|
| Status |
Public on Apr 24, 2018 |
| Title |
ChIP_Growing_H3K4me1_Rep1 |
| Sample type |
SRA |
| |
|
| Source name |
IMR90
|
| Organism |
Homo sapiens |
| Characteristics |
vector 1: ER:HRAS(G12V)
4oht: No
chip antibody: H3K4me1 (Clone CMA302; in house; Kimura et al., 2008; also available from MBL life sciences, CAT MABI0302)
passage: 23-28
|
| Treatment protocol |
For RIS samples,IMR90 ER:HRAS(G12V) cells are treated for 6 days with 4OHT.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Fixed cells were lysed and sonicated to generate 200-400 bp chromatin fragments before immunoprecipitation
Libraries were prepared using the NEBnext ultra II DNA-library prep kit for Illumina (E7645) according to manufacturers instructions except that size selection was performed during the final bead purification step using SPRIselect beads (B23319, Beckman Coulter)
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
ChIP-Seq
|
| Data processing |
Reads were mapped to the human reference (hg19) with BWA (version 0.7.12)
Peak calling was performed with MACS2 (version 2.1.0) 84.
Coverage files were generated using MACS2 (version 2.1.0).
Genome_build: hg19
Supplementary_files_format_and_content: .narrowPeak = peaks
Supplementary_files_format_and_content: .bedgraph = coverage data
|
| |
|
| Submission date |
Sep 07, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Shamith Samarajiwa |
| Organization name |
Imperial College London
|
| Department |
Genetics and Genomics Section Department of Metabolism, Digestion and Reproduction
|
| Lab |
Computational Biology & Data Science
|
| Street address |
ICTEM Building, Hammersmith Campus, Du Cane Road,
|
| City |
London |
| ZIP/Postal code |
W12 0NN |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL16791 |
| Series (2) |
| GSE103589 |
NOTCH-mediated non-cell autonomous regulation of chromatin structure during senescence [ChIP-Seq] |
| GSE103590 |
NOTCH-mediated non-cell autonomous regulation of chromatin structure during senescence |
|
| Relations |
| BioSample |
SAMN07614478 |
| SRA |
SRX3166969 |
