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Sample GSM5417201

Query DataSets for GSM5417201

Status

Public on Jul 04, 2024

Title

U2OS_siCtrl_HiC_rep1

Sample type

SRA

Source name

U2OS cells

Organism

Homo sapiens

Characteristics

cell type: U2OS cells
genotype: control
treatment: untreated

Extracted molecule

genomic DNA

Extraction protocol

The cross-linked cells were lysed in lysis buffer,fragmentation of the genome using restriction enzymes
Hi-C libraries were prepared for sequencing using standard Illumina protocols

Library strategy

Hi-C

Library source

genomic

Library selection

other

Instrument model

Illumina HiSeq 4000

Data processing

Raw sequencing data was first filtered by Trimmomatic (version: 0.36), low-quality reads were discarded and adaptor sequences were trimmed
The BWA package was used to map the sequences against the human reference genome with the parameter -n 0. Mapped reads with MAPQ quality scores ≥20 were chosen for further analysis.
We applied the ICE method to normalize the interaction matrix for different resolutions
If a region between two adjacent boundaries was less than 400 kb, the region was marked as a TAD boundary
The Juicer pipeline’s HiCCUPS was applied for discovery of locally enriched peaks
Genome_build: hg19
Supplementary_files_format_and_content: all the locally enriched peaks were determined by HiCCUPS

Submission date

Jul 04, 2021

Last update date

Jul 04, 2024

Contact name

wenhui Zhao

E-mail(s)

ZHAOWENHUI@CQU.EDU.CN

Organization name

Peking University

Street address

5 Yiheyuan Road, Haidian District