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Sample GSM2790946 Query DataSets for GSM2790946
Status Public on Jan 31, 2018
Title Hind III digested HepG2 genome DNA
Sample type SRA
 
Source name HepG2
Organism Homo sapiens
Characteristics cell line: HepG2
cell type: primary epithelial cells
fragment method: Enzyme digestion
Growth protocol HeLa, HepG2 and 293T cells were grown in Dulbecco’s Modified Eagle’s Medium (DMEM, GIBCO), GM12878 cells were cultured in RPMI 1640, which were all supplemented with 10% fetal bovine serum (FBS, GIBCO) with 100 μg/mL streptomycin and 100 units/mL penicillin at 37°C in 5% CO2.
Extracted molecule genomic DNA
Extraction protocol The nuclei of 100,000 GM12878, HeLa, HepG2, and 293T cells, and various numbers of HepG2 cells (50,000, 10,000, 5,000, 2,500, and 500) were extracted.
Nuclei then tagmented by Tn5 transposome with different barcoded Tn5 adaptors.The denatured tagmented gDNA was ligated with variant single strand adaptors. Then elongated, purified with Ampure XP beads and amplified with Illumina compatible primers. The genome DNA of HepG2 were digested with Hind III and sonicated, and genome DNA libraries were constructed with SALP protocol.
 
Library strategy OTHER
Library source genomic
Library selection other
Instrument model HiSeq X Ten
 
Data processing The raw reads data were separated according to the barcode using a homemade Perl scripts.
All reads were cut to 30 bp and aligned to the human genome (hg19) using Bowtie program (version 1.1.2)
Peak calling was performed with macs2 with the following parameters: -f BEDPE –keep-dup=2.
Genome_build: hg19
Supplementary_files_format_and_content: bigwig
 
Submission date Sep 22, 2017
Last update date May 15, 2019
Contact name Jian Wu
E-mail(s) wujian2010@outlook.com
Organization name Southeast University
Street address Sipailou 2#, Sipailou 2#
City NanJing
State/province Jiangsu
ZIP/Postal code 210096
Country China
 
Platform ID GPL20795
Series (1)
GSE104162 SALP, a new NGS library construction method especially useful for the high-throughput characterization of chromatin openness states
Relations
BioSample SAMN07689050
SRA SRX3206852

Supplementary file Size Download File type/resource
GSM2790946_HH.bw 86.2 Mb (ftp)(http) BW
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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