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Sample GSM862720 Query DataSets for GSM862720
Status Public on Apr 10, 2012
Title RenLab-HiC-mESC-HindIII, replicate one
Sample type SRA
 
Source name Mouse ES
Organism Mus musculus
Characteristics strain: 129S4/SvJae
cell line: mESC line J1
restriction enzyme: HindIII
Treatment protocol None
Growth protocol mESC line J1 was maintained on mitomycin C-inactivated MEF feeder layers in DME containing 15% fetal calf serum, leukemia inhibiting factor, penicillin/streptomycin, L-glutamine and non-essential amino acids. All ES cells were passaged on 0.2 % gelatin twice to deplete feeder cells before harvest for experiments. H1 and IMR90 cells were grown as described in: Hawkins, R.D. et al. Distinct epigenomic landscapes of pluripotent and lineage-committed human cells. Cell Stem Cell 6, 479-91
Extracted molecule genomic DNA
Extraction protocol Hi-C experiment were conducted in biological replicates using HindIII according to previous publication (Lieberman-Aiden, E. et al. Comprehensive mapping of long-range interactions reveals folding principles of the human genome. Science 326, 289-93 (2009).).
 
Library strategy OTHER
Library source genomic
Library selection other
Instrument model Illumina HiSeq 2000
 
Data processing fastq: Illumina's HiSeq Control Software
hic.summary.txt:The paired-end Hi-C reads were mapped to mouse genome build mm9 and human genome hg18 using an in-house pipeline based on BWA using default parameter. BWA SAMPE was used to merged the pairs. Duplicated reads from the same biological library were removed.
Genome Build:
J1_mESC_HindIII_ori_HiC.nodup.summary.txt: mm9
 
Submission date Jan 17, 2012
Last update date Jan 25, 2019
Contact name Feng Yue
E-mail fyue@ucsd.edu
Organization name Ludwig Institue for Cancer Research
Street address 9500 Gilman Dr.
City La Jolla
State/province CA
ZIP/Postal code 92093
Country USA
 
Platform ID GPL13112
Series (2)
GSE35156 Conserved Topological Domains in Mammalian Genomes Identified by High-resolution Analysis of Chromatin Interactions
GSE51334 DNA replication-timing boundaries separate stable chromosome domains with cell-type-specific functions
Relations
Reanalyzed by GSE87112
Reanalyzed by GSE101715
SRA SRX116341
BioSample SAMN00773751

Supplementary data files not provided
Raw data provided as supplementary file
Processed data is available on Series record

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