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Sample GSM7040752 Query DataSets for GSM7040752
Status Public on Jun 20, 2023
Title ChIP-seq of H3K4me1 in WT
Sample type SRA
 
Source name mES
Organism Mus musculus
Characteristics cell line: mES
cell type: mouse embryonic stem cell
chip antibody: H3K4me1
Extracted molecule genomic DNA
Extraction protocol For ChIP-seq,cells were crosslinked with 1% formaldehyde for 10 min and quenched with glycine for 5 min at the room temperature. Fixed cells were sonicated and immunoprecipitated with the mixture of beads and antibody overnight at 4 ℃. ChIP-DNA was purified using PCR purification kit (Qiagen) and performed for qPCR using iTaq Universal SYBR Green Supermix (Bio-Rad) on CFX96 (Bio-Rad).
ChIP-seq libraries were prepared with Illumina's ChIP-seq sample prep kit (0801-0303). NEBNext® DNA Library Prep Master Mix Set for Illumina.
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina NovaSeq 6000
 
Data processing For quantification of repetitive genomic regions, we allowed multiple-mapping reads using Bowtie2 parameter ‘–fast -k 1’.
Peak calling was performed with the MACS2 and TE-specific peaks were selected by overlapping with the RepeatMasker from UCSC (mm9.rmsk) using bedtools
Assembly: mm9
Supplementary files format and content: bigWig
 
Submission date Feb 13, 2023
Last update date Jun 20, 2023
Contact name Xiaoxu Liu
E-mail(s) liuxiaoxu1010@126.com
Organization name Southeast University
Department Institute of Life Sciences
Lab the Key Laboratory of Developmental Genes and Human Disease
Street address 2 Sipailou
City Nanjing
State/province Jiangsu
ZIP/Postal code 210018
Country China
 
Platform ID GPL24247
Series (2)
GSE207397 ELL3 promotes stem cell native to primed transition through LINE-based enhancers [ChIP-Seq]
GSE208227 ELL3 promotes stem cell native to primed transition through LINE-based enhancers
Relations
BioSample SAMN33270271
SRA SRX19352283

Supplementary file Size Download File type/resource
GSM7040752_ChIP-seq_of_H3K4me1_in_Non_T_shRNA_2iL.multiple.bw 66.9 Mb (ftp)(http) BW
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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