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| Status |
Public on Nov 12, 2020 |
| Title |
12d-TNFa treatment+withdraw-10d, ATAC-seq, rep1 |
| Sample type |
SRA |
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| Source name |
12d-TNFa treated HEK 293 cells+withdraw-10d
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| Organism |
Homo sapiens |
| Characteristics |
cell line: HEK 293 transfected with reporter construct
cell type: somatic cell
tissue source: embryonic kidney
treatment: TNF-α treatment 12 days, then withdraw to recover 10 days
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| Treatment protocol |
The final concentration of TNF (high, default) is 50 ng/mL.
The final concentration of TNF (low, specified) is 0.4 ng/mL.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
45,000 cells were collected and resuspended in 50 μL cold ATAC-Resuspension Buffer (10 mM Tris-HCl pH 7.4, 10 mM NaCl and 3 mM MgCl2 in sterile water) containing 0.1% NP40, 0.1% Tween-20, and 0.01% Digitonin. Then the cells were incubated on ice for 3 minutes. The nuclei were washed with 1 mL cold ATAC-Resuspension Buffer containing 0.1% Tween-20 and centrifuged at 500 g and 4 ℃ for 10 minutes. The cell pellet were resuspended in 50 μL transposition mix (10 μL 5×TTBL, 5 μL TTE Mix V50, 16.5 μL PBS, 0.5 μL 1% digitonin, 0.5 μL 10% Tween-20, 17.5 μL ddH2O) with TruePrep DNA Library Prep Kit V2 for Illumina (Vazyme TD501) and incubated at 37 ℃ for 30 minutes with shaking in a thermomixer. The reactions were cleaned up with DNA Clean & Concentrator-5 (Zymo Research D4014).
The ATAC-seq libraries are prepared as previously described (Corces et al., 2017) with minor modifications. After transposition reaction, the libraries were constructed through PCR amplification with TruePrep Index Kit V2 for Illumina (Vazyme TD202) to barcode samples.
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| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
B1210-1_L3_Q804603
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| Data processing |
ATAC-seq basecalls performed by Berry Genomics, Co. Ltd. Beijing.
ATAC-seq reads were mapped to UCSC hg38 genome by Bowtie2 (2.3.4.2)
ATAC-seq data were filtered using samtools rmdup to remove potential PCR duplicates
Genome_build: hg38
Supplementary_files_format_and_content: wig files were generated using IGV tools with fragment extension of average fragments size.
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| Submission date |
Nov 11, 2020 |
| Last update date |
Nov 14, 2020 |
| Contact name |
Zhuqiang Zhang |
| E-mail(s) |
[email protected]
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| Organization name |
Institute of Biophysics, CAS
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| Street address |
15 Datun Road, Chaoyang District.
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| City |
Beijing |
| State/province |
--- |
| ZIP/Postal code |
100101 |
| Country |
China |
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| Platform ID |
GPL24676 |
| Series (1) |
| GSE152146 |
TNF induced inflammatory transcription dynamics and epigenetic changes |
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| Relations |
| BioSample |
SAMN16770457 |
| SRA |
SRX9486243 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4904184_B1210-1.bigwig |
220.2 Mb |
(ftp)(http) |
BIGWIG |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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