|
| Status |
Public on Aug 24, 2017 |
| Title |
CAPTURE-ChIP-seq_K562_sgHS1-5-rep2 |
| 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 ChIP-seq analysis using the Illumina NextSeq500, 10-20 ng of ChIP 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 |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
Processed data file: CAPTURE-ChIP-seq_K562_sgHS1-5_vs_sgGal4_merged.txt
|
| Data processing |
Sequencing reads were aligned to human genome assembly hg19 (NCBI version 37) using Bowtie v1.0.0 with the following parameters: --best --strata -k 2 -m 2 for HBG samples and --best --strata -k 1 -m 1 for the rest samples. Duplicate reads were removed after the aligment with the Picard command-line tools.
Peak detection was performed with the Model-based Analysis of ChIP-Seq (MACS) algorithm (http://liulab.dfci.harvard.edu/MACS/).
The wig files were generated by a moving window of size 200bp. The tag count in the windown was further normalized by total read count for ChIP-seq data generated by NextSeq500.
Genome_build: hg19
Supplementary_files_format_and_content: wig file, peak bed file
|
| |
|
| 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 |
| GSE99177 |
ChIP-seq analysis of dCas9 chromatin occupancy by dCas9/sgRNA-mediated CAPTURE |
|
| Relations |
| BioSample |
SAMN07155074 |
| SRA |
SRX2842049 |
