|
| Status |
Public on Feb 20, 2020 |
| Title |
CAPTURE-3C-seq_K562_sgHS1-5_rep1 |
| Sample type |
SRA |
| |
|
| Source name |
Human K562 cells
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Human K562 cells
streptavidin dynabeads: ThermoFisher 65602
|
| Treatment protocol |
G1E-ER4 cells were treated with 10-7 M β-estradiol to induce erythroid differentiation.
|
| Growth protocol |
Human K562 cells were cultured in IMDM supplemented with 10% heat-inactivated fetal bovine serum (FBS). G1E-ER4 cells were cultured in IMDM medium containing 15% FBS, 50 ng/mL recombinant SCF, and 2 U/ml recombinant human erythropoietin (EPO).
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
For 3C-seq analysis using the Illumina NextSeq500, 10 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 |
CAPTURE-3C-seq_K562_sgHS1-5_combined_interaction
|
| Data processing |
Library strategy: 3C-seq
Sequencing reads were aligned to human genome assembly hg19 or mm10 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, mm10
Supplementary_files_format_and_content: Pairwise Interaction Format
|
| |
|
| Submission date |
Oct 18, 2019 |
| Last update date |
Feb 20, 2020 |
| Contact name |
Jian Xu |
| E-mail(s) |
Jian.Xu@stjude.org
|
| Phone |
9015955208
|
| Organization name |
St. Jude Children's Research Hospital
|
| Department |
Pathology
|
| Street address |
262 Danny Thomas Place, MS 345
|
| City |
Memphis |
| State/province |
Tennessee |
| ZIP/Postal code |
38105 |
| Country |
USA |
| |
|
| Platform ID |
GPL18573 |
| Series (2) |
| GSE139109 |
CAPTURE-3C-seq analysis of cis-element-mediated long-range DNA interactions in K562 and G1E-ER4 cells |
| GSE139117 |
Analysis of CRE-mediated chromatin interactions by CAPTURE2.0 |
|
| Relations |
| BioSample |
SAMN13059579 |
| SRA |
SRX7023634 |
