|
| Status |
Public on Feb 26, 2021 |
| Title |
RNA-Seq splenic NK - WT 3 |
| 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 |
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 |
SAMN18058581 |
| SRA |
SRX10170260 |
