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Sample GSM2515902 Query DataSets for GSM2515902
Status Public on Apr 26, 2017
Title human pluripotent stem cells, naïve, control, 2
Sample type genomic
 
Source name human pluripotent stem cells
Organism Homo sapiens
Characteristics cell type: human pluripotent stem cells, naïve
shRNA: control
Growth protocol Human induced pluripotent stem cells were cultured on Matrigel [BD Biosciences] in MEF conditioned medium (MEF-CM) supplemented with 8 ng/ml bFGF [Invitrogen] or maintained on irradiated feeder MEFs (iMEFs) with hPSC medium (DMEM/F12 [Gibco] with 20% Knockout Serum Replacement [Gibco], 100 mM b-mercaptoethanol, 100 mM nonessential amino acid [Gibco], 1 mM L-glutamine [Gibco], and 10 ng/ml bFGF, as previously described (Werbowetski-Ogilvie et al., 2009). Cells were routinely passaged every 5-7 days by mechanical transfer using 1 mg/ml Collagenase IV [Invitrogen]. For the derivation of naïve hPSCs, cells in primed pluripotent states were switched into hPSC medium supplemented with 1 mM MEK inhibitor PD0325901, 3 mM GSK3 inhibitor CHIR99021, and 10 ng/ml LIF (abbreviated LIF/2i) as previously reported (Buecker et al., 2010; Hanna et al., 2010; Li et al., 2009) or de novo reprogramming of somatic cells in naïve conditions. We also established naïve hPSCs using 10 ng/ml LIF and a combination of inhibitors for MEK/ERK (1 mM PD0325901), GSK3 (0.3 mM CHIR99021), LCF/SRC (1 mM WH-4-023), BRAF (0.5 mM SB590885) and ROCK (10 mM Y-27632) (5i)(Theunissen et al., 2014). Emerging colonies with a mESC-like morphology (appeared after 10-20 days of culture) were individually picked and subcultured by trypsinization or mechanical passaging onto feeder-free Matrigel or iMEFs with LIF/2i
Extracted molecule genomic DNA
Extraction protocol genomic DNA was extracted and purified from samples using Qiagen Dneasy Blood and Tissue Kit according to standard instructions
Label Cy5 and Cy3
Label protocol Standard Illumina Protocol
 
Hybridization protocol bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Human MethylationEpic Beadchip using standard Illumina protocol
Scan protocol Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting
Description hPSC_LIF2i_shCTRL-2
Data processing Partek Genomics Suite 6.6 methylation workflow
 
Submission date Feb 28, 2017
Last update date Apr 28, 2017
Contact name Mickie Bhatia
E-mail(s) mbhatia@mcmaster.ca
Organization name McMaster University
Department Stem Cell and Cancer Research Institute (SCC-RI)
Street address 1200 Main Street West
City Hamilton
State/province Ontario
ZIP/Postal code L8N 3Z5
Country Canada
 
Platform ID GPL21145
Series (2)
GSE95505 Lineage specific differentiation is influenced by state of human pluripotency
GSE95531 Lineage specific differentiation is influenced by state of human pluripotency [methylation]

Data table header descriptions
ID_REF
VALUE Normalized (SWAN Normalization) Beta values

Data table
ID_REF VALUE
cg09835024 0.0311757
cg14361672 0.716467
cg12950382 0.896008
cg02115394 0.156133
cg12480843 0.0429394
cg26724186 0.866007
cg00617867 0.957512
cg13773083 0.378427
cg17236668 0.945996
cg19607165 0.189149
cg08770523 0.0376238
cg24040570 0.0629811
cg24652288 0.870178
cg09387925 0.037878
cg01675618 0.0335181
cg11947782 0.90154
cg11945228 0.0317248
cg21650422 0.017754
cg08360726 0.0594225
cg05738196 0.104036

Total number of rows: 867867

Table truncated, full table size 17019 Kbytes.




Supplementary file Size Download File type/resource
GSM2515902_200526580002_R04C01_Grn.idat.gz 7.0 Mb (ftp)(http) IDAT
GSM2515902_200526580002_R04C01_Red.idat.gz 7.1 Mb (ftp)(http) IDAT
Processed data included within Sample table

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