|
| Status |
Public on Jan 27, 2014 |
| Title |
KDM5B_mESC |
| Sample type |
SRA |
| |
|
| Source name |
ES cells
|
| Organism |
Mus musculus |
| Characteristics |
cell line: R1 ES cell
antibody: Anti-KDM5B antibody (Abcam; ab50958)
|
| Growth protocol |
ES cells were cultured on irradiated MEFs in DMEM, 15% FBS media containing LIF (ESGRO) at 37oC with 5% CO2. For ChIP experiments ES cells were cultured on gelatin-coated dishes in ES cell media containing 1.5 µM CHIR9901 (GSK3 inhibitor) for several passages to remove feeder cells. ES cells were passed by washing with PBS, and dissociating with trypsin. For differentiation, ES cells were cultured in low attachment binding dishes to promote 3D formation in ES cell media without LIF.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
ES cells were crosslinked with formaldehyde and subsequently sonicated. Sonicated cell extracts were used for ChIP assays.
ChIP-enriched DNA was end-repaired using the End-It DNA End-Repair kit (Epicentre), followed by addition of a single A nucleotide, and ligation of PE adapters (Illumina) or custom indexed adapters. PCR was performed using Phusion High Fidelity PCR master mix
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina Genome Analyzer IIx |
| |
|
| Description |
Chromatin IP against KDM5B
|
| Data processing |
Basecalls performed using GAPipeline 1.3.2 or CASAVA 1.0
Sequence reads were obtained and mapped to the mouse (mm8) genomes with Bowtie (0.12.7).Uniquely mapped reads were kept for each lane, and for positions where multiple reads were mapped, only one read was retained (except for RNA-Seq libraries).
The RBPM measure (reads per base per million reads) was used to generate graph files.
Genome_build: mm8
Supplementary_files_format_and_content: BED
|
| |
|
| Submission date |
Dec 06, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Benjamin L Kidder |
| E-mail(s) |
benjamin.kidder@wayne.edu
|
| Organization name |
Wayne State University
|
| Department |
Oncology
|
| Lab |
Laboratory of Epigenomics
|
| Street address |
4100 John R St
|
| City |
Detroit |
| State/province |
MI |
| ZIP/Postal code |
48201 |
| Country |
USA |
| |
|
| Platform ID |
GPL11002 |
| Series (2) |
| GSE53087 |
KDM5B focuses H3K4 methylation near promoters and enhancers during embryonic stem cell self-renewal and differentiation [ChIP-Seq] |
| GSE53093 |
KDM5B focuses H3K4 methylation near promoters and enhancers during embryonic stem cell self-renewal and differentiation |
|
| Relations |
| Reanalyzed by |
GSE63286 |
| BioSample |
SAMN02438004 |
| SRA |
SRX388392 |
