|
| Status |
Public on Oct 08, 2016 |
| Title |
input_HeLa |
| Sample type |
SRA |
| |
|
| Source name |
HeLa Kyoto
|
| Organism |
Homo sapiens |
| Characteristics |
antibody: none
cross-linking: 45 min DSG, 10 min Formaldehyde
down sampling: 0.58
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were prepped using 5ng of ChIP material and the Kapa Hyper Prep Kit for Illumina Sequencing (Kapa Biosystems) according to manufacturer's protocol.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Mapping was performed with an in-house Ruby script using BWA alignment to the hg19(build37) genome allowing one mismatch.
Data were filtered on quality and duplicates were removed using samtools.
Peaks were called using MACS 2.0 with the indicated p-value.
ZMYND8_ZMYND8KO was randomly down sampled to have the same number of reads as ZMYND8_v2 using samtools. MBD3_ZMYND8KO is down sampled to have similar read count as MBD3_v1. GFP-GATAD2B is down sampled to have similar read counts as GFP-GATAD2A and GFP-Wtcells.
Genome_build: hg19(build37)
Supplementary_files_format_and_content: Bed files contain filtered, aligned reads and called peaks.
|
| |
|
| Submission date |
Apr 01, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Cornelia Gijsbertha Spruijt |
| E-mail(s) |
nellekespruijt@hotmail.com
|
| Organization name |
Radboud University
|
| Department |
RIMLS
|
| Lab |
Proteomics and Chromatin Biology
|
| Street address |
Geert Grooteplein 26-28
|
| City |
Nijmegen |
| ZIP/Postal code |
6525 GA |
| Country |
Netherlands |
| |
|
| Platform ID |
GPL11154 |
| Series (2) |
| GSE79834 |
ZMYND8 co-localizes with NuRD on target genes and regulates recruitment of GATAD2A/NuRD to sites of DNA damage [ChIP-seq] |
| GSE79836 |
ZMYND8 co-localizes with NuRD on target genes and regulates recruitment of GATAD2A/NuRD to sites of DNA damage |
|
| Relations |
| BioSample |
SAMN04600202 |
| SRA |
SRX1674500 |
