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Sample GSM5348404 Query DataSets for GSM5348404
Status Public on May 31, 2021
Title ESCs, SS18-ChIP-0h
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: no doxycycline
chip antibody: SS18 (CST, 21792)
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 Protein-DNA complexes were isolated with antibody and Tn5-proteinA/G.
The ChIP DNA library for sequencing was constructed with NovoNGS CUT&Tag 2.0 High-Sensitivity Kit for Illumina (novoprotein) according to manufacturer’s instructions.
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina NovaSeq 6000
 
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 (GRCm38)
Supplementary_files_format_and_content: bigWig files
 
Submission date May 30, 2021
Last update date May 31, 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 GPL24247
Series (2)
GSE135451 SS18 is a phase-separation protein relocating from pluripotent to somatic loci during mESC differentiation
GSE175818 SS18 is a phase-separation protein relocating from pluripotent to somatic loci during mESC differentiation [ChIP-Seq Dataset 3]
Relations
BioSample SAMN19459945
SRA SRX11030054

Supplementary file Size Download File type/resource
GSM5348404_SS18-ChIP-0h.bw 15.7 Mb (ftp)(http) BW
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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