% FBS [Hyclone], 5% KnockOut Serum Replacement [Invitrogen], 1 mM glutamine [Invitrogen], 1% nonessential amino acids [Invitrogen], 0.1 mM β-mercaptoethanol [Sigma], and 4 ng/ml FGF2 [R&D Systems]). Cultures were passaged every 5 to 7 days either manually or enzymatically with collagenase type IV (Invitrogen; 1.5 mg/ml). hiPS cell lines were passaged 15-25 times prior to ChIP-Seq and gene expression analysis.
| | Sample_molecule_ch1 | polyA RNA
| | Sample_extract_protocol_ch1 | RNA was isolated from hES and hiPS cells, which were mechanically separated from feeder cells, with the RNeasy Mini Kit (QIAGEN).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | 5 µg total RNA was used to prepare biotinylated cRNA according to the manufacturer’s protocol (Affymetrix One Cycle cDNA Synthesis Kit). Briefly, this method involves SuperScript II-directed reverse transcription using a T7-Oligo-dT promoter primer to create first strand cDNA. RNase H-mediated second strand cDNA synthesis is followed by T7 RNA Polymerase directed in vitro transcription, which incorporates a biotinylated nucleotide during cRNA amplification.
| | Sample_hyb_protocol | Samples were prepared for hybridization using 15 µg biotinylated cRNA in a 1X hybridization cocktail with additional hybridization cocktail components provided in the GeneChip Hybridization, Wash and Stain Kit (Affymetrix). GeneChip arrays (Human U133 Plus 2.0) were hybridized in a GeneChip Hybridization Oven at 45 degrees C for 16 hours at 60 RPM. Washing was performed 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 using default settings.
| | Sample_data_processing | Images were extracted and analyzed using the default settings of GeneChip Operating Software v1.4.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Garrett,M,Frampton
| | Sample_contact_email | frampton@mit.edu
| | Sample_contact_laboratory | Richard Young
| | Sample_contact_department | Biology
| | Sample_contact_institute | Whitehead Instute - MIT
| | Sample_contact_address | 9 Cambridge Center
| | Sample_contact_city | Cambridge
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02142
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM574nnn/GSM574061/suppl/GSM574061.CEL.gz
| | Sample_series_id | GSE22499
| | Sample_series_id | GSE23402
| | Sample_data_row_count | 54675
| | |
|
GSM574062 | GPL570 |
|
hES_BG01_rep2_081006_10
|
hES line BG01
|
cell line: hES line BG01
|
Gene expression data from hES line BG01
|
| Sample_geo_accession | GSM574062
| | Sample_status | Public on Aug 09 2010
| | Sample_submission_date | Aug 03 2010
| | Sample_last_update_date | Sep 15 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | All primary human fibroblasts cells described in this paper (PDB-AG20442 and GM-M01660) were purchased from the Coriell Cell Repository (Camden, NJ). Fibroblasts were cultured in fibroblast medium (Dulbecco's modified Eagle's medium [DMEM] supplemented with 15% fetal bovine serum [FBS; Hyclone], 1 mM glutamine [Invitrogen], 1% nonessential amino acids [Invitrogen], and penicillin/streptomycin [Invitrogen]).
| | Sample_growth_protocol_ch1 | hiPS cell lines iPS A1, iPS C1, iPS4, iPS A6 (Hockemeyer et al. 2009); hiPS cell lines iPS PDB2lox-17, iPS PDB2lox-21, iPS PDB2lox-5, iPS PDB2lox-22, iPS PDB1lox-17puro-5, iPS PDB1lox-17puro-10, iPS PDB1lox-17puro-33, iPS PDB1lox-21puro-20, iPS PDB1lox-21puro-26, and iPS PDB1lox-21puro-28 (Soldner et al. 2009); hES cell lines BG01 and BG03 (National Institutes of Health code: BG01 and BG03; BresaGen, Inc., Athens, GA); hES cell lines WIBR1, WIBR2, WIBR3, and WIBR7 (Lengner et al., 2010; Whitehead Institute Center for Human Stem Cell Research) and hES cell line H9 (NIH Code:WA09, Wisconsin Alumni Research Foundation, Madison, WI) were maintained on mitomycin C-inactivated mouse embryonic fibroblast (MEF) feeder layers in hESC medium (DMEM/F12 [Invitrogen] supplemented with 15% FBS [Hyclone], 5% KnockOut Serum Replacement [Invitrogen], 1 mM glutamine [Invitrogen], 1% nonessential amino acids [Invitrogen], 0.1 mM β-mercaptoethanol [Sigma], and 4 ng/ml FGF2 [R&D Systems]). Cultures were passaged every 5 to 7 days either manually or enzymatically with collagenase type IV (Invitrogen; 1.5 mg/ml). hiPS cell lines were passaged 15-25 times prior to ChIP-Seq and gene expression analysis.
| | Sample_molecule_ch1 | polyA RNA
| | Sample_extract_protocol_ch1 | RNA was isolated from hES and hiPS cells, which were mechanically separated from feeder cells, with the RNeasy Mini Kit (QIAGEN).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | 5 µg total RNA was used to prepare biotinylated cRNA according to the manufacturer’s protocol (Affymetrix One Cycle cDNA Synthesis Kit). Briefly, this method involves SuperScript II-directed reverse transcription using a T7-Oligo-dT promoter primer to create first strand cDNA. RNase H-mediated second strand cDNA synthesis is followed by T7 RNA Polymerase directed in vitro transcription, which incorporates a biotinylated nucleotide during cRNA amplification.
| | Sample_hyb_protocol | Samples were prepared for hybridization using 15 µg biotinylated cRNA in a 1X hybridization cocktail with additional hybridization cocktail components provided in the GeneChip Hybridization, Wash and Stain Kit (Affymetrix). GeneChip arrays (Human U133 Plus 2.0) were hybridized in a GeneChip Hybridization Oven at 45 degrees C for 16 hours at 60 RPM. Washing was performed 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 using default settings.
| | Sample_data_processing | Images were extracted and analyzed using the default settings of GeneChip Operating Software v1.4.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Garrett,M,Frampton
| | Sample_contact_email | frampton@mit.edu
| | Sample_contact_laboratory | Richard Young
| | Sample_contact_department | Biology
| | Sample_contact_institute | Whitehead Instute - MIT
| | Sample_contact_address | 9 Cambridge Center
| | Sample_contact_city | Cambridge
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02142
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM574nnn/GSM574062/suppl/GSM574062.CEL.gz
| | Sample_series_id | GSE22499
| | Sample_series_id | GSE23402
| | Sample_data_row_count | 54675
| | |
|
GSM574063 | GPL570 |
|
hES_BG01_rep3_081006_13
|
hES line BG01
|
cell line: hES line BG01
|
Gene expression data from hES line BG01
|
| Sample_geo_accession | GSM574063
| | Sample_status | Public on Aug 09 2010
| | Sample_submission_date | Aug 03 2010
| | Sample_last_update_date | Sep 15 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | All primary human fibroblasts cells described in this paper (PDB-AG20442 and GM-M01660) were purchased from the Coriell Cell Repository (Camden, NJ). Fibroblasts were cultured in fibroblast medium (Dulbecco's modified Eagle's medium [DMEM] supplemented with 15% fetal bovine serum [FBS; Hyclone], 1 mM glutamine [Invitrogen], 1% nonessential amino acids [Invitrogen], and penicillin/streptomycin [Invitrogen]).
| | Sample_growth_protocol_ch1 | hiPS cell lines iPS A1, iPS C1, iPS4, iPS A6 (Hockemeyer et al. 2009); hiPS cell lines iPS PDB2lox-17, iPS PDB2lox-21, iPS PDB2lox-5, iPS PDB2lox-22, iPS PDB1lox-17puro-5, iPS PDB1lox-17puro-10, iPS PDB1lox-17puro-33, iPS PDB1lox-21puro-20, iPS PDB1lox-21puro-26, and iPS PDB1lox-21puro-28 (Soldner et al. 2009); hES cell lines BG01 and BG03 (National Institutes of Health code: BG01 and BG03; BresaGen, Inc., Athens, GA); hES cell lines WIBR1, WIBR2, WIBR3, and WIBR7 (Lengner et al., 2010; Whitehead Institute Center for Human Stem Cell Research) and hES cell line H9 (NIH Code:WA09, Wisconsin Alumni Research Foundation, Madison, WI) were maintained on mitomycin C-inactivated mouse embryonic fibroblast (MEF) feeder layers in hESC medium (DMEM/F12 [Invitrogen] supplemented with 15% FBS [Hyclone], 5% KnockOut Serum Replacement [Invitrogen], 1 mM glutamine [Invitrogen], 1% nonessential amino acids [Invitrogen], 0.1 mM β-mercaptoethanol [Sigma], and 4 ng/ml FGF2 [R&D Systems]). Cultures were passaged every 5 to 7 days either manually or enzymatically with collagenase type IV (Invitrogen; 1.5 mg/ml). hiPS cell lines were passaged 15-25 times prior to ChIP-Seq and gene expression analysis.
| | Sample_molecule_ch1 | polyA RNA
| | Sample_extract_protocol_ch1 | RNA was isolated from hES and hiPS cells, which were mechanically separated from feeder cells, with the RNeasy Mini Kit (QIAGEN).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | 5 µg total RNA was used to prepare biotinylated cRNA according to the manufacturer’s protocol (Affymetrix One Cycle cDNA Synthesis Kit). Briefly, this method involves SuperScript II-directed reverse transcription using a T7-Oligo-dT promoter primer to create first strand cDNA. RNase H-mediated second strand cDNA synthesis is followed by T7 RNA Polymerase directed in vitro transcription, which incorporates a biotinylated nucleotide during cRNA amplification.
| | Sample_hyb_protocol | Samples were prepared for hybridization using 15 µg biotinylated cRNA in a 1X hybridization cocktail with additional hybridization cocktail components provided in the GeneChip Hybridization, Wash and Stain Kit (Affymetrix). GeneChip arrays (Human U133 Plus 2.0) were hybridized in a GeneChip Hybridization Oven at 45 degrees C for 16 hours at 60 RPM. Washing was performed 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 using default settings.
| | Sample_data_processing | Images were extracted and analyzed using the default settings of GeneChip Operating Software v1.4.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Garrett,M,Frampton
| | Sample_contact_email | frampton@mit.edu
| | Sample_contact_laboratory | Richard Young
| | Sample_contact_department | Biology
| | Sample_contact_institute | Whitehead Instute - MIT
| | Sample_contact_address | 9 Cambridge Center
| | Sample_contact_city | Cambridge
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02142
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM574nnn/GSM574063/suppl/GSM574063.CEL.gz
| | Sample_series_id | GSE22499
| | Sample_series_id | GSE23402
| | Sample_data_row_count | 54675
| | |
|
GSM574064 | GPL570 |
|
hES_BG01_rep4_081006_14
|
hES line BG01
|
cell line: hES line BG01
|
Gene expression data from hES line BG01
|
| Sample_geo_accession | GSM574064
| | Sample_status | Public on Aug 09 2010
| | Sample_submission_date | Aug 03 2010
| | Sample_last_update_date | Sep 15 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | All primary human fibroblasts cells described in this paper (PDB-AG20442 and GM-M01660) were purchased from the Coriell Cell Repository (Camden, NJ). Fibroblasts were cultured in fibroblast medium (Dulbecco's modified Eagle's medium [DMEM] supplemented with 15% fetal bovine serum [FBS; Hyclone], 1 mM glutamine [Invitrogen], 1% nonessential amino acids [Invitrogen], and penicillin/streptomycin [Invitrogen]).
| | Sample_growth_protocol_ch1 | hiPS cell lines iPS A1, iPS C1, iPS4, iPS A6 (Hockemeyer et al. 2009); hiPS cell lines iPS PDB2lox-17, iPS PDB2lox-21, iPS PDB2lox-5, iPS PDB2lox-22, iPS PDB1lox-17puro-5, iPS PDB1lox-17puro-10, iPS PDB1lox-17puro-33, iPS PDB1lox-21puro-20, iPS PDB1lox-21puro-26, and iPS PDB1lox-21puro-28 (Soldner et al. 2009); hES cell lines BG01 and BG03 (National Institutes of Health code: BG01 and BG03; BresaGen, Inc., Athens, GA); hES cell lines WIBR1, WIBR2, WIBR3, and WIBR7 (Lengner et al., 2010; Whitehead Institute Center for Human Stem Cell Research) and hES cell line H9 (NIH Code:WA09, Wisconsin Alumni Research Foundation, Madison, WI) were maintained on mitomycin C-inactivated mouse embryonic fibroblast (MEF) feeder layers in hESC medium (DMEM/F12 [Invitrogen] supplemented with 15% FBS [Hyclone], 5% KnockOut Serum Replacement [Invitrogen], 1 mM glutamine [Invitrogen], 1% nonessential amino acids [Invitrogen], 0.1 mM β-mercaptoethanol [Sigma], and 4 ng/ml FGF2 [R&D Systems]). Cultures were passaged every 5 to 7 days either manually or enzymatically with collagenase type IV (Invitrogen; 1.5 mg/ml). hiPS cell lines were passaged 15-25 times prior to ChIP-Seq and gene expression analysis.
| | Sample_molecule_ch1 | polyA RNA
| | Sample_extract_protocol_ch1 | RNA was isolated from hES and hiPS cells, which were mechanically separated from feeder cells, with the RNeasy Mini Kit (QIAGEN).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | 5 µg total RNA was used to prepare biotinylated cRNA according to the manufacturer’s protocol (Affymetrix One Cycle cDNA Synthesis Kit). Briefly, this method involves SuperScript II-directed reverse transcription using a T7-Oligo-dT promoter primer to create first strand cDNA. RNase H-mediated second strand cDNA synthesis is followed by T7 RNA Polymerase directed in vitro transcription, which incorporates a biotinylated nucleotide during cRNA amplification.
| | Sample_hyb_protocol | Samples were prepared for hybridization using 15 µg biotinylated cRNA in a 1X hybridization cocktail with additional hybridization cocktail components provided in the GeneChip Hybridization, Wash and Stain Kit (Affymetrix). GeneChip arrays (Human U133 Plus 2.0) were hybridized in a GeneChip Hybridization Oven at 45 degrees C for 16 hours at 60 RPM. Washing was performed 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 using default settings.
| | Sample_data_processing | Images were extracted and analyzed using the default settings of GeneChip Operating Software v1.4.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Garrett,M,Frampton
| | Sample_contact_email | frampton@mit.edu
| | Sample_contact_laboratory | Richard Young
| | Sample_contact_department | Biology
| | Sample_contact_institute | Whitehead Instute - MIT
| | Sample_contact_address | 9 Cambridge Center
| | Sample_contact_city | Cambridge
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02142
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM574nnn/GSM574064/suppl/GSM574064.CEL.gz
| | Sample_series_id | GSE22499
| | Sample_series_id | GSE23402
| | Sample_data_row_count | 54675
| | |
|
GSM574065 | GPL570 |
|
hES_BG01_rep5_120208_1
|
hES line BG01
|
cell line: hES line BG01
|
Gene expression data from hES line BG01
|
| Sample_geo_accession | GSM574065
| | Sample_status | Public on Aug 09 2010
| | Sample_submission_date | Aug 03 2010
| | Sample_last_update_date | Sep 15 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | All primary human fibroblasts cells described in this paper (PDB-AG20442 and GM-M01660) were purchased from the Coriell Cell Repository (Camden, NJ). Fibroblasts were cultured in fibroblast medium (Dulbecco's modified Eagle's medium [DMEM] supplemented with 15% fetal bovine serum [FBS; Hyclone], 1 mM glutamine [Invitrogen], 1% nonessential amino acids [Invitrogen], and penicillin/streptomycin [Invitrogen]).
| | Sample_growth_protocol_ch1 | hiPS cell lines iPS A1, iPS C1, iPS4, iPS A6 (Hockemeyer et al. 2009); hiPS cell lines iPS PDB2lox-17, iPS PDB2lox-21, iPS PDB2lox-5, iPS PDB2lox-22, iPS PDB1lox-17puro-5, iPS PDB1lox-17puro-10, iPS PDB1lox-17puro-33, iPS PDB1lox-21puro-20, iPS PDB1lox-21puro-26, and iPS PDB1lox-21puro-28 (Soldner et al. 2009); hES cell lines BG01 and BG03 (National Institutes of Health code: BG01 and BG03; BresaGen, Inc., Athens, GA); hES cell lines WIBR1, WIBR2, WIBR3, and WIBR7 (Lengner et al., 2010; Whitehead Institute Center for Human Stem Cell Research) and hES cell line H9 (NIH Code:WA09, Wisconsin Alumni Research Foundation, Madison, WI) were maintained on mitomycin C-inactivated mouse embryonic fibroblast (MEF) feeder layers in hESC medium (DMEM/F12 [Invitrogen] supplemented with 15% FBS [Hyclone], 5% KnockOut Serum Replacement [Invitrogen], 1 mM glutamine [Invitrogen], 1% nonessential amino acids [Invitrogen], 0.1 mM β-mercaptoethanol [Sigma], and 4 ng/ml FGF2 [R&D Systems]). Cultures were passaged every 5 to 7 days either manually or enzymatically with collagenase type IV (Invitrogen; 1.5 mg/ml). hiPS cell lines were passaged 15-25 times prior to ChIP-Seq and gene expression analysis.
| | Sample_molecule_ch1 | polyA RNA
| | Sample_extract_protocol_ch1 | RNA was isolated from hES and hiPS cells, which were mechanically separated from feeder cells, with the RNeasy Mini Kit (QIAGEN).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | 5 µg total RNA was used to prepare biotinylated cRNA according to the manufacturer’s protocol (Affymetrix One Cycle cDNA Synthesis Kit). Briefly, this method involves SuperScript II-directed reverse transcription using a T7-Oligo-dT promoter primer to create first strand cDNA. RNase H-mediated second strand cDNA synthesis is followed by T7 RNA Polymerase directed in vitro transcription, which incorporates a biotinylated nucleotide during cRNA amplification.
| | Sample_hyb_protocol | Samples were prepared for hybridization using 15 µg biotinylated cRNA in a 1X hybridization cocktail with additional hybridization cocktail components provided in the GeneChip Hybridization, Wash and Stain Kit (Affymetrix). GeneChip arrays (Human U133 Plus 2.0) were hybridized in a GeneChip Hybridization Oven at 45 degrees C for 16 hours at 60 RPM. Washing was performed 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 using default settings.
| | Sample_data_processing | Images were extracted and analyzed using the default settings of GeneChip Operating Software v1.4.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Garrett,M,Frampton
| | Sample_contact_email | frampton@mit.edu
| | Sample_contact_laboratory | Richard Young
| | Sample_contact_department | Biology
| | Sample_contact_institute | Whitehead Instute - MIT
| | Sample_contact_address | 9 Cambridge Center
| | Sample_contact_city | Cambridge
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02142
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM574nnn/GSM574065/suppl/GSM574065.CEL.gz
| | Sample_series_id | GSE22499
| | Sample_series_id | GSE23402
| | Sample_data_row_count | 54675
| | |
|
GSM574066 | GPL570 |
|
hES_BG03_rep1_090811_5
|
hES line BG03
|
cell line: hES line BG03
|
Gene expression data from hES line BG03
|
| Sample_geo_accession | GSM574066
| | Sample_status | Public on Aug 09 2010
| | Sample_submission_date | Aug 03 2010
| | Sample_last_update_date | Sep 15 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | All primary human fibroblasts cells described in this paper (PDB-AG20442 and GM-M01660) were purchased from the Coriell Cell Repository (Camden, NJ). Fibroblasts were cultured in fibroblast medium (Dulbecco's modified Eagle's medium [DMEM] supplemented with 15% fetal bovine serum [FBS; Hyclone], 1 mM glutamine [Invitrogen], 1% nonessential amino acids [Invitrogen], and penicillin/streptomycin [Invitrogen]).
| | Sample_growth_protocol_ch1 | hiPS cell lines iPS A1, iPS C1, iPS4, iPS A6 (Hockemeyer et al. 2009); hiPS cell lines iPS PDB2lox-17, iPS PDB2lox-21, iPS PDB2lox-5, iPS PDB2lox-22, iPS PDB1lox-17puro-5, iPS PDB1lox-17puro-10, iPS PDB1lox-17puro-33, iPS PDB1lox-21puro-20, iPS PDB1lox-21puro-26, and iPS PDB1lox-21puro-28 (Soldner et al. 2009); hES cell lines BG01 and BG03 (National Institutes of Health code: BG01 and BG03; BresaGen, Inc., Athens, GA); hES cell lines WIBR1, WIBR2, WIBR3, and WIBR7 (Lengner et al., 2010; Whitehead Institute Center for Human Stem Cell Research) and hES cell line H9 (NIH Code:WA09, Wisconsin Alumni Research Foundation, Madison, WI) were maintained on mitomycin C-inactivated mouse embryonic fibroblast (MEF) feeder layers in hESC medium (DMEM/F12 [Invitrogen] supplemented with 15% FBS [Hyclone], 5% KnockOut Serum Replacement [Invitrogen], 1 mM glutamine [Invitrogen], 1% nonessential amino acids [Invitrogen], 0.1 mM β-mercaptoethanol [Sigma], and 4 ng/ml FGF2 [R&D Systems]). Cultures were passaged every 5 to 7 days either manually or enzymatically with collagenase type IV (Invitrogen; 1.5 mg/ml). hiPS cell lines were passaged 15-25 times prior to ChIP-Seq and gene expression analysis.
| | Sample_molecule_ch1 | polyA RNA
| | Sample_extract_protocol_ch1 | RNA was isolated from hES and hiPS cells, which were mechanically separated from feeder cells, with the RNeasy Mini Kit (QIAGEN).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | 5 µg total RNA was used to prepare biotinylated cRNA according to the manufacturer’s protocol (Affymetrix One Cycle cDNA Synthesis Kit). Briefly, this method involves SuperScript II-directed reverse transcription using a T7-Oligo-dT promoter primer to create first strand cDNA. RNase H-mediated second strand cDNA synthesis is followed by T7 RNA Polymerase directed in vitro transcription, which incorporates a biotinylated nucleotide during cRNA amplification.
| | Sample_hyb_protocol | Samples were prepared for hybridization using 15 µg biotinylated cRNA in a 1X hybridization cocktail with additional hybridization cocktail components provided in the GeneChip Hybridization, Wash and Stain Kit (Affymetrix). GeneChip arrays (Human U133 Plus 2.0) were hybridized in a GeneChip Hybridization Oven at 45 degrees C for 16 hours at 60 RPM. Washing was performed 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 using default settings.
| | Sample_data_processing | Images were extracted and analyzed using the default settings of GeneChip Operating Software v1.4.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Garrett,M,Frampton
| | Sample_contact_email | frampton@mit.edu
| | Sample_contact_laboratory | Richard Young
| | Sample_contact_department | Biology
| | Sample_contact_institute | Whitehead Instute - MIT
| | Sample_contact_address | 9 Cambridge Center
| | Sample_contact_city | Cambridge
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02142
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM574nnn/GSM574066/suppl/GSM574066.CEL.gz
| | Sample_series_id | GSE22499
| | Sample_series_id | GSE23402
| | Sample_data_row_count | 54675
| | |
|
GSM574067 | GPL570 |
|
hES_BG03_rep2_090811_6
|
hES line BG03
|
cell line: hES line BG03
|
Gene expression data from hES line BG03
|
| Sample_geo_accession | GSM574067
| | Sample_status | Public on Aug 09 2010
| | Sample_submission_date | Aug 03 2010
| | Sample_last_update_date | Sep 15 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | All primary human fibroblasts cells described in this paper (PDB-AG20442 and GM-M01660) were purchased from the Coriell Cell Repository (Camden, NJ). Fibroblasts were cultured in fibroblast medium (Dulbecco's modified Eagle's medium [DMEM] supplemented with 15% fetal bovine serum [FBS; Hyclone], 1 mM glutamine [Invitrogen], 1% nonessential amino acids [Invitrogen], and penicillin/streptomycin [Invitrogen]).
| | Sample_growth_protocol_ch1 | hiPS cell lines iPS A1, iPS C1, iPS4, iPS A6 (Hockemeyer et al. 2009); hiPS cell lines iPS PDB2lox-17, iPS PDB2lox-21, iPS PDB2lox-5, iPS PDB2lox-22, iPS PDB1lox-17puro-5, iPS PDB1lox-17puro-10, iPS PDB1lox-17puro-33, iPS PDB1lox-21puro-20, iPS PDB1lox-21puro-26, and iPS PDB1lox-21puro-28 (Soldner et al. 2009); hES cell lines BG01 and BG03 (National Institutes of Health code: BG01 and BG03; BresaGen, Inc., Athens, GA); hES cell lines WIBR1, WIBR2, WIBR3, and WIBR7 (Lengner et al., 2010; Whitehead Institute Center for Human Stem Cell Research) and hES cell line H9 (NIH Code:WA09, Wisconsin Alumni Research Foundation, Madison, WI) were maintained on mitomycin C-inactivated mouse embryonic fibroblast (MEF) feeder layers in hESC medium (DMEM/F12 [Invitrogen] supplemented with 15% FBS [Hyclone], 5% KnockOut Serum Replacement [Invitrogen], 1 mM glutamine [Invitrogen], 1% nonessential amino acids [Invitrogen], 0.1 mM β-mercaptoethanol [Sigma], and 4 ng/ml FGF2 [R&D Systems]). Cultures were passaged every 5 to 7 days either manually or enzymatically with collagenase type IV (Invitrogen; 1.5 mg/ml). hiPS cell lines were passaged 15-25 times prior to ChIP-Seq and gene expression analysis.
| | Sample_molecule_ch1 | polyA RNA
| | Sample_extract_protocol_ch1 | RNA was isolated from hES and hiPS cells, which were mechanically separated from feeder cells, with the RNeasy Mini Kit (QIAGEN).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | 5 µg total RNA was used to prepare biotinylated cRNA according to the manufacturer’s protocol (Affymetrix One Cycle cDNA Synthesis Kit). Briefly, this method involves SuperScript II-directed reverse transcription using a T7-Oligo-dT promoter primer to create first strand cDNA. RNase H-mediated second strand cDNA synthesis is followed by T7 RNA Polymerase directed in vitro transcription, which incorporates a biotinylated nucleotide during cRNA amplification.
| | Sample_hyb_protocol | Samples were prepared for hybridization using 15 µg biotinylated cRNA in a 1X hybridization cocktail with additional hybridization cocktail components provided in the GeneChip Hybridization, Wash and Stain Kit (Affymetrix). GeneChip arrays (Human U133 Plus 2.0) were hybridized in a GeneChip Hybridization Oven at 45 degrees C for 16 hours at 60 RPM. Washing was performed 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 using default settings.
| | Sample_data_processing | Images were extracted and analyzed using the default settings of GeneChip Operating Software v1.4.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Garrett,M,Frampton
| | Sample_contact_email | frampton@mit.edu
| | Sample_contact_laboratory | Richard Young
| | Sample_contact_department | Biology
| | Sample_contact_institute | Whitehead Instute - MIT
| | Sample_contact_address | 9 Cambridge Center
| | Sample_contact_city | Cambridge
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02142
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM574nnn/GSM574067/suppl/GSM574067.CEL.gz
| | Sample_series_id | GSE22499
| | Sample_series_id | GSE23402
| | Sample_data_row_count | 54675
| | |
|
GSM574068 | GPL570 |
|
hES_H9_rep1_081006_15
|
hES line H9
|
cell line: hES line H9
|
Gene expression data from hES line H9
|
| Sample_geo_accession | GSM574068
| | Sample_status | Public on Aug 09 2010
| | Sample_submission_date | Aug 03 2010
| | Sample_last_update_date | Sep 15 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | All primary human fibroblasts cells described in this paper (PDB-AG20442 and GM-M01660) were purchased from the Coriell Cell Repository (Camden, NJ). Fibroblasts were cultured in fibroblast medium (Dulbecco's modified Eagle's medium [DMEM] supplemented with 15% fetal bovine serum [FBS; Hyclone], 1 mM glutamine [Invitrogen], 1% nonessential amino acids [Invitrogen], and penicillin/streptomycin [Invitrogen]).
| | Sample_growth_protocol_ch1 | hiPS cell lines iPS A1, iPS C1, iPS4, iPS A6 (Hockemeyer et al. 2009); hiPS cell lines iPS PDB2lox-17, iPS PDB2lox-21, iPS PDB2lox-5, iPS PDB2lox-22, iPS PDB1lox-17puro-5, iPS PDB1lox-17puro-10, iPS PDB1lox-17puro-33, iPS PDB1lox-21puro-20, iPS PDB1lox-21puro-26, and iPS PDB1lox-21puro-28 (Soldner et al. 2009); hES cell lines BG01 and BG03 (National Institutes of Health code: BG01 and BG03; BresaGen, Inc., Athens, GA); hES cell lines WIBR1, WIBR2, WIBR3, and WIBR7 (Lengner et al., 2010; Whitehead Institute Center for Human Stem Cell Research) and hES cell line H9 (NIH Code:WA09, Wisconsin Alumni Research Foundation, Madison, WI) were maintained on mitomycin C-inactivated mouse embryonic fibroblast (MEF) feeder layers in hESC medium (DMEM/F12 [Invitrogen] supplemented with 15% FBS [Hyclone], 5% KnockOut Serum Replacement [Invitrogen], 1 mM glutamine [Invitrogen], 1% nonessential amino acids [Invitrogen], 0.1 mM β-mercaptoethanol [Sigma], and 4 ng/ml FGF2 [R&D Systems]). Cultures were passaged every 5 to 7 days either manually or enzymatically with collagenase type IV (Invitrogen; 1.5 mg/ml). hiPS cell lines were passaged 15-25 times prior to ChIP-Seq and gene expression analysis.
| | Sample_molecule_ch1 | polyA RNA
| | Sample_extract_protocol_ch1 | RNA was isolated from hES and hiPS cells, which were mechanically separated from feeder cells, with the RNeasy Mini Kit (QIAGEN).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | 5 µg total RNA was used to prepare biotinylated cRNA according to the manufacturer’s protocol (Affymetrix One Cycle cDNA Synthesis Kit). Briefly, this method involves SuperScript II-directed reverse transcription using a T7-Oligo-dT promoter primer to create first strand cDNA. RNase H-mediated second strand cDNA synthesis is followed by T7 RNA Polymerase directed in vitro transcription, which incorporates a biotinylated nucleotide during cRNA amplification.
| | Sample_hyb_protocol | Samples were prepared for hybridization using 15 µg biotinylated cRNA in a 1X hybridization cocktail with additional hybridization cocktail components provided in the GeneChip Hybridization, Wash and Stain Kit (Affymetrix). GeneChip arrays (Human U133 Plus 2.0) were hybridized in a GeneChip Hybridization Oven at 45 degrees C for 16 hours at 60 RPM. Washing was performed 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 using default settings.
| | Sample_data_processing | Images were extracted and analyzed using the default settings of GeneChip Operating Software v1.4.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Garrett,M,Frampton
| | Sample_contact_email | frampton@mit.edu
| | Sample_contact_laboratory | Richard Young
| | Sample_contact_department | Biology
| | Sample_contact_institute | Whitehead Instute - MIT
| | Sample_contact_address | 9 Cambridge Center
| | Sample_contact_city | Cambridge
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02142
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM574nnn/GSM574068/suppl/GSM574068.CEL.gz
| | Sample_series_id | GSE22499
| | Sample_series_id | GSE23402
| | Sample_data_row_count | 54675
| | |
|
GSM574069 | GPL570 |
|
hES_H9_rep2_120208_15
|
hES line H9
|
cell line: hES line H9
|
Gene expression data from hES line H9
|
| Sample_geo_accession | GSM574069
| | Sample_status | Public on Aug 09 2010
| | Sample_submission_date | Aug 03 2010
| | Sample_last_update_date | Sep 15 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | All primary human fibroblasts cells described in this paper (PDB-AG20442 and GM-M01660) were purchased from the Coriell Cell Repository (Camden, NJ). Fibroblasts were cultured in fibroblast medium (Dulbecco's modified Eagle's medium [DMEM] supplemented with 15% fetal bovine serum [FBS; Hyclone], 1 mM glutamine [Invitrogen], 1% nonessential amino acids [Invitrogen], and penicillin/streptomycin [Invitrogen]).
| | Sample_growth_protocol_ch1 | hiPS cell lines iPS A1, iPS C1, iPS4, iPS A6 (Hockemeyer et al. 2009); hiPS cell lines iPS PDB2lox-17, iPS PDB2lox-21, iPS PDB2lox-5, iPS PDB2lox-22, iPS PDB1lox-17puro-5, iPS PDB1lox-17puro-10, iPS PDB1lox-17puro-33, iPS PDB1lox-21puro-20, iPS PDB1lox-21puro-26, and iPS PDB1lox-21puro-28 (Soldner et al. 2009); hES cell lines BG01 and BG03 (National Institutes of Health code: BG01 and BG03; BresaGen, Inc., Athens, GA); hES cell lines WIBR1, WIBR2, WIBR3, and WIBR7 (Lengner et al., 2010; Whitehead Institute Center for Human Stem Cell Research) and hES cell line H9 (NIH Code:WA09, Wisconsin Alumni Research Foundation, Madison, WI) were maintained on mitomycin C-inactivated mouse embryonic fibroblast (MEF) feeder layers in hESC medium (DMEM/F12 [Invitrogen] supplemented with 15% FBS [Hyclone], 5% KnockOut Serum Replacement [Invitrogen], 1 mM glutamine [Invitrogen], 1% nonessential amino acids [Invitrogen], 0.1 mM β-mercaptoethanol [Sigma], and 4 ng/ml FGF2 [R&D Systems]). Cultures were passaged every 5 to 7 days either manually or enzymatically with collagenase type IV (Invitrogen; 1.5 mg/ml). hiPS cell lines were passaged 15-25 times prior to ChIP-Seq and gene expression analysis.
| | Sample_molecule_ch1 | polyA RNA
| | Sample_extract_protocol_ch1 | RNA was isolated from hES and hiPS cells, which were mechanically separated from feeder cells, with the RNeasy Mini Kit (QIAGEN).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | 5 µg total RNA was used to prepare biotinylated cRNA according to the manufacturer’s protocol (Affymetrix One Cycle cDNA Synthesis Kit). Briefly, this method involves SuperScript II-directed reverse transcription using a T7-Oligo-dT promoter primer to create first strand cDNA. RNase H-mediated second strand cDNA synthesis is followed by T7 RNA Polymerase directed in vitro transcription, which incorporates a biotinylated nucleotide during cRNA amplification.
| | Sample_hyb_protocol | Samples were prepared for hybridization using 15 µg biotinylated cRNA in a 1X hybridization cocktail with additional hybridization cocktail components provided in the GeneChip Hybridization, Wash and Stain Kit (Affymetrix). GeneChip arrays (Human U133 Plus 2.0) were hybridized in a GeneChip Hybridization Oven at 45 degrees C for 16 hours at 60 RPM. Washing was performed 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 using default settings.
| | Sample_data_processing | Images were extracted and analyzed using the default settings of GeneChip Operating Software v1.4.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Garrett,M,Frampton
| | Sample_contact_email | frampton@mit.edu
| | Sample_contact_laboratory | Richard Young
| | Sample_contact_department | Biology
| | Sample_contact_institute | Whitehead Instute - MIT
| | Sample_contact_address | 9 Cambridge Center
| | Sample_contact_city | Cambridge
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02142
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM574nnn/GSM574069/suppl/GSM574069.CEL.gz
| | Sample_series_id | GSE22499
| | Sample_series_id | GSE23402
| | Sample_data_row_count | 54675
| | |
|
GSM574070 | GPL570 |
|
hES_WIBR1_rep1_090811_7
|
hES line WIBR1
|
cell line: hES line WIBR1
|
Gene expression data from hES line WIBR1
|
| Sample_geo_accession | GSM574070
| | Sample_status | Public on Aug 09 2010
| | Sample_submission_date | Aug 03 2010
| | Sample_last_update_date | Sep 15 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | All primary human fibroblasts cells described in this paper (PDB-AG20442 and GM-M01660) were purchased from the Coriell Cell Repository (Camden, NJ). Fibroblasts were cultured in fibroblast medium (Dulbecco's modified Eagle's medium [DMEM] supplemented with 15% fetal bovine serum [FBS; Hyclone], 1 mM glutamine [Invitrogen], 1% nonessential amino acids [Invitrogen], and penicillin/streptomycin [Invitrogen]).
| | Sample_growth_protocol_ch1 | hiPS cell lines iPS A1, iPS C1, iPS4, iPS A6 (Hockemeyer et al. 2009); hiPS cell lines iPS PDB2lox-17, iPS PDB2lox-21, iPS PDB2lox-5, iPS PDB2lox-22, iPS PDB1lox-17puro-5, iPS PDB1lox-17puro-10, iPS PDB1lox-17puro-33, iPS PDB1lox-21puro-20, iPS PDB1lox-21puro-26, and iPS PDB1lox-21puro-28 (Soldner et al. 2009); hES cell lines BG01 and BG03 (National Institutes of Health code: BG01 and BG03; BresaGen, Inc., Athens, GA); hES cell lines WIBR1, WIBR2, WIBR3, and WIBR7 (Lengner et al., 2010; Whitehead Institute Center for Human Stem Cell Research) and hES cell line H9 (NIH Code:WA09, Wisconsin Alumni Research Foundation, Madison, WI) were maintained on mitomycin C-inactivated mouse embryonic fibroblast (MEF) feeder layers in hESC medium (DMEM/F12 [Invitrogen] supplemented with 15% FBS [Hyclone], 5% KnockOut Serum Replacement [Invitrogen], 1 mM glutamine [Invitrogen], 1% nonessential amino acids [Invitrogen], 0.1 mM β-mercaptoethanol [Sigma], and 4 ng/ml FGF2 [R&D Systems]). Cultures were passaged every 5 to 7 days either manually or enzymatically with collagenase type IV (Invitrogen; 1.5 mg/ml). hiPS cell lines were passaged 15-25 times prior to ChIP-Seq and gene expression analysis.
| | Sample_molecule_ch1 | polyA RNA
| | Sample_extract_protocol_ch1 | RNA was isolated from hES and hiPS cells, which were mechanically separated from feeder cells, with the RNeasy Mini Kit (QIAGEN).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | 5 µg total RNA was used to prepare biotinylated cRNA according to the manufacturer’s protocol (Affymetrix One Cycle cDNA Synthesis Kit). Briefly, this method involves SuperScript II-directed reverse transcription using a T7-Oligo-dT promoter primer to create first strand cDNA. RNase H-mediated second strand cDNA synthesis is followed by T7 RNA Polymerase directed in vitro transcription, which incorporates a biotinylated nucleotide during cRNA amplification.
| | Sample_hyb_protocol | Samples were prepared for hybridization using 15 µg biotinylated cRNA in a 1X hybridization cocktail with additional hybridization cocktail components provided in the GeneChip Hybridization, Wash and Stain Kit (Affymetrix). GeneChip arrays (Human U133 Plus 2.0) were hybridized in a GeneChip Hybridization Oven at 45 degrees C for 16 hours at 60 RPM. Washing was performed 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 using default settings.
| | Sample_data_processing | Images were extracted and analyzed using the default settings of GeneChip Operating Software v1.4.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Garrett,M,Frampton
| | Sample_contact_email | frampton@mit.edu
| | Sample_contact_laboratory | Richard Young
| | Sample_contact_department | Biology
| | Sample_contact_institute | Whitehead Instute - MIT
| | Sample_contact_address | 9 Cambridge Center
| | Sample_contact_city | Cambridge
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02142
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM574nnn/GSM574070/suppl/GSM574070.CEL.gz
| | Sample_series_id | GSE22499
| | Sample_series_id | GSE23402
| | Sample_data_row_count | 54675
| | |
|
GSM574071 | GPL570 |
|
hES_WIBR1_rep2_090811_11
|
hES line WIBR1
|
cell line: hES line WIBR1
|
Gene expression data from hES line WIBR1
|
| Sample_geo_accession | GSM574071
| | Sample_status | Public on Aug 09 2010
| | Sample_submission_date | Aug 03 2010
| | Sample_last_update_date | Sep 15 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | All primary human fibroblasts cells described in this paper (PDB-AG20442 and GM-M01660) were purchased from the Coriell Cell Repository (Camden, NJ). Fibroblasts were cultured in fibroblast medium (Dulbecco's modified Eagle's medium [DMEM] supplemented with 15% fetal bovine serum [FBS; Hyclone], 1 mM glutamine [Invitrogen], 1% nonessential amino acids [Invitrogen], and penicillin/streptomycin [Invitrogen]).
| | Sample_growth_protocol_ch1 | hiPS cell lines iPS A1, iPS C1, iPS4, iPS A6 (Hockemeyer et al. 2009); hiPS cell lines iPS PDB2lox-17, iPS PDB2lox-21, iPS PDB2lox-5, iPS PDB2lox-22, iPS PDB1lox-17puro-5, iPS PDB1lox-17puro-10, iPS PDB1lox-17puro-33, iPS PDB1lox-21puro-20, iPS PDB1lox-21puro-26, and iPS PDB1lox-21puro-28 (Soldner et al. 2009); hES cell lines BG01 and BG03 (National Institutes of Health code: BG01 and BG03; BresaGen, Inc., Athens, GA); hES cell lines WIBR1, WIBR2, WIBR3, and WIBR7 (Lengner et al., 2010; Whitehead Institute Center for Human Stem Cell Research) and hES cell line H9 (NIH Code:WA09, Wisconsin Alumni Research Foundation, Madison, WI) were maintained on mitomycin C-inactivated mouse embryonic fibroblast (MEF) feeder layers in hESC medium (DMEM/F12 [Invitrogen] supplemented with 15% FBS [Hyclone], 5% KnockOut Serum Replacement [Invitrogen], 1 mM glutamine [Invitrogen], 1% nonessential amino acids [Invitrogen], 0.1 mM β-mercaptoethanol [Sigma], and 4 ng/ml FGF2 [R&D Systems]). Cultures were passaged every 5 to 7 days either manually or enzymatically with collagenase type IV (Invitrogen; 1.5 mg/ml). hiPS cell lines were passaged 15-25 times prior to ChIP-Seq and gene expression analysis.
| | Sample_molecule_ch1 | polyA RNA
| | Sample_extract_protocol_ch1 | RNA was isolated from hES and hiPS cells, which were mechanically separated from feeder cells, with the RNeasy Mini Kit (QIAGEN).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | 5 µg total RNA was used to prepare biotinylated cRNA according to the manufacturer’s protocol (Affymetrix One Cycle cDNA Synthesis Kit). Briefly, this method involves SuperScript II-directed reverse transcription using a T7-Oligo-dT promoter primer to create first strand cDNA. RNase H-mediated second strand cDNA synthesis is followed by T7 RNA Polymerase directed in vitro transcription, which incorporates a biotinylated nucleotide during cRNA amplification.
| | Sample_hyb_protocol | Samples were prepared for hybridization using 15 µg biotinylated cRNA in a 1X hybridization cocktail with additional hybridization cocktail components provided in the GeneChip Hybridization, Wash and Stain Kit (Affymetrix). GeneChip arrays (Human U133 Plus 2.0) were hybridized in a GeneChip Hybridization Oven at 45 degrees C for 16 hours at 60 RPM. Washing was performed 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 using default settings.
| | Sample_data_processing | Images were extracted and analyzed using the default settings of GeneChip Operating Software v1.4.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Garrett,M,Frampton
| | Sample_contact_email | frampton@mit.edu
| | Sample_contact_laboratory | Richard Young
| | Sample_contact_department | Biology
| | Sample_contact_institute | Whitehead Instute - MIT
| | Sample_contact_address | 9 Cambridge Center
| | Sample_contact_city | Cambridge
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02142
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM574nnn/GSM574071/suppl/GSM574071.CEL.gz
| | Sample_series_id | GSE22499
| | Sample_series_id | GSE23402
| | Sample_data_row_count | 54675
| | |
|
GSM574072 | GPL570 |
|
hES_WIBR2_rep1_090811_8
|
hES line WIBR2
|
cell line: hES line WIBR2
|
Gene expression data from hES line WIBR2
|
| Sample_geo_accession | GSM574072
| | Sample_status | Public on Aug 09 2010
| | Sample_submission_date | Aug 03 2010
| | Sample_last_update_date | Sep 15 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | All primary human fibroblasts cells described in this paper (PDB-AG20442 and GM-M01660) were purchased from the Coriell Cell Repository (Camden, NJ). Fibroblasts were cultured in fibroblast medium (Dulbecco's modified Eagle's medium [DMEM] supplemented with 15% fetal bovine serum [FBS; Hyclone], 1 mM glutamine [Invitrogen], 1% nonessential amino acids [Invitrogen], and penicillin/streptomycin [Invitrogen]).
| | Sample_growth_protocol_ch1 | hiPS cell lines iPS A1, iPS C1, iPS4, iPS A6 (Hockemeyer et al. 2009); hiPS cell lines iPS PDB2lox-17, iPS PDB2lox-21, iPS PDB2lox-5, iPS PDB2lox-22, iPS PDB1lox-17puro-5, iPS PDB1lox-17puro-10, iPS PDB1lox-17puro-33, iPS PDB1lox-21puro-20, iPS PDB1lox-21puro-26, and iPS PDB1lox-21puro-28 (Soldner et al. 2009); hES cell lines BG01 and BG03 (National Institutes of Health code: BG01 and BG03; BresaGen, Inc., Athens, GA); hES cell lines WIBR1, WIBR2, WIBR3, and WIBR7 (Lengner et al., 2010; Whitehead Institute Center for Human Stem Cell Research) and hES cell line H9 (NIH Code:WA09, Wisconsin Alumni Research Foundation, Madison, WI) were maintained on mitomycin C-inactivated mouse embryonic fibroblast (MEF) feeder layers in hESC medium (DMEM/F12 [Invitrogen] supplemented with 15% FBS [Hyclone], 5% KnockOut Serum Replacement [Invitrogen], 1 mM glutamine [Invitrogen], 1% nonessential amino acids [Invitrogen], 0.1 mM β-mercaptoethanol [Sigma], and 4 ng/ml FGF2 [R&D Systems]). Cultures were passaged every 5 to 7 days either manually or enzymatically with collagenase type IV (Invitrogen; 1.5 mg/ml). hiPS cell lines were passaged 15-25 times prior to ChIP-Seq and gene expression analysis.
| | Sample_molecule_ch1 | polyA RNA
| | Sample_extract_protocol_ch1 | RNA was isolated from hES and hiPS cells, which were mechanically separated from feeder cells, with the RNeasy Mini Kit (QIAGEN).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | 5 µg total RNA was used to prepare biotinylated cRNA according to the manufacturer’s protocol (Affymetrix One Cycle cDNA Synthesis Kit). Briefly, this method involves SuperScript II-directed reverse transcription using a T7-Oligo-dT promoter primer to create first strand cDNA. RNase H-mediated second strand cDNA synthesis is followed by T7 RNA Polymerase directed in vitro transcription, which incorporates a biotinylated nucleotide during cRNA amplification.
| | Sample_hyb_protocol | Samples were prepared for hybridization using 15 µg biotinylated cRNA in a 1X hybridization cocktail with additional hybridization cocktail components provided in the GeneChip Hybridization, Wash and Stain Kit (Affymetrix). GeneChip arrays (Human U133 Plus 2.0) were hybridized in a GeneChip Hybridization Oven at 45 degrees C for 16 hours at 60 RPM. Washing was performed 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 using default settings.
| | Sample_data_processing | Images were extracted and analyzed using the default settings of GeneChip Operating Software v1.4.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Garrett,M,Frampton
| | Sample_contact_email | frampton@mit.edu
| | Sample_contact_laboratory | Richard Young
| | Sample_contact_department | Biology
| | Sample_contact_institute | Whitehead Instute - MIT
| | Sample_contact_address | 9 Cambridge Center
| | Sample_contact_city | Cambridge
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02142
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM574nnn/GSM574072/suppl/GSM574072.CEL.gz
| | Sample_series_id | GSE22499
| | Sample_series_id | GSE23402
| | Sample_data_row_count | 54675
| | |
|
GSM574073 | GPL570 |
|
hES_WIBR2_rep2_090811_12
|
hES line WIBR2
|
cell line: hES line WIBR2
|
Gene expression data from hES line WIBR2
|
| Sample_geo_accession | GSM574073
| | Sample_status | Public on Aug 09 2010
| | Sample_submission_date | Aug 03 2010
| | Sample_last_update_date | Sep 15 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | All primary human fibroblasts cells described in this paper (PDB-AG20442 and GM-M01660) were purchased from the Coriell Cell Repository (Camden, NJ). Fibroblasts were cultured in fibroblast medium (Dulbecco's modified Eagle's medium [DMEM] supplemented with 15% fetal bovine serum [FBS; Hyclone], 1 mM glutamine [Invitrogen], 1% nonessential amino acids [Invitrogen], and penicillin/streptomycin [Invitrogen]).
| | Sample_growth_protocol_ch1 | hiPS cell lines iPS A1, iPS C1, iPS4, iPS A6 (Hockemeyer et al. 2009); hiPS cell lines iPS PDB2lox-17, iPS PDB2lox-21, iPS PDB2lox-5, iPS PDB2lox-22, iPS PDB1lox-17puro-5, iPS PDB1lox-17puro-10, iPS PDB1lox-17puro-33, iPS PDB1lox-21puro-20, iPS PDB1lox-21puro-26, and iPS PDB1lox-21puro-28 (Soldner et al. 2009); hES cell lines BG01 and BG03 (National Institutes of Health code: BG01 and BG03; BresaGen, Inc., Athens, GA); hES cell lines WIBR1, WIBR2, WIBR3, and WIBR7 (Lengner et al., 2010; Whitehead Institute Center for Human Stem Cell Research) and hES cell line H9 (NIH Code:WA09, Wisconsin Alumni Research Foundation, Madison, WI) were maintained on mitomycin C-inactivated mouse embryonic fibroblast (MEF) feeder layers in hESC medium (DMEM/F12 [Invitrogen] supplemented with 15% FBS [Hyclone], 5% KnockOut Serum Replacement [Invitrogen], 1 mM glutamine [Invitrogen], 1% nonessential amino acids [Invitrogen], 0.1 mM β-mercaptoethanol [Sigma], and 4 ng/ml FGF2 [R&D Systems]). Cultures were passaged every 5 to 7 days either manually or enzymatically with collagenase type IV (Invitrogen; 1.5 mg/ml). hiPS cell lines were passaged 15-25 times prior to ChIP-Seq and gene expression analysis.
| | Sample_molecule_ch1 | polyA RNA
| | Sample_extract_protocol_ch1 | RNA was isolated from hES and hiPS cells, which were mechanically separated from feeder cells, with the RNeasy Mini Kit (QIAGEN).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | 5 µg total RNA was used to prepare biotinylated cRNA according to the manufacturer’s protocol (Affymetrix One Cycle cDNA Synthesis Kit). Briefly, this method involves SuperScript II-directed reverse transcription using a T7-Oligo-dT promoter primer to create first strand cDNA. RNase H-mediated second strand cDNA synthesis is followed by T7 RNA Polymerase directed in vitro transcription, which incorporates a biotinylated nucleotide during cRNA amplification.
| | Sample_hyb_protocol | Samples were prepared for hybridization using 15 µg biotinylated cRNA in a 1X hybridization cocktail with additional hybridization cocktail components provided in the GeneChip Hybridization, Wash and Stain Kit (Affymetrix). GeneChip arrays (Human U133 Plus 2.0) were hybridized in a GeneChip Hybridization Oven at 45 degrees C for 16 hours at 60 RPM. Washing was performed 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 using default settings.
| | Sample_data_processing | Images were extracted and analyzed using the default settings of GeneChip Operating Software v1.4.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Garrett,M,Frampton
| | Sample_contact_email | frampton@mit.edu
| | Sample_contact_laboratory | Richard Young
| | Sample_contact_department | Biology
| | Sample_contact_institute | Whitehead Instute - MIT
| | Sample_contact_address | 9 Cambridge Center
| | Sample_contact_city | Cambridge
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02142
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM574nnn/GSM574073/suppl/GSM574073.CEL.gz
| | Sample_series_id | GSE22499
| | Sample_series_id | GSE23402
| | Sample_data_row_count | 54675
| | |
|
GSM574074 | GPL570 |
|
hES_WIBR3_rep1_090811_1
|
hES line WIBR3
|
cell line: hES line WIBR3
|
Gene expression data from hES line WIBR3
|
| Sample_geo_accession | GSM574074
| | Sample_status | Public on Aug 09 2010
| | Sample_submission_date | Aug 03 2010
| | Sample_last_update_date | Sep 15 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | All primary human fibroblasts cells described in this paper (PDB-AG20442 and GM-M01660) were purchased from the Coriell Cell Repository (Camden, NJ). Fibroblasts were cultured in fibroblast medium (Dulbecco's modified Eagle's medium [DMEM] supplemented with 15% fetal bovine serum [FBS; Hyclone], 1 mM glutamine [Invitrogen], 1% nonessential amino acids [Invitrogen], and penicillin/streptomycin [Invitrogen]).
| | Sample_growth_protocol_ch1 | hiPS cell lines iPS A1, iPS C1, iPS4, iPS A6 (Hockemeyer et al. 2009); hiPS cell lines iPS PDB2lox-17, iPS PDB2lox-21, iPS PDB2lox-5, iPS PDB2lox-22, iPS PDB1lox-17puro-5, iPS PDB1lox-17puro-10, iPS PDB1lox-17puro-33, iPS PDB1lox-21puro-20, iPS PDB1lox-21puro-26, and iPS PDB1lox-21puro-28 (Soldner et al. 2009); hES cell lines BG01 and BG03 (National Institutes of Health code: BG01 and BG03; BresaGen, Inc., Athens, GA); hES cell lines WIBR1, WIBR2, WIBR3, and WIBR7 (Lengner et al., 2010; Whitehead Institute Center for Human Stem Cell Research) and hES cell line H9 (NIH Code:WA09, Wisconsin Alumni Research Foundation, Madison, WI) were maintained on mitomycin C-inactivated mouse embryonic fibroblast (MEF) feeder layers in hESC medium (DMEM/F12 [Invitrogen] supplemented with 15% FBS [Hyclone], 5% KnockOut Serum Replacement [Invitrogen], 1 mM glutamine [Invitrogen], 1% nonessential amino acids [Invitrogen], 0.1 mM β-mercaptoethanol [Sigma], and 4 ng/ml FGF2 [R&D Systems]). Cultures were passaged every 5 to 7 days either manually or enzymatically with collagenase type IV (Invitrogen; 1.5 mg/ml). hiPS cell lines were passaged 15-25 times prior to ChIP-Seq and gene expression analysis.
| | Sample_molecule_ch1 | polyA RNA
| | Sample_extract_protocol_ch1 | RNA was isolated from hES and hiPS cells, which were mechanically separated from feeder cells, with the RNeasy Mini Kit (QIAGEN).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | 5 µg total RNA was used to prepare biotinylated cRNA according to the manufacturer’s protocol (Affymetrix One Cycle cDNA Synthesis Kit). Briefly, this method involves SuperScript II-directed reverse transcription using a T7-Oligo-dT promoter primer to create first strand cDNA. RNase H-mediated second strand cDNA synthesis is followed by T7 RNA Polymerase directed in vitro transcription, which incorporates a biotinylated nucleotide during cRNA amplification.
| | Sample_hyb_protocol | Samples were prepared for hybridization using 15 µg biotinylated cRNA in a 1X hybridization cocktail with additional hybridization cocktail components provided in the GeneChip Hybridization, Wash and Stain Kit (Affymetrix). GeneChip arrays (Human U133 Plus 2.0) were hybridized in a GeneChip Hybridization Oven at 45 degrees C for 16 hours at 60 RPM. Washing was performed 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 using default settings.
| | Sample_data_processing | Images were extracted and analyzed using the default settings of GeneChip Operating Software v1.4.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Garrett,M,Frampton
| | Sample_contact_email | frampton@mit.edu
| | Sample_contact_laboratory | Richard Young
| | Sample_contact_department | Biology
| | Sample_contact_institute | Whitehead Instute - MIT
| | Sample_contact_address | 9 Cambridge Center
| | Sample_contact_city | Cambridge
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02142
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM574nnn/GSM574074/suppl/GSM574074.CEL.gz
| | Sample_series_id | GSE22499
| | Sample_series_id | GSE23402
| | Sample_data_row_count | 54675
| | |
|
GSM574075 | GPL570 |
|
hES_WIBR3_rep2_090811_2
|
hES line WIBR3
|
cell line: hES line WIBR3
|
Gene expression data from hES line WIBR3
|
| Sample_geo_accession | GSM574075
| | Sample_status | Public on Aug 09 2010
| | Sample_submission_date | Aug 03 2010
| | Sample_last_update_date | Sep 15 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | All primary human fibroblasts cells described in this paper (PDB-AG20442 and GM-M01660) were purchased from the Coriell Cell Repository (Camden, NJ). Fibroblasts were cultured in fibroblast medium (Dulbecco's modified Eagle's medium [DMEM] supplemented with 15% fetal bovine serum [FBS; Hyclone], 1 mM glutamine [Invitrogen], 1% nonessential amino acids [Invitrogen], and penicillin/streptomycin [Invitrogen]).
| | Sample_growth_protocol_ch1 | hiPS cell lines iPS A1, iPS C1, iPS4, iPS A6 (Hockemeyer et al. 2009); hiPS cell lines iPS PDB2lox-17, iPS PDB2lox-21, iPS PDB2lox-5, iPS PDB2lox-22, iPS PDB1lox-17puro-5, iPS PDB1lox-17puro-10, iPS PDB1lox-17puro-33, iPS PDB1lox-21puro-20, iPS PDB1lox-21puro-26, and iPS PDB1lox-21puro-28 (Soldner et al. 2009); hES cell lines BG01 and BG03 (National Institutes of Health code: BG01 and BG03; BresaGen, Inc., Athens, GA); hES cell lines WIBR1, WIBR2, WIBR3, and WIBR7 (Lengner et al., 2010; Whitehead Institute Center for Human Stem Cell Research) and hES cell line H9 (NIH Code:WA09, Wisconsin Alumni Research Foundation, Madison, WI) were maintained on mitomycin C-inactivated mouse embryonic fibroblast (MEF) feeder layers in hESC medium (DMEM/F12 [Invitrogen] supplemented with 15% FBS [Hyclone], 5% KnockOut Serum Replacement [Invitrogen], 1 mM glutamine [Invitrogen], 1% nonessential amino acids [Invitrogen], 0.1 mM β-mercaptoethanol [Sigma], and 4 ng/ml FGF2 [R&D Systems]). Cultures were passaged every 5 to 7 days either manually or enzymatically with collagenase type IV (Invitrogen; 1.5 mg/ml). hiPS cell lines were passaged 15-25 times prior to ChIP-Seq and gene expression analysis.
| | Sample_molecule_ch1 | polyA RNA
| | Sample_extract_protocol_ch1 | RNA was isolated from hES and hiPS cells, which were mechanically separated from feeder cells, with the RNeasy Mini Kit (QIAGEN).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | 5 µg total RNA was used to prepare biotinylated cRNA according to the manufacturer’s protocol (Affymetrix One Cycle cDNA Synthesis Kit). Briefly, this method involves SuperScript II-directed reverse transcription using a T7-Oligo-dT promoter primer to create first strand cDNA. RNase H-mediated second strand cDNA synthesis is followed by T7 RNA Polymerase directed in vitro transcription, which incorporates a biotinylated nucleotide during cRNA amplification.
| | Sample_hyb_protocol | Samples were prepared for hybridization using 15 µg biotinylated cRNA in a 1X hybridization cocktail with additional hybridization cocktail components provided in the GeneChip Hybridization, Wash and Stain Kit (Affymetrix). GeneChip arrays (Human U133 Plus 2.0) were hybridized in a GeneChip Hybridization Oven at 45 degrees C for 16 hours at 60 RPM. Washing was performed 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 using default settings.
| | Sample_data_processing | Images were extracted and analyzed using the default settings of GeneChip Operating Software v1.4.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Garrett,M,Frampton
| | Sample_contact_email | frampton@mit.edu
| | Sample_contact_laboratory | Richard Young
| | Sample_contact_department | Biology
| | Sample_contact_institute | Whitehead Instute - MIT
| | Sample_contact_address | 9 Cambridge Center
| | Sample_contact_city | Cambridge
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02142
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM574nnn/GSM574075/suppl/GSM574075.CEL.gz
| | Sample_series_id | GSE22499
| | Sample_series_id | GSE23402
| | Sample_data_row_count | 54675
| | |
|
GSM574076 | GPL570 |
|
hES_WIBR7_rep1_090811_3
|
hES line WIBR7
|
cell line: hES line WIBR7
|
Gene expression data from hES line WIBR7
|
| Sample_geo_accession | GSM574076
| | Sample_status | Public on Aug 09 2010
| | Sample_submission_date | Aug 03 2010
| | Sample_last_update_date | Sep 15 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | All primary human fibroblasts cells described in this paper (PDB-AG20442 and GM-M01660) were purchased from the Coriell Cell Repository (Camden, NJ). Fibroblasts were cultured in fibroblast medium (Dulbecco's modified Eagle's medium [DMEM] supplemented with 15% fetal bovine serum [FBS; Hyclone], 1 mM glutamine [Invitrogen], 1% nonessential amino acids [Invitrogen], and penicillin/streptomycin [Invitrogen]).
| | Sample_growth_protocol_ch1 | hiPS cell lines iPS A1, iPS C1, iPS4, iPS A6 (Hockemeyer et al. 2009); hiPS cell lines iPS PDB2lox-17, iPS PDB2lox-21, iPS PDB2lox-5, iPS PDB2lox-22, iPS PDB1lox-17puro-5, iPS PDB1lox-17puro-10, iPS PDB1lox-17puro-33, iPS PDB1lox-21puro-20, iPS PDB1lox-21puro-26, and iPS PDB1lox-21puro-28 (Soldner et al. 2009); hES cell lines BG01 and BG03 (National Institutes of Health code: BG01 and BG03; BresaGen, Inc., Athens, GA); hES cell lines WIBR1, WIBR2, WIBR3, and WIBR7 (Lengner et al., 2010; Whitehead Institute Center for Human Stem Cell Research) and hES cell line H9 (NIH Code:WA09, Wisconsin Alumni Research Foundation, Madison, WI) were maintained on mitomycin C-inactivated mouse embryonic fibroblast (MEF) feeder layers in hESC medium (DMEM/F12 [Invitrogen] supplemented with 15% FBS [Hyclone], 5% KnockOut Serum Replacement [Invitrogen], 1 mM glutamine [Invitrogen], 1% nonessential amino acids [Invitrogen], 0.1 mM β-mercaptoethanol [Sigma], and 4 ng/ml FGF2 [R&D Systems]). Cultures were passaged every 5 to 7 days either manually or enzymatically with collagenase type IV (Invitrogen; 1.5 mg/ml). hiPS cell lines were passaged 15-25 times prior to ChIP-Seq and gene expression analysis.
| | Sample_molecule_ch1 | polyA RNA
| | Sample_extract_protocol_ch1 | RNA was isolated from hES and hiPS cells, which were mechanically separated from feeder cells, with the RNeasy Mini Kit (QIAGEN).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | 5 µg total RNA was used to prepare biotinylated cRNA according to the manufacturer’s protocol (Affymetrix One Cycle cDNA Synthesis Kit). Briefly, this method involves SuperScript II-directed reverse transcription using a T7-Oligo-dT promoter primer to create first strand cDNA. RNase H-mediated second strand cDNA synthesis is followed by T7 RNA Polymerase directed in vitro transcription, which incorporates a biotinylated nucleotide during cRNA amplification.
| | Sample_hyb_protocol | Samples were prepared for hybridization using 15 µg biotinylated cRNA in a 1X hybridization cocktail with additional hybridization cocktail components provided in the GeneChip Hybridization, Wash and Stain Kit (Affymetrix). GeneChip arrays (Human U133 Plus 2.0) were hybridized in a GeneChip Hybridization Oven at 45 degrees C for 16 hours at 60 RPM. Washing was performed 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 using default settings.
| | Sample_data_processing | Images were extracted and analyzed using the default settings of GeneChip Operating Software v1.4.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Garrett,M,Frampton
| | Sample_contact_email | frampton@mit.edu
| | Sample_contact_laboratory | Richard Young
| | Sample_contact_department | Biology
| | Sample_contact_institute | Whitehead Instute - MIT
| | Sample_contact_address | 9 Cambridge Center
| | Sample_contact_city | Cambridge
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02142
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM574nnn/GSM574076/suppl/GSM574076.CEL.gz
| | Sample_series_id | GSE22499
| | Sample_series_id | GSE23402
| | Sample_data_row_count | 54675
| | |
|
GSM574077 | GPL570 |
|
hES_WIBR7_rep2_090811_4
|
hES line WIBR7
|
cell line: hES line WIBR7
|
Gene expression data from hES line WIBR7
|
| Sample_geo_accession | GSM574077
| | Sample_status | Public on Aug 09 2010
| | Sample_submission_date | Aug 03 2010
| | Sample_last_update_date | Sep 15 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | All primary human fibroblasts cells described in this paper (PDB-AG20442 and GM-M01660) were purchased from the Coriell Cell Repository (Camden, NJ). Fibroblasts were cultured in fibroblast medium (Dulbecco's modified Eagle's medium [DMEM] supplemented with 15% fetal bovine serum [FBS; Hyclone], 1 mM glutamine [Invitrogen], 1% nonessential amino acids [Invitrogen], and penicillin/streptomycin [Invitrogen]).
| | Sample_growth_protocol_ch1 | hiPS cell lines iPS A1, iPS C1, iPS4, iPS A6 (Hockemeyer et al. 2009); hiPS cell lines iPS PDB2lox-17, iPS PDB2lox-21, iPS PDB2lox-5, iPS PDB2lox-22, iPS PDB1lox-17puro-5, iPS PDB1lox-17puro-10, iPS PDB1lox-17puro-33, iPS PDB1lox-21puro-20, iPS PDB1lox-21puro-26, and iPS PDB1lox-21puro-28 (Soldner et al. 2009); hES cell lines BG01 and BG03 (National Institutes of Health code: BG01 and BG03; BresaGen, Inc., Athens, GA); hES cell lines WIBR1, WIBR2, WIBR3, and WIBR7 (Lengner et al., 2010; Whitehead Institute Center for Human Stem Cell Research) and hES cell line H9 (NIH Code:WA09, Wisconsin Alumni Research Foundation, Madison, WI) were maintained on mitomycin C-inactivated mouse embryonic fibroblast (MEF) feeder layers in hESC medium (DMEM/F12 [Invitrogen] supplemented with 15% FBS [Hyclone], 5% KnockOut Serum Replacement [Invitrogen], 1 mM glutamine [Invitrogen], 1% nonessential amino acids [Invitrogen], 0.1 mM β-mercaptoethanol [Sigma], and 4 ng/ml FGF2 [R&D Systems]). Cultures were passaged every 5 to 7 days either manually or enzymatically with collagenase type IV (Invitrogen; 1.5 mg/ml). hiPS cell lines were passaged 15-25 times prior to ChIP-Seq and gene expression analysis.
| | Sample_molecule_ch1 | polyA RNA
| | Sample_extract_protocol_ch1 | RNA was isolated from hES and hiPS cells, which were mechanically separated from feeder cells, with the RNeasy Mini Kit (QIAGEN).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | 5 µg total RNA was used to prepare biotinylated cRNA according to the manufacturer’s protocol (Affymetrix One Cycle cDNA Synthesis Kit). Briefly, this method involves SuperScript II-directed reverse transcription using a T7-Oligo-dT promoter primer to create first strand cDNA. RNase H-mediated second strand cDNA synthesis is followed by T7 RNA Polymerase directed in vitro transcription, which incorporates a biotinylated nucleotide during cRNA amplification.
| | Sample_hyb_protocol | Samples were prepared for hybridization using 15 µg biotinylated cRNA in a 1X hybridization cocktail with additional hybridization cocktail components provided in the GeneChip Hybridization, Wash and Stain Kit (Affymetrix). GeneChip arrays (Human U133 Plus 2.0) were hybridized in a GeneChip Hybridization Oven at 45 degrees C for 16 hours at 60 RPM. Washing was performed 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 using default settings.
| | Sample_data_processing | Images were extracted and analyzed using the default settings of GeneChip Operating Software v1.4.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Garrett,M,Frampton
| | Sample_contact_email | frampton@mit.edu
| | Sample_contact_laboratory | Richard Young
| | Sample_contact_department | Biology
| | Sample_contact_institute | Whitehead Instute - MIT
| | Sample_contact_address | 9 Cambridge Center
| | Sample_contact_city | Cambridge
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02142
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM574nnn/GSM574077/suppl/GSM574077.CEL.gz
| | Sample_series_id | GSE22499
| | Sample_series_id | GSE23402
| | Sample_data_row_count | 54675
| | |
|
GSM574078 | GPL570 |
|
hiPS_4_rep1_081006_5
|
hiPS line 4
|
cell line: hiPS line 4
|
Gene expression data from hiPS line 4
|
| Sample_geo_accession | GSM574078
| | Sample_status | Public on Aug 09 2010
| | Sample_submission_date | Aug 03 2010
| | Sample_last_update_date | Sep 15 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | All primary human fibroblasts cells described in this paper (PDB-AG20442 and GM-M01660) were purchased from the Coriell Cell Repository (Camden, NJ). Fibroblasts were cultured in fibroblast medium (Dulbecco's modified Eagle's medium [DMEM] supplemented with 15% fetal bovine serum [FBS; Hyclone], 1 mM glutamine [Invitrogen], 1% nonessential amino acids [Invitrogen], and penicillin/streptomycin [Invitrogen]).
| | Sample_growth_protocol_ch1 | hiPS cell lines iPS A1, iPS C1, iPS4, iPS A6 (Hockemeyer et al. 2009); hiPS cell lines iPS PDB2lox-17, iPS PDB2lox-21, iPS PDB2lox-5, iPS PDB2lox-22, iPS PDB1lox-17puro-5, iPS PDB1lox-17puro-10, iPS PDB1lox-17puro-33, iPS PDB1lox-21puro-20, iPS PDB1lox-21puro-26, and iPS PDB1lox-21puro-28 (Soldner et al. 2009); hES cell lines BG01 and BG03 (National Institutes of Health code: BG01 and BG03; BresaGen, Inc., Athens, GA); hES cell lines WIBR1, WIBR2, WIBR3, and WIBR7 (Lengner et al., 2010; Whitehead Institute Center for Human Stem Cell Research) and hES cell line H9 (NIH Code:WA09, Wisconsin Alumni Research Foundation, Madison, WI) were maintained on mitomycin C-inactivated mouse embryonic fibroblast (MEF) feeder layers in hESC medium (DMEM/F12 [Invitrogen] supplemented with 15% FBS [Hyclone], 5% KnockOut Serum Replacement [Invitrogen], 1 mM glutamine [Invitrogen], 1% nonessential amino acids [Invitrogen], 0.1 mM β-mercaptoethanol [Sigma], and 4 ng/ml FGF2 [R&D Systems]). Cultures were passaged every 5 to 7 days either manually or enzymatically with collagenase type IV (Invitrogen; 1.5 mg/ml). hiPS cell lines were passaged 15-25 times prior to ChIP-Seq and gene expression analysis.
| | Sample_molecule_ch1 | polyA RNA
| | Sample_extract_protocol_ch1 | RNA was isolated from hES and hiPS cells, which were mechanically separated from feeder cells, with the RNeasy Mini Kit (QIAGEN).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | 5 µg total RNA was used to prepare biotinylated cRNA according to the manufacturer’s protocol (Affymetrix One Cycle cDNA Synthesis Kit). Briefly, this method involves SuperScript II-directed reverse transcription using a T7-Oligo-dT promoter primer to create first strand cDNA. RNase H-mediated second strand cDNA synthesis is followed by T7 RNA Polymerase directed in vitro transcription, which incorporates a biotinylated nucleotide during cRNA amplification.
| | Sample_hyb_protocol | Samples were prepared for hybridization using 15 µg biotinylated cRNA in a 1X hybridization cocktail with additional hybridization cocktail components provided in the GeneChip Hybridization, Wash and Stain Kit (Affymetrix). GeneChip arrays (Human U133 Plus 2.0) were hybridized in a GeneChip Hybridization Oven at 45 degrees C for 16 hours at 60 RPM. Washing was performed 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 using default settings.
| | Sample_data_processing | Images were extracted and analyzed using the default settings of GeneChip Operating Software v1.4.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Garrett,M,Frampton
| | Sample_contact_email | frampton@mit.edu
| | Sample_contact_laboratory | Richard Young
| | Sample_contact_department | Biology
| | Sample_contact_institute | Whitehead Instute - MIT
| | Sample_contact_address | 9 Cambridge Center
| | Sample_contact_city | Cambridge
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02142
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM574nnn/GSM574078/suppl/GSM574078.CEL.gz
| | Sample_series_id | GSE22499
| | Sample_series_id | GSE23402
| | Sample_data_row_count | 54675
| | |
|
GSM574079 | GPL570 |
|
hiPS_4_rep2_081006_6
|
hiPS line 4
|
cell line: hiPS line 4
|
Gene expression data from hiPS line 4
|
| Sample_geo_accession | GSM574079
| | Sample_status | Public on Aug 09 2010
| | Sample_submission_date | Aug 03 2010
| | Sample_last_update_date | Sep 15 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | All primary human fibroblasts cells described in this paper (PDB-AG20442 and GM-M01660) were purchased from the Coriell Cell Repository (Camden, NJ). Fibroblasts were cultured in fibroblast medium (Dulbecco's modified Eagle's medium [DMEM] supplemented with 15% fetal bovine serum [FBS; Hyclone], 1 mM glutamine [Invitrogen], 1% nonessential amino acids [Invitrogen], and penicillin/streptomycin [Invitrogen]).
| | Sample_growth_protocol_ch1 | hiPS cell lines iPS A1, iPS C1, iPS4, iPS A6 (Hockemeyer et al. 2009); hiPS cell lines iPS PDB2lox-17, iPS PDB2lox-21, iPS PDB2lox-5, iPS PDB2lox-22, iPS PDB1lox-17puro-5, iPS PDB1lox-17puro-10, iPS PDB1lox-17puro-33, iPS PDB1lox-21puro-20, iPS PDB1lox-21puro-26, and iPS PDB1lox-21puro-28 (Soldner et al. 2009); hES cell lines BG01 and BG03 (National Institutes of Health code: BG01 and BG03; BresaGen, Inc., Athens, GA); hES cell lines WIBR1, WIBR2, WIBR3, and WIBR7 (Lengner et al., 2010; Whitehead Institute Center for Human Stem Cell Research) and hES cell line H9 (NIH Code:WA09, Wisconsin Alumni Research Foundation, Madison, WI) were maintained on mitomycin C-inactivated mouse embryonic fibroblast (MEF) feeder layers in hESC medium (DMEM/F12 [Invitrogen] supplemented with 15% FBS [Hyclone], 5% KnockOut Serum Replacement [Invitrogen], 1 mM glutamine [Invitrogen], 1% nonessential amino acids [Invitrogen], 0.1 mM β-mercaptoethanol [Sigma], and 4 ng/ml FGF2 [R&D Systems]). Cultures were passaged every 5 to 7 days either manually or enzymatically with collagenase type IV (Invitrogen; 1.5 mg/ml). hiPS cell lines were passaged 15-25 times prior to ChIP-Seq and gene expression analysis.
| | Sample_molecule_ch1 | polyA RNA
| | Sample_extract_protocol_ch1 | RNA was isolated from hES and hiPS cells, which were mechanically separated from feeder cells, with the RNeasy Mini Kit (QIAGEN).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | 5 µg total RNA was used to prepare biotinylated cRNA according to the manufacturer’s protocol (Affymetrix One Cycle cDNA Synthesis Kit). Briefly, this method involves SuperScript II-directed reverse transcription using a T7-Oligo-dT promoter primer to create first strand cDNA. RNase H-mediated second strand cDNA synthesis is followed by T7 RNA Polymerase directed in vitro transcription, which incorporates a biotinylated nucleotide during cRNA amplification.
| | Sample_hyb_protocol | Samples were prepared for hybridization using 15 µg biotinylated cRNA in a 1X hybridization cocktail with additional hybridization cocktail components provided in the GeneChip Hybridization, Wash and Stain Kit (Affymetrix). GeneChip arrays (Human U133 Plus 2.0) were hybridized in a GeneChip Hybridization Oven at 45 degrees C for 16 hours at 60 RPM. Washing was performed 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 using default settings.
| | Sample_data_processing | Images were extracted and analyzed using the default settings of GeneChip Operating Software v1.4.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Garrett,M,Frampton
| | Sample_contact_email | frampton@mit.edu
| | Sample_contact_laboratory | Richard Young
| | Sample_contact_department | Biology
| | Sample_contact_institute | Whitehead Instute - MIT
| | Sample_contact_address | 9 Cambridge Center
| | Sample_contact_city | Cambridge
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02142
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM574nnn/GSM574079/suppl/GSM574079.CEL.gz
| | Sample_series_id | GSE22499
| | Sample_series_id | GSE23402
| | Sample_data_row_count | 54675
| | |
|
GSM574080 | GPL570 |
|
hiPS_A1_rep1_081006_1
|
hiPS line A1
|
cell line: hiPS line A1
|
Gene expression data from hiPS line A1
|
| Sample_geo_accession | GSM574080
| | Sample_status | Public on Aug 09 2010
| | Sample_submission_date | Aug 03 2010
| | Sample_last_update_date | Sep 15 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | All primary human fibroblasts cells described in this paper (PDB-AG20442 and GM-M01660) were purchased from the Coriell Cell Repository (Camden, NJ). Fibroblasts were cultured in fibroblast medium (Dulbecco's modified Eagle's medium [DMEM] supplemented with 15% fetal bovine serum [FBS; Hyclone], 1 mM glutamine [Invitrogen], 1% nonessential amino acids [Invitrogen], and penicillin/streptomycin [Invitrogen]).
| | Sample_growth_protocol_ch1 | hiPS cell lines iPS A1, iPS C1, iPS4, iPS A6 (Hockemeyer et al. 2009); hiPS cell lines iPS PDB2lox-17, iPS PDB2lox-21, iPS PDB2lox-5, iPS PDB2lox-22, iPS PDB1lox-17puro-5, iPS PDB1lox-17puro-10, iPS PDB1lox-17puro-33, iPS PDB1lox-21puro-20, iPS PDB1lox-21puro-26, and iPS PDB1lox-21puro-28 (Soldner et al. 2009); hES cell lines BG01 and BG03 (National Institutes of Health code: BG01 and BG03; BresaGen, Inc., Athens, GA); hES cell lines WIBR1, WIBR2, WIBR3, and WIBR7 (Lengner et al., 2010; Whitehead Institute Center for Human Stem Cell Research) and hES cell line H9 (NIH Code:WA09, Wisconsin Alumni Research Foundation, Madison, WI) were maintained on mitomycin C-inactivated mouse embryonic fibroblast (MEF) feeder layers in hESC medium (DMEM/F12 [Invitrogen] supplemented with 15% FBS [Hyclone], 5% KnockOut Serum Replacement [Invitrogen], 1 mM glutamine [Invitrogen], 1% nonessential amino acids [Invitrogen], 0.1 mM β-mercaptoethanol [Sigma], and 4 ng/ml FGF2 [R&D Systems]). Cultures were passaged every 5 to 7 days either manually or enzymatically with collagenase type IV (Invitrogen; 1.5 mg/ml). hiPS cell lines were passaged 15-25 times prior to ChIP-Seq and gene expression analysis.
| | Sample_molecule_ch1 | polyA RNA
| | Sample_extract_protocol_ch1 | RNA was isolated from hES and hiPS cells, which were mechanically separated from feeder cells, with the RNeasy Mini Kit (QIAGEN).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | 5 µg total RNA was used to prepare biotinylated cRNA according to the manufacturer’s protocol (Affymetrix One Cycle cDNA Synthesis Kit). Briefly, this method involves SuperScript II-directed reverse transcription using a T7-Oligo-dT promoter primer to create first strand cDNA. RNase H-mediated second strand cDNA synthesis is followed by T7 RNA Polymerase directed in vitro transcription, which incorporates a biotinylated nucleotide during cRNA amplification.
| | Sample_hyb_protocol | Samples were prepared for hybridization using 15 µg biotinylated cRNA in a 1X hybridization cocktail with additional hybridization cocktail components provided in the GeneChip Hybridization, Wash and Stain Kit (Affymetrix). GeneChip arrays (Human U133 Plus 2.0) were hybridized in a GeneChip Hybridization Oven at 45 degrees C for 16 hours at 60 RPM. Washing was performed 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 using default settings.
| | Sample_data_processing | Images were extracted and analyzed using the default settings of GeneChip Operating Software v1.4.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Garrett,M,Frampton
| | Sample_contact_email | frampton@mit.edu
| | Sample_contact_laboratory | Richard Young
| | Sample_contact_department | Biology
| | Sample_contact_institute | Whitehead Instute - MIT
| | Sample_contact_address | 9 Cambridge Center
| | Sample_contact_city | Cambridge
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02142
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM574nnn/GSM574080/suppl/GSM574080.CEL.gz
| | Sample_series_id | GSE22499
| | Sample_series_id | GSE23402
| | Sample_data_row_count | 54675
| | |
|
GSM574081 | GPL570 |
|
hiPS_A1_rep2_081006_2
|
hiPS line A1
|
cell line: hiPS line A1
|
Gene expression data from hiPS line A1
|
| Sample_geo_accession | GSM574081
| | Sample_status | Public on Aug 09 2010
| | Sample_submission_date | Aug 03 2010
| | Sample_last_update_date | Sep 15 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | All primary human fibroblasts cells described in this paper (PDB-AG20442 and GM-M01660) were purchased from the Coriell Cell Repository (Camden, NJ). Fibroblasts were cultured in fibroblast medium (Dulbecco's modified Eagle's medium [DMEM] supplemented with 15% fetal bovine serum [FBS; Hyclone], 1 mM glutamine [Invitrogen], 1% nonessential amino acids [Invitrogen], and penicillin/streptomycin [Invitrogen]).
| | Sample_growth_protocol_ch1 | hiPS cell lines iPS A1, iPS C1, iPS4, iPS A6 (Hockemeyer et al. 2009); hiPS cell lines iPS PDB2lox-17, iPS PDB2lox-21, iPS PDB2lox-5, iPS PDB2lox-22, iPS PDB1lox-17puro-5, iPS PDB1lox-17puro-10, iPS PDB1lox-17puro-33, iPS PDB1lox-21puro-20, iPS PDB1lox-21puro-26, and iPS PDB1lox-21puro-28 (Soldner et al. 2009); hES cell lines BG01 and BG03 (National Institutes of Health code: BG01 and BG03; BresaGen, Inc., Athens, GA); hES cell lines WIBR1, WIBR2, WIBR3, and WIBR7 (Lengner et al., 2010; Whitehead Institute Center for Human Stem Cell Research) and hES cell line H9 (NIH Code:WA09, Wisconsin Alumni Research Foundation, Madison, WI) were maintained on mitomycin C-inactivated mouse embryonic fibroblast (MEF) feeder layers in hESC medium (DMEM/F12 [Invitrogen] supplemented with 15% FBS [Hyclone], 5% KnockOut Serum Replacement [Invitrogen], 1 mM glutamine [Invitrogen], 1% nonessential amino acids [Invitrogen], 0.1 mM β-mercaptoethanol [Sigma], and 4 ng/ml FGF2 [R&D Systems]). Cultures were passaged every 5 to 7 days either manually or enzymatically with collagenase type IV (Invitrogen; 1.5 mg/ml). hiPS cell lines were passaged 15-25 times prior to ChIP-Seq and gene expression analysis.
| | Sample_molecule_ch1 | polyA RNA
| | Sample_extract_protocol_ch1 | RNA was isolated from hES and hiPS cells, which were mechanically separated from feeder cells, with the RNeasy Mini Kit (QIAGEN).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | 5 µg total RNA was used to prepare biotinylated cRNA according to the manufacturer’s protocol (Affymetrix One Cycle cDNA Synthesis Kit). Briefly, this method involves SuperScript II-directed reverse transcription using a T7-Oligo-dT promoter primer to create first strand cDNA. RNase H-mediated second strand cDNA synthesis is followed by T7 RNA Polymerase directed in vitro transcription, which incorporates a biotinylated nucleotide during cRNA amplification.
| | Sample_hyb_protocol | Samples were prepared for hybridization using 15 µg biotinylated cRNA in a 1X hybridization cocktail with additional hybridization cocktail components provided in the GeneChip Hybridization, Wash and Stain Kit (Affymetrix). GeneChip arrays (Human U133 Plus 2.0) were hybridized in a GeneChip Hybridization Oven at 45 degrees C for 16 hours at 60 RPM. Washing was performed 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 using default settings.
| | Sample_data_processing | Images were extracted and analyzed using the default settings of GeneChip Operating Software v1.4.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Garrett,M,Frampton
| | Sample_contact_email | frampton@mit.edu
| | Sample_contact_laboratory | Richard Young
| | Sample_contact_department | Biology
| | Sample_contact_institute | Whitehead Instute - MIT
| | Sample_contact_address | 9 Cambridge Center
| | Sample_contact_city | Cambridge
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02142
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM574nnn/GSM574081/suppl/GSM574081.CEL.gz
| | Sample_series_id | GSE22499
| | Sample_series_id | GSE23402
| | Sample_data_row_count | 54675
| | |
|
GSM574082 | GPL570 |
|
hiPS_A6_rep1_081006_3
|
hiPS line A6
|
cell line: hiPS line A6
|
Gene expression data from hiPS line A6
|
| Sample_geo_accession | GSM574082
| | Sample_status | Public on Aug 09 2010
| | Sample_submission_date | Aug 03 2010
| | Sample_last_update_date | Sep 15 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | All primary human fibroblasts cells described in this paper (PDB-AG20442 and GM-M01660) were purchased from the Coriell Cell Repository (Camden, NJ). Fibroblasts were cultured in fibroblast medium (Dulbecco's modified Eagle's medium [DMEM] supplemented with 15% fetal bovine serum [FBS; Hyclone], 1 mM glutamine [Invitrogen], 1% nonessential amino acids [Invitrogen], and penicillin/streptomycin [Invitrogen]).
| | Sample_growth_protocol_ch1 | hiPS cell lines iPS A1, iPS C1, iPS4, iPS A6 (Hockemeyer et al. 2009); hiPS cell lines iPS PDB2lox-17, iPS PDB2lox-21, iPS PDB2lox-5, iPS PDB2lox-22, iPS PDB1lox-17puro-5, iPS PDB1lox-17puro-10, iPS PDB1lox-17puro-33, iPS PDB1lox-21puro-20, iPS PDB1lox-21puro-26, and iPS PDB1lox-21puro-28 (Soldner et al. 2009); hES cell lines BG01 and BG03 (National Institutes of Health code: BG01 and BG03; BresaGen, Inc., Athens, GA); hES cell lines WIBR1, WIBR2, WIBR3, and WIBR7 (Lengner et al., 2010; Whitehead Institute Center for Human Stem Cell Research) and hES cell line H9 (NIH Code:WA09, Wisconsin Alumni Research Foundation, Madison, WI) were maintained on mitomycin C-inactivated mouse embryonic fibroblast (MEF) feeder layers in hESC medium (DMEM/F12 [Invitrogen] supplemented with 15% FBS [Hyclone], 5% KnockOut Serum Replacement [Invitrogen], 1 mM glutamine [Invitrogen], 1% nonessential amino acids [Invitrogen], 0.1 mM β-mercaptoethanol [Sigma], and 4 ng/ml FGF2 [R&D Systems]). Cultures were passaged every 5 to 7 days either manually or enzymatically with collagenase type IV (Invitrogen; 1.5 mg/ml). hiPS cell lines were passaged 15-25 times prior to ChIP-Seq and gene expression analysis.
| | Sample_molecule_ch1 | polyA RNA
| | Sample_extract_protocol_ch1 | RNA was isolated from hES and hiPS cells, which were mechanically separated from feeder cells, with the RNeasy Mini Kit (QIAGEN).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | 5 µg total RNA was used to prepare biotinylated cRNA according to the manufacturer’s protocol (Affymetrix One Cycle cDNA Synthesis Kit). Briefly, this method involves SuperScript II-directed reverse transcription using a T7-Oligo-dT promoter primer to create first strand cDNA. RNase H-mediated second strand cDNA synthesis is followed by T7 RNA Polymerase directed in vitro transcription, which incorporates a biotinylated nucleotide during cRNA amplification.
| | Sample_hyb_protocol | Samples were prepared for hybridization using 15 µg biotinylated cRNA in a 1X hybridization cocktail with additional hybridization cocktail components provided in the GeneChip Hybridization, Wash and Stain Kit (Affymetrix). GeneChip arrays (Human U133 Plus 2.0) were hybridized in a GeneChip Hybridization Oven at 45 degrees C for 16 hours at 60 RPM. Washing was performed 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 using default settings.
| | Sample_data_processing | Images were extracted and analyzed using the default settings of GeneChip Operating Software v1.4.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Garrett,M,Frampton
| | Sample_contact_email | frampton@mit.edu
| | Sample_contact_laboratory | Richard Young
| | Sample_contact_department | Biology
| | Sample_contact_institute | Whitehead Instute - MIT
| | Sample_contact_address | 9 Cambridge Center
| | Sample_contact_city | Cambridge
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02142
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM574nnn/GSM574082/suppl/GSM574082.CEL.gz
| | Sample_series_id | GSE22499
| | Sample_series_id | GSE23402
| | Sample_data_row_count | 54675
| | |
|
GSM574083 | GPL570 |
|
hiPS_A6_rep2_081006_4
|
hiPS line A6
|
cell line: hiPS line A6
|
Gene expression data from hiPS line A6
|
| Sample_geo_accession | GSM574083
| | Sample_status | Public on Aug 09 2010
| | Sample_submission_date | Aug 03 2010
| | Sample_last_update_date | Sep 15 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | All primary human fibroblasts cells described in this paper (PDB-AG20442 and GM-M01660) were purchased from the Coriell Cell Repository (Camden, NJ). Fibroblasts were cultured in fibroblast medium (Dulbecco's modified Eagle's medium [DMEM] supplemented with 15% fetal bovine serum [FBS; Hyclone], 1 mM glutamine [Invitrogen], 1% nonessential amino acids [Invitrogen], and penicillin/streptomycin [Invitrogen]).
| | Sample_growth_protocol_ch1 | hiPS cell lines iPS A1, iPS C1, iPS4, iPS A6 (Hockemeyer et al. 2009); hiPS cell lines iPS PDB2lox-17, iPS PDB2lox-21, iPS PDB2lox-5, iPS PDB2lox-22, iPS PDB1lox-17puro-5, iPS PDB1lox-17puro-10, iPS PDB1lox-17puro-33, iPS PDB1lox-21puro-20, iPS PDB1lox-21puro-26, and iPS PDB1lox-21puro-28 (Soldner et al. 2009); hES cell lines BG01 and BG03 (National Institutes of Health code: BG01 and BG03; BresaGen, Inc., Athens, GA); hES cell lines WIBR1, WIBR2, WIBR3, and WIBR7 (Lengner et al., 2010; Whitehead Institute Center for Human Stem Cell Research) and hES cell line H9 (NIH Code:WA09, Wisconsin Alumni Research Foundation, Madison, WI) were maintained on mitomycin C-inactivated mouse embryonic fibroblast (MEF) feeder layers in hESC medium (DMEM/F12 [Invitrogen] supplemented with 15% FBS [Hyclone], 5% KnockOut Serum Replacement [Invitrogen], 1 mM glutamine [Invitrogen], 1% nonessential amino acids [Invitrogen], 0.1 mM β-mercaptoethanol [Sigma], and 4 ng/ml FGF2 [R&D Systems]). Cultures were passaged every 5 to 7 days either manually or enzymatically with collagenase type IV (Invitrogen; 1.5 mg/ml). hiPS cell lines were passaged 15-25 times prior to ChIP-Seq and gene expression analysis.
| | Sample_molecule_ch1 | polyA RNA
| | Sample_extract_protocol_ch1 | RNA was isolated from hES and hiPS cells, which were mechanically separated from feeder cells, with the RNeasy Mini Kit (QIAGEN).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | 5 µg total RNA was used to prepare biotinylated cRNA according to the manufacturer’s protocol (Affymetrix One Cycle cDNA Synthesis Kit). Briefly, this method involves SuperScript II-directed reverse transcription using a T7-Oligo-dT promoter primer to create first strand cDNA. RNase H-mediated second strand cDNA synthesis is followed by T7 RNA Polymerase directed in vitro transcription, which incorporates a biotinylated nucleotide during cRNA amplification.
| | Sample_hyb_protocol | Samples were prepared for hybridization using 15 µg biotinylated cRNA in a 1X hybridization cocktail with additional hybridization cocktail components provided in the GeneChip Hybridization, Wash and Stain Kit (Affymetrix). GeneChip arrays (Human U133 Plus 2.0) were hybridized in a GeneChip Hybridization Oven at 45 degrees C for 16 hours at 60 RPM. Washing was performed 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 using default settings.
| | Sample_data_processing | Images were extracted and analyzed using the default settings of GeneChip Operating Software v1.4.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Garrett,M,Frampton
| | Sample_contact_email | frampton@mit.edu
| | Sample_contact_laboratory | Richard Young
| | Sample_contact_department | Biology
| | Sample_contact_institute | Whitehead Instute - MIT
| | Sample_contact_address | 9 Cambridge Center
| | Sample_contact_city | Cambridge
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02142
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM574nnn/GSM574083/suppl/GSM574083.CEL.gz
| | Sample_series_id | GSE22499
| | Sample_series_id | GSE23402
| | Sample_data_row_count | 54675
| | |
|
GSM574084 | GPL570 |
|
hiPS_C1_rep1_081006_11
|
hiPS line C1
|
cell line: hiPS line C1
|
Gene expression data from hiPS line C1
|
| Sample_geo_accession | GSM574084
| | Sample_status | Public on Aug 09 2010
| | Sample_submission_date | Aug 03 2010
| | Sample_last_update_date | Sep 15 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | All primary human fibroblasts cells described in this paper (PDB-AG20442 and GM-M01660) were purchased from the Coriell Cell Repository (Camden, NJ). Fibroblasts were cultured in fibroblast medium (Dulbecco's modified Eagle's medium [DMEM] supplemented with 15% fetal bovine serum [FBS; Hyclone], 1 mM glutamine [Invitrogen], 1% nonessential amino acids [Invitrogen], and penicillin/streptomycin [Invitrogen]).
| | Sample_growth_protocol_ch1 | hiPS cell lines iPS A1, iPS C1, iPS4, iPS A6 (Hockemeyer et al. 2009); hiPS cell lines iPS PDB2lox-17, iPS PDB2lox-21, iPS PDB2lox-5, iPS PDB2lox-22, iPS PDB1lox-17puro-5, iPS PDB1lox-17puro-10, iPS PDB1lox-17puro-33, iPS PDB1lox-21puro-20, iPS PDB1lox-21puro-26, and iPS PDB1lox-21puro-28 (Soldner et al. 2009); hES cell lines BG01 and BG03 (National Institutes of Health code: BG01 and BG03; BresaGen, Inc., Athens, GA); hES cell lines WIBR1, WIBR2, WIBR3, and WIBR7 (Lengner et al., 2010; Whitehead Institute Center for Human Stem Cell Research) and hES cell line H9 (NIH Code:WA09, Wisconsin Alumni Research Foundation, Madison, WI) were maintained on mitomycin C-inactivated mouse embryonic fibroblast (MEF) feeder layers in hESC medium (DMEM/F12 [Invitrogen] supplemented with 15% FBS [Hyclone], 5% KnockOut Serum Replacement [Invitrogen], 1 mM glutamine [Invitrogen], 1% nonessential amino acids [Invitrogen], 0.1 mM β-mercaptoethanol [Sigma], and 4 ng/ml FGF2 [R&D Systems]). Cultures were passaged every 5 to 7 days either manually or enzymatically with collagenase type IV (Invitrogen; 1.5 mg/ml). hiPS cell lines were passaged 15-25 times prior to ChIP-Seq and gene expression analysis.
| | Sample_molecule_ch1 | polyA RNA
| | Sample_extract_protocol_ch1 | RNA was isolated from hES and hiPS cells, which were mechanically separated from feeder cells, with the RNeasy Mini Kit (QIAGEN).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | 5 µg total RNA was used to prepare biotinylated cRNA according to the manufacturer’s protocol (Affymetrix One Cycle cDNA Synthesis Kit). Briefly, this method involves SuperScript II-directed reverse transcription using a T7-Oligo-dT promoter primer to create first strand cDNA. RNase H-mediated second strand cDNA synthesis is followed by T7 RNA Polymerase directed in vitro transcription, which incorporates a biotinylated nucleotide during cRNA amplification.
| | Sample_hyb_protocol | Samples were prepared for hybridization using 15 µg biotinylated cRNA in a 1X hybridization cocktail with additional hybridization cocktail components provided in the GeneChip Hybridization, Wash and Stain Kit (Affymetrix). GeneChip arrays (Human U133 Plus 2.0) were hybridized in a GeneChip Hybridization Oven at 45 degrees C for 16 hours at 60 RPM. Washing was performed 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 using default settings.
| | Sample_data_processing | Images were extracted and analyzed using the default settings of GeneChip Operating Software v1.4.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Garrett,M,Frampton
| | Sample_contact_email | frampton@mit.edu
| | Sample_contact_laboratory | Richard Young
| | Sample_contact_department | Biology
| | Sample_contact_institute | Whitehead Instute - MIT
| | Sample_contact_address | 9 Cambridge Center
| | Sample_contact_city | Cambridge
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02142
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM574nnn/GSM574084/suppl/GSM574084.CEL.gz
| | Sample_series_id | GSE22499
| | Sample_series_id | GSE23402
| | Sample_data_row_count | 54675
| | |
|
GSM574085 | GPL570 |
|
hiPS_C1_rep2_081006_12
|
hiPS line C1
|
cell line: hiPS line C1
|
Gene expression data from hiPS line C1
|
| Sample_geo_accession | GSM574085
| | Sample_status | Public on Aug 09 2010
| | Sample_submission_date | Aug 03 2010
| | Sample_last_update_date | Sep 15 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | All primary human fibroblasts cells described in this paper (PDB-AG20442 and GM-M01660) were purchased from the Coriell Cell Repository (Camden, NJ). Fibroblasts were cultured in fibroblast medium (Dulbecco's modified Eagle's medium [DMEM] supplemented with 15% fetal bovine serum [FBS; Hyclone], 1 mM glutamine [Invitrogen], 1% nonessential amino acids [Invitrogen], and penicillin/streptomycin [Invitrogen]).
| | Sample_growth_protocol_ch1 | hiPS cell lines iPS A1, iPS C1, iPS4, iPS A6 (Hockemeyer et al. 2009); hiPS cell lines iPS PDB2lox-17, iPS PDB2lox-21, iPS PDB2lox-5, iPS PDB2lox-22, iPS PDB1lox-17puro-5, iPS PDB1lox-17puro-10, iPS PDB1lox-17puro-33, iPS PDB1lox-21puro-20, iPS PDB1lox-21puro-26, and iPS PDB1lox-21puro-28 (Soldner et al. 2009); hES cell lines BG01 and BG03 (National Institutes of Health code: BG01 and BG03; BresaGen, Inc., Athens, GA); hES cell lines WIBR1, WIBR2, WIBR3, and WIBR7 (Lengner et al., 2010; Whitehead Institute Center for Human Stem Cell Research) and hES cell line H9 (NIH Code:WA09, Wisconsin Alumni Research Foundation, Madison, WI) were maintained on mitomycin C-inactivated mouse embryonic fibroblast (MEF) feeder layers in hESC medium (DMEM/F12 [Invitrogen] supplemented with 15% FBS [Hyclone], 5% KnockOut Serum Replacement [Invitrogen], 1 mM glutamine [Invitrogen], 1% nonessential amino acids [Invitrogen], 0.1 mM β-mercaptoethanol [Sigma], and 4 ng/ml FGF2 [R&D Systems]). Cultures were passaged every 5 to 7 days either manually or enzymatically with collagenase type IV (Invitrogen; 1.5 mg/ml). hiPS cell lines were passaged 15-25 times prior to ChIP-Seq and gene expression analysis.
| | Sample_molecule_ch1 | polyA RNA
| | Sample_extract_protocol_ch1 | RNA was isolated from hES and hiPS cells, which were mechanically separated from feeder cells, with the RNeasy Mini Kit (QIAGEN).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | 5 µg total RNA was used to prepare biotinylated cRNA according to the manufacturer’s protocol (Affymetrix One Cycle cDNA Synthesis Kit). Briefly, this method involves SuperScript II-directed reverse transcription using a T7-Oligo-dT promoter primer to create first strand cDNA. RNase H-mediated second strand cDNA synthesis is followed by T7 RNA Polymerase directed in vitro transcription, which incorporates a biotinylated nucleotide during cRNA amplification.
| | Sample_hyb_protocol | Samples were prepared for hybridization using 15 µg biotinylated cRNA in a 1X hybridization cocktail with additional hybridization cocktail components provided in the GeneChip Hybridization, Wash and Stain Kit (Affymetrix). GeneChip arrays (Human U133 Plus 2.0) were hybridized in a GeneChip Hybridization Oven at 45 degrees C for 16 hours at 60 RPM. Washing was performed 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 using default settings.
| | Sample_data_processing | Images were extracted and analyzed using the default settings of GeneChip Operating Software v1.4.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Garrett,M,Frampton
| | Sample_contact_email | frampton@mit.edu
| | Sample_contact_laboratory | Richard Young
| | Sample_contact_department | Biology
| | Sample_contact_institute | Whitehead Instute - MIT
| | Sample_contact_address | 9 Cambridge Center
| | Sample_contact_city | Cambridge
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02142
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM574nnn/GSM574085/suppl/GSM574085.CEL.gz
| | Sample_series_id | GSE22499
| | Sample_series_id | GSE23402
| | Sample_data_row_count | 54675
| | |
|
GSM574086 | GPL570 |
|
hiPS_PDB1lox_17puro_10_rep1_120208_9
|
hiPS_PDB1lox_17puro_10
|
cell line: hiPS_PDB1lox_17puro_10
|
Gene expression data from hiPS_PDB1lox_17puro_10
|
| Sample_geo_accession | GSM574086
| | Sample_status | Public on Aug 09 2010
| | Sample_submission_date | Aug 03 2010
| | Sample_last_update_date | Sep 15 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | All primary human fibroblasts cells described in this paper (PDB-AG20442 and GM-M01660) were purchased from the Coriell Cell Repository (Camden, NJ). Fibroblasts were cultured in fibroblast medium (Dulbecco's modified Eagle's medium [DMEM] supplemented with 15% fetal bovine serum [FBS; Hyclone], 1 mM glutamine [Invitrogen], 1% nonessential amino acids [Invitrogen], and penicillin/streptomycin [Invitrogen]).
| | Sample_growth_protocol_ch1 | hiPS cell lines iPS A1, iPS C1, iPS4, iPS A6 (Hockemeyer et al. 2009); hiPS cell lines iPS PDB2lox-17, iPS PDB2lox-21, iPS PDB2lox-5, iPS PDB2lox-22, iPS PDB1lox-17puro-5, iPS PDB1lox-17puro-10, iPS PDB1lox-17puro-33, iPS PDB1lox-21puro-20, iPS PDB1lox-21puro-26, and iPS PDB1lox-21puro-28 (Soldner et al. 2009); hES cell lines BG01 and BG03 (National Institutes of Health code: BG01 and BG03; BresaGen, Inc., Athens, GA); hES cell lines WIBR1, WIBR2, WIBR3, and WIBR7 (Lengner et al., 2010; Whitehead Institute Center for Human Stem Cell Research) and hES cell line H9 (NIH Code:WA09, Wisconsin Alumni Research Foundation, Madison, WI) were maintained on mitomycin C-inactivated mouse embryonic fibroblast (MEF) feeder layers in hESC medium (DMEM/F12 [Invitrogen] supplemented with 15% FBS [Hyclone], 5% KnockOut Serum Replacement [Invitrogen], 1 mM glutamine [Invitrogen], 1% nonessential amino acids [Invitrogen], 0.1 mM β-mercaptoethanol [Sigma], and 4 ng/ml FGF2 [R&D Systems]). Cultures were passaged every 5 to 7 days either manually or enzymatically with collagenase type IV (Invitrogen; 1.5 mg/ml). hiPS cell lines were passaged 15-25 times prior to ChIP-Seq and gene expression analysis.
| | Sample_molecule_ch1 | polyA RNA
| | Sample_extract_protocol_ch1 | RNA was isolated from hES and hiPS cells, which were mechanically separated from feeder cells, with the RNeasy Mini Kit (QIAGEN).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | 5 µg total RNA was used to prepare biotinylated cRNA according to the manufacturer’s protocol (Affymetrix One Cycle cDNA Synthesis Kit). Briefly, this method involves SuperScript II-directed reverse transcription using a T7-Oligo-dT promoter primer to create first strand cDNA. RNase H-mediated second strand cDNA synthesis is followed by T7 RNA Polymerase directed in vitro transcription, which incorporates a biotinylated nucleotide during cRNA amplification.
| | Sample_hyb_protocol | Samples were prepared for hybridization using 15 µg biotinylated cRNA in a 1X hybridization cocktail with additional hybridization cocktail components provided in the GeneChip Hybridization, Wash and Stain Kit (Affymetrix). GeneChip arrays (Human U133 Plus 2.0) were hybridized in a GeneChip Hybridization Oven at 45 degrees C for 16 hours at 60 RPM. Washing was performed 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 using default settings.
| | Sample_data_processing | Images were extracted and analyzed using the default settings of GeneChip Operating Software v1.4.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Garrett,M,Frampton
| | Sample_contact_email | frampton@mit.edu
| | Sample_contact_laboratory | Richard Young
| | Sample_contact_department | Biology
| | Sample_contact_institute | Whitehead Instute - MIT
| | Sample_contact_address | 9 Cambridge Center
| | Sample_contact_city | Cambridge
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02142
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM574nnn/GSM574086/suppl/GSM574086.CEL.gz
| | Sample_series_id | GSE22499
| | Sample_series_id | GSE23402
| | Sample_data_row_count | 54675
| | |
|
GSM574087 | GPL570 |
|
hiPS_PDB1lox_17puro_33_rep1_120208_10
|
hiPS_PDB1lox_17puro_33
|
cell line: hiPS_PDB1lox_17puro_33
|
Gene expression data from hiPS_PDB1lox_17puro_33
|
| Sample_geo_accession | GSM574087
| | Sample_status | Public on Aug 09 2010
| | Sample_submission_date | Aug 03 2010
| | Sample_last_update_date | Sep 15 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | All primary human fibroblasts cells described in this paper (PDB-AG20442 and GM-M01660) were purchased from the Coriell Cell Repository (Camden, NJ). Fibroblasts were cultured in fibroblast medium (Dulbecco's modified Eagle's medium [DMEM] supplemented with 15% fetal bovine serum [FBS; Hyclone], 1 mM glutamine [Invitrogen], 1% nonessential amino acids [Invitrogen], and penicillin/streptomycin [Invitrogen]).
| | Sample_growth_protocol_ch1 | hiPS cell lines iPS A1, iPS C1, iPS4, iPS A6 (Hockemeyer et al. 2009); hiPS cell lines iPS PDB2lox-17, iPS PDB2lox-21, iPS PDB2lox-5, iPS PDB2lox-22, iPS PDB1lox-17puro-5, iPS PDB1lox-17puro-10, iPS PDB1lox-17puro-33, iPS PDB1lox-21puro-20, iPS PDB1lox-21puro-26, and iPS PDB1lox-21puro-28 (Soldner et al. 2009); hES cell lines BG01 and BG03 (National Institutes of Health code: BG01 and BG03; BresaGen, Inc., Athens, GA); hES cell lines WIBR1, WIBR2, WIBR3, and WIBR7 (Lengner et al., 2010; Whitehead Institute Center for Human Stem Cell Research) and hES cell line H9 (NIH Code:WA09, Wisconsin Alumni Research Foundation, Madison, WI) were maintained on mitomycin C-inactivated mouse embryonic fibroblast (MEF) feeder layers in hESC medium (DMEM/F12 [Invitrogen] supplemented with 15% FBS [Hyclone], 5% KnockOut Serum Replacement [Invitrogen], 1 mM glutamine [Invitrogen], 1% nonessential amino acids [Invitrogen], 0.1 mM β-mercaptoethanol [Sigma], and 4 ng/ml FGF2 [R&D Systems]). Cultures were passaged every 5 to 7 days either manually or enzymatically with collagenase type IV (Invitrogen; 1.5 mg/ml). hiPS cell lines were passaged 15-25 times prior to ChIP-Seq and gene expression analysis.
| | Sample_molecule_ch1 | polyA RNA
| | Sample_extract_protocol_ch1 | RNA was isolated from hES and hiPS cells, which were mechanically separated from feeder cells, with the RNeasy Mini Kit (QIAGEN).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | 5 µg total RNA was used to prepare biotinylated cRNA according to the manufacturer’s protocol (Affymetrix One Cycle cDNA Synthesis Kit). Briefly, this method involves SuperScript II-directed reverse transcription using a T7-Oligo-dT promoter primer to create first strand cDNA. RNase H-mediated second strand cDNA synthesis is followed by T7 RNA Polymerase directed in vitro transcription, which incorporates a biotinylated nucleotide during cRNA amplification.
| | Sample_hyb_protocol | Samples were prepared for hybridization using 15 µg biotinylated cRNA in a 1X hybridization cocktail with additional hybridization cocktail components provided in the GeneChip Hybridization, Wash and Stain Kit (Affymetrix). GeneChip arrays (Human U133 Plus 2.0) were hybridized in a GeneChip Hybridization Oven at 45 degrees C for 16 hours at 60 RPM. Washing was performed 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 using default settings.
| | Sample_data_processing | Images were extracted and analyzed using the default settings of GeneChip Operating Software v1.4.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Garrett,M,Frampton
| | Sample_contact_email | frampton@mit.edu
| | Sample_contact_laboratory | Richard Young
| | Sample_contact_department | Biology
| | Sample_contact_institute | Whitehead Instute - MIT
| | Sample_contact_address | 9 Cambridge Center
| | Sample_contact_city | Cambridge
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02142
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM574nnn/GSM574087/suppl/GSM574087.CEL.gz
| | Sample_series_id | GSE22499
| | Sample_series_id | GSE23402
| | Sample_data_row_count | 54675
| | |
|
GSM574088 | GPL570 |
|
hiPS_PDB1lox_17puro_5_rep1_120208_8
|
hiPS_PDB1lox_17puro_5
|
cell line: hiPS_PDB1lox_17puro_5
|
Gene expression data from hiPS_PDB1lox_17puro_5
|
| Sample_geo_accession | GSM574088
| | Sample_status | Public on Aug 09 2010
| | Sample_submission_date | Aug 03 2010
| | Sample_last_update_date | Sep 15 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | All primary human fibroblasts cells described in this paper (PDB-AG20442 and GM-M01660) were purchased from the Coriell Cell Repository (Camden, NJ). Fibroblasts were cultured in fibroblast medium (Dulbecco's modified Eagle's medium [DMEM] supplemented with 15% fetal bovine serum [FBS; Hyclone], 1 mM glutamine [Invitrogen], 1% nonessential amino acids [Invitrogen], and penicillin/streptomycin [Invitrogen]).
| | Sample_growth_protocol_ch1 | hiPS cell lines iPS A1, iPS C1, iPS4, iPS A6 (Hockemeyer et al. 2009); hiPS cell lines iPS PDB2lox-17, iPS PDB2lox-21, iPS PDB2lox-5, iPS PDB2lox-22, iPS PDB1lox-17puro-5, iPS PDB1lox-17puro-10, iPS PDB1lox-17puro-33, iPS PDB1lox-21puro-20, iPS PDB1lox-21puro-26, and iPS PDB1lox-21puro-28 (Soldner et al. 2009); hES cell lines BG01 and BG03 (National Institutes of Health code: BG01 and BG03; BresaGen, Inc., Athens, GA); hES cell lines WIBR1, WIBR2, WIBR3, and WIBR7 (Lengner et al., 2010; Whitehead Institute Center for Human Stem Cell Research) and hES cell line H9 (NIH Code:WA09, Wisconsin Alumni Research Foundation, Madison, WI) were maintained on mitomycin C-inactivated mouse embryonic fibroblast (MEF) feeder layers in hESC medium (DMEM/F12 [Invitrogen] supplemented with 15% FBS [Hyclone], 5% KnockOut Serum Replacement [Invitrogen], 1 mM glutamine [Invitrogen], 1% nonessential amino acids [Invitrogen], 0.1 mM β-mercaptoethanol [Sigma], and 4 ng/ml FGF2 [R&D Systems]). Cultures were passaged every 5 to 7 days either manually or enzymatically with collagenase type IV (Invitrogen; 1.5 mg/ml). hiPS cell lines were passaged 15-25 times prior to ChIP-Seq and gene expression analysis.
| | Sample_molecule_ch1 | polyA RNA
| | Sample_extract_protocol_ch1 | RNA was isolated from hES and hiPS cells, which were mechanically separated from feeder cells, with the RNeasy Mini Kit (QIAGEN).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | 5 µg total RNA was used to prepare biotinylated cRNA according to the manufacturer’s protocol (Affymetrix One Cycle cDNA Synthesis Kit). Briefly, this method involves SuperScript II-directed reverse transcription using a T7-Oligo-dT promoter primer to create first strand cDNA. RNase H-mediated second strand cDNA synthesis is followed by T7 RNA Polymerase directed in vitro transcription, which incorporates a biotinylated nucleotide during cRNA amplification.
| | Sample_hyb_protocol | Samples were prepared for hybridization using 15 µg biotinylated cRNA in a 1X hybridization cocktail with additional hybridization cocktail components provided in the GeneChip Hybridization, Wash and Stain Kit (Affymetrix). GeneChip arrays (Human U133 Plus 2.0) were hybridized in a GeneChip Hybridization Oven at 45 degrees C for 16 hours at 60 RPM. Washing was performed 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 using default settings.
| | Sample_data_processing | Images were extracted and analyzed using the default settings of GeneChip Operating Software v1.4.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Garrett,M,Frampton
| | Sample_contact_email | frampton@mit.edu
| | Sample_contact_laboratory | Richard Young
| | Sample_contact_department | Biology
| | Sample_contact_institute | Whitehead Instute - MIT
| | Sample_contact_address | 9 Cambridge Center
| | Sample_contact_city | Cambridge
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02142
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM574nnn/GSM574088/suppl/GSM574088.CEL.gz
| | Sample_series_id | GSE22499
| | Sample_series_id | GSE23402
| | Sample_data_row_count | 54675
| | |
|
GSM574089 | GPL570 |
|
hiPS_PDB1lox_17puro_5_rep2_090811_13
|
hiPS_PDB1lox_17puro_5
|
cell line: hiPS_PDB1lox_17puro_5
|
Gene expression data from hiPS_PDB1lox_17puro_5
|
| Sample_geo_accession | GSM574089
| | Sample_status | Public on Aug 09 2010
| | Sample_submission_date | Aug 03 2010
| | Sample_last_update_date | Sep 15 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | All primary human fibroblasts cells described in this paper (PDB-AG20442 and GM-M01660) were purchased from the Coriell Cell Repository (Camden, NJ). Fibroblasts were cultured in fibroblast medium (Dulbecco's modified Eagle's medium [DMEM] supplemented with 15% fetal bovine serum [FBS; Hyclone], 1 mM glutamine [Invitrogen], 1% nonessential amino acids [Invitrogen], and penicillin/streptomycin [Invitrogen]).
| | Sample_growth_protocol_ch1 | hiPS cell lines iPS A1, iPS C1, iPS4, iPS A6 (Hockemeyer et al. 2009); hiPS cell lines iPS PDB2lox-17, iPS PDB2lox-21, iPS PDB2lox-5, iPS PDB2lox-22, iPS PDB1lox-17puro-5, iPS PDB1lox-17puro-10, iPS PDB1lox-17puro-33, iPS PDB1lox-21puro-20, iPS PDB1lox-21puro-26, and iPS PDB1lox-21puro-28 (Soldner et al. 2009); hES cell lines BG01 and BG03 (National Institutes of Health code: BG01 and BG03; BresaGen, Inc., Athens, GA); hES cell lines WIBR1, WIBR2, WIBR3, and WIBR7 (Lengner et al., 2010; Whitehead Institute Center for Human Stem Cell Research) and hES cell line H9 (NIH Code:WA09, Wisconsin Alumni Research Foundation, Madison, WI) were maintained on mitomycin C-inactivated mouse embryonic fibroblast (MEF) feeder layers in hESC medium (DMEM/F12 [Invitrogen] supplemented with 15% FBS [Hyclone], 5% KnockOut Serum Replacement [Invitrogen], 1 mM glutamine [Invitrogen], 1% nonessential amino acids [Invitrogen], 0.1 mM β-mercaptoethanol [Sigma], and 4 ng/ml FGF2 [R&D Systems]). Cultures were passaged every 5 to 7 days either manually or enzymatically with collagenase type IV (Invitrogen; 1.5 mg/ml). hiPS cell lines were passaged 15-25 times prior to ChIP-Seq and gene expression analysis.
| | Sample_molecule_ch1 | polyA RNA
| | Sample_extract_protocol_ch1 | RNA was isolated from hES and hiPS cells, which were mechanically separated from feeder cells, with the RNeasy Mini Kit (QIAGEN).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | 5 µg total RNA was used to prepare biotinylated cRNA according to the manufacturer’s protocol (Affymetrix One Cycle cDNA Synthesis Kit). Briefly, this method involves SuperScript II-directed reverse transcription using a T7-Oligo-dT promoter primer to create first strand cDNA. RNase H-mediated second strand cDNA synthesis is followed by T7 RNA Polymerase directed in vitro transcription, which incorporates a biotinylated nucleotide during cRNA amplification.
| | Sample_hyb_protocol | Samples were prepared for hybridization using 15 µg biotinylated cRNA in a 1X hybridization cocktail with additional hybridization cocktail components provided in the GeneChip Hybridization, Wash and Stain Kit (Affymetrix). GeneChip arrays (Human U133 Plus 2.0) were hybridized in a GeneChip Hybridization Oven at 45 degrees C for 16 hours at 60 RPM. Washing was performed 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 using default settings.
| | Sample_data_processing | Images were extracted and analyzed using the default settings of GeneChip Operating Software v1.4.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Garrett,M,Frampton
| | Sample_contact_email | frampton@mit.edu
| | Sample_contact_laboratory | Richard Young
| | Sample_contact_department | Biology
| | Sample_contact_institute | Whitehead Instute - MIT
| | Sample_contact_address | 9 Cambridge Center
| | Sample_contact_city | Cambridge
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02142
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM574nnn/GSM574089/suppl/GSM574089.CEL.gz
| | Sample_series_id | GSE22499
| | Sample_series_id | GSE23402
| | Sample_data_row_count | 54675
| | |
|
GSM574090 | GPL570 |
|
hiPS_PDB1lox_21puro_20_rep1_120208_11
|
hiPS_PDB1lox_21puro_20
|
cell line: hiPS_PDB1lox_21puro_20
|
Gene expression data from hiPS_PDB1lox_21puro_20
|
| Sample_geo_accession | GSM574090
| | Sample_status | Public on Aug 09 2010
| | Sample_submission_date | Aug 03 2010
| | Sample_last_update_date | Sep 15 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | All primary human fibroblasts cells described in this paper (PDB-AG20442 and GM-M01660) were purchased from the Coriell Cell Repository (Camden, NJ). Fibroblasts were cultured in fibroblast medium (Dulbecco's modified Eagle's medium [DMEM] supplemented with 15% fetal bovine serum [FBS; Hyclone], 1 mM glutamine [Invitrogen], 1% nonessential amino acids [Invitrogen], and penicillin/streptomycin [Invitrogen]).
| | Sample_growth_protocol_ch1 | hiPS cell lines iPS A1, iPS C1, iPS4, iPS A6 (Hockemeyer et al. 2009); hiPS cell lines iPS PDB2lox-17, iPS PDB2lox-21, iPS PDB2lox-5, iPS PDB2lox-22, iPS PDB1lox-17puro-5, iPS PDB1lox-17puro-10, iPS PDB1lox-17puro-33, iPS PDB1lox-21puro-20, iPS PDB1lox-21puro-26, and iPS PDB1lox-21puro-28 (Soldner et al. 2009); hES cell lines BG01 and BG03 (National Institutes of Health code: BG01 and BG03; BresaGen, Inc., Athens, GA); hES cell lines WIBR1, WIBR2, WIBR3, and WIBR7 (Lengner et al., 2010; Whitehead Institute Center for Human Stem Cell Research) and hES cell line H9 (NIH Code:WA09, Wisconsin Alumni Research Foundation, Madison, WI) were maintained on mitomycin C-inactivated mouse embryonic fibroblast (MEF) feeder layers in hESC medium (DMEM/F12 [Invitrogen] supplemented with 15% FBS [Hyclone], 5% KnockOut Serum Replacement [Invitrogen], 1 mM glutamine [Invitrogen], 1% nonessential amino acids [Invitrogen], 0.1 mM β-mercaptoethanol [Sigma], and 4 ng/ml FGF2 [R&D Systems]). Cultures were passaged every 5 to 7 days either manually or enzymatically with collagenase type IV (Invitrogen; 1.5 mg/ml). hiPS cell lines were passaged 15-25 times prior to ChIP-Seq and gene expression analysis.
| | Sample_molecule_ch1 | polyA RNA
| | Sample_extract_protocol_ch1 | RNA was isolated from hES and hiPS cells, which were mechanically separated from feeder cells, with the RNeasy Mini Kit (QIAGEN).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | 5 µg total RNA was used to prepare biotinylated cRNA according to the manufacturer’s protocol (Affymetrix One Cycle cDNA Synthesis Kit). Briefly, this method involves SuperScript II-directed reverse transcription using a T7-Oligo-dT promoter primer to create first strand cDNA. RNase H-mediated second strand cDNA synthesis is followed by T7 RNA Polymerase directed in vitro transcription, which incorporates a biotinylated nucleotide during cRNA amplification.
| | Sample_hyb_protocol | Samples were prepared for hybridization using 15 µg biotinylated cRNA in a 1X hybridization cocktail with additional hybridization cocktail components provided in the GeneChip Hybridization, Wash and Stain Kit (Affymetrix). GeneChip arrays (Human U133 Plus 2.0) were hybridized in a GeneChip Hybridization Oven at 45 degrees C for 16 hours at 60 RPM. Washing was performed 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 using default settings.
| | Sample_data_processing | Images were extracted and analyzed using the default settings of GeneChip Operating Software v1.4.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Garrett,M,Frampton
| | Sample_contact_email | frampton@mit.edu
| | Sample_contact_laboratory | Richard Young
| | Sample_contact_department | Biology
| | Sample_contact_institute | Whitehead Instute - MIT
| | Sample_contact_address | 9 Cambridge Center
| | Sample_contact_city | Cambridge
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02142
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM574nnn/GSM574090/suppl/GSM574090.CEL.gz
| | Sample_series_id | GSE22499
| | Sample_series_id | GSE23402
| | Sample_data_row_count | 54675
| | |
|
GSM574091 | GPL570 |
|
hiPS_PDB1lox_21puro_26_rep1_120208_12
|
hiPS_PDB1lox_21puro_26
|
cell line: hiPS_PDB1lox_21puro_26
|
Gene expression data from hiPS_PDB1lox_21puro_26
|
| Sample_geo_accession | GSM574091
| | Sample_status | Public on Aug 09 2010
| | Sample_submission_date | Aug 03 2010
| | Sample_last_update_date | Sep 15 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | All primary human fibroblasts cells described in this paper (PDB-AG20442 and GM-M01660) were purchased from the Coriell Cell Repository (Camden, NJ). Fibroblasts were cultured in fibroblast medium (Dulbecco's modified Eagle's medium [DMEM] supplemented with 15% fetal bovine serum [FBS; Hyclone], 1 mM glutamine [Invitrogen], 1% nonessential amino acids [Invitrogen], and penicillin/streptomycin [Invitrogen]).
| | Sample_growth_protocol_ch1 | hiPS cell lines iPS A1, iPS C1, iPS4, iPS A6 (Hockemeyer et al. 2009); hiPS cell lines iPS PDB2lox-17, iPS PDB2lox-21, iPS PDB2lox-5, iPS PDB2lox-22, iPS PDB1lox-17puro-5, iPS PDB1lox-17puro-10, iPS PDB1lox-17puro-33, iPS PDB1lox-21puro-20, iPS PDB1lox-21puro-26, and iPS PDB1lox-21puro-28 (Soldner et al. 2009); hES cell lines BG01 and BG03 (National Institutes of Health code: BG01 and BG03; BresaGen, Inc., Athens, GA); hES cell lines WIBR1, WIBR2, WIBR3, and WIBR7 (Lengner et al., 2010; Whitehead Institute Center for Human Stem Cell Research) and hES cell line H9 (NIH Code:WA09, Wisconsin Alumni Research Foundation, Madison, WI) were maintained on mitomycin C-inactivated mouse embryonic fibroblast (MEF) feeder layers in hESC medium (DMEM/F12 [Invitrogen] supplemented with 15% FBS [Hyclone], 5% KnockOut Serum Replacement [Invitrogen], 1 mM glutamine [Invitrogen], 1% nonessential amino acids [Invitrogen], 0.1 mM β-mercaptoethanol [Sigma], and 4 ng/ml FGF2 [R&D Systems]). Cultures were passaged every 5 to 7 days either manually or enzymatically with collagenase type IV (Invitrogen; 1.5 mg/ml). hiPS cell lines were passaged 15-25 times prior to ChIP-Seq and gene expression analysis.
| | Sample_molecule_ch1 | polyA RNA
| | Sample_extract_protocol_ch1 | RNA was isolated from hES and hiPS cells, which were mechanically separated from feeder cells, with the RNeasy Mini Kit (QIAGEN).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | 5 µg total RNA was used to prepare biotinylated cRNA according to the manufacturer’s protocol (Affymetrix One Cycle cDNA Synthesis Kit). Briefly, this method involves SuperScript II-directed reverse transcription using a T7-Oligo-dT promoter primer to create first strand cDNA. RNase H-mediated second strand cDNA synthesis is followed by T7 RNA Polymerase directed in vitro transcription, which incorporates a biotinylated nucleotide during cRNA amplification.
| | Sample_hyb_protocol | Samples were prepared for hybridization using 15 µg biotinylated cRNA in a 1X hybridization cocktail with additional hybridization cocktail components provided in the GeneChip Hybridization, Wash and Stain Kit (Affymetrix). GeneChip arrays (Human U133 Plus 2.0) were hybridized in a GeneChip Hybridization Oven at 45 degrees C for 16 hours at 60 RPM. Washing was performed 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 using default settings.
| | Sample_data_processing | Images were extracted and analyzed using the default settings of GeneChip Operating Software v1.4.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Garrett,M,Frampton
| | Sample_contact_email | frampton@mit.edu
| | Sample_contact_laboratory | Richard Young
| | Sample_contact_department | Biology
| | Sample_contact_institute | Whitehead Instute - MIT
| | Sample_contact_address | 9 Cambridge Center
| | Sample_contact_city | Cambridge
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02142
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM574nnn/GSM574091/suppl/GSM574091.CEL.gz
| | Sample_series_id | GSE22499
| | Sample_series_id | GSE23402
| | Sample_data_row_count | 54675
| | |
|
GSM574092 | GPL570 |
|
hiPS_PDB1lox_21puro_26_rep2_090811_14
|
hiPS_PDB1lox_21puro_26
|
cell line: hiPS_PDB1lox_21puro_26
|
Gene expression data from hiPS_PDB1lox_21puro_26
|
| Sample_geo_accession | GSM574092
| | Sample_status | Public on Aug 09 2010
| | Sample_submission_date | Aug 03 2010
| | Sample_last_update_date | Sep 15 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | All primary human fibroblasts cells described in this paper (PDB-AG20442 and GM-M01660) were purchased from the Coriell Cell Repository (Camden, NJ). Fibroblasts were cultured in fibroblast medium (Dulbecco's modified Eagle's medium [DMEM] supplemented with 15% fetal bovine serum [FBS; Hyclone], 1 mM glutamine [Invitrogen], 1% nonessential amino acids [Invitrogen], and penicillin/streptomycin [Invitrogen]).
| | Sample_growth_protocol_ch1 | hiPS cell lines iPS A1, iPS C1, iPS4, iPS A6 (Hockemeyer et al. 2009); hiPS cell lines iPS PDB2lox-17, iPS PDB2lox-21, iPS PDB2lox-5, iPS PDB2lox-22, iPS PDB1lox-17puro-5, iPS PDB1lox-17puro-10, iPS PDB1lox-17puro-33, iPS PDB1lox-21puro-20, iPS PDB1lox-21puro-26, and iPS PDB1lox-21puro-28 (Soldner et al. 2009); hES cell lines BG01 and BG03 (National Institutes of Health code: BG01 and BG03; BresaGen, Inc., Athens, GA); hES cell lines WIBR1, WIBR2, WIBR3, and WIBR7 (Lengner et al., 2010; Whitehead Institute Center for Human Stem Cell Research) and hES cell line H9 (NIH Code:WA09, Wisconsin Alumni Research Foundation, Madison, WI) were maintained on mitomycin C-inactivated mouse embryonic fibroblast (MEF) feeder layers in hESC medium (DMEM/F12 [Invitrogen] supplemented with 15% FBS [Hyclone], 5% KnockOut Serum Replacement [Invitrogen], 1 mM glutamine [Invitrogen], 1% nonessential amino acids [Invitrogen], 0.1 mM β-mercaptoethanol [Sigma], and 4 ng/ml FGF2 [R&D Systems]). Cultures were passaged every 5 to 7 days either manually or enzymatically with collagenase type IV (Invitrogen; 1.5 mg/ml). hiPS cell lines were passaged 15-25 times prior to ChIP-Seq and gene expression analysis.
| | Sample_molecule_ch1 | polyA RNA
| | Sample_extract_protocol_ch1 | RNA was isolated from hES and hiPS cells, which were mechanically separated from feeder cells, with the RNeasy Mini Kit (QIAGEN).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | 5 µg total RNA was used to prepare biotinylated cRNA according to the manufacturer’s protocol (Affymetrix One Cycle cDNA Synthesis Kit). Briefly, this method involves SuperScript II-directed reverse transcription using a T7-Oligo-dT promoter primer to create first strand cDNA. RNase H-mediated second strand cDNA synthesis is followed by T7 RNA Polymerase directed in vitro transcription, which incorporates a biotinylated nucleotide during cRNA amplification.
| | Sample_hyb_protocol | Samples were prepared for hybridization using 15 µg biotinylated cRNA in a 1X hybridization cocktail with additional hybridization cocktail components provided in the GeneChip Hybridization, Wash and Stain Kit (Affymetrix). GeneChip arrays (Human U133 Plus 2.0) were hybridized in a GeneChip Hybridization Oven at 45 degrees C for 16 hours at 60 RPM. Washing was performed 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 using default settings.
| | Sample_data_processing | Images were extracted and analyzed using the default settings of GeneChip Operating Software v1.4.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Garrett,M,Frampton
| | Sample_contact_email | frampton@mit.edu
| | Sample_contact_laboratory | Richard Young
| | Sample_contact_department | Biology
| | Sample_contact_institute | Whitehead Instute - MIT
| | Sample_contact_address | 9 Cambridge Center
| | Sample_contact_city | Cambridge
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02142
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM574nnn/GSM574092/suppl/GSM574092.CEL.gz
| | Sample_series_id | GSE22499
| | Sample_series_id | GSE23402
| | Sample_data_row_count | 54675
| | |
|
GSM574093 | GPL570 |
|
hiPS_PDB1lox_21puro_28_rep1_120208_13
|
hiPS_PDB1lox_21puro_28
|
cell line: hiPS_PDB1lox_21puro_28
|
Gene expression data from hiPS_PDB1lox_21puro_28
|
| Sample_geo_accession | GSM574093
| | Sample_status | Public on Aug 09 2010
| | Sample_submission_date | Aug 03 2010
| | Sample_last_update_date | Sep 15 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | All primary human fibroblasts cells described in this paper (PDB-AG20442 and GM-M01660) were purchased from the Coriell Cell Repository (Camden, NJ). Fibroblasts were cultured in fibroblast medium (Dulbecco's modified Eagle's medium [DMEM] supplemented with 15% fetal bovine serum [FBS; Hyclone], 1 mM glutamine [Invitrogen], 1% nonessential amino acids [Invitrogen], and penicillin/streptomycin [Invitrogen]).
| | Sample_growth_protocol_ch1 | hiPS cell lines iPS A1, iPS C1, iPS4, iPS A6 (Hockemeyer et al. 2009); hiPS cell lines iPS PDB2lox-17, iPS PDB2lox-21, iPS PDB2lox-5, iPS PDB2lox-22, iPS PDB1lox-17puro-5, iPS PDB1lox-17puro-10, iPS PDB1lox-17puro-33, iPS PDB1lox-21puro-20, iPS PDB1lox-21puro-26, and iPS PDB1lox-21puro-28 (Soldner et al. 2009); hES cell lines BG01 and BG03 (National Institutes of Health code: BG01 and BG03; BresaGen, Inc., Athens, GA); hES cell lines WIBR1, WIBR2, WIBR3, and WIBR7 (Lengner et al., 2010; Whitehead Institute Center for Human Stem Cell Research) and hES cell line H9 (NIH Code:WA09, Wisconsin Alumni Research Foundation, Madison, WI) were maintained on mitomycin C-inactivated mouse embryonic fibroblast (MEF) feeder layers in hESC medium (DMEM/F12 [Invitrogen] supplemented with 15% FBS [Hyclone], 5% KnockOut Serum Replacement [Invitrogen], 1 mM glutamine [Invitrogen], 1% nonessential amino acids [Invitrogen], 0.1 mM β-mercaptoethanol [Sigma], and 4 ng/ml FGF2 [R&D Systems]). Cultures were passaged every 5 to 7 days either manually or enzymatically with collagenase type IV (Invitrogen; 1.5 mg/ml). hiPS cell lines were passaged 15-25 times prior to ChIP-Seq and gene expression analysis.
| | Sample_molecule_ch1 | polyA RNA
| | Sample_extract_protocol_ch1 | RNA was isolated from hES and hiPS cells, which were mechanically separated from feeder cells, with the RNeasy Mini Kit (QIAGEN).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | 5 µg total RNA was used to prepare biotinylated cRNA according to the manufacturer’s protocol (Affymetrix One Cycle cDNA Synthesis Kit). Briefly, this method involves SuperScript II-directed reverse transcription using a T7-Oligo-dT promoter primer to create first strand cDNA. RNase H-mediated second strand cDNA synthesis is followed by T7 RNA Polymerase directed in vitro transcription, which incorporates a biotinylated nucleotide during cRNA amplification.
| | Sample_hyb_protocol | Samples were prepared for hybridization using 15 µg biotinylated cRNA in a 1X hybridization cocktail with additional hybridization cocktail components provided in the GeneChip Hybridization, Wash and Stain Kit (Affymetrix). GeneChip arrays (Human U133 Plus 2.0) were hybridized in a GeneChip Hybridization Oven at 45 degrees C for 16 hours at 60 RPM. Washing was performed 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 using default settings.
| | Sample_data_processing | Images were extracted and analyzed using the default settings of GeneChip Operating Software v1.4.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Garrett,M,Frampton
| | Sample_contact_email | frampton@mit.edu
| | Sample_contact_laboratory | Richard Young
| | Sample_contact_department | Biology
| | Sample_contact_institute | Whitehead Instute - MIT
| | Sample_contact_address | 9 Cambridge Center
| | Sample_contact_city | Cambridge
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02142
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM574nnn/GSM574093/suppl/GSM574093.CEL.gz
| | Sample_series_id | GSE22499
| | Sample_series_id | GSE23402
| | Sample_data_row_count | 54675
| | |
|
GSM574094 | GPL570 |
|
hiPS_PDB2lox_17_rep1_120208_5
|
hiPS_PDB2lox_17
|
cell line: hiPS_PDB2lox_17
|
Gene expression data from hiPS_PDB2lox_17
|
| Sample_geo_accession | GSM574094
| | Sample_status | Public on Aug 09 2010
| | Sample_submission_date | Aug 03 2010
| | Sample_last_update_date | Sep 15 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | All primary human fibroblasts cells described in this paper (PDB-AG20442 and GM-M01660) were purchased from the Coriell Cell Repository (Camden, NJ). Fibroblasts were cultured in fibroblast medium (Dulbecco's modified Eagle's medium [DMEM] supplemented with 15% fetal bovine serum [FBS; Hyclone], 1 mM glutamine [Invitrogen], 1% nonessential amino acids [Invitrogen], and penicillin/streptomycin [Invitrogen]).
| | Sample_growth_protocol_ch1 | hiPS cell lines iPS A1, iPS C1, iPS4, iPS A6 (Hockemeyer et al. 2009); hiPS cell lines iPS PDB2lox-17, iPS PDB2lox-21, iPS PDB2lox-5, iPS PDB2lox-22, iPS PDB1lox-17puro-5, iPS PDB1lox-17puro-10, iPS PDB1lox-17puro-33, iPS PDB1lox-21puro-20, iPS PDB1lox-21puro-26, and iPS PDB1lox-21puro-28 (Soldner et al. 2009); hES cell lines BG01 and BG03 (National Institutes of Health code: BG01 and BG03; BresaGen, Inc., Athens, GA); hES cell lines WIBR1, WIBR2, WIBR3, and WIBR7 (Lengner et al., 2010; Whitehead Institute Center for Human Stem Cell Research) and hES cell line H9 (NIH Code:WA09, Wisconsin Alumni Research Foundation, Madison, WI) were maintained on mitomycin C-inactivated mouse embryonic fibroblast (MEF) feeder layers in hESC medium (DMEM/F12 [Invitrogen] supplemented with 15% FBS [Hyclone], 5% KnockOut Serum Replacement [Invitrogen], 1 mM glutamine [Invitrogen], 1% nonessential amino acids [Invitrogen], 0.1 mM β-mercaptoethanol [Sigma], and 4 ng/ml FGF2 [R&D Systems]). Cultures were passaged every 5 to 7 days either manually or enzymatically with collagenase type IV (Invitrogen; 1.5 mg/ml). hiPS cell lines were passaged 15-25 times prior to ChIP-Seq and gene expression analysis.
| | Sample_molecule_ch1 | polyA RNA
| | Sample_extract_protocol_ch1 | RNA was isolated from hES and hiPS cells, which were mechanically separated from feeder cells, with the RNeasy Mini Kit (QIAGEN).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | 5 µg total RNA was used to prepare biotinylated cRNA according to the manufacturer’s protocol (Affymetrix One Cycle cDNA Synthesis Kit). Briefly, this method involves SuperScript II-directed reverse transcription using a T7-Oligo-dT promoter primer to create first strand cDNA. RNase H-mediated second strand cDNA synthesis is followed by T7 RNA Polymerase directed in vitro transcription, which incorporates a biotinylated nucleotide during cRNA amplification.
| | Sample_hyb_protocol | Samples were prepared for hybridization using 15 µg biotinylated cRNA in a 1X hybridization cocktail with additional hybridization cocktail components provided in the GeneChip Hybridization, Wash and Stain Kit (Affymetrix). GeneChip arrays (Human U133 Plus 2.0) were hybridized in a GeneChip Hybridization Oven at 45 degrees C for 16 hours at 60 RPM. Washing was performed 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 using default settings.
| | Sample_data_processing | Images were extracted and analyzed using the default settings of GeneChip Operating Software v1.4.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Garrett,M,Frampton
| | Sample_contact_email | frampton@mit.edu
| | Sample_contact_laboratory | Richard Young
| | Sample_contact_department | Biology
| | Sample_contact_institute | Whitehead Instute - MIT
| | Sample_contact_address | 9 Cambridge Center
| | Sample_contact_city | Cambridge
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02142
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM574nnn/GSM574094/suppl/GSM574094.CEL.gz
| | Sample_series_id | GSE22499
| | Sample_series_id | GSE23402
| | Sample_data_row_count | 54675
| | |
|
GSM574095 | GPL570 |
|
hiPS_PDB2lox_17_rep2_090811_9
|
hiPS_PDB2lox_17
|
cell line: hiPS_PDB2lox_17
|
Gene expression data from hiPS_PDB2lox_17
|
| Sample_geo_accession | GSM574095
| | Sample_status | Public on Aug 09 2010
| | Sample_submission_date | Aug 03 2010
| | Sample_last_update_date | Sep 15 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | All primary human fibroblasts cells described in this paper (PDB-AG20442 and GM-M01660) were purchased from the Coriell Cell Repository (Camden, NJ). Fibroblasts were cultured in fibroblast medium (Dulbecco's modified Eagle's medium [DMEM] supplemented with 15% fetal bovine serum [FBS; Hyclone], 1 mM glutamine [Invitrogen], 1% nonessential amino acids [Invitrogen], and penicillin/streptomycin [Invitrogen]).
| | Sample_growth_protocol_ch1 | hiPS cell lines iPS A1, iPS C1, iPS4, iPS A6 (Hockemeyer et al. 2009); hiPS cell lines iPS PDB2lox-17, iPS PDB2lox-21, iPS PDB2lox-5, iPS PDB2lox-22, iPS PDB1lox-17puro-5, iPS PDB1lox-17puro-10, iPS PDB1lox-17puro-33, iPS PDB1lox-21puro-20, iPS PDB1lox-21puro-26, and iPS PDB1lox-21puro-28 (Soldner et al. 2009); hES cell lines BG01 and BG03 (National Institutes of Health code: BG01 and BG03; BresaGen, Inc., Athens, GA); hES cell lines WIBR1, WIBR2, WIBR3, and WIBR7 (Lengner et al., 2010; Whitehead Institute Center for Human Stem Cell Research) and hES cell line H9 (NIH Code:WA09, Wisconsin Alumni Research Foundation, Madison, WI) were maintained on mitomycin C-inactivated mouse embryonic fibroblast (MEF) feeder layers in hESC medium (DMEM/F12 [Invitrogen] supplemented with 15% FBS [Hyclone], 5% KnockOut Serum Replacement [Invitrogen], 1 mM glutamine [Invitrogen], 1% nonessential amino acids [Invitrogen], 0.1 mM β-mercaptoethanol [Sigma], and 4 ng/ml FGF2 [R&D Systems]). Cultures were passaged every 5 to 7 days either manually or enzymatically with collagenase type IV (Invitrogen; 1.5 mg/ml). hiPS cell lines were passaged 15-25 times prior to ChIP-Seq and gene expression analysis.
| | Sample_molecule_ch1 | polyA RNA
| | Sample_extract_protocol_ch1 | RNA was isolated from hES and hiPS cells, which were mechanically separated from feeder cells, with the RNeasy Mini Kit (QIAGEN).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | 5 µg total RNA was used to prepare biotinylated cRNA according to the manufacturer’s protocol (Affymetrix One Cycle cDNA Synthesis Kit). Briefly, this method involves SuperScript II-directed reverse transcription using a T7-Oligo-dT promoter primer to create first strand cDNA. RNase H-mediated second strand cDNA synthesis is followed by T7 RNA Polymerase directed in vitro transcription, which incorporates a biotinylated nucleotide during cRNA amplification.
| | Sample_hyb_protocol | Samples were prepared for hybridization using 15 µg biotinylated cRNA in a 1X hybridization cocktail with additional hybridization cocktail components provided in the GeneChip Hybridization, Wash and Stain Kit (Affymetrix). GeneChip arrays (Human U133 Plus 2.0) were hybridized in a GeneChip Hybridization Oven at 45 degrees C for 16 hours at 60 RPM. Washing was performed 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 using default settings.
| | Sample_data_processing | Images were extracted and analyzed using the default settings of GeneChip Operating Software v1.4.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Garrett,M,Frampton
| | Sample_contact_email | frampton@mit.edu
| | Sample_contact_laboratory | Richard Young
| | Sample_contact_department | Biology
| | Sample_contact_institute | Whitehead Instute - MIT
| | Sample_contact_address | 9 Cambridge Center
| | Sample_contact_city | Cambridge
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02142
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM574nnn/GSM574095/suppl/GSM574095.CEL.gz
| | Sample_series_id | GSE22499
| | Sample_series_id | GSE23402
| | Sample_data_row_count | 54675
| | |
|
GSM574096 | GPL570 |
|
hiPS_PDB2lox_21_rep1_120208_23
|
hiPS_PDB2lox_21
|
cell line: hiPS_PDB2lox_21
|
Gene expression data from hiPS_PDB2lox_21
|
| Sample_geo_accession | GSM574096
| | Sample_status | Public on Aug 09 2010
| | Sample_submission_date | Aug 03 2010
| | Sample_last_update_date | Sep 15 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | All primary human fibroblasts cells described in this paper (PDB-AG20442 and GM-M01660) were purchased from the Coriell Cell Repository (Camden, NJ). Fibroblasts were cultured in fibroblast medium (Dulbecco's modified Eagle's medium [DMEM] supplemented with 15% fetal bovine serum [FBS; Hyclone], 1 mM glutamine [Invitrogen], 1% nonessential amino acids [Invitrogen], and penicillin/streptomycin [Invitrogen]).
| | Sample_growth_protocol_ch1 | hiPS cell lines iPS A1, iPS C1, iPS4, iPS A6 (Hockemeyer et al. 2009); hiPS cell lines iPS PDB2lox-17, iPS PDB2lox-21, iPS PDB2lox-5, iPS PDB2lox-22, iPS PDB1lox-17puro-5, iPS PDB1lox-17puro-10, iPS PDB1lox-17puro-33, iPS PDB1lox-21puro-20, iPS PDB1lox-21puro-26, and iPS PDB1lox-21puro-28 (Soldner et al. 2009); hES cell lines BG01 and BG03 (National Institutes of Health code: BG01 and BG03; BresaGen, Inc., Athens, GA); hES cell lines WIBR1, WIBR2, WIBR3, and WIBR7 (Lengner et al., 2010; Whitehead Institute Center for Human Stem Cell Research) and hES cell line H9 (NIH Code:WA09, Wisconsin Alumni Research Foundation, Madison, WI) were maintained on mitomycin C-inactivated mouse embryonic fibroblast (MEF) feeder layers in hESC medium (DMEM/F12 [Invitrogen] supplemented with 15% FBS [Hyclone], 5% KnockOut Serum Replacement [Invitrogen], 1 mM glutamine [Invitrogen], 1% nonessential amino acids [Invitrogen], 0.1 mM β-mercaptoethanol [Sigma], and 4 ng/ml FGF2 [R&D Systems]). Cultures were passaged every 5 to 7 days either manually or enzymatically with collagenase type IV (Invitrogen; 1.5 mg/ml). hiPS cell lines were passaged 15-25 times prior to ChIP-Seq and gene expression analysis.
| | Sample_molecule_ch1 | polyA RNA
| | Sample_extract_protocol_ch1 | RNA was isolated from hES and hiPS cells, which were mechanically separated from feeder cells, with the RNeasy Mini Kit (QIAGEN).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | 5 µg total RNA was used to prepare biotinylated cRNA according to the manufacturer’s protocol (Affymetrix One Cycle cDNA Synthesis Kit). Briefly, this method involves SuperScript II-directed reverse transcription using a T7-Oligo-dT promoter primer to create first strand cDNA. RNase H-mediated second strand cDNA synthesis is followed by T7 RNA Polymerase directed in vitro transcription, which incorporates a biotinylated nucleotide during cRNA amplification.
| | Sample_hyb_protocol | Samples were prepared for hybridization using 15 µg biotinylated cRNA in a 1X hybridization cocktail with additional hybridization cocktail components provided in the GeneChip Hybridization, Wash and Stain Kit (Affymetrix). GeneChip arrays (Human U133 Plus 2.0) were hybridized in a GeneChip Hybridization Oven at 45 degrees C for 16 hours at 60 RPM. Washing was performed 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 using default settings.
| | Sample_data_processing | Images were extracted and analyzed using the default settings of GeneChip Operating Software v1.4.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Garrett,M,Frampton
| | Sample_contact_email | frampton@mit.edu
| | Sample_contact_laboratory | Richard Young
| | Sample_contact_department | Biology
| | Sample_contact_institute | Whitehead Instute - MIT
| | Sample_contact_address | 9 Cambridge Center
| | Sample_contact_city | Cambridge
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02142
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM574nnn/GSM574096/suppl/GSM574096.CEL.gz
| | Sample_series_id | GSE22499
| | Sample_series_id | GSE23402
| | Sample_data_row_count | 54675
| | |
|
GSM574097 | GPL570 |
|
hiPS_PDB2lox_21_rep2_090811_10
|
hiPS_PDB2lox_21
|
cell line: hiPS_PDB2lox_21
|
Gene expression data from hiPS_PDB2lox_21
|
| Sample_geo_accession | GSM574097
| | Sample_status | Public on Aug 09 2010
| | Sample_submission_date | Aug 03 2010
| | Sample_last_update_date | Sep 15 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | All primary human fibroblasts cells described in this paper (PDB-AG20442 and GM-M01660) were purchased from the Coriell Cell Repository (Camden, NJ). Fibroblasts were cultured in fibroblast medium (Dulbecco's modified Eagle's medium [DMEM] supplemented with 15% fetal bovine serum [FBS; Hyclone], 1 mM glutamine [Invitrogen], 1% nonessential amino acids [Invitrogen], and penicillin/streptomycin [Invitrogen]).
| | Sample_growth_protocol_ch1 | hiPS cell lines iPS A1, iPS C1, iPS4, iPS A6 (Hockemeyer et al. 2009); hiPS cell lines iPS PDB2lox-17, iPS PDB2lox-21, iPS PDB2lox-5, iPS PDB2lox-22, iPS PDB1lox-17puro-5, iPS PDB1lox-17puro-10, iPS PDB1lox-17puro-33, iPS PDB1lox-21puro-20, iPS PDB1lox-21puro-26, and iPS PDB1lox-21puro-28 (Soldner et al. 2009); hES cell lines BG01 and BG03 (National Institutes of Health code: BG01 and BG03; BresaGen, Inc., Athens, GA); hES cell lines WIBR1, WIBR2, WIBR3, and WIBR7 (Lengner et al., 2010; Whitehead Institute Center for Human Stem Cell Research) and hES cell line H9 (NIH Code:WA09, Wisconsin Alumni Research Foundation, Madison, WI) were maintained on mitomycin C-inactivated mouse embryonic fibroblast (MEF) feeder layers in hESC medium (DMEM/F12 [Invitrogen] supplemented with 15% FBS [Hyclone], 5% KnockOut Serum Replacement [Invitrogen], 1 mM glutamine [Invitrogen], 1% nonessential amino acids [Invitrogen], 0.1 mM β-mercaptoethanol [Sigma], and 4 ng/ml FGF2 [R&D Systems]). Cultures were passaged every 5 to 7 days either manually or enzymatically with collagenase type IV (Invitrogen; 1.5 mg/ml). hiPS cell lines were passaged 15-25 times prior to ChIP-Seq and gene expression analysis.
| | Sample_molecule_ch1 | polyA RNA
| | Sample_extract_protocol_ch1 | RNA was isolated from hES and hiPS cells, which were mechanically separated from feeder cells, with the RNeasy Mini Kit (QIAGEN).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | 5 µg total RNA was used to prepare biotinylated cRNA according to the manufacturer’s protocol (Affymetrix One Cycle cDNA Synthesis Kit). Briefly, this method involves SuperScript II-directed reverse transcription using a T7-Oligo-dT promoter primer to create first strand cDNA. RNase H-mediated second strand cDNA synthesis is followed by T7 RNA Polymerase directed in vitro transcription, which incorporates a biotinylated nucleotide during cRNA amplification.
| | Sample_hyb_protocol | Samples were prepared for hybridization using 15 µg biotinylated cRNA in a 1X hybridization cocktail with additional hybridization cocktail components provided in the GeneChip Hybridization, Wash and Stain Kit (Affymetrix). GeneChip arrays (Human U133 Plus 2.0) were hybridized in a GeneChip Hybridization Oven at 45 degrees C for 16 hours at 60 RPM. Washing was performed 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 using default settings.
| | Sample_data_processing | Images were extracted and analyzed using the default settings of GeneChip Operating Software v1.4.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Garrett,M,Frampton
| | Sample_contact_email | frampton@mit.edu
| | Sample_contact_laboratory | Richard Young
| | Sample_contact_department | Biology
| | Sample_contact_institute | Whitehead Instute - MIT
| | Sample_contact_address | 9 Cambridge Center
| | Sample_contact_city | Cambridge
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02142
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM574nnn/GSM574097/suppl/GSM574097.CEL.gz
| | Sample_series_id | GSE22499
| | Sample_series_id | GSE23402
| | Sample_data_row_count | 54675
| | |
|
GSM574098 | GPL570 |
|
hiPS_PDB2lox_22_rep1_120208_25
|
hiPS_PDB2lox_22
|
cell line: hiPS_PDB2lox_22
|
Gene expression data from hiPS_PDB2lox_22
|
| Sample_geo_accession | GSM574098
| | Sample_status | Public on Aug 09 2010
| | Sample_submission_date | Aug 03 2010
| | Sample_last_update_date | Sep 15 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | All primary human fibroblasts cells described in this paper (PDB-AG20442 and GM-M01660) were purchased from the Coriell Cell Repository (Camden, NJ). Fibroblasts were cultured in fibroblast medium (Dulbecco's modified Eagle's medium [DMEM] supplemented with 15% fetal bovine serum [FBS; Hyclone], 1 mM glutamine [Invitrogen], 1% nonessential amino acids [Invitrogen], and penicillin/streptomycin [Invitrogen]).
| | Sample_growth_protocol_ch1 | hiPS cell lines iPS A1, iPS C1, iPS4, iPS A6 (Hockemeyer et al. 2009); hiPS cell lines iPS PDB2lox-17, iPS PDB2lox-21, iPS PDB2lox-5, iPS PDB2lox-22, iPS PDB1lox-17puro-5, iPS PDB1lox-17puro-10, iPS PDB1lox-17puro-33, iPS PDB1lox-21puro-20, iPS PDB1lox-21puro-26, and iPS PDB1lox-21puro-28 (Soldner et al. 2009); hES cell lines BG01 and BG03 (National Institutes of Health code: BG01 and BG03; BresaGen, Inc., Athens, GA); hES cell lines WIBR1, WIBR2, WIBR3, and WIBR7 (Lengner et al., 2010; Whitehead Institute Center for Human Stem Cell Research) and hES cell line H9 (NIH Code:WA09, Wisconsin Alumni Research Foundation, Madison, WI) were maintained on mitomycin C-inactivated mouse embryonic fibroblast (MEF) feeder layers in hESC medium (DMEM/F12 [Invitrogen] supplemented with 15% FBS [Hyclone], 5% KnockOut Serum Replacement [Invitrogen], 1 mM glutamine [Invitrogen], 1% nonessential amino acids [Invitrogen], 0.1 mM β-mercaptoethanol [Sigma], and 4 ng/ml FGF2 [R&D Systems]). Cultures were passaged every 5 to 7 days either manually or enzymatically with collagenase type IV (Invitrogen; 1.5 mg/ml). hiPS cell lines were passaged 15-25 times prior to ChIP-Seq and gene expression analysis.
| | Sample_molecule_ch1 | polyA RNA
| | Sample_extract_protocol_ch1 | RNA was isolated from hES and hiPS cells, which were mechanically separated from feeder cells, with the RNeasy Mini Kit (QIAGEN).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | 5 µg total RNA was used to prepare biotinylated cRNA according to the manufacturer’s protocol (Affymetrix One Cycle cDNA Synthesis Kit). Briefly, this method involves SuperScript II-directed reverse transcription using a T7-Oligo-dT promoter primer to create first strand cDNA. RNase H-mediated second strand cDNA synthesis is followed by T7 RNA Polymerase directed in vitro transcription, which incorporates a biotinylated nucleotide during cRNA amplification.
| | Sample_hyb_protocol | Samples were prepared for hybridization using 15 µg biotinylated cRNA in a 1X hybridization cocktail with additional hybridization cocktail components provided in the GeneChip Hybridization, Wash and Stain Kit (Affymetrix). GeneChip arrays (Human U133 Plus 2.0) were hybridized in a GeneChip Hybridization Oven at 45 degrees C for 16 hours at 60 RPM. Washing was performed 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 using default settings.
| | Sample_data_processing | Images were extracted and analyzed using the default settings of GeneChip Operating Software v1.4.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Garrett,M,Frampton
| | Sample_contact_email | frampton@mit.edu
| | Sample_contact_laboratory | Richard Young
| | Sample_contact_department | Biology
| | Sample_contact_institute | Whitehead Instute - MIT
| | Sample_contact_address | 9 Cambridge Center
| | Sample_contact_city | Cambridge
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02142
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM574nnn/GSM574098/suppl/GSM574098.CEL.gz
| | Sample_series_id | GSE22499
| | Sample_series_id | GSE23402
| | Sample_data_row_count | 54675
| | |
|
GSM574099 | GPL570 |
|
hiPS_PDB2lox_5_rep1_120208_19
|
hiPS_PDB2lox_5
|
cell line: hiPS_PDB2lox_5
|
Gene expression data from hiPS_PDB2lox_5
|
| Sample_geo_accession | GSM574099
| | Sample_status | Public on Aug 09 2010
| | Sample_submission_date | Aug 03 2010
| | Sample_last_update_date | Sep 15 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | All primary human fibroblasts cells described in this paper (PDB-AG20442 and GM-M01660) were purchased from the Coriell Cell Repository (Camden, NJ). Fibroblasts were cultured in fibroblast medium (Dulbecco's modified Eagle's medium [DMEM] supplemented with 15% fetal bovine serum [FBS; Hyclone], 1 mM glutamine [Invitrogen], 1% nonessential amino acids [Invitrogen], and penicillin/streptomycin [Invitrogen]).
| | Sample_growth_protocol_ch1 | hiPS cell lines iPS A1, iPS C1, iPS4, iPS A6 (Hockemeyer et al. 2009); hiPS cell lines iPS PDB2lox-17, iPS PDB2lox-21, iPS PDB2lox-5, iPS PDB2lox-22, iPS PDB1lox-17puro-5, iPS PDB1lox-17puro-10, iPS PDB1lox-17puro-33, iPS PDB1lox-21puro-20, iPS PDB1lox-21puro-26, and iPS PDB1lox-21puro-28 (Soldner et al. 2009); hES cell lines BG01 and BG03 (National Institutes of Health code: BG01 and BG03; BresaGen, Inc., Athens, GA); hES cell lines WIBR1, WIBR2, WIBR3, and WIBR7 (Lengner et al., 2010; Whitehead Institute Center for Human Stem Cell Research) and hES cell line H9 (NIH Code:WA09, Wisconsin Alumni Research Foundation, Madison, WI) were maintained on mitomycin C-inactivated mouse embryonic fibroblast (MEF) feeder layers in hESC medium (DMEM/F12 [Invitrogen] supplemented with 15% FBS [Hyclone], 5% KnockOut Serum Replacement [Invitrogen], 1 mM glutamine [Invitrogen], 1% nonessential amino acids [Invitrogen], 0.1 mM β-mercaptoethanol [Sigma], and 4 ng/ml FGF2 [R&D Systems]). Cultures were passaged every 5 to 7 days either manually or enzymatically with collagenase type IV (Invitrogen; 1.5 mg/ml). hiPS cell lines were passaged 15-25 times prior to ChIP-Seq and gene expression analysis.
| | Sample_molecule_ch1 | polyA RNA
| | Sample_extract_protocol_ch1 | RNA was isolated from hES and hiPS cells, which were mechanically separated from feeder cells, with the RNeasy Mini Kit (QIAGEN).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | 5 µg total RNA was used to prepare biotinylated cRNA according to the manufacturer’s protocol (Affymetrix One Cycle cDNA Synthesis Kit). Briefly, this method involves SuperScript II-directed reverse transcription using a T7-Oligo-dT promoter primer to create first strand cDNA. RNase H-mediated second strand cDNA synthesis is followed by T7 RNA Polymerase directed in vitro transcription, which incorporates a biotinylated nucleotide during cRNA amplification.
| | Sample_hyb_protocol | Samples were prepared for hybridization using 15 µg biotinylated cRNA in a 1X hybridization cocktail with additional hybridization cocktail components provided in the GeneChip Hybridization, Wash and Stain Kit (Affymetrix). GeneChip arrays (Human U133 Plus 2.0) were hybridized in a GeneChip Hybridization Oven at 45 degrees C for 16 hours at 60 RPM. Washing was performed 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 using default settings.
| | Sample_data_processing | Images were extracted and analyzed using the default settings of GeneChip Operating Software v1.4.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Garrett,M,Frampton
| | Sample_contact_email | frampton@mit.edu
| | Sample_contact_laboratory | Richard Young
| | Sample_contact_department | Biology
| | Sample_contact_institute | Whitehead Instute - MIT
| | Sample_contact_address | 9 Cambridge Center
| | Sample_contact_city | Cambridge
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02142
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM574nnn/GSM574099/suppl/GSM574099.CEL.gz
| | Sample_series_id | GSE22499
| | Sample_series_id | GSE23402
| | Sample_data_row_count | 54675
| | |
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