NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM7226718 Query DataSets for GSM7226718
Status Public on Jun 07, 2023
Title mesenteric lymph nodes, PBS, rep3
Sample type SRA
 
Source name mesenteric lymph node
Organism Mus musculus
Characteristics cell type: mesenteric lymph node
genotype: WT
treatment: PBS control
time: 48 hours post T1L infection
Extracted molecule polyA RNA
Extraction protocol RNA from mesenteric lymph node was prepared using the RNeasy Mini Kit (Qiagen, 74136)
libraries were prepared using the Illumina TruSeq protocol
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2000
 
Data processing Reads were aligned to mouse reference genome mm10 (GRCm38).
Raw FASTQ files were processed using kallisto (v0.46.0) to obtain abundances (TPM) as well as the counts (Bray et al., 2016).
Sleuth (v0.30.0), an R (v4.2.0)/ Bioconductor package was used to identify differentially expressed transcripts among the groups of interest.
Assembly: mm10
Supplementary files format and content: Excel files include normalized reads
 
Submission date Apr 25, 2023
Last update date Jun 07, 2023
Contact name Reinhard Hinterleitner
E-mail(s) REINHARD@pitt.edu
Organization name University of Pittsburgh
Department Immunology
Street address 5051 Centre Avenue
City PITTSBURGH
State/province PA
ZIP/Postal code 15213
Country USA
 
Platform ID GPL13112
Series (1)
GSE230558 A gut commensal protist protects against virus-mediated loss of oral tolerance_2
Relations
BioSample SAMN34369755
SRA SRX20097522

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap