Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Transcriptome analysis of alternative splicing under heat stress condition in atcyp18-1 mutant compared to wild type of Arabidopsis

ABSTRACT: To investigate whether the observed changes in pre-mRNA splicing led to AtCYP18-1 depletion, we conducted RNA-sequencing to analyse the quantitative profiling of alternative splicing

ORGANISM(S): Arabidopsis thaliana

PROVIDER: GSE159796 | GEO | 2020/10/22

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Transriptome analysis of alternative splicing under heat stress condition in atcyp18-2 mutant compared to Wild type (Col-0) of Arabidopsis

Project description:To investigate whether the observed changes in pre-mRNA splicing led to AtCYP18-2 depletion, we conducted RNA-sequencing to analyse the quantitative profiling of alternative splicing

2021-02-16 | GSE166755 | GEO

Transcriptome analysis of alternative splicing under heat stress condition in atcyp18-1 mutant compared to wild type of Arabidopsis

Project description:Transcriptome analysis of alternative splicing under heat stress condition in atcyp18-1 mutant compared to wild type of Arabidopsis

| PRJNA670492 | ENA

Transriptome analysis of alternative splicing under heat stress condition in atcyp18-2 mutant compared to Wild type (Col-0) of Arabidopsis

Project description:Transriptome analysis of alternative splicing under heat stress condition in atcyp18-2 mutant compared to Wild type (Col-0) of Arabidopsis

| PRJNA701911 | ENA

Transcriptome analysis of alternative splicing under ABA exposure in osfkbp20-1b mutant compared to wild-type (ZH11) of rice

Project description:To investigate whether observed changes in pre-mRNA splicing led to OsFKBP20-1b depletion, we analyzed RNA-seq to identify the quantitative profiling and alternative splicing

2023-04-24 | GSE197599 | GEO

Arabidopsis thaliana cao mutant alternative splicing exploration by RNAseq

Project description:The early flowering Arabidopsis cäö mutant is defective in the BRR2a helicase involved in splicing. In order to get some explanation about the phenotype, we compared the expression profiles of wt and mutant with RNA-seq. In addtion, the same RNA-seq data was used to measure the extent of intron retention in the cäö mutant

2016-12-31 | GSE65287 | GEO

Alternative splicing in Col-0 and sc35-scl mutant in Arabidopsis tlianaha

Project description:Serine/arginine-rich (SR) proteins are important splicing factors which play significant roles in spliceosome assembly and splicing regulation. However, little is known regarding their biological functions in plants. Here, we analyzed the phenotypes of mutants upon depleting different subfamilies of Arabidopsis SR proteins. We found that loss of the functions of SC35 and SC35-like (SCL) proteins cause pleiotropic changes in plant morphology and development, including serrated leaves, late flowering, shorter roots and abnormal silique phyllotaxy. Using RNA-seq, we found that SC35 and SCL proteins play roles in the pre-mRNA splicing. Motif analysis revealed that SC35 and SCL proteins preferentially bind to a specific RNA sequence containing the AGAAGA motif. In addition, the transcriptions of a subset of genes are affected by the deletion of SC35 and SCL proteins which interact with NRPB4, a specific subunit of RNA polymerase II. The splicing of FLOWERING LOCUS C (FLC) intron1 and transcription of FLC were significantly regulated by SC35 and SCL proteins to control Arabidopsis flowering. Therefore, our findings provide mechanistic insight into the functions of plant SC35 and SCL proteins in the regulation of splicing and transcription to maintain the proper expression of genes and development.

2017-01-26 | GSE93910 | GEO

Integrative analysis of gene expression and alternative splicing in microalgae grown under heterotrophic condition.

Project description:Heterotrophic cultures are the most effective approach to overcome low growth rate challenge in the most commercial microalgae. However, the mechanism through which heterotrophic condition regulates algae metabolism are not completely clear. Alternative Splicing (AS) is a common posttranscriptional process by which transcriptome and proteome plasticity increases at different environmental conditions. To identify and characterize of AS events in Auxenochlorella protothecoides microalga grown in autotrophic and heterotrophic, RNA-Seq data were analysed. We found that AS increased with the transition from autotrophic to heterotrophic condition. 705 and 660 differentially expressed (DEG) and spliced (DAS) genes were identified for A.protothecoides was transferred from autotrophic to heterotrophic condition, respectively. Moreover, there was slight coverage between DEG and DAS genes. Furthermore, functional analysis showed that the DAS genes are most frequently related to ion binding and stimulus response. The results also indicated that prevalence of Intron retention is associated with down-regulation of the genes involved in carotenoid biosynthesis. This study provides valuable insights into transcriptional and posttranscriptional plasticity of microalgae during growth mode change.

| S-EPMC7299362 | biostudies-literature

Heat stress induced alternative splicing in a species-dependent manner

Project description:Patterns of alternative splicing during heat stress in Arabidopsis thaliana and Boechera depauperata indicate complex and species-specific interactions between differential expression and alternative splicing.

2018-03-21 | GSE107820 | GEO

Cell type and culture condition-dependent alternative splicing in human breast cancer cells

Project description:We used splicing-sensitive microarrays to detect differences in alternative splicing between two breast cancer cell lines MCF7 (estrogen receptor positive) and MDA-MB-231 (estrogen receptor negative), as well as cultured human mammary epithelial cells (HMEC). Several splicing alterations in genes, including CD44, FAS, RBM9, HnRNPA/B, APLP2, and MYL6, were detected by the microarray, and verified by RT-PCR. We also compared splicing in these breast cancer cells cultured in either two-dimensional flat dishes (2-D) or in three-dimensional Matrigel (3-D) conditions. Only a subset of the splicing differences that distinguish MCF7 cells from MDA-MB-231 cells under 2-D culture condition is retained under 3-D conditions, suggesting that alternative splicing events are influenced by the geometry of the culture conditions of these cells. Keywords: Splicing-sensitive microarray

2005-12-30 | GSE3042 | GEO

The evolution of alternative splicing in glioblastoma under therapy.

Project description:Alternative splicing is a rich source of tumor-specific neoantigen targets for immunotherapy. This holds promise for glioblastomas (GBMs), the most common primary tumors of the adult brain, which are resistant to standard-of-care therapy. Although most clinical trials enroll patients at recurrence, most preclinical studies have been done with specimens from primary disease. There are limited expression data from GBMs at recurrence and surprisingly little is known about the evolution of splicing patterns under therapy. We profiled 29 primary-recurrent paired human GBM specimens via RNA sequencing. We describe the landscape of alternative splicing in GBM at recurrence and contrast that to primary and non-malignant brain-tissue specimens. By screening single-cell atlases, we identify cell-type specific splicing patterns and novel splicing events in cell-surface proteins that are suitable targets for engineered T-cell therapies. We identify recurrent-specific isoforms of mitogen-activated kinase pathway genes that enhance invasiveness and are preferentially expressed by stem-like cells. These studies shed light on gene expression in recurrent GBM and identify novel targets for therapeutic development.

2020-12-10 | GSE155434 | 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