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SRX2683645: GSM2559431: WT_infected_18h_Salmonella TCRgd+_2; Mus musculus; RNA-Seq
1 ILLUMINA (NextSeq 500) run: 24.4M spots, 1.9G bases, 720.3Mb downloads

Submitted by: NCBI (GEO)
Study: Intestinal epithelial and intraepithelial T cell crosstalk mediates a dynamic response to infection
show Abstracthide Abstract
Oral infection of mice with Salmonella Typhimurium leads to rapid changes in small intestinal TCRgd IEL behavior. How these changes are induced is currently unknown. By analyzing the transcriptome of TCRgd and intestinal epithelial cells in the steady state and after infection, we find a potential role for epithelial cell MYD88 expression in regulating the IEL response. By additionally analyzing the transcriptome of epithelial cell-specific, conditional Myd88 knockout animals after Salmonella infection, we address the role of epithelial cell Myd88 signaling in regulating the IEL and EC response to Salmonella infection. Overall design: 3 types of mice were used: wildtype C57BL/6 mice, Villin-Cre Myd88ff and Cre negative control mice (C57BL/6 background). Wildtype mice were naïve or orally infected with 10^8 CFU of Salmonella enterica serovar Typhimurium (SL1344) and IELs were harvested from the small intestine after 18 hours. Villin-Cre Myd88ff and Cre negative control mice were treated with Tamoxifen. 1 week after Tamoxifen treatment, mice were orally infected with 10^8 CFU of Salmonella enterica serovar Typhimurium (SL1344) and IELs were harvested from the small intestine after 18 hours.
Sample: WT_infected_18h_Salmonella TCRgd+_2
SAMN06651615 • SRS2080852 • All experiments • All runs
Organism: Mus musculus
Library:
Instrument: NextSeq 500
Strategy: RNA-Seq
Source: TRANSCRIPTOMIC
Selection: cDNA
Layout: SINGLE
Construction protocol: Intraepithelial lymphocytes were isolated as previously described(Mucida et al., 2007). Briefly, small and large intestines were removed and placed in chilled HBSS media (Gibco) containing 2% FCS. The intestines were carefully cleaned from the mesentery and flushed of fecal content. Intestines were opened longitudinally and then cut into 1 cm pieces. The intestinal tissue was transferred to a 50 ml Falcon tubes containing 25 ml of cold HBSS complemented with 2% FCS and 5 mM EDTA and shaken (2x) at 230 rpm for 20 min at 37°C. The tissue suspension was passed through a stainless steel sieve into 50-ml conical tubes and the cells were pelleted by centrifugation at 1200 rpm for 10 min at 4°C. The cell pellet was resuspended in complete HBSS, layered over a discontinuous 40/70% Percoll gradient, and centrifuged at 2000 rpm for 30 min. Cells from the 40/70% interface were collected, washed and resuspended in complete RPMI media. These purified cells constituted the intraepithelial lymphocyte (IEL) population. Cells were sorted using a FACS ARIAII with markers as shown above. Total RNA was extracted using the RNAeasy kit from Qiagen. For total RNA from TCRgd IELs, RNA libraries were prepared using the SMART-Seq™ v4 Ultra™ Low Input RNA kit (ClonTech Labs) . For total RNA from intestinal epithelial cells, RNA libraries were prepared using TruSeq® Stranded mRNA Sample Preparation. All samples were sequenced using 75 base pair single end reading on a NextSeq 500 instrument (Illumina) at High Output setting.
Experiment attributes:
GEO Accession: GSM2559431
Links:
Runs: 1 run, 24.4M spots, 1.9G bases, 720.3Mb
Run# of Spots# of BasesSizePublished
SRR538866224,387,9151.9G720.3Mb2017-09-21

ID:
3868685

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