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Sample GSM1282174 Query DataSets for GSM1282174
Status Public on Jan 27, 2014
Title shKdm5b_nLIF_d3_Input_mESC
Sample type SRA
 
Source name shKdm5b noLIF day3 ES cells
Organism Mus musculus
Characteristics cell line: R1 ES cell
antibody: NULL
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 ┬ÁM 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 HiSeq 2000
 
Description Direct sequencing following sonication of x-linked chromatin
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 GPL13112
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
BioSample SAMN02437995
SRA SRX388440

Supplementary file Size Download File type/resource
GSM1282174_GA3868-Index10-CCAACT-shKdm5b-LIF-d3-Input-m1_6_0_noDup.bed.gz 135.8 Mb (ftp)(http) BED
GSM1282174_GA3868-Index10-CCAACT-shKdm5b-LIF-d3-Input-m1_noDup_RPBM.bedgraph.gz 45.7 Mb (ftp)(http) BEDGRAPH
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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