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Sample GSM8324582 Query DataSets for GSM8324582
Status Public on Jun 13, 2024
Title n5-pH6_6
Sample type SRA
 
Source name CD8+ T cell
Organism Mus musculus
Characteristics cell type: CD8+ T cell
treatment: 24 hours culture at pH6.6
Growth protocol DMEM low glucose, glutamax, pyruvate supplemented with 10% FBS, 1% NEAA, 1% P/S, 50uM b-mercaptoethanol - Cultured at 37°C/5% CO2
Extracted molecule total RNA
Extraction protocol Ficoll to remove dead cells, washes twice with PBS, then RNA extraction using Qiagen RNeasy extraction kit
Illumina Truseq stranded mRNA
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2500
 
Data processing Purity-filtered reads were adapters and quality trimmed with Cutadapt (v. 1.8, Martin 2011). Reads matching to ribosomal RNA sequences were removed with fastq_screen (v. 0.9.3).
Remaining reads were further filtered for low complexity with reaper (v. 15-065, Davis et al. 2013).
Reads were aligned against Mus musculus build GRCm38 genome using STAR (v. 2.5.2b, Dobin et al. 2013). The number of read counts per gene locus was summarized with htseq-count (v. 0.6.1, Anders et al. 2014) using Ensembl 86 gene annotation. Quality of the RNA-seq data alignment was assessed using RSeQC (v. 2.3.7, Wang et al. 2012)
Assembly: GRCm38
Supplementary files format and content: tab-delimited text file includes raw counts per sample
 
Submission date Jun 12, 2024
Last update date Jun 13, 2024
Contact name Isaac Crespo
E-mail(s) Isaac.crespo-casajus@chuv.ch
Organization name Ludwig Cancer Research,UNIL
Department Oncology
Lab Hi-TIDe: T cell systems engineering group
Street address Bugnon 25A
City Lausanne
State/province Vaud
ZIP/Postal code 1005
Country Switzerland
 
Platform ID GPL17021
Series (1)
GSE269681 Acidity perturbs IL-2 responsiveness, mTORC1 and c-Myc in CD8+ T cells
Relations
BioSample SAMN41806337
SRA SRX24892179

Supplementary file Size Download File type/resource
GSM8324582_32.processed_counts.txt.gz 168.5 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA

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