Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

RNAseq for finding splicing events in Arabidopsis prefoldin and lsm8 mutants in different environmental conditions

ABSTRACT: RNAseq for finding splicing events in Arabidopsis prefoldin and lsm8 mutants in different environmental conditions

PROVIDER: PRJNA513852 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR8422200_1.fastq.gz	Fastqsanger.gz
	SRR8422200_2.fastq.gz	Fastqsanger.gz
	SRR8422210_1.fastq.gz	Fastqsanger.gz
	SRR8422210_2.fastq.gz	Fastqsanger.gz
	SRR8422220_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 56

Similar Datasets

RNAseq for finding splicing events in Arabidopsis prefoldin and lsm8 mutants in different environmental conditions

Project description:This GEO submission includes RNAseq raw data (fastq) and processed data (using ASpli 1.6.0) from samples obtained in the wild type and the single prefoldin4 and lsm8 mutants in three different environmental conditions as well as in the triple prefoldin2 prefoldin4 prefoldin6 mutant growth in standard conditions.

2019-01-09 | GSE124812 | GEO

RNAseq in Arabidopsis prefoldin mutants

Project description:RNAseq in Arabidopsis prefoldin mutants

| PRJNA575853 | ENA

ChIP-seq data of prefoldin subunit PFDN5 in HCT116 human colon carcinoma cells

Project description:Prefoldin is a heterohexameric complex conserved from archaea to humans that plays a cochaperone role during the co-translational folding of actin and tubulin monomers. Additional functions of prefoldin in the cell nucleus have been described, including a positive contribution to transcription elongation and chromatin dynamics in yeast. Here we show that prefoldin perturbations provoked transcriptional alterations across the genome of human cells. We detected genome-wide prefoldin binding to transcribed genes and found that this binding negatively correlate with the impact of prefoldin depletion on gene expression. Moreover, lack of prefoldin caused significant global decrease in the levels of Ser2 and Ser5 phosphorylation of the RNA polymerase II carboxy-terminal domain (CTD). Altogether the reported results indicate that human prefoldin is able to act locally on the genome to modulate gene expression by influencing phosphorylation of elongating RNA polymerase II, and thereby regulating co-transcriptional splicing.

2021-05-04 | GSE171466 | GEO

Prefoldin 6 mediates longevity response from heat shock factor 1 to FOXO in C. elegans

Project description:Heat shock factor 1 (HSF-1) and forkhead box O (FOXO) are key transcription factors that protect cells from various stresses. InCaenorhabditis elegans, HSF-1 and FOXO together promote a long life span when insulin/IGF-1 signaling (IIS) is reduced. However, it remains poorly understood how HSF-1 and FOXO cooperate to confer IIS-mediated longevity. Here, we show that prefoldin 6 (PFD-6), a component of the molecular chaperone prefoldin-like complex, relays longevity response from HSF-1 to FOXO under reduced IIS. We found that PFD-6 was specifically required for reduced IIS-mediated longevity by acting in the intestine and hypodermis. We showed that HSF-1 increased the levels of PFD-6 proteins, which in turn directly bound FOXO and enhanced its transcriptional activity. Our work suggests that the prefoldin-like chaperone complex mediates longevity response from HSF-1 to FOXO to increase the life span in animals with reduced IIS.

2023-10-04 | GSE244495 | GEO

RNA-seq data of prefoldin subunits PFDN2 and PFDN5 knockdowns in HCT116 human colon carcinoma cells

Project description:We report gene expression data from total RNA-seq of HCT116 human colon carcinoma cells treated with siRNA against PFDN2 and PFDN5 (both part of a complex known as prefoldin). Cells were independently treated with one of the previously mentioned siRNAs or with an exogenous control siRNA (luciferase GL2). All cells were treated with the different siRNAs for 24 hours, then serum-starved them for 48 hours, and finally stimulated by adding serum for 90 minutes. Samples were taken before and after serum stimulation. Prefoldin depletion provoked transcriptional alterations across the genome of human cells. Severe pre-mRNA splicing defects were also detected, particularly under serum stimulation conditions. We found a significant impairment of co-transcriptional splicing during transcription elongation.

2021-05-04 | GSE155231 | GEO

Differential splicing events in aging Drosophila eye

Project description:Differential splicing events in aging Drosophila eye

| PRJNA417508 | ENA

Human prefoldin modulates co-transcriptional pre-mRNA splicing.

Project description:Prefoldin is a heterohexameric complex conserved from archaea to humans that plays a cochaperone role during the co-translational folding of actin and tubulin monomers. Additional functions of prefoldin have been described, including a positive contribution to transcription elongation and chromatin dynamics in yeast. Here we show that prefoldin perturbations provoked transcriptional alterations across the human genome. Severe pre-mRNA splicing defects were also detected, particularly after serum stimulation. We found impairment of co-transcriptional splicing during transcription elongation, which explains why the induction of long genes with a high number of introns was affected the most. We detected genome-wide prefoldin binding to transcribed genes and found that it correlated with the negative impact of prefoldin depletion on gene expression. Lack of prefoldin caused global decrease in Ser2 and Ser5 phosphorylation of the RNA polymerase II carboxy-terminal domain. It also reduced the recruitment of the CTD kinase CDK9 to transcribed genes, and the association of splicing factors PRP19 and U2AF65 to chromatin, which is known to depend on CTD phosphorylation. Altogether the reported results indicate that human prefoldin is able to act locally on the genome to modulate gene expression by influencing phosphorylation of elongating RNA polymerase II, and thereby regulating co-transcriptional splicing.

| S-EPMC8216451 | biostudies-literature

RNAseq in Arabidopsis prefoldin mutants

Project description:This GEO submission includes RNAseq raw data (fastq.gz) and processed data (using DESeq2) from samples obtained in the wild type and the pfd4 and 6x_pfd mutants

2020-12-22 | GSE138432 | GEO

Finding cellular origin of mouse kidney organoids

Project description:Finding cellular origin of mouse kidney organoids

| PRJEB17924 | ENA

Differential splicing events in aging Drosophila eye

Project description:Purpose: The goal of this study was to identify differential splicing events in the Drosophila eye during aging.

2018-06-20 | GSE106652 | GEO