|
Status |
Public on Apr 10, 2012 |
Title |
RenLab-HiC-IMR90, replicate two |
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_replicate.nodup.hic.summary.txt: hg18
|
|
|
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 |
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 |
SRX128222 |
BioSample |
SAMN00810007 |