NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM862724 Query DataSets for GSM862724
Status Public on Apr 10, 2012
Title RenLab-HiC-IMR90, replicate one
Sample type SRA
 
Source name Human IMR90
Organism Homo sapiens
Characteristics cell line: IMR90 fetal lung fibroblast cell line
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:
IMR90_HindIII_HiC.nodup.summary.txt: hg18
 
Submission date Jan 17, 2012
Last update date May 23, 2013
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 GPL11154
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
SRA SRX116345
BioSample SAMN00773755

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

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