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Sample GSM6176452 Query DataSets for GSM6176452
Status Public on Aug 19, 2022
Title Naive P14 cells 2
Sample type SRA
 
Source name splenic CD8+ T cells
Organism Mus musculus
Characteristics cell type: CD8+ T cells
strain: C57BL/6
tissue: spleen
Extracted molecule total RNA
Extraction protocol 10000 cells were sorted of each population. Rneasy Plus Mini Kit (Quiagen) was used for RNA isolation according to the manufacturer's protocol.
SMART-Seq V4 Ultra Low Input RNA Kit (Takara) was used according to the manufacturer's protocol for library contruction.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NovaSeq 6000
 
Description bulkRNA-Seq of 10000 cells
Data processing RNA-seq reads were aligned to the mouse reference genome GRCm38/mm10 using STAR (Version 2.5.4). Read counts per gene locus were obtained using htseq-count (Version 0.11.4).
R package DESeq2 (version 1.26.0) was used to perform size factor normalization and differential expression analysis. Batch effects were identified using sva (Version 3.34.0) and subsequently modelled in the design formula of DESeq2.
Assembly: mm10
Supplementary files format and content: Matrix table, in txt format, with raw read counts per gene locus from htseq-count.
 
Submission date May 23, 2022
Last update date Aug 19, 2022
Contact name Lorenz Kretschmer
E-mail(s) lorenz.kretschmer@tum.de
Organization name TU Munich
Department Institute for Medical Microbiology, Immunology and Hygiene
Lab Dr. Veit R. Buchholz
Street address Trogerstr. 30
City Munich
State/province Bavaria
ZIP/Postal code 81675
Country Germany
 
Platform ID GPL24247
Series (2)
GSE203575 c-Myb instructs both stemness and functional exhaustion of CD8+ T cells during chronic infection [bulkRNA-seq]
GSE205608 c-Myb instructs both stemness and functional exhaustion of CD8+ T cells during chronic infection
Relations
BioSample SAMN28596931
SRA SRX15413945

Supplementary file Size Download File type/resource
GSM6176452_Sample16_htseq_count.txt.gz 81.9 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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