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Sample GSM4727959 Query DataSets for GSM4727959
Status Public on Dec 04, 2020
Title H3K4me3.ES.2
Sample type SRA
Source name E14
Organism Mus musculus
Characteristics histone mark: H3K4me3
cell line: E14
condition: Naive
replicate: Rep 2
Growth protocol ES cells were cultured in 2iL, FS cells were cultured in A3XR, AF cells were cultured in AF and AFX cells were cultured in AFX
Extracted molecule genomic DNA
Extraction protocol Chromatin was cross-linked with 1% formaldehyde for 10 minutes at RT and quenched with 125 mM Glycine for 5 minutes at RT with rotation. After cell pellets were lysed, sonication was performed for 16 cycle on High setting, 30sec ON/30 sec OFF cycle by Bioruptor (Diagnode), 2x107 cells per 300 µl in Bioruptor tube (Diagnode). 10% inputs were collected for the later library construction. Chromatin was immunoprecipitated with 2 µg of each antibodies and 20 µl of Protein G Dynabeads (Invitrogen) were used against 3x106 cells. After the washes, DNA was eluted and each samples were treated with 2.5 µg/ml RNase A at 37˚C for 30 minutes followed by 87.5 µg/ml Proteinase K at 55˚C for 1 hour. DNA was purified with PCR clean-up kit (Qiagen).
Libraries were prepared by NEXTflex Rapid DNA-Seq Kit 2.0 bundle with 96 HT barcodes (ParkinElmer).
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina HiSeq 4000
Data processing The quality of the data was assessed using FastQC and MultiQC
The reads were aligned using bwa mem v0.7.10-r789 (default parameters) and BAM files sorted with samtools v1.9
MT, X, Y chromosomes and scaffolds were removed from BAM files
Peaks were called using macs2 v2.2.6 (-f BAMPE -q 0.05)
Genome browser tracks were created using deepTools bamCoverage v3.3.1 (--binSize 5 -of bigwig)
Genome_build: GRCm38.p6
Supplementary_files_format_and_content: Bigwig tracks, created after removal of MT, X, Y chromosomes and scaffolds
Submission date Aug 14, 2020
Last update date Dec 05, 2020
Contact name Irina Mohorianu
Organization name University of Cambridge
Department Wellcome-MRC Cambridge Stem Cell Institute
Street address Puddicombe Way
City Cambridge
ZIP/Postal code CB2 0AW
Country United Kingdom
Platform ID GPL21103
Series (2)
GSE156261 Capture of mouse and human stem cells with features of formative pluripotency [ChIP-seq]
GSE156589 Capture of mouse and human stem cells with features of formative pluripotency
BioSample SAMN15822288
SRA SRX8948725

Supplementary file Size Download File type/resource 295.4 Mb (ftp)(http) BW
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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