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Sample GSM6862365

Query DataSets for GSM6862365

Status

Public on Dec 22, 2022

Title

LCMVDiv1.2

Sample type

SRA

Source name

Spleen

Organism

Mus musculus

Characteristics

tissue: Spleen
cell type: P14 CD8 T cell
sequencing batch: 2

Extracted molecule

total RNA

Extraction protocol

Cell sorting was performed by FACS Aria II (BD Biosciences). For RNA-seq of P14s in LCMV Arm or in TRAMPC1-GP bearing mice, Live, CD4-CD14-CD19-, CD45.1+CD8+CD44+PD1+ were sorted. For RNA-seq of endogenous CD8 T cells from tumor, Live, CD4-CD14-CD19-Ly6G-, CD8+CD44+PD1+ 127+ or TIM3+ were sorted. performed by FACS Aria II (BD Biosciences). For RNA-seq of P14s in LCMV Arm or in TRAMPC1-GP bearing mice, Live, CD4-CD14-CD19-, CD45.1+CD8+CD44+PD1+ were sorted. For RNA-seq of endogenous CD8 T cells from tumor, Live, CD4-CD14-CD19-Ly6G-, CD8+CD44+PD1+ 127+ or TIM3+ were sorted. Qiagen micro RNA/DNA all prep columns were used for RNA extraction.

Library strategy

RNA-Seq

Library source

transcriptomic

Library selection

cDNA

Instrument model

Illumina HiSeq 3000

Description

P14 TCR transgenic CD8 T cells specific for GP33 epitope of LCMV. Activated P14s sorted from LCMV Armstrong infection, TDLN and tumor of TRAMPC1-GP bearing mice, or naïve spleen.

Data processing

Aligned with HISAT2
Reads counted with subread/featurecounts
normalization and differential expression with DESEQ2
Assembly: mm10
Supplementary files format and content:CSV file with raw counts for all genes and samples

Submission date

Dec 20, 2022

Last update date

Jan 04, 2023

Contact name

Haydn Kissick

E-mail(s)

haydn.kissick@emory.edu

Phone

6172598364

Organization name

Emory University