|
Status |
Public on Jul 31, 2022 |
Title |
T_cell_LCMV_KO-3 |
Sample type |
SRA |
|
|
Source name |
T cells
|
Organism |
Mus musculus |
Characteristics |
tissue: T cells genotype: SRSF-1 KO treatment: LCMV acute infection 8 days
|
Treatment protocol |
Mice were infected via intraperitoneal injection (i.p.) with 105 PFU and maintained for 8 days in the Animal Research facility at BIDMC. On day 8 post infection, mice were euthanized, and tissues were collected for downstream procedures
|
Growth protocol |
Total T cells were isolated from spleens by magnetic assisted cell sorting (MACS), using the Pan T cell isolation kit (Miltenyi Biotech).
|
Extracted molecule |
total RNA |
Extraction protocol |
Total RNA was extracted using the RNeasy mini kit (Qiagen) and submitted for RNA sequencing to the Molecular Biology Core Facilities at the Dana-Farber Cancer Institute (DFCI) Libraries were prepared using Roche Kapa mRNA HyperPrep strand specific sample preparation kits from 200ng of purified total RNA according to the manufacturer’s protocol on a Beckman Coulter Biomek i7
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|
|
Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina NovaSeq 6000 |
|
|
Data processing |
Qubit fluorometer and Agilent TapeStation 4200 Uniquely dual indexed libraries were pooled in an equimolar ratio and shallowly sequenced on an Illumina MiSeq to further evaluate library quality and pool balance. The final pool was sequenced on an Illumina NovaSeq 6000 targeting 40 million 150bp read pairs per library at the Dana-Farber Cancer Institute Molecular Biology Core Facilities Sequenced reads were aligned to the UCSC mm10 reference genome assembly and gene counts were quantified using STAR (v2.7.3a) Differential gene expression testing was performed by DESeq2 (v1.22.1) and RNAseq analysis was performed using the VIPER snakemake pipeline Assembly: mm10 Supplementary files format and content: STAR_Gene_Counts.csv : raw read counts
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|
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Submission date |
Apr 19, 2022 |
Last update date |
Jul 31, 2022 |
Contact name |
Sean Lawler |
E-mail(s) |
sean_lawler@brown.edu
|
Organization name |
Brigham and Women's Hospital
|
Street address |
75 Francis St
|
City |
Boston |
State/province |
MA |
ZIP/Postal code |
02115 |
Country |
USA |
|
|
Platform ID |
GPL24247 |
Series (1) |
GSE201028 |
Effect of SRSF1 splicing factor knockdown in the physiology and function of cytotoxic CD8 T lymphocytes and a potential molecular mechanism in viral immunopathogenesis |
|
Relations |
BioSample |
SAMN27629960 |
SRA |
SRX14908262 |