|
| Status |
Public on Jul 12, 2017 |
| Title |
Hi-C 500 mESCs rep2 |
| Sample type |
SRA |
| |
|
| Source name |
Embryonic stem cell
|
| Organism |
Mus musculus |
| Characteristics |
strain: R1
developmental stage: Embryonic stem cell
|
| Growth protocol |
mESCs were cultured routinely in LIF and serum medium.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
HiC libraries were prepared using in situ Hi-C developed by Rao et al. with some modification
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
HiSeq X Ten |
| |
|
| Description |
mESC_500_rep12_allValidPairs.txt
|
| Data processing |
Library strategy: HiC-Seq
Basecalls performed using CASAVA version 1.8
Hi-C reads are processed using HiCPro version2.7.1b and replicates of same stage were pooled together
Compartment analysis are done as previously described. (Dixon et al., 2015)
TAD calling is done using Insulation score method as previously described ( Crane et al., 2015)
Genome_build: mm9
Supplementary_files_format_and_content: The files including all the valid interaction pairs ( described as Servant et al., 2015). The valid pairs are stored using a simple tab-delimited text format ; read name / chr_reads1 / pos_reads1 / strand_reads1 / chr_reads2 / pos_reads2 / strand_reads2 / fragment_size [/ allele_specific_tag]
|
| |
|
| Submission date |
Jun 16, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Zhenhai Du |
| E-mail(s) |
duzhenhai93220@gmail.com
|
| Organization name |
Tsinghua University
|
| Street address |
Qinghua Yuan, Haidian District
|
| City |
Beijing |
| ZIP/Postal code |
100084 |
| Country |
China |
| |
|
| Platform ID |
GPL21273 |
| Series (1) |
| GSE82185 |
Allelic reprogramming of 3D chromatin architecture during early mammalian development |
|
| Relations |
| BioSample |
SAMN05258675 |
| SRA |
SRX1853318 |
