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Sample GSM5107417 Query DataSets for GSM5107417
Status Public on Feb 26, 2021
Title RNA-Seq splenic NK - MUT 5
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 total RNA
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. 3-5 x 10^5 NK cells from each mouse were used for isolation of total RNA using the RNeasy Plus Micro Kit (Qiagen)
Libraries were generated with the SMART-seq HT Kit (Takara Bio no. 634438)
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
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 splice-aware STAR aligner.
The featureCounts program was used to to generate counts for each gene based on how many aligned reads overlapped the exons of that gene
These counts were then normalized and used to test for differential expression using negative binomial generalized linear models implemented by the DESeq2 R package.
Genome_build: mm10
Supplementary_files_format_and_content: counts.raw.csv consist of counts for each gene based on aligned reads; counts.normalized.csv consists of raw counts that have been normalized to library size
 
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)
GSE167550 The NK cell stress response status modulates anti-tumor immunity [RNA-seq]
GSE167552 The stress response regulator HSF1 modulates natural killer cell anti-tumour immunity
Relations
BioSample SAMN18058578
SRA SRX10170261

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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