Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Deciphering isoform switching and specific isoform usage during biofilm lifestyle by Candida glabrata analysed through global transcriptomic approach

ABSTRACT: Methodology: RNA was extracted using Hi-PurA yeast RNA purification kit from biofilm and planktonic growth phase and sequenced by Illumina Hi-Seq 2500 and platform with 250bp paired chemistry and analysed by IsoformSwitchAnalyseR tool of bioconductor Results: Differential transcript expression (DTE) and differential transcript utilization (DTU) of C. glabrata showed that it utilized 292 significant transcripts isoforms during biofilm formation via isoform switching process. Conclusion: Investigation of the present study elucidated that the switched isoform and predicted proteins encoded in biofilm growth mode of this pathogen could be used as a potential target for the development of novel antifungal targets.

ORGANISM(S): Nakaseomyces glabratus

PROVIDER: GSE162024 | GEO | 2021/06/09

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Global transcriptomic portrait of biofilm lifestyle in the clincial isolate of Candida glabrata

Project description:Aim: of the study was to compare the transcriptomic profiling of planktonic and biofilm growth phase of clinical isolate of Candida glabrata Methodology: RNA was extracted using Hi-PurA yeast RNA purification kit from biofilm and planktonic growth phase and sequenced by Illumina Hi-Seq 2500 platform with 250bp paired chemistry Results: we got 959 significantly Differential Expressed Genes DEGs (logFC => 1.5) acconts for 18.11 % in which 596 (11.26 %) are getting downregulated and 363 (6.85%) upregulated in the biofilm growth mode. We validated 8 genes by qPCR Conclusion: Comprehensive analysis of the large expression gene sets generated from experimental conditions (Planktonic vs Biofilm) by RNA Seq revealed the unique network of genes associated with this intricate and complex process. We observed that Differentially Expressed Genes (DEGs) associated with Glyoxylate and Dicarboxylate metabolism, Carbon-Carbon lyase activity

2021-06-09 | GSE152789 | GEO

Deciphering isoform switching and specific isoform usage during biofilm lifestyle by Candida glabrata analysed through global transcriptomic approach

Project description:Deciphering isoform switching and specific isoform usage during biofilm lifestyle by Candida glabrata analysed through global transcriptomic approach

| PRJNA680327 | ENA

Depletion of the RNA-binding protein PURA triggers changes in posttranscriptional gene regulation and loss of P-bodies

Project description:The RNA-binding protein PURA has been implicated in the rare, monogenetic, neurodevelopmental disorder PURA Syndrome. PURA binds both DNA and RNA and has been associated with various cellular functions. Only little is known about its main cellular functions and the molecular pathways affected upon PURA depletion. Here, we show that PURA is predominantly located in the cytoplasm, where it binds to thousands of mRNAs. Many of these transcripts change abundance in response to PURA depletion. The encoded proteins suggest a role for PURA in immune responses, mitochondrial function, autophagy and processing (P)-body activity. Intriguingly, reduced PURA levels decrease the expression of the integral P-body components LSM14A and DDX6, and strongly affect P-body formation in human cells. Furthermore, PURA knockdown results in stabilization of P-body-enriched transcripts, whereas other mRNAs decrease. Hence, reduced PURA levels, as reported in patients with PURA Syndrome, influence the formation and composition of this phase-separated RNA processing machinery. Our study on PURA provides a blueprint for the comprehensive understanding of the tight connection between P-body-associated RNA regulation and neurodevelopmental disorders.

2022-12-19 | PXD030266 | Pride

p73 isoform antibodies

Project description:Epitope mapping of novel p73 isoform antibodies

| PRJEB80529 | ENA

Isoform-specific depletion of U2AF1

Project description:Isoform-specific depletion of U2AF1

| PRJEB6651 | ENA

Isoform-specific depletion of U2AF1

Project description:RNA-Seq data of U2AF1 isoform depletion experiments.

2015-03-16 | E-MTAB-2682 | biostudies-arrayexpress

Exploring the Dynamics and Consequences of Differential Transcript Usage in Cardiomyocyte Fate Specification

Project description:Cardiovascular research often relies on in vitro models using induced pluripotent stem cells (iPSCs) differentiating into induced cardiomyocytes (iCM). Little is known about the changes in transcript variants, termed differential transcript usage (DTU), which greatly influence cellular programs. In this study, we explored the DTU landscape during the iPSC-to-iCM differentiation and its relation to iCM fate. We found that DTU is consistently displayed by a subset of genes during iCM differentiation. DTU largely operates on a distinct set of genes than DGE, and both impact different biological processes. The DTU is used more often by protein coding in the late stage of iCM differentiation. The DTU-displaying genes are linked with functions specific to CMs, including ion signaling and cell junction organization, and their expression is cell-type specific. The RNA binding proteins (RBPs) involved in shaping the alternative splicing during the iCM differentiation experience early directed gene expression changes in their expression. Our research emphasizes that analyzing transcript variant expression levels is crucial for uncovering novel genes and functions, and for mapping fine-tuning gene expression and cardiomyocyte-specific functions during cell differentiation.

2024-08-18 | GSE274653 | GEO

Alternative Isoform Regulation in Human Tissue Transcriptomes

Project description:Through alternative processing of pre-mRNAs, individual mammalian genes often produce multiple mRNA and protein isoforms that may have related, distinct or even opposing functions. Here we report an in-depth analysis of 15 diverse human tissue and cell line transcriptomes based on deep sequencing of cDNA fragments, yielding a digital inventory of gene and mRNA isoform expression. Analysis of mappings of sequence reads to exon-exon junctions indicated that ~94% of human genes undergo alternative splicing (AS), ~86% with a minor isoform frequency of 15% or more. Differences in isoform-specific read densities indicated that a majority of AS and alternative cleavage and polyadenylation (APA) events exhibit variation between tissues. Variations in alternative mRNA isoform expression between 6 individuals were also detected in cerebellar cortex, with ~2- to 3-fold less isoform variation observed between individuals than between tissues. Extreme or 'switch-like' regulation of splicing between tissues was associated with increased sequence conservation and with generation of full-length open reading frames. Patterns of AS and APA were strongly correlated across tissues, suggesting coordinated regulation, and sequence conservation of known regulatory motifs in both regulated introns and 3' UTRs suggested common involvement of the same factors in regulation of tissue-specific splicing and polyadenylation. Exam mRNA expression in 15 human tissues and cell lines

2008-09-30 | E-GEOD-12946 | biostudies-arrayexpress

Saccharomyces cerevisiae Transcript Isoform mapping

Project description:Extensive transcriptional heterogeneity revealed by isoform profiling

2013-05-06 | GSE39128 | GEO

RNAseq of PURA knockdown in HeLa cells

Project description:Here, we show that PURA predominantly resides in the cytoplasm, where it binds to a large set of transcripts. Many of these transcripts change abundance in response to PURA depletion, in parts reflected in altered protein expression levels. A closer inspection of the regulated proteins indicates a role of PURA in immune responses, mitochondrial function, autophagy and processing (P)-body activity.

2022-12-12 | GSE193900 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data