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Sample GSM7225697 Query DataSets for GSM7225697
Status Public on Apr 30, 2023
Title mLN_control_2
Sample type SRA
 
Source name mesenteric lymph node
Organism Mus musculus
Characteristics tissue: mesenteric lymph node
cell type: transferred CD45.1+CD8+ OTI T cells
genotype: WT
Sex: Female
treatment: Lm-OVA infection in recipient mice
Extracted molecule total RNA
Extraction protocol RNA was harvested using Rneasy micro plus kit (Qiagen).
Nextera Smarter following manufacture's protocol
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 4000
 
Description Standard_TMDI_raw_counts.txt
Data processing Read were mapped to the UCSC mm10 mouse genome with STAR v.2.7.4.
The biological QC was performed with picard tools
Table of counts was prepared with HTseq v0.9.1.
After normalization, the differential expression analysis was performed with the package edgeR (v1.34.1) in R.
PCA were obtained using Deseq2
Assembly: UCSC mm10 mouse genome
Supplementary files format and content: txt file containing raw counts of each sample (naïve, mLN, LILP)
Supplementary files format and content: excel file containing raw counts of each sample (highOVA, lowOVA)
 
Submission date Apr 25, 2023
Last update date Apr 30, 2023
Contact name Liqing Cheng
E-mail(s) Liqing.Cheng@unige.ch
Organization name University of Geneva
Street address 1 rue Michel-Servet 1
City Geneva
ZIP/Postal code 1211
Country Switzerland
 
Platform ID GPL21103
Series (1)
GSE230515 Local antigen is required for CD8+ tissue resident memory T cell (Trm) generation in large intestine
Relations
BioSample SAMN34361376
SRA SRX20094572

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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