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Sample GSM2099820 Query DataSets for GSM2099820
Status Public on Jan 09, 2018
Title ChIP_D2_0_E14_H3K4me1
Sample type SRA
 
Source name E14, mouse embryonic stem cell line
Organism Mus musculus
Characteristics genotype: wild type
cell line: E14
antibody: H3K4me1
Growth protocol Mouse embryonic stem cell lines E14 and Mll3/4 double knockout were cultured in mouse ES cell media: DMEM 85%, 15% fetal bovine serum (Hyclone), penicillin/streptomycin, 1× non-essential amino acids (Gibco), 1× GlutaMax, 1000 U/ml LIF (Millipore), 0.4 mM β-mercaptoethanol. Mouse ES cells were initially cultured on 0.1% gelatin-coated petridish with CF-1 irradiated mouse embryonic fibroblasts (GlobalStem) and were passaged twice on 0.1% gelatin-coated feeder-free plates before harvesting.
Extracted molecule genomic DNA
Extraction protocol ChIP-seq: Cells were lysed in RIPA buffer (10 mM Tris-HCl pH 8.0, 140 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% SDS, 0.1% sodium deoxycholate) supplemented with protease inhibitor (details see Yan et al). Hi-C and 4C-seq: Briefly, 2 million cells were cross-linked with 1% formaldehyde for 10min at RT and reaction was quenched using 125 mM of Glycine for 5 min at RT. Nuclei were isolated and directly applied for digestion using 4 cutter restriction enzyme MboI (NEB) at 37 °C o/n.
All libraries were constructed using standard illumina TruSeq LT library prep.
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina HiSeq 4000
 
Data processing base-calling use bcl2fastq version 2.17
alignment was performed using bowtie for ChIP-seq, bwa for Hi-C, Tophat for RNA-seq, 4cseqpipe for 4C-seq
Genome_build: mm9
 
Submission date Mar 26, 2016
Last update date May 15, 2019
Contact name Jian Yan
E-mail(s) jian.yan618@gmail.com
Organization name City University of Hong Kong
Department Biomedical Sciences
Lab Jian Yan
Street address 83 Tat Chee Ave
City Kowloon
ZIP/Postal code 999077
Country Hong Kong
 
Platform ID GPL21103
Series (1)
GSE74055 Histone H3 lysine 4 monomethylation modulates longrange chromatin interactions at enhancers
Relations
BioSample SAMN04590673
SRA SRX1670190

Supplementary file Size Download File type/resource
GSM2099820_ChIP_D2_0_E14_H3K4me1.bw 42.1 Mb (ftp)(http) BW
SRA Run SelectorHelp
Processed data provided as supplementary file
Raw data are available in SRA

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