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Sample GSM4007598 Query DataSets for GSM4007598
Status Public on May 18, 2021
Title ESCs, H3K27ac-ChIP-seq.8h
Sample type SRA
 
Source name mouse embryonic stem cells (mESCs)
Organism Mus musculus
Characteristics cell type: OG2 transgenetic mouse embryonic stem cells (OG2ES)
strain: 1/2 129SVJ+3/8 C57B6+1/8 CBA
genotype: c-Jun_TetOn_mESC
treatment: treated with doxycycline for 8h
chip antibody: H3K27ac (Abcam, ab4729)
Treatment protocol Treated with 2µg/ml doxycycline
Growth protocol Mouse ESCs were cultured on feeder free with mESC-2i medium (DMEM, 15%FBS, NEAA, GlutaMAX, PD0325901, Chir99021, LIF)
Extracted molecule genomic DNA
Extraction protocol Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with antibody.
The ChIP DNA library for sequencing was constructed with VAHTS Turbo DNA Library Prep Kit for Illumina (Vazyme) according to manufacturer’s instructions
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina NextSeq 500
 
Data processing bcl2fastq conversion software v2.17 used for basecalling.
The ChIP-seq datasets were aligned to the mouse Genome mm10 using Bowtie2 (version 2.2.5) with the parameters --very-sensitive --end-to-end --no-unal.
Bowtie2 SAM output files were converted to sorted BAM files using SAMtools. Multiple mapped reads were discarded. When multiple reads mapped to the same genomic position, only one read were retained.
The samtools and bedtools suites were used to generate bigwig files for visualization in the IGV browser
Peaks were called using MACS2 software with the default parameters.
Genome_build: mm10
Supplementary_files_format_and_content: bigwig
 
Submission date Aug 05, 2019
Last update date May 18, 2021
Contact name kuang junqi
E-mail(s) kuangjunqi@westlake.edu.cn
Organization name westlake University
Street address No.18 Shilongshan Road
City hangzhou
ZIP/Postal code 310024
Country China
 
Platform ID GPL19057
Series (2)
GSE135396 SS18 is a phase-separation protein relocating from pluripotent to somatic loci during mESC differentiation [ChIP-Seq Dataset 1]
GSE135451 SS18 is a phase-separation protein relocating from pluripotent to somatic loci during mESC differentiation
Relations
BioSample SAMN12497458
SRA SRX6657513

Supplementary file Size Download File type/resource
GSM4007598_H3K27ac-ChIP-seq.8h.bw 73.3 Mb (ftp)(http) BW
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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