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| Status |
Public on Jan 16, 2024 |
| Title |
Noncrosslink |
| Sample type |
SRA |
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| Source name |
293T cells
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| Organism |
Homo sapiens |
| Characteristics |
cell line: 293T
sample type: non-crosslink
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| 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.
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| 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.
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| 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.
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| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
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| 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
Supplementary_files_format_and_content: narrowPeak files were generated using macs2
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| Submission date |
Jul 19, 2021 |
| Last update date |
Jan 16, 2024 |
| Contact name |
Haizhu Zhang |
| E-mail(s) |
zhz2230@qq.com
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| Phone |
18621062295
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| Organization name |
Fudan University
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| Department |
Institutes of Biomedical Sciences
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| Lab |
He Fuchu Lab
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| Street address |
No. 131 Dong'an Road, Xuhui District
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| City |
Shanghai |
| ZIP/Postal code |
200032 |
| Country |
China |
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| 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] |
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| Relations |
| 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 Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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