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Sample GSM5321309 Query DataSets for GSM5321309
Status Public on Jan 16, 2024
Title HeLa-1-0min
Sample type SRA
 
Source name HeLa
Organism Homo sapiens
Characteristics antibody: NFKB1
cell type: HeLa
Treatment protocol 1.ATAC-seq was applied to 293T, HeLa, HepG2 and MCF7 cell line. 2.ATAC-seq was applied to mouse liver rhythm model.3. ChIP-seq was applied to different cells with different treatment.
Growth protocol Cell lines 293T were maintained in Dulbecco’s Modified Eagle’s Medium (DMEM) supplemented with 10% fetal bovine serum (FBS) and Pen-Strep (100 U / ml penicillin, 100 mg / ml streptomycin) at 37℃, 5% CO2.
Extracted molecule genomic DNA
Extraction protocol Cells were harvested and wash once with cold 1x PBS buffer, and then resuspended in 1 mL cold lysis buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% NP-40, 1mM PMSF). This cell lysis reaction was incubated on ice for 10 min.
DNA libraries were prepared for sequencing using TruePrepTM DNA Library Prep Kit V2 for Illumina().
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina NovaSeq 6000
 
Data processing Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 or mm10 whole genome using bowtie2 v2.2.6 with parameters with the parameters -X2000 and -m1.
Remove mitochondrial DNA with removeChrom.py
Peak calling with macs2 v 2.2.1
Motif finding with homer(findMotifsGenome.pl)
Genome_build: hg19 and mm10
Supplementary_files_format_and_content: narrowPeak files were generated using macs2
 
Submission date May 18, 2021
Last update date Jan 16, 2024
Contact name Haizhu Zhang
E-mail(s) zhz2230@qq.com
Phone 18621062295
Organization name Fudan University
Department Institutes of Biomedical Sciences
Lab He Fuchu Lab
Street address No. 131 Dong'an Road, Xuhui District
City Shanghai
ZIP/Postal code 200032
Country China
 
Platform ID GPL24676
Series (2)
GSE174642 Proteome-wide profiling of Transcriptional Machinery on Accessible Chromatin by biotinylated transposon (various cell lines II)
GSE174643 Proteome-wide profiling of Transcriptional Machinery on Accessible Chromatin by biotinylated transposon
Relations
BioSample SAMN19243586
SRA SRX10921871

Supplementary file Size Download File type/resource
GSM5321309_R21038977-ZHZ008-HeLa-2-0min_peaks.narrowPeak.gz 12.5 Kb (ftp)(http) NARROWPEAK
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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