|
| Status |
Public on May 28, 2015 |
| Title |
H3K9me3_sgSETDB1 |
| Sample type |
SRA |
| |
|
| Source name |
HeLa cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: HeLa
cell type: epithelial
disrupted gene: SETDB1
antibody: anti-H3K9me3 Abcam ab8898
|
| Treatment protocol |
Transfected with pool of Cas9/sgRNA expression plasmids, and sorted for knockout cells that become GFP+ owing to de-repression of a silent GFP reporter construct
|
| Growth protocol |
RPMI + 10% FCS + Penicillin/Streptomycin
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Crosslinking: 1% formaldehyde; Shearing: Bioruptor (Diagenode) to target size of 300bp; IP: 5ug primary antibody overnight
Illumina TruSeq ChIP Sample Prep Kit
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
ChIP-seq reads were aligned to the reference human genome hg19 using Bowtie2 with default settings.
Data were imported into SeqMonk analysis software with minimum mapping quality of 20.
Genome was considered as a series of 1 kb 'windows' and the number of H3K9me3 ChIP-seq reads in each window quantitated for each sample, correcting for total read counts.
Windows containing low (H3K9me3 score <40) levels of H3K9me3 were filtered out.
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text file showing the H3K9me3 score for each cell type for each window.
|
| |
|
| Submission date |
Nov 07, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Iva Tchasovnikarova |
| E-mail(s) |
it257@cam.ac.uk
|
| Organization name |
University of Cambridge
|
| Department |
The Gurdon Institute
|
| Lab |
Tchasovnikarova Lab
|
| Street address |
Tennis Court Road
|
| City |
Cambridge |
| ZIP/Postal code |
CB2 1QN |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL16791 |
| Series (1) |
| GSE63116 |
H3K9me3 ChIP-seq in HeLa cells lacking TASOR, MPP8, periphilin and SETDB1 |
|
| Relations |
| BioSample |
SAMN03169292 |
| SRA |
SRX755642 |
