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Sample GSM4171645 Query DataSets for GSM4171645
Status Public on Nov 16, 2019
Title in_vitro-matured_SCbeta_ATAC_72h
Sample type SRA
Source name HUES 8 hESC line
Organism Homo sapiens
Characteristics cell line: HUES 8 hESC line
cell type: hPSC-derived beta cell
Stage: entrained to circadian metabolic rhythms
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).
Extracted molecule genomic DNA
Extraction protocol Live cells (typically ~50,000) were pelleted and tagmentation was performed at 37ºC for 30min as described in (Buenrostro et al., 2013). Briefly, cell pellets were resuspended in buffer containing Tn5 Transposase (Nextera DNA Sample Preparation kit; Illumina), incubated at 37ºC for 30min, and DNA was isolated using the MinElute PCR purification kit (Qiagen).
Tagmented DNA was PCR-amplified for 10 cycles and purified using AMPure XP magnetic beads (Beckman Coulter). Double-sided AMPure cleanup to remove high-molecular-weight fragments was conducted by incubation of double-concentrated AMPure beads added at 0.55x volume to the PCR reactions, followed by cleanup with a 1x AMPure volume. Sequencing libraries were pooled and sequenced on a HiSeq 2500 instrument.
Library strategy ATAC-seq
Library source genomic
Library selection other
Instrument model Illumina HiSeq 2500
Data processing Sequencing reads were mapped to the human hg19 reference genome assembly using bowtie2 (Langmead and Salzberg, 2012) with default parameters. Peak calling was performed using MACS2 (Zhang et al., 2008) with default parameters, “--nomodel --shift 37 --extsize 73” to bypass building a ChIP-based shifting model and instead shift read 5’-ends and extend in the 5'->3' direction by a half-nucleosome size (73bp), and “--broad --qvalue 0.01” to composite broad regions of read enrichment with a minimum FDR q-value cutoff of 0.01.
Genome_build: hg19
Supplementary_files_format_and_content: Tab delimited file with peak coordinates
Submission date Nov 15, 2019
Last update date Nov 20, 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 GPL16791
Series (2)
GSE139817 Chromatin dynamics reveal circadian control of human in vitro islet maturation
GSE140499 Chromatin dynamics reveal circadian control of human in vitro islet maturation [ATAC-seq]
BioSample SAMN13293868
SRA SRX7157627

Supplementary file Size Download File type/resource
GSM4171645_in_vitro-matured_SCbeta_ATAC_72h.peaks.bed.gz 1.8 Mb (ftp)(http) BED
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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