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Sample GSM6048789 Query DataSets for GSM6048789
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
 
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
 
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

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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