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Sample GSM1145400 Query DataSets for GSM1145400
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
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]
BioSample SAMN02152305
SRA SRX283868

Supplementary file Size Download File type/resource
GSM1145400_GA4712-shKdm5b-4TF-MEF-48h-H3K4me2-ChIP-Index10-CCAACT-m1_5_15_noDup.bed.gz 18.3 Mb (ftp)(http) BED
GSM1145400_GA4712-shKdm5b-4TF-MEF-48h-H3K4me2-ChIP-Index10-CCAACT-m1_noDup_RPBM.bedgraph.gz 7.7 Mb (ftp)(http) BEDGRAPH
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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