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Sample GSM5462310 Query DataSets for GSM5462310
Status Public on Jan 16, 2024
Title Noncrosslink
Sample type SRA
Source name 293T cells
Organism Homo sapiens
Characteristics cell line: 293T
sample type: non-crosslink
Treatment protocol In the group with crosslinking, 293T cells were fixed with 1% formaldehyde for 10 min and quenched with 0.125 M glycine for 5 min at room temperature. After permeabilization with lysis buffer, the transposed reaction was performed. Then, a reverse-crosslinking solution was added (with final concentration of 50 mM Tris–Cl, 1 mM EDTA, 1% SDS, 0.2 M NaCl, 5 ng/mL proteinase K). The mixture was incubated with shaking in a heat block at 65 °C, at 1,000 rpm overnight for the crosslinking reversion. After purification, DNA libraries were prepared and sequencing was performed. In the group without crosslinking, living cells were prepared following the original ATAC-seq protocol.
Growth protocol Human 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 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 at room temperature for 10 min.
DNA libraries were prepared for sequencing using TruePrepTM DNA Library Prep Kit V2 for Illumina.
Library strategy ATAC-seq
Library source genomic
Library selection other
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
Peak calling with macs2 v 2.2.1
Motif finding with homer(
Genome_build: hg19
Supplementary_files_format_and_content: narrowPeak files were generated using macs2
Submission date Jul 19, 2021
Last update date Jan 16, 2024
Contact name Haizhu Zhang
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)
GSE174643 Proteome-wide profiling of Transcriptional Machinery on Accessible Chromatin by biotinylated transposon
GSE180398 Proteome-wide profiling of Transcriptional Machinery on Accessible Chromatin with biotinylated transposons [ATAC-seq]
BioSample SAMN20307299
SRA SRX11500240

Supplementary file Size Download File type/resource
GSM5462310_NC_peak_peaks.narrowPeak.gz 987.5 Kb (ftp)(http) NARROWPEAK
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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