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Sample GSM5107410 Query DataSets for GSM5107410
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)
 
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 SAMN18058556
SRA SRX10170254

Supplementary file Size Download File type/resource
GSM5107410_MUT-26.bed.gz 665.4 Kb (ftp)(http) BED
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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