|
| Status |
Public on Aug 24, 2017 |
| Title |
CAPTURE-3C-seq_K562_sgHS2-rep3 |
| Sample type |
SRA |
| |
|
| Source name |
Human K562 cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: K562
streptavidin dynabeads: ThermoFisher 65602
|
| Growth protocol |
Human K562 cells were cultured in IMDM supplemented with 10% heat-inactivated fetal bovine serum (FBS) and 2% penicillin-streptomycin. KH2 cells were cultured on primary embryonic fibroblasts in standard ES medium and differentiated to EBs by LIF withdrawal for 8 days.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
For 3C-seq analysis using the Illumina NextSeq500, 10-20 ng of 3C DNA was processed for library generation using the NEBNext ChIP-seq Library Prep Master Mix following the manufacturer’s protocol (New England Biolabs). Raw reads that aligned to exactly one location in the reference human genome (hg19) were retained for downstream data analysis.
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
Processed data file: CAPTURE-3C-seq_K562_sgHS2-combined_interaction.txt
|
| Data processing |
Library strategy: 3C-seq
Sequencing reads were aligned to human genome assembly hg19 (NCBI version 37) using Bowtie2 v2.2.8 with default parameters. The reads with low mapping qualit and duplicate reads were removed after the aligment with the Picard command-line tools.
After preprocessing and filtering, we generated the list of count numbers of read pairs from the bait region to any chromosomal regions. A pair of reads that located within two different regions is considered an interaction between them.
The interaction significance between the bait region and another chromosomal region was calculated by a Bayesian-Mixture Model. The PETs from bait region to any chromosomal regions were reported in Pairwise interaction format (http://wiki.wubrowse.org/Long-range).
Genome_build: hg19
Supplementary_files_format_and_content: Pairwise Interaction Format
|
| |
|
| Submission date |
May 22, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Jian Xu |
| E-mail(s) |
Jian.Xu@UTSouthwestern.edu
|
| Phone |
214-648-6125
|
| Organization name |
UT Southwestern Medical Center
|
| Department |
Children's Research Institute
|
| Street address |
6000 Harry Hines Blvd. NL12.138B
|
| City |
Dallas |
| State/province |
TX |
| ZIP/Postal code |
75235 |
| Country |
USA |
| |
|
| Platform ID |
GPL18573 |
| Series (2) |
| GSE88817 |
In situ CAPTURE of chromatin interactions by biotinylated dCas9 |
| GSE99174 |
CAPTURE-3C-seq analysis of cis-element-mediated long-range DNA interactions |
|
| Relations |
| BioSample |
SAMN07152426 |
| SRA |
SRX2841232 |
