|
| Status |
Public on Jun 02, 2023 |
| Title |
NK92_SAHA_ATAC_rep2 |
| Sample type |
SRA |
| |
|
| Source name |
NK92
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: NK Cells
passages: 12 passages
cell line: NK92
treatment: SAHA treated
|
| Treatment protocol |
NK92 was treated with 1000nM SAHA for 24 hours.
|
| Growth protocol |
NK92 cells were cultured α-MEM medium supplemented with 20% FBS, 55μM 2-mercaptoethanoland 100U/ml IL-2, 100U/ml Penicillin and 100μg/ml Streptomycin.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
ATAC-seq was performed using the protocol from Corces et al., 2015 with small modifications. Nuclear pellets at 5x10^4 were permeabilized and tagmented by Tn5 enzyme.
Tagmentation was performed using Nextera DNA library preparation kit (illumina #15028212) according to manufacturer's instructions. Reverse-crosslinked DNA was amplified using Nextera PCR primers. Libraries were paired-end sequenced on Illumina HiSeq 2500 platform.
|
| |
|
| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
sequnced using Illumina HiSeq 2500 platform
Raw ATAC-seq reads were trimmed for adaptor sequence, and aligned to the hg19 genome assembly using bowtie2 v2.3.5.1 with the following setting: --end-to-end --very-sensitive --maxins 2000
aligned files were filtered for MAPQ > 30 and sorting, deduplication were processed using PICARD v2.27.4
filtered reads were shifted and reads in nucleome-free regions were extracted using deeptools alignmentSieve with the following setting: --maxFragmentLength 140 --ATACshift
peaks were called using macs2 v2.2.7.1 with the following setting: -f BAMPE -g hs and all peaks in blacklist regions were removed
normalized abundance file, bigwig files were generated applying CPM normalization using deeptools v3.5.1
Assembly: hg19
Supplementary files format and content: narrowPeak, CPM normalized bigwig
|
| |
|
| Submission date |
Mar 19, 2023 |
| Last update date |
Jun 02, 2023 |
| Contact name |
Hyoung-Pyo Kim |
| E-mail(s) |
kimhp@yuhs.ac
|
| Organization name |
Yonsei University College of Medicine
|
| Department |
Department of Tropical Medicine
|
| Street address |
Yonsei-ro 50-1
|
| City |
Seoul |
| ZIP/Postal code |
03722 |
| Country |
South Korea |
| |
|
| Platform ID |
GPL16791 |
| Series (2) |
| GSE227661 |
Genome-wide transcriptional, epigenetic, and topological changes occurring in human natural killer cells in response to HDAC inhibitor [ATAC-seq] |
| GSE227664 |
Genome-wide transcriptional, epigenetic, and topological changes occurring in human natural killer cells in response to HDAC inhibitor |
|
| Relations |
| BioSample |
SAMN33819388 |
| SRA |
SRX19719532 |
