Similar Datasets
Project description:To investigate the role of RNA Pol II CTD acetylation we performed comprehensive deacetylase inhibition using common small-molecule inhibitors and performed ChIP-seq from mouse cells using antibodies against RNA Polymerase II CTD modifications: (8WG16, unmodified heptads; K7ac, acetylated heptads; 4H8, S5-phosphorylated heptads). In addition, we tested the effect of knockdown of RPRD1B, a key transcription regulator that recruits RPAP2, a CTD S5-phosphatase.
2019-01-12 | GSE124996 | GEO
Project description:This study aimed to evaluate the gene expression signature of HSC-3 cells and its subline adapted to suspension culture (HSC-3-S5). Total RNAs were isolated from HSC-3 cells and HSC-3-S5 cells, and gene expression signatures were examined using gene expression microarray.
2023-09-01 | GSE235020 | GEO
Project description:Faecalibacterium duncaniae A2-165 is a rod-shaped, non-motile, and Extremely Sensitive to Oxygen microorganism, belonging to one of the most abundant genera in the human gut microbiome. A decreased abundance of Faecalibacterium species is correlated to Inflammatory Bowel Diseases (IBDs), highlighting this genus as a marker of gut health and a promising Next-Generation Probiotic. Many studies have demonstrated the anti-inflammatory effect of the most studied species, F. duncaniae A2-165, on mouse models of IBDs, associating the disease amelioration and suppression of inflammatory markers with large amounts of butyrate produced by the bacteria, and the presence of the MAM protein. However, many factors in F. duncaniae metabolism could contribute to its importance in the gut. To address this issue, this study characterized the proteome of F. duncaniae A2-165 in the stationary phase through a LC-MS/MS label-free proteomics approach.We quantified 1.280 proteins in total, corresponding to 44,7% of the in silico predicted proteome, with clear distinction between insoluble and soluble protein abunndaces. The subcellular localization prediction of the quantified proteins revealed 802 cytoplasmic proteins, 265 membrane proteins, six extracellular proteins, eight cell wall proteins, and 199 unknown localization proteins. Differential abundance analysis between insoluble and soluble fraction showed 290 proteins more abundant and 330 less abundant in the insoluble fraction. Functional analysis of these proteins showed a predominance of transporter proteins in the insoluble fraction, while metabolism of amino acids, carbohydrates and nucleotides were predominant in the soluble fraction. Further analysis of enriched pathways for each fraction showed energy metabolism, carbon cycle, and amino acid metabolism enriched in the soluble, and ABC transporters, quorum sensing, and oxidative phosphorylation in the insoluble. Moreover, we could confirm the presence of proteins associated to the bacteria’s mechanism of action, notably the key butyrate production pathway ButCoAT, the MAM protein and the ABC transporter exporter, and shikimate pathway enzymes.
2026-01-27 | PXD071138 | Pride
Project description:The shoot apical meristem (SAM) comprises a group of undifferentiated cells that divide to maintain the plant meristem and also give rise to all shoot organs. SAM fate is specified by class III HOMEODOMAIN-LEUCINE ZIPPER (HD-ZIP III) transcription factors, which are targets of miR166/165. In Arabidopsis, AGO10 is a critical regulator of SAM maintenance, and here we demonstrate that AGO10 specifically interacts with miR166/165. The association is determined by a distinct structure of the miR166/165 duplex. Deficient loading of miR166 into AGO10 results in a defective SAM. Notably, the miRNA-binding ability of AGO10, but not its catalytic activity, is required for SAM development, and AGO10 has a higher binding affinity for miR166 than does AGO1, a principal contributor to miRNA-mediated silencing. We propose that AGO10 functions as a decoy for miR166/165 to maintain the SAM, preventing their incorporation into AGO1 complexes and the subsequent repression of HD-ZIP III gene expression.
2012-08-04 | GSE39885 | GEO
Project description:Individualized outcome prediction classifiers were successfully constructed through expression profiling of ncRNAs in 165 CRC cases.
2016-12-28 | GSE92928 | GEO
Project description:Nocardioides sp. S5 strain:S5 Genome sequencing
| PRJNA392418 | ENA
Project description:Citrobacter sp. S5 strain:S5 Genome sequencing
| PRJNA1166959 | ENA