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Sample GSM7113532 Query DataSets for GSM7113532
Status Public on Jun 03, 2024
Title HepG2_5_ctr_H3K9me2_CUTTAG
Sample type SRA
 
Source name liver
Organism Homo sapiens
Characteristics tissue: liver
cell line: HepG2
cell type: HCC
cut&tag antibody: H3K9me2 ab1220 Abcam
treatment: Control
Extracted molecule genomic DNA
Extraction protocol The CUT&Tag experiments were performed using the Hyperactive Universal CUT&Tag Assay Kit for Illumina (Vazyme Biotech Co., Ltd., TD903) according to the manufacturer’s instructions.
The library was constructed by TruePrep® Index Kit V2 for Illumina kit and PCR amplification
 
Library strategy OTHER
Library source genomic
Library selection other
Instrument model Illumina NovaSeq 6000
 
Data processing The sequencing reads obtained from the Illumina platform were subjected to quality control using FastQC (v0.11.9) to assess the quality of the reads.
Adapter trimming and read filtering were performed using Trim-galore (0.6.5-1).
The filtered reads were then aligned to the human genome (UCSC hg38) using Bowtie2 version 2.2.6 with parameters.
The aligned reads were processed by MACS2 (v2.2.7.1) to call peaks and transformed to bigwig formatted files by bamCoverage function in Deeptools (v3.5.1) with default parameters.
Assembly: hg38
Supplementary files format and content: bigwig
Library strategy: CUT&Tag
 
Submission date Mar 23, 2023
Last update date Jun 03, 2024
Contact name Boshi Wang
E-mail(s) wbs137@126.com
Organization name Shanghai Cancer Institute
Street address No.800 Dongchuan Road
City Shanghai
ZIP/Postal code 200240
Country China
 
Platform ID GPL24676
Series (1)
GSE228071 Exploring the epigenetic regulatory role of KDM1A inhibition in HCC cells [HepG2_SP2509_CUTTag_seq]
Relations
BioSample SAMN33872263
SRA SRX19758119

Supplementary file Size Download File type/resource
GSM7113532_HepG2_5_ctr_H3K9me2_CUTTAG.sorted.bw 1.0 Gb (ftp)(http) BW
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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