NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM892305 Query DataSets for GSM892305
Status Public on Apr 10, 2012
Title RenLab-HiC-cortex, replicate two
Sample type SRA
 
Source name Mouse ES
Organism Mus musculus
Characteristics strain: C57Bl/6
tissue: cortex
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
 
Description equivalent to Sample GSM938751
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:
cortex_HindIII_replicate_Hic.nodup.hic.summary.txt: mm9
 
Submission date Mar 09, 2012
Last update date May 15, 2019
Contact name Feng Yue
E-mail(s) 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 (1)
GSE35156 Conserved Topological Domains in Mammalian Genomes Identified by High-resolution Analysis of Chromatin Interactions
Relations
SRA SRX128220
BioSample SAMN00810005

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap