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Sample GSM2309023 Query DataSets for GSM2309023
Status Public on Mar 23, 2017
Title HiC_hESC
Sample type SRA
 
Source name Human Embryonic Stem Cells
Organism Homo sapiens
Characteristics cell line: H9 ESC
cell type: Human Embryonic Stem Cells
Growth protocol Human ESC (H9/WA09; obtained from WiCell) were cultured at 37°C in 5% CO2 in air in Pluripro media and matrix (Cell Guidance Systems). ESC were routinely verified as mycoplasma-free using a PCR-based assay. ESC were differentiated into NEC using a previously described protocol (Rada-Iglesias, A. Nature 470, 279–283 (2011)) and samples were harvested on day 7.
Extracted molecule genomic DNA
Extraction protocol DNA was extracted as described in Wilson, N.K. et al., Blood 127, e12–e23 (2016).
Hi-C and PCHi-C libraries were generated as described in Wilson, N.K. et al., Blood 127, e12–e23 (2016). For PCHi-C, ligation products containing promoter sequences were captured using a custom-made RNA capture bait system (SureSelect Target Enrichment, Agilent Technologies) designed as previously described in Mifsud, B. et al. Nat. Genet. 47, 598–606 (2015), and containing 37,608 biotinylated RNAs targeting 22,076 HindIII restriction fragment ends. Libraries were paired-end sequenced on an Illumina HiSeq 1000 machine at the Babraham Institute Sequencing Facility.
 
Library strategy OTHER
Library source genomic
Library selection other
Instrument model Illumina HiSeq 2000
 
Data processing Library strategy: Hi-C-seq
Standard Illumina base-calling pipeline.
PCHi-C/Hi-C reads were mapped and filtered with HiCUP (v0.4.2) and Bowtie(v1.0.0). Significant interactions were called with CHiCAGO(v0.1.4). RNA-Seq mapping was performed with TopHat (v2.0.8b).
Genome_build: Hg19
Supplementary_files_format_and_content: Hi-C interaction file (Tabix format); RNA-Seq raw counts per gene
 
Submission date Sep 12, 2016
Last update date May 15, 2019
Contact name Steven William Wingett
E-mail(s) steven.wingett@babraham.ac.uk
Organization name Babraham Institute
Department Bioinformatics
Street address Babraham Research Park
City Cambridge
State/province Cambs
ZIP/Postal code CB22 3AT
Country United Kingdom
 
Platform ID GPL11154
Series (1)
GSE86821 Global rewiring of cis-regulatory units upon lineage commitment of human embryonic stem cells
Relations
BioSample SAMN05762671
SRA SRX2159278

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data not provided for this record

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