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| Status |
Public on Dec 17, 2019 |
| Title |
SCbeta_WGBS_rep1 |
| Sample type |
SRA |
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| Source name |
HUES 8 hESC line
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| Organism |
Homo sapiens |
| Characteristics |
cell line: HUES 8 hESC line
cell type: hPSC-derived beta cell
Stage: Stage 6 day 15
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| 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 37ºC 5% CO2 incubator. Directed hPSC differentiation into islet cells was conducted as described in the methods of (Alvarez-Dominguez et al. 2019).
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| 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.
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| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
RANDOM |
| Instrument model |
Illumina HiSeq 4000 |
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| 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
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| Submission date |
Dec 16, 2019 |
| Last update date |
Dec 17, 2019 |
| Contact name |
Juan R Alvarez-Dominguez |
| Organization name |
Harvard University
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| Department |
Stem Cell and Regenerative Biology
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| Street address |
7 Divinity Ave
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| City |
Cambridge |
| State/province |
MA |
| ZIP/Postal code |
02138 |
| Country |
USA |
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| 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] |
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| Relations |
| BioSample |
SAMN13575117 |
| SRA |
SRX7388217 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4221051_SCbeta_WGBS_rep1.bb |
239.9 Mb |
(ftp)(http) |
BB |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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