Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

ABSTRACT: Genome-wide analysis of transcription in dek3 mutants and DEK3-over expressors

PROVIDER: PRJNA472184 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR7187470_1.fastq.gz	Fastqsanger.gz
	SRR7187470_2.fastq.gz	Fastqsanger.gz
	SRR7187480_1.fastq.gz	Fastqsanger.gz
	SRR7187480_2.fastq.gz	Fastqsanger.gz
	SRR7187490_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 108

Similar Datasets

Genome-wide analysis of transcription in dek3 mutants and DEK3-over expressors

Project description:Genome-wide analysis of transcription in dek3 mutants and DEK3-over expressors

| PRJNA472045 | ENA

Genome-wide analysis of transcription in dek3 mutants and DEK3-over expressors [8 time points]

Project description:Genome-wide analysis of transcription in dek3 mutants and DEK3-over expressors [8 time points]

| PRJNA472047 | ENA

Genome-wide analysis of transcription in dek3 mutants and DEK3-over expressors [2 temperatures at 2 time points]

Project description:Genome-wide analysis of transcription in dek3 mutants and DEK3-over expressors [2 temperatures at 2 time points]

| PRJNA471342 | ENA

RNA-Seq of Col-0, dek3-2, dek4-2, and dek3-2 dek4-2 (dd-2) 7-day-old seedlings in Arabidopsis

Project description:Evolutionarily conserved DEK domain-containing proteins have been implicated in multiple chromatin-related processes, mRNA splicing, and transcriptional regulation in eukaryotes. Here, we show that two DEK proteins, DEK3 and DEK4, redundantly control the floral transition in Arabidopsis. DEK3 and DEK4 directly associate with chromatin of related flowering repressors, FLOWERING LOCUS C (FLC), and its two homologs, MADS AFFECTING FLOWERING4 (MAF4) and MAF5, to promote their expression. The binding of DEK3 and DEK4 to histone octamer in vivo affects histone modifications at FLC, MAF4 and MAF5 loci. In addition, DEK3 and DEK4 interact with RNA polymerase II and promote the association of RNA polymerase II with FLC, MAF4 and MAF5 chromatin to promote their expression. Our results show that DEK3 and DEK4 directly interact with chromatin to facilitate the transcription of key flowering repressors and thus prevent precocious flowering in Arabidopsis.

2021-05-04 | GSE163742 | GEO

Expression profiling of mouse livers with inducible over-expression of microRNA Mir483

Project description:In this study we generated mice with inducible over-expression of microRNA Mir483, using a transgene inserted at the Rosa26 locus. Whole transcriptome analysis was performed by RNA-seq in livers collected from 15-week old adult mice (over-expressors and controls).

2024-02-26 | GSE256304 | GEO

Genes Associated with MUC5AC Expression in the Human Airway Epithelium

Project description:To help define the genes associated with mucus synthesis and secretion in the human small airway epithelium, we hypothesized that comparison of the transcriptomes of the small airway epithelium of individuals that express high vs low levels of MUC5AC, a major secretory mucin and the major component of airway mucus, could be used as a probe to identify the genes related to human small airway mucus production / secretion. Genome-wide comparison between healthy nonsmokers grouped as “high MUC5AC expressors” vs “low MUC5AC expressors” identified significantly up-regulated and down-regulated genes in the high vs low expressors. Based on the literature, genes in the up-regulated list were used to identify a 73 “MUC5AC-associated core gene” list with 9 categories: mucus components; mucus-producing cell differentiation-related transcription factor; mucus-producing cell differentiation-related pathway or mediator; post-translational modification of mucin; vesicle transport; endoplasmic reticulum stress-related; secretory granule-associated; mucus secretion-related regulator and mucus hypersecretory-related ion channel. The identification of the genes associated with increased small airway mucin production in humans should be useful in identifying therapeutic targets to treat small airway mucus hypersecretion.

2017-02-09 | GSE34450 | GEO

ChIP-chip data of Rrm3-Flag in wild-type and rpb1-1 cells

Project description:Transcription is a major contributor to genome instability.A main cause of transcription-associated instability relies on the capacity of transcription to stall replication. Such genome instability is increased in RNAPII mutants. ChIP-chips performed in asynchronous cultures showed an increase of the Rrm3 binding signal all over the genome in rpb1-1 compared to wild-type.

2014-12-04 | GSE55184 | GEO

Targeting the fitness cost of antibiotic resistance via the non-essential genome

Project description:Mutations in the rifampicin (Rif)-binding site of RNA polymerase (RNAP) impart antibiotic resistance and inextricably affect transcription initiation, elongation, and termination properties as well. At each step of the transcription cycle, RNAP responds to non-essential transcription factors, signaling molecules, and substrate availability. As such, the non- essential genome and its impact on fitness cost potentially represent an untapped resource for new combination therapies. Using transposon sequencing (Tn-seq), we present a genome- wide analysis of resistance cost in a clinically common rpoB H526Y mutant. Our data show that cost-compounding genes include factors that promote high transcription elongation rate, whereas cost-mitigating genes function in cell wall synthesis and division. We demonstrate that cell wall synthesis and division defects in rpoB H526Y are a consequence of an abnormally high transcription elongation rate, which is further exacerbated by superfluous activity of the uracil salvage pathway and indifference of the mutant RNAP to alarmone ppGpp. Leveraging on this knowledge, we identified drugs that are highly potent against rpoB H526Y and other RifR alleles from the same phenotypic class. Thus, genome-wide analysis of fitness cost of antibiotic resistant mutants should expedite discovery of new combination therapies and delineate cellular pathways that underlie molecular mechanisms of cost.

2021-11-25 | PXD027810 | Pride

Pol II localization in yeast termination mutants

Project description:RNA Polymerase II was mapped over 4% of the yeast genome by ChIP, in wild-type and a handful of mutants in transcriptional termination factors. Keywords: ChIP-chip, transcription termination

2006-11-21 | GSE6301 | GEO

Binding in wild type, D and SoxN mutant embryos: SoxN vs D.

Project description:Genome-wide binding of transcription factors SoxN and D in stage 12-17 wild type embryos (SoxNDam and DDam), of SoxN in D mutants (D-SoxNDam) and of D in SoxN mutants (SoxN-DDam).

2014-04-23 | GSE47228 | 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