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| Status |
Public on Jan 16, 2024 |
| Title |
Hela-15 ATAC-seq |
| Sample type |
SRA |
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| Source name |
HeLa cells
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| Organism |
Homo sapiens |
| Characteristics |
cell line: HeLa
treatment: 20ng/mL TNF-α for 15min
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| Treatment protocol |
1.Final concentration of 20 ng/mL TNF-α was added into the cell culture medium and HeLa cells were incubated in 37 °C for 15 min, 30 min and 60 min. Cells were harvested in cold 1x PBS buffer and counted.
2.When the density of MCF7 cells was up to 70%, DMEM was changed to Phenol Red-free DMEM with 2.5% FBS for 24 h and then Phenol Red-free DMEM only for 24 h. Final concentration of 100 nM 17β-estradiol(E2) and 2 uM 4-hydroxytamoxifen(4-HT) were added into the cell culture medium, cells were incubated in 37 °C for 2 h. Cells were harvested in cold 1x PBS buffer and counted.
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| Growth protocol |
Human cell lines HeLa, HepG2 and MCF-7 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. Mouse C2C12 were cultured in DMEM supplemented with 10% FBS, 2 mM -glutamine, 100 U/ml penicillin and 100 g of streptomycin (1% Pen/Strep) at 37℃, 5% CO2. For myogenic differentiation, cells were shifted to DMEM containing 2% horse serum (differentiation medium).
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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 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.
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| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
HiSeq X Ten |
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| Description |
s15_TKD180600256
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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 and mm10
Supplementary_files_format_and_content: narrowPeak files were generated using macs2
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| Submission date |
Jul 10, 2019 |
| 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 |
GPL20795 |
| Series (2) |
| GSE134086 |
Proteome-wide profiling of Transcriptional Machinery on Accessible Chromatin by biotinylated transposon (various cell lines I) |
| GSE174643 |
Proteome-wide profiling of Transcriptional Machinery on Accessible Chromatin by biotinylated transposon |
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| Relations |
| BioSample |
SAMN12249492 |
| SRA |
SRX6427763 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM3936827_s15_peaks.narrowPeak.gz |
161.8 Kb |
(ftp)(http) |
NARROWPEAK |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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