Shaped Chain Elongating Microbiome
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ABSTRACT:
PROVIDER: PRJNA686230 | ENA |
REPOSITORIES: ENA
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Project description:Chain elongating microbiome Raw sequence reads
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Project description:The study by Allaart et al. (2023) investigates whether different environmental conditions can alter chain-elongating microbial communities to exhibit different catabolic stoichiometries. In support of the study, we provide whole-cell lysate shotgun proteomics data that compare the tested conditions. Contact: M.T.Allaart@tudelft.nl
2023-10-24 | PXD040972 | Pride
Project description:This study evaluated transcriptomic responses to submergence in elongating and non-elongating leaves of rice near-isogenic lines with and without SUB1A using RNA-Seq. SUB1A is an ERF transcription factor gene and the key regulator of submergence tolerance in rice, restricting underwater elongation and avoiding starvation under the stress. Submergence induces mRNA accumulation of SUB1A similarly in elongating and non-elongating leaves. This study uncovered SUB1A-dependent and independent regulation of adaptive responses to submergence in the two functionally distinct leaves at the global level.
2022-08-01 | GSE181336 | GEO
Project description:The human stool samples were collected and processed for in vitro culturing under anaerobic condition using rapidAIM assay with or without SAHA, an lysine deacetylase inhibitor, for evaluating the effects of SAHA on human gut microbiome. Metaproteomics were used to analyze the microbiome composition and functions.
2022-03-01 | PXD016388 | Pride
Project description:Early life exposure to antibiotics alters the gut microbiome. These alterations lead to changes in metabolic homeostasis and an increase in host adiposity. We used microarrays to identify metabolic genes that may be up- or down-regulated secondary to antibiotic exposure. Low dose antibiotics have been widely used as growth promoters in the agricultural industry since the 1950’s, yet the mechanisms for this effect are unclear. Because antimicrobial agents of different classes and varying activity are effective across several vertebrate species, we hypothesized that such subtherapeutic administration alters the population structure of the gut microbiome as well as its metabolic capabilities. We generated a model of adiposity by giving subtherapeutic antibiotic therapy (STAT) to young mice and evaluated changes in the composition and capabilities of the gut microbiome. STAT administration increased adiposity in young mice and altered hormones related to metabolism. We observed substantial taxonomic changes in the microbiome, changes in copies of key genes involved in the metabolism of carbohydrates to short-chain fatty acids (SCFA), increases in colonic SCFA levels, and alterations in the regulation of hepatic metabolism of lipids and cholesterol. In this model, we demonstrate the alteration of early life murine metabolic homeostasis through antibiotic manipulation. C57BL6 mice were divided into low-dose penicillin or control groups. Given antibiotics via drinking water after weaning. Sacrificed and liver sections collected for RNA extraction.
2012-06-30 | E-GEOD-38880 | biostudies-arrayexpress
Project description:Emerging data has highlighted the importance of short-chain fatty acids (SCFAs) on ruminal microbiome and derived metabolism profiling, and ruminal epithelial health and nutritional absorption in ruminants. However, little is known about the roles of SCFAs on ileal microbiome profiles. Here, we combined infusion of three SCFAs, to study their different roles in ileal microbiome succession profiling using a in vivo goat model.
2023-08-14 | GSE240818 | GEO
Project description:We reasoned that the pi-RISC, by virtue of the enormous sequence portfolio of piRNAs, might mediate elimination of a large variety of mRNAs in late stages of spermiogenesis. Both Miwi-null and Caf1-null mice showed early spermiogenic arrest, preventing us from determining the role of MIWI and CAF1 in elongating spermatids using the existing genetic models. We therefore used microarrays to detail the global effect of MIWI or CAF1 on mRNA levels in mouse elongating spermatids. Using GFP+ elongating spermatids sorted from mouse testes transduced with shMiwi:GFP, shCaf1:GFP, or control pSilencer:GFP, we performed transcriptome profiling on Affymetrix mouse arrays.
2014-07-11 | E-GEOD-59291 | biostudies-arrayexpress