|
| Status |
Public on Jul 01, 2012 |
| Title |
RenLab-HiC-cortex_replicate two |
| Sample type |
SRA |
| |
|
| Source name |
Mouse cortex
|
| 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 |
Cortex 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).) with modifications for tissue samples. In brief, cortex from 8-week old male C57Bl/6 mice were dissected, minced and fixed with 1% formaldehyde for 20 minutes at room temperature. After fixation, samples were homogenized and counted for cell numbers with Trypan Blue.
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
equivalent to Sample GSM892305
|
| Data processing |
fastq: Illumina's HiSeq Control Software
hic.summary.txt:The paired-end Hi-C reads were mapped to mouse genome build mm9 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.gz: mm9
|
| |
|
| Submission date |
May 29, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Bing Ren |
| E-mail(s) |
biren@ucsd.edu
|
| Organization name |
University of California, San Diego
|
| Street address |
9500 Gilman Drive
|
| City |
La Jolla |
| State/province |
CA |
| ZIP/Postal code |
92093 |
| Country |
USA |
| |
|
| Platform ID |
GPL13112 |
| Series (2) |
| GSE29184 |
A draft map of cis-regulatory sequences in the mouse genome |
| GSE34587 |
A draft map of cis-regulatory sequences in the mouse genome [HiC] |
|
| Relations |
| Reanalyzed by |
GSE87112 |
| SRA |
SRX150197 |
| BioSample |
SAMN00998882 |
