|
| Status |
Public on Aug 24, 2017 |
| Title |
ATAC-seq_K562_Control-rep2 |
| Sample type |
SRA |
| |
|
| Source name |
Human K562 cells
|
| Organism |
Homo sapiens |
| Characteristics |
genotype/variation: control
cell line: K562
|
| 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 ATAC-seq analysis using the Illumina NextSeq500, ~50,000 cells were processed for tagmentation followed by DNA isolation and library generation. Raw reads that aligned to exactly one location in the reference human genome (hg19) were retained for downstream data analysis.
|
| |
|
| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Sequencing reads were aligned to human genome assembly hg19 (NCBI version 37) or mouse genome assembly (mm9) using Bowtie v1.0.0 with the following parameters: --best --strata -k 1 -m 1. 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 ATAC-seq data generated by NextSeq500.
Genome_build: hg19 or mm9
Supplementary_files_format_and_content: wig file and peak bed file
|
| |
|
| Submission date |
Jul 06, 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 |
| GSE99173 |
ATAC-seq analysis in K562 cells with or without HBD-1k region knockout, mouse KH2 embryonic stem cells (ESCs) and differentiated KH2 Embryoid bodies (EBs) |
|
| Relations |
| BioSample |
SAMN07328104 |
| SRA |
SRX2987810 |
