|
| Status |
Public on May 15, 2017 |
| Title |
H3K27ac_K562_shNT |
| Sample type |
SRA |
| |
|
| Source name |
Human K562 cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: K562
chip antibody: Abcam ab4729
|
| Treatment protocol |
NA
|
| Growth protocol |
Human K562 cells were cultured in IMDM supplemented with 10% heat-inactivated fetal bovine serum (FBS) and 2% penicillin-streptomycin.
|
| 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 |
ChIP DNA
|
| Data processing |
Sequencing reads were aligned to human genome assembly hg19 (NCBI version 37) using Bowtie v0.12.7 with the following parameters: -v 2 -m 3 --strata --best. 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 in unit RPKM (# read per kb per million total reads) for ChIP-seq data generated by NextSeq500.
Genome_build: hg19
Supplementary_files_format_and_content: wig file and peak bed file
|
| |
|
| Submission date |
Sep 13, 2016 |
| 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) |
| GSE86864 |
ChIP-seq analysis of H3K27ac in K562 cells with shRNA-mediated depeltion of TFAM expression |
| GSE86912 |
Quantitative Proteomic and Transcriptomic Analysis Reveals Post-Transcriptional Regulation of Mitochondrial Biogenesis during Erythropoiesis |
|
| Relations |
| BioSample |
SAMN05768191 |
| SRA |
SRX2161993 |
