|
| Status |
Public on Oct 14, 2013 |
| Title |
shKdm5b_4TF-MEF_H3K4me2_48h |
| Sample type |
SRA |
| |
|
| Source name |
shKdm5b 4TF-MEFs
|
| Organism |
Mus musculus |
| Characteristics |
cell type: mouse embryonic fibroblasts
antibody: Anti-H3K4me2 antibody (Abcam: ab32356)
|
| Growth protocol |
shLuc and shKdm5b 4TF-MEFs were grown in ESC media (LIF and GSK3i) without feeders and in the presence of 2ug/mL doxycyclin.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
4TF-MEFs 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 HiSeq 2000 |
| |
|
| Description |
Chromatin IP against H3K4me2
|
| 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). See BED files included in this submission.
The RBPM measure (reads per base per million reads) was used to generate bedgraph files.
Genome_build: mm8
|
| |
|
| Submission date |
May 21, 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 |
GPL13112 |
| Series (2) |
| GSE46893 |
Extended self-renewal and accelerated reprogramming in the absence of Kdm5b |
| GSE47123 |
Extended self-renewal and accelerated reprogramming in the absence of Kdm5b [ChIP-Seq] |
|
| Relations |
| BioSample |
SAMN02152305 |
| SRA |
SRX283868 |
