Ontology highlight
ABSTRACT:
PROVIDER: PRJNA944604 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Metabolic landscape of the male mouse gut identifies different niches determined by microbial activities
2023-03-13 | MSV000091478 | GNPS
Project description:Metabolic landscape of the male mouse gut identifies different niches determined by microbial activities
2023-03-13 | MSV000091478 | MassIVE
Project description:<p>Sertoli cell-only syndrome is severe form of human male infertility in which most seminiferous tubules appear to lack all spermatogenic cells, including spermatogonial stem cells (SSCs). However, a few small tubule segments of some patients have active spermatogenesis and, thus, functional stem cell niches and SSCs. Normally SSCs replicate, migrate and refill adjacent empty niches, but this does not appear to occur in SCO syndrome. We hypothesized that this failure occurs because most niches are dysfunctional. As Sertoli cells are essential to formation of these niches, we used RNAseq to compare the transcriptomes of human testes with qualitatively normal (complete) spermatogenesis (n=4) with the transcriptomes of human testes with SCO syndrome (n=7). We then focused our analysis on the expression of transcripts that bioinformatic analyses identified as Sertoli cell signature transcripts. Results show that Sertoli cells in SCO testes express abnormally low levels of GDNF, FGF8 and BMP4, all of which are important regulators of mouse SSCs and/or progenitor spermatogonia. Sertoli cells in SCO testes express significantly reduced levels of transcripts for proteins that polarize the Sertoli cell plasma membrane and regulate the trafficking of cell adhesion and gap junction proteins in and out of that plasma membrane.</p>
| phs001777 | dbGaP
Project description:Ustilago maydis is an important plant pathogen causing corn-smut disease and an effective biotechnological production host. The lack of a comprehensive metabolic overview hinders a full understanding of the organism’s environmental adaptation and a full use of its metabolic potential. Here, we report the first genome scale metabolic model (GSMM) of Ustilago maydis (iUma22) for the simulation of metabolic activities. iUma22 was reconstructed from sequencing and annotation using PathwayTools, the biomass equation was derived from literature values and from the codon composition. The final model contains over 25% of annotated genes (6,909) in the sequenced genome. Substrate utilization was corrected by Biolog-Phenotype arrays and exponential batch cultivations were used to test growth predictions. The growth data revealed a metabolic phenotype shift at high glucose uptake rates and the model allowed its quantification. A pan-genome of four different U. maydis strains revealed missing metabolic pathways in iUma22. The new model allows studies of metabolic adaptations to different environmental niches as well as for biotechnological applications.
2024-05-22 | MODEL2203250001 | BioModels
Project description:Mammalian sex is determined by a network of antagonistic genes that are well characterized. However, its non-coding regulation is still largely unknown. Here we explore the 3D chromatin landscape of sex determination in vivo. We integrate Hi-C with ChIP-seq experiments using METALoci, a novel genome spatial auto-correlation analysis approach that identifies 3D regulatory hubs across the genome. We uncover a prominent rewiring of chromatin interactions during sex determination. By combining predictive approaches and validations in transgenic mice we identify a novel Fgf9 regulatory hub, which deletion results in male-to-female sex reversal.
2022-11-21 | GSE217616 | GEO
Project description:Mammalian sex is determined by a network of antagonistic genes that are well characterized. However, its non-coding regulation is still largely unknown. Here we explore the 3D chromatin landscape of sex determination in vivo. We integrate Hi-C with ChIP-seq experiments using METALoci, a novel genome spatial auto-correlation analysis approach that identifies 3D regulatory hubs across the genome. We uncover a prominent rewiring of chromatin interactions during sex determination. By combining predictive approaches and validations in transgenic mice we identify a novel Fgf9 regulatory hub, which deletion results in male-to-female sex reversal.
2022-11-21 | GSE217617 | GEO
Project description:Adult male and female C56BL6J mice were subjected to 8 weeks of small mouse cage (SMC) intervention to model physical inactivity. Widely-used physical inactivity models such as hindlimb unloading and immobilization do not phenocopy metabolic adaptations that occur with human sedentary behavior, whereas many aspects of metabolic adaptations with SMC appear to reproduce this effect. The RNAseq analyses were performed in muscles from these mice to capture changes in skeletal muscle gene expression landscape.
2024-03-06 | GSE260612 | GEO
Project description:Total mRNA seq was perfomed on widtype and Ret null male mouse embryonic gut at E10.5
2018-04-01 | GSE99232 | GEO
Project description:The human gut microbiota is a metabolic organ whose cellular composition is determined by a dynamic process of selection and competition. To identify microbial genes required for establishment of human symbionts in the gut, we developed an approach (insertion-sequencing, or INSeq) based on a mutagenic transposon that allows capture of adjacent chromosomal DNA to define its genomic location. We used massively parallel sequencing to monitor the relative abundance of tens of thousands of transposon mutants of a saccharolytic human gut bacterium, Bacteroides thetaiotaomicron, as they established themselves in wild-type and immunodeficient gnotobiotic mice, in the presence or absence of other human gut commensals. In vivo selection transforms this population, revealing functions necessary for survival in the gut: we show how this selection is influenced by community composition and competition for nutrients (vitamin B12). INSeq provides a broadly applicable platform to explore microbial adaptation to the gut and other ecosystems. Keywords: Other 57 samples analyzed, 1 of these is the reference (input) sample
2009-09-15 | E-GEOD-17712 | biostudies-arrayexpress