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Sample GSM4832448 Query DataSets for GSM4832448
Status Public on Jan 01, 2021
Title WT_embryonic stem cells - H3K9me3_rep1
Sample type SRA
 
Source name WT_ESCs_H3K9me3
Organism Mus musculus
Characteristics strain: 129Sv
genotype: Wild type
cell type: Embryonic stem cells
chip antibody: H3K9me3 (Active Motif no. 39162)
Extracted molecule genomic DNA
Extraction protocol Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were prepared for sequencing using standard Illumina protocols
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina Genome Analyzer IIx
 
Description Normalized tag counts
Data processing Sequenced reads were trimmed for adaptor sequence, low quality and low complexity reads, then mapped to mm9 reference genome using bowtie2
ChIP-seq peaks were called with MACS2 (version 2.2.4) with the parameters “--nomodel --keep-dup all –shift = 73” over input files.
Genome_build: mm9
Supplementary_files_format_and_content: Signal tracks for each sample were generated using the bamCompare function of deeptools and were normalized by calculating the reads per kilobase of transcript per million mapped reads.
 
Submission date Oct 19, 2020
Last update date Jan 03, 2021
Contact name Yixin Huang
E-mail(s) 1710944@tongji.edu.cn
Organization name Tongji University
Street address Siping Road
City Shanghai
ZIP/Postal code 200092
Country China
 
Platform ID GPL11002
Series (2)
GSE132746 Dcaf11 facilitates telomere elongation in early embryos and embryonic stem cells (ESCs) through activating the Zscan4-mediated alternative lengthening telomere (ALT) mechanism
GSE159552 ULI-NChIP-seq Analysis of Wild Type(WT) and Dcaf11 overexpresion(OE) ESCs [ChIP-seq]
Relations
BioSample SAMN16475294
SRA SRX9298988

Supplementary file Size Download File type/resource
GSM4832448_WT.1.bw 131.8 Mb (ftp)(http) BW
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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