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SRX4140995: GSM3165065: 4C-WT-4-LPS; Mus musculus; RNA-Seq
1 ILLUMINA (Illumina HiSeq 3000) run: 7.7M spots, 1.2G bases, 468.2Mb downloads

Submitted by: NCBI (GEO)
Study: Casp8- and Casp11-dependent gene expression in ileal mucosa of LPS-challenged male mice
show Abstracthide Abstract
The execution of shock following high dose E. coli lipopolysaccharide (LPS) or bacterial sepsis in mice required pro-apoptotic caspase-8 in addition to pro-pyroptotic caspase-11 and gasdermin d. Hematopoietic cells produced MyD88- and TRIF-dependent inflammatory cytokines sufficient to initiate LPS shock independent of caspase-8 or caspase-11. Both proteases had to be present to support tissue injury, dependent upon TNF and interferon ?, first observed in the small intestine and later in spleen and thymus. Caspase-11 enhanced the activation of caspase-8 and extrinsic cell death machinery within the lower small intestine. Neither caspase-8 nor caspase-11 was individually sufficient for shock, but collaborated to amplify the inflammatory signals associated with tissue injury. Therefore, combined pyroptotic and apoptotic signaling mediated endotoxemia independent of RIPK1 kinase activity and RIPK3 function. These observations bring to light the relevance of tissue compartmentalization during inflammatory signaling in vivo where cytokines execute diverse cell death pathways and tissue damage. Overall design: Ileum was harvested from Wt (C57BL/6), Casp8-RIPK3-deficient and Casp11-deficient mice (5 male for each group) at 1.5 h post challenge with high dose LPS (54 mg/kg). Excised tissues were maintained in RNAlater solution for 24 h and RNA was harvested from mucosa.
Sample: 4C-WT-4-LPS
SAMN09281538 • SRS3354816 • All experiments • All runs
Organism: Mus musculus
Library:
Instrument: Illumina HiSeq 3000
Strategy: RNA-Seq
Source: TRANSCRIPTOMIC
Selection: cDNA
Layout: SINGLE
Construction protocol: For transcriptome (RNASeq/RefSeq) analysis , ileum from each WT, Casp8–/–Ripk3–/– and Casp11-negative mouse (5 male mice per group) harvested at 1.5 hpc was placed in RNAlater (Thermo-Fisher) at 4C. 24 h post-harvest, intestines were cleaned with cold RNAlater and mucus was scraped, homogenized and pelleted as described for immunoblot analysis. RNA isolation and further steps for transcriptome analysis were carried out as described (Sandler et al., 2014) in the NHP Genomics Core, Yerkes National Primate Research Center. Briefly, total RNA was isolated from mucus pellet for each sample using RNeasy Micro and RNA integrity was tested using Agilent Bioanalyzer capillary electrophoresis. cDNA libraries were prepared using Illumina Stranded RNATruSeq kits and barcoded as well as sequenced on an Illumina HiSeq 3000. Five million 150-base pair mapping reads were obtained per sample, with >90% reads having Q-Scores of >30 (>99.9% estimated accuracy for 150 base reads).
Experiment attributes:
GEO Accession: GSM3165065
Links:
Runs: 1 run, 7.7M spots, 1.2G bases, 468.2Mb
Run# of Spots# of BasesSizePublished
SRR72345867,680,1731.2G468.2Mb2018-08-08

ID:
5627263

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