|
Status |
Public on Feb 05, 2020 |
Title |
Foreskin fibroblasts, ATAC-seq quiescence rep2 |
Sample type |
SRA |
|
|
Source name |
foreskin fibroblast
|
Organism |
Homo sapiens |
Characteristics |
cell line: BJ cell type: human diploid foreskin fibroblasts cell state: quiescence
|
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.
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|
|
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 |
SAMN13981965 |
SRA |
SRX7671727 |