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Sample GSM8278849 Query DataSets for GSM8278849
Status Public on Jun 03, 2024
Title paneth cells, PBS, rep 2
Sample type SRA
 
Source name purified paneth cells
Organism Mus musculus
Characteristics tissue: purified paneth cells
strain: C57BL/6J
treatment: PBS
time: 15h
Treatment protocol mice were injected with PBS or TNF. The small intestine was isolaed after 15h and PC were purified using a cell sorter for RNA isolation
Extracted molecule total RNA
Extraction protocol RNA was obtained with the Aurum Total RNA Mini kit (Bio-Rad) according to the manufacturer’s protocol
RNA was used to generate a sequencing libary for the Element AVITI accoring to the manufacturers instructions from the AVITI 150 cycles Cloudbreak sequencing kit single-end reads
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Element AVITI
 
Data processing Reads were quality checked with fastqc and quality filtered with trimmomatic (v0.39; parameters:SLIDINGWINDOW:4:30 MINLEN:50)
Reads were aligned to the mm10 reference genome with the STAR aligner (v2.7.10a) and read counts were directly obtained using the "--quantMode GeneCounts" parameter for STAR
Differential expression analysis was done using the DESeq2 package, with the FDR set at 5%
Assembly: mm39
Supplementary files format and content: matrix of raw counts for all samples
 
Submission date May 17, 2024
Last update date Jun 03, 2024
Contact name Steven Timmermans
Organization name VIB-UGent
Street address Technologiepark 71
City Gent
ZIP/Postal code 9052
Country Belgium
 
Platform ID GPL34475
Series (1)
GSE267790 PanethcellTNF-signalinginducesbacterialsepsis: PC transcriptome 15h ater TNF
Relations
BioSample SAMN41439972
SRA SRX24594977

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA

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