Project description:Cornea exhibits distinct curvature-dependent mechanical environments that influence stromal cell phenotype and extracellular matrix remodeling. In this study, we employed a hydraulically-controlled cornea-on-a-chip platform to systematically vary curvature and examine transcriptional and phenotypic responses of human corneal keratocytes. RNA sequencing revealed differential expression profiles associated with curvature states that mimic pathological conditions such as cornea plana and keratoconus. Curvature-dependent regulation of extracellular matrix genes, cytoskeletal organization, and signaling pathways was validated with qPCR and immunostaining. These findings provide transcriptomic insights into how corneal tissue geometry contributes to disease progression and may inform future therapeutic strategies for corneal ectatic disorders.

2025-09-30 | GSE308374 | GEO

Tropheryma whipplei proteome - Analyses of new genomic, transcriptomic or proteomic data commonly result in trashing many unidentified data escaping the ‘canonical’ DNA-RNA-protein scheme

Project description:Analyses of new genomic, transcriptomic or proteomic data commonly result in trashing many unidentified data escaping the ‘canonical’ DNA-RNA-protein scheme. Testing systematic exchanges of nucleotides over long stretches produces inversed RNA pieces (here named “swinger” RNA) differing from their template DNA. These may explain some trashed data. Here analyses of genomic, transcriptomic and proteomic data of the pathogenic Tropheryma whipplei according to canonical genomic, transcriptomic and translational 'rules' resulted in trashing 58.9% of DNA, 37.7% RNA and about 85% of mass spectra (corresponding to peptides). In the trash, we found numerous DNA/RNA fragments compatible with “swinger” polymerization. Genomic sequences covered by «swinger» DNA and RNA are 3X more frequent than expected by chance and explained 12.4 and 20.8% of the rejected DNA and RNA sequences, respectively. As for peptides, several match with “swinger” RNAs, including some chimera, translated from both regular, and «swinger» transcripts, notably for ribosomal RNAs. Congruence of DNA, RNA and peptides resulting from the same swinging process suggest that systematic nucleotide exchanges increase coding potential, and may add to evolutionary diversification of bacterial populations.

2017-12-18 | PXD006238 | Pride

tfGorAlbo

Project description:Gordius_albopunctatus, genomic and transcriptomic data

| PRJEB78907 | ENA