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Sample GSM4221052 Query DataSets for GSM4221052
Status Public on Dec 17, 2019
Title PH_WGBS_rep1
Sample type SRA
 
Source name HUES 8 hESC line
Organism Homo sapiens
Characteristics cell line: HUES 8 hESC line
cell type: hPSC-derived poly-hormonal cell
Stage: Stage 6 day 15
Growth protocol Undifferentiated stem cells were maintained as aggregates in supplemented mTeSR1 medium (StemCell Technologies) using spinner flasks (Corning) set at a 70rpm rotation rate in a 37ÂșC 5% CO2 incubator. Directed hPSC differentiation into islet cells was conducted as described in the methods of (Alvarez-Dominguez et al. 2019).
Extracted molecule genomic DNA
Extraction protocol DNA was fragmented with a Covaris S2 sonicator for 6min, purified using the DNA Clean and Concentrator kit (Zymo Research), and bisulfite conversion was performed using the EZ DNA Methylation-Gold kit (Zymo Research).
Sequencing libraries were generated using the Accel-NGS Methyl-Seq DNA library kit (Swift Biosciences), pooled, and sequenced on a HiSeq 4000 instrument.
 
Library strategy Bisulfite-Seq
Library source genomic
Library selection RANDOM
Instrument model Illumina HiSeq 4000
 
Data processing Sequencing reads were mapped to the human hg19 reference genome assembly using BSMap (Xi and Li, 2009) in bisulfite mode with default parameters. CpG methylation was called as described in (Ziller et al., 2013), excluding low-quality, duplicate, and >10%-mismatched reads.
Genome_build: hg19
Supplementary_files_format_and_content: bed. Column headers are: Chr, Start, End, methylatedCpG/TotalCpG, Score, Strand
 
Submission date Dec 16, 2019
Last update date Dec 17, 2019
Contact name Juan R Alvarez-Dominguez
Organization name Harvard University
Department Stem Cell and Regenerative Biology
Street address 7 Divinity Ave
City Cambridge
State/province MA
ZIP/Postal code 02138
Country USA
 
Platform ID GPL20301
Series (2)
GSE139817 Chromatin dynamics reveal circadian control of human in vitro islet maturation
GSE140501 Chromatin dynamics reveal circadian control of human in vitro islet maturation [WGBS]
Relations
BioSample SAMN13575116
SRA SRX7388218

Supplementary file Size Download File type/resource
GSM4221052_PH_WGBS_rep1.bb 250.7 Mb (ftp)(http) BB
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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