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GEO help: Mouse over screen elements for information. |
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Status |
Public on Jun 07, 2023 |
Title |
mesenteric lymph nodes, PBS, rep3 |
Sample type |
SRA |
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Source name |
mesenteric lymph node
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Organism |
Mus musculus |
Characteristics |
cell type: mesenteric lymph node genotype: WT treatment: PBS control time: 48 hours post T1L infection
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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
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Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina HiSeq 2000 |
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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
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Submission date |
Apr 25, 2023 |
Last update date |
Jun 07, 2023 |
Contact name |
Reinhard Hinterleitner |
E-mail(s) |
REINHARD@pitt.edu
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Organization name |
University of Pittsburgh
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Department |
Immunology
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Street address |
5051 Centre Avenue
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City |
PITTSBURGH |
State/province |
PA |
ZIP/Postal code |
15213 |
Country |
USA |
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Platform ID |
GPL13112 |
Series (1) |
GSE230558 |
A gut commensal protist protects against virus-mediated loss of oral tolerance_2 |
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Relations |
BioSample |
SAMN34369755 |
SRA |
SRX20097522 |
Supplementary data files not provided |
SRA Run Selector |
Raw data are available in SRA |
Processed data are available on Series record |
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