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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
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
BioSample SAMN33270271
SRA SRX19352283

Supplementary file Size Download File type/resource 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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