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Sample GSM5006018 Query DataSets for GSM5006018
Status Public on Jan 16, 2024
Title G200
Sample type SRA
Source name 293T cells
Organism Homo sapiens
Characteristics cell line: 293T
Treatment protocol Q Sepharose was added to 1.5 mL EP tubes, and washed gently with 20 mM NaCl for 3 times, for every time, the Q Sepharose was centrifuged for 2 min at 300 × g at room temperature. Cells were crosslinked, permeabilized and incubated with transposons. After tagmentation with transposons, the mixture was incubated with Q Sepharose for 10 min and shortly centrifuged for 30 s at 300× g. The supernatant was collected into a new tube as FT (flow-through). The Q Sepharose was then washed with 20 mM, 100 mM, 200 mM, 300 mM, 500 mM, 700 mM, and 1000 mM NaCl successively. The supernatant was collected into new tubes. For ATAC-seq, a reverse-crosslinked solution (with final concentration of 50 mM Tris–HCl, 1 mM EDTA, 1% SDS, 0.2 M NaCl, 5 ng/ml proteinase K) was added to each group. The mixture was incubated at 65 °C at 1,000 r.p.m. with shaking in a heat block overnight, then purified with Qiagen Mini-purification kit and eluted in 17 μL Quiagen EB elution buffer. Sequencing libraries were prepared using TruePrep Index Kit V2 for Illumina (Vazyme TD202) and purified using VAHTS DNA Clean Beads (Vazyme N411).
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 Jan 05, 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)
GSE164299 Proteome-wide profiling of Transcriptional Machinery on Accessible Chromatin by biotinylated transposon [fractionation]
GSE174643 Proteome-wide profiling of Transcriptional Machinery on Accessible Chromatin by biotinylated transposon
BioSample SAMN17218426
SRA SRX9786179

Supplementary file Size Download File type/resource
GSM5006018_G200.peak_peaks.narrowPeak.gz 374.2 Kb (ftp)(http) NARROWPEAK
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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