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Sample GSM8281697 Query DataSets for GSM8281697
Status Public on Jun 03, 2024
Title paneth cells, IFNAR1 KO, PBS, rep 3
Sample type SRA
Source name small intestine
Organism Mus musculus
Characteristics cell type: purified paneth cells
genotype: IFNAR1 KO
strain: C57BL/6J
treatment: PBS
time: 15h
tissue: small intestine
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
Description PBS-3
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 mm39 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 20, 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)
GSE267927 PanethcellTNF-signalinginducesbacterialsepsis: PC transcriptome 15h ater TNF in IFNARKO mice
BioSample SAMN41463933
SRA SRX24614247

Supplementary data files not provided
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Raw data are available in SRA

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