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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Aug 15, 2020 |
| Title |
RNA-seq of WT liver with DEX, Zn and untreated controls |
| Organism |
Mus musculus |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
The cytokine TNF drives inflammatory diseases, e.g. Crohn disease. In a mouse model of TNF-induced systemic inflammatory response syndrome (SIRS), severe impact on intestinal epithelial cells (IECs) is observed. Zinc confers complete protection in this model. We found that zinc no longer protects in animals which lack glucocorticoids (GCs), or express mutant versions of their receptor GR in IECs, nor in mice which lack gut microbiota. RNA-seq studies in IECs showed that zinc caused reduction of expression of constitutive (STAT1-induced) interferon-stimulated response (ISRE) genes and Interferon Regulatory Factor (IRF) genes. Since some of these genes are involved in TNF-induced cell death in intestinal crypt Paneth cells, and since zinc has direct effects on the composition of the gut microbiota (such as several Staphylococcus species) and on TNF-induced Paneth cell death, we postulate a new zinc-related anti-inflammatory mechanism. Zinc modulates the gut microbiota, causing less induction of ISRE/IRF genes in crypt cells, less TNF-induced necroptosis in Paneth cells and less fatal evasion of gut bacteria into the system.
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| Overall design |
Examination of changes in gene expresion in liver of mice after treatment with DEX, Zinc or DEX+Zinc and a control group a total of 12 samples was sequenced in 4 conditions with 3 (biological) replicates/condition
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| Contributor(s) |
Souffriau J, Timmermans S, Vanderhaeghen T, Wallaeys C, Van Looveren K, Aelbrecht L, Dewaele S, Vandewalle J, Goossens E, Verbanck S, Boyen F, Eggermont M, De Commer L, De Rycke R, De Bruyne M, Tito R, Ballegeer M, Vandevyver S, Velho T, Moita LF, Hochepied T, De Bosscher K, Raes J, Van Immerseel F, Beyaert R, Libert C |
| Citation(s) |
32914580 |
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| Submission date |
Aug 14, 2020 |
| Last update date |
Oct 13, 2020 |
| Contact name |
Steven Timmermans |
| Organization name |
VIB-UGent
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| Street address |
Technologiepark 71
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| City |
Gent |
| ZIP/Postal code |
9052 |
| Country |
Belgium |
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| Platforms (1) |
| GPL19057 |
Illumina NextSeq 500 (Mus musculus) |
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| Samples (12)
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| GSM4728276 |
normal drinking water + DEX injection, rep1 [liver_HD-1] |
| GSM4728277 |
normal drinking water + DEX injection, rep2 [liver_HD-2] |
| GSM4728278 |
normal drinking water + DEX injection, rep3 [liver_HD-3] |
| GSM4728279 |
normal drinking water + PBS injection,(control) rep1 [liver_HP-1] |
| GSM4728280 |
normal drinking water + PBS injection,(control) rep2 [liver_HP-2] |
| GSM4728281 |
normal drinking water + PBS injection,(control) rep3 [liver_HP-3] |
| GSM4728282 |
zinc supplemented drinking water + DEX injection, rep1 [liver_ZD-1] |
| GSM4728283 |
zinc supplemented drinking water + DEX injection, rep2 [liver_ZD-2] |
| GSM4728284 |
zinc supplemented drinking water + DEX injection, rep3 [liver_ZD-3] |
| GSM4728285 |
zinc supplemented drinking water + PBS injection, rep1 [liver_ZP-1] |
| GSM4728286 |
zinc supplemented drinking water + PBS injection, rep2 [liver_ZP-2] |
| GSM4728287 |
zinc supplemented drinking water + PBS injection, rep3 [liver_ZP-3] |
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| Relations |
| BioProject |
PRJNA657263 |
| SRA |
SRP277546 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE156282_counts.txt.gz |
560.7 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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