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Sample GSM2203842 Query DataSets for GSM2203842
Status Public on Jul 12, 2017
Title Hi-C 500 mESCs rep2
Sample type SRA
Source name Embryonic stem cell
Organism Mus musculus
Characteristics strain: R1
developmental stage: Embryonic stem cell
Growth protocol mESCs were cultured routinely in LIF and serum medium.
Extracted molecule genomic DNA
Extraction protocol HiC libraries were prepared using in situ Hi-C developed by Rao et al. with some modification
Library strategy OTHER
Library source genomic
Library selection other
Instrument model HiSeq X Ten
Description mESC_500_rep12_allValidPairs.txt
Data processing Library strategy: HiC-Seq
Basecalls performed using CASAVA version 1.8
Hi-C reads are processed using HiCPro version2.7.1b and replicates of same stage were pooled together
Compartment analysis are done as previously described. (Dixon et al., 2015)
TAD calling is done using Insulation score method as previously described ( Crane et al., 2015)
Genome_build: mm9
Supplementary_files_format_and_content: The files including all the valid interaction pairs ( described as Servant et al., 2015). The valid pairs are stored using a simple tab-delimited text format ; read name / chr_reads1 / pos_reads1 / strand_reads1 / chr_reads2 / pos_reads2 / strand_reads2 / fragment_size [/ allele_specific_tag]
Submission date Jun 16, 2016
Last update date May 15, 2019
Contact name Zhenhai Du
Organization name Tsinghua University
Street address Qinghua Yuan, Haidian District
City Beijing
ZIP/Postal code 100084
Country China
Platform ID GPL21273
Series (1)
GSE82185 Allelic reprogramming of 3D chromatin architecture during early mammalian development
BioSample SAMN05258675
SRA SRX1853318

Supplementary file Size Download File type/resource
GSM2203842_mESC_500_rep2_allValidPairs.txt.gz 1.2 Gb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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