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| Status |
Public on Jun 20, 2024 |
| Title |
293T_WT_ATAC |
| Sample type |
SRA |
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| Source name |
HEK293T
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| Organism |
Homo sapiens |
| Characteristics |
cell line: HEK293T
cell type: Human embryonic kidney
genotype: WT
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| Growth protocol |
DMEM, 15% fetal bovine serum, 2mM glutamine, 1x penicillin/streptomycin. Cells were cultured at 37C at 5% CO2.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
ATAC-seq was performed as previously described (Li et al. 2021). Briefly, 5×104 cells were collected and washed with cold PBS and centrifuged at 500 g for 5 minutes. Then, the cells were lysed by 50 μl cold lysis buffer (Novoprotein, 10 mM Tris-HCl, 10 mM NaCl, 3 mM MgCl, 0.1% NP-40, 0.1% Tween-20, 1% Digitonin) and incubated on ice for 5 minutes. The cells were furthered added with 950 μl cold wash buffer (Novoprotein, 10 mM Tris-HCl, 10 mM NaCl, 3 mM MgCl, 0.1% Tween-20) and centrifuged at 500 g for 5 minutes
The pellet was resuspended with 40 μl tagmentation buffer (Novoprotein, N248, 0.3×pbs, 0.1% Tween-20, 0.01% Digitonin, 1×TD buffer, 1×pA-Tn5 transposome Mix) incubated at 37 ℃ for 30 min. The reaction was stopped by adding 10 μl stop buffer (Novoprotein, N248) at 55 ℃ for 5 min. The DNA was further purified with 100 μl Tagment DNA Extract Beads (Novoprotein, N245) and eluted with 37 μl Elution buffer. The purifyied DNA was amplified with 5×AmpliMix (Novoprotein, N248) using N501 and N701 index primer((Novoprotein, N239). The purified DNA libraries were size selected with NovoNGS® DNA Clean Beads (Novoprotein, N240)
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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 |
ATAC-seq reads were aligned to human genome hg38. The aligned reads were removed with Picard MarkDuplicates, Blacklisted regions were removed from the BAM file with bedtools intersect, and the deduplicated BAM files were normalized (Bins Per Million mapped reads, BPM) to generate bigwig file with the bamCoverage command from deepTools 3.3.0.
Assembly: hg38
Supplementary files format and content: bigWig, narrowPeak
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| Submission date |
Jun 17, 2024 |
| Last update date |
Jun 21, 2024 |
| Contact name |
Lijun Xiang |
| E-mail(s) |
xiang-lijun@m.scnu.edu.cn
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| Phone |
+86-15626099434
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| Organization name |
South China Normal University
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| Department |
Guangzhou Key Laboratory of Insect Development Regulation and Application Research
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| Lab |
Qili Feng lab
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| Street address |
No.55, West of Zhongshan Avenue
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| City |
Guangzhou |
| State/province |
Guangdong |
| ZIP/Postal code |
510631 |
| Country |
China |
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| Platform ID |
GPL24676 |
| Series (2) |
| GSE221437 |
DNA 5-methylcytosine regulates genome-wide formation of G-quadruplex structures |
| GSE270033 |
DNA 5-methylcytosine regulates genome-wide formation of G-quadruplex structures [ATAC-seq] |
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| Relations |
| SRA |
SRX24946425 |
| BioSample |
SAMN41872851 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM8333110_HEK293T_WT_ATAC.bw |
34.2 Mb |
(ftp)(http) |
BW |
| GSM8333110_HEK293T_WT_ATAC_peaks.narrowPeak.gz |
547.6 Kb |
(ftp)(http) |
NARROWPEAK |
SRA Run Selector |
| Raw data are available in SRA |
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