|
| Status |
Public on Feb 26, 2021 |
| Title |
ATAC-Seq splenic NK - WT 5 |
| Sample type |
SRA |
| |
|
| Source name |
splenic NK cells
|
| Organism |
Mus musculus |
| Characteristics |
genotype: wild-type
|
| Treatment protocol |
Spleens were isolated from mice wild-type (WT) for HSF1 or those bearing serine to alanine mutations in amino acids 303 and 307 (S303/7A or MUT) under steady state conditions
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Single-cell suspension of splenocytes was enriched for NK using DX5 Microbeads (Miltenyi) before sort purification for NK cells (CD49b+,CD3e-). Each mouse served as a biological replicate. 2 x 10^5 NK cells from each mouse were used for the ATAC-seq protocol
Assay for transposase-accessible chromatin (ATAC) and library preparation was performed as previously described (Buenrostro J.D. et al, Curr Protoc Mol Biol, 2015)
|
| |
|
| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Reads were trimmed for adapter sequences and low-quality score bases using Trimmomatic; reads that were properly paired and had a unique alignment (mapping quality > 30) were retained
Trimmed reads were aligned to the Mus musculus genome (mm10/GRCm38) using the Bowtie2 aligner (v2.3.4.1)
Duplicate reads were removed using sambamba markdup.
Peaks were determined algorithmically using Model-based Analysis of ChIP-Seq 2 algorithm (v1.4.2) with q < 0.05
Differential peaks were called using negative binomial generalized linear models implemented by the DESeq2 analysis in the DiffBind (v3.0.12) package
Genome_build: mm10
Supplementary_files_format_and_content: Preprocessed bed files for all biological replicates consist of peaks determined algorithmicaly using MACS 2 with q < 0.05
|
| |
|
| Submission date |
Feb 25, 2021 |
| Last update date |
Feb 26, 2021 |
| Contact name |
Kathryn Grace Hockemeyer |
| Organization name |
NYU Langone Health
|
| Department |
Pathology
|
| Lab |
Aifantis
|
| Street address |
550 1st Avenue
|
| City |
New York |
| State/province |
New York |
| ZIP/Postal code |
10016 |
| Country |
USA |
| |
|
| Platform ID |
GPL24247 |
| Series (2) |
| GSE167549 |
The NK cell stress response status modulates anti-tumor immunity [ATAC-seq] |
| GSE167552 |
The stress response regulator HSF1 modulates natural killer cell anti-tumour immunity |
|
| Relations |
| BioSample |
SAMN18058561 |
| SRA |
SRX10170251 |
