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Sample GSM4295145 Query DataSets for GSM4295145
Status Public on Feb 05, 2020
Title Foreskin fibroblasts, ATAC-seq reversal of senescence rep1
Sample type SRA
 
Source name foreskin fibroblast
Organism Homo sapiens
Characteristics cell line: BJ
cell type: human diploid foreskin fibroblasts
cell state: reversal of senescence
Growth protocol Human diploid BJ fibroblasts purchased from American Type Culture Collection were cultured in DMEM supplemented with 10% fetal bovine serum (FBS) and penicillin and streptomycin.
Extracted molecule genomic DNA
Extraction protocol ~25,000 cells were harvested and then lysed in cold lysis buffer (10 mM Tris-HCl, 10 mM NaCl, 3 mM MgCl2, 0.5% Igepal CA-630) for 10 min. Centrifuge at 500× g for 10 min at 4℃. Discard the supernatant and resuspend pellet in a 50 ul transposition mix (TruePrep™ DNA Library Prep Kit V2 for Illumina, TD501). Incubate the transposition system at 37℃ for 1 hour and purify transposed DNA using Zymo DNA Clean & Concentrator™-5 kit. Finally ATAC-seq libraries were PCR amplified for 10 cycles and purified using Zymo DNA Clean & Concentrator™-5 kit.
Illumina HiSeq 2500
 
Library strategy ATAC-seq
Library source genomic
Library selection other
Instrument model Illumina HiSeq 2500
 
Data processing ATAC-seq reads were mapped to hg19 genome using bowtie2 (-X2000 --no-mixed --no-discordant).
Duplicate reads were removed by genomic positions.
NFR reads were used to call peaks using MACS2 (--keep-dup all -f BEDPE).
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: *.narrowPeak: Open peaks.
 
Submission date Feb 04, 2020
Last update date Dec 18, 2020
Contact name Xianglin Zhang
E-mail(s) xl-zhang15@mails.tsinghua.edu.cn
Phone 15101669184
Organization name Tsinghua University
Street address Haidian District
City Beijing
State/province Beijing
ZIP/Postal code 100084
Country China
 
Platform ID GPL16791
Series (1)
GSE133292 The loss of heterochromatin is associated with multiscale three-dimensional genome reorganization and aberrant transcription during cellular senescence
Relations
BioSample SAMN13981960
SRA SRX7671732

Supplementary file Size Download File type/resource
GSM4295145_RS1.narrowPeak.gz 5.2 Mb (ftp)(http) NARROWPEAK
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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