|
Status |
Public on Feb 26, 2021 |
Title |
ATAC-Seq splenic NK - MUT 26 |
Sample type |
SRA |
|
|
Source name |
splenic NK cells
|
Organism |
Mus musculus |
Characteristics |
genotype: HSF1-S303/7A
|
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)
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|
|
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
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|
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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 |
SAMN18058556 |
SRA |
SRX10170254 |