Browse
Submit Data
Databases
API
Help

Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

12 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

First insights into the unexplored two-component system YehU/YehT in Escherichia coli

ABSTRACT: To identify YehT-regulated genes, the transcriptome profiles of E. coli cells overproducing either the response regulator (RR) YehT or the RR KdpE (control) were comparatively analyzed. The expression level of 32 genes varied more than 8-fold.

ORGANISM(S): Escherichia coli

SUBMITTER: Luitpold Fried

PROVIDER: E-MTAB-984 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Identification of a target gene and activating stimulus for the YpdA/YpdB histidine kinase/response regulator system in Escherichia coli

Project description:To identify YpdB-regulated genes, the transcriptome profiles of E. coli cells overproducing either the response regulator (RR) YpdB or the RR YehS (control) were comparatively analyzed. The expression level of 15 genes varied more than 1.9-fold.

2012-10-30 | E-MTAB-1347 | biostudies-arrayexpress

Network analysis of gene expression in mice provides new evidence of involvement of the mTOR pathway in antipsychotic-induced extrapyramidal symptoms

Project description:To identify potential candidate genes for future pharmacogenetic studies of antipsychotic (AP)-induced extrapyramidal symptoms (EPS), we used gene expression arrays to analyze changes induced by risperidone in mice strains with different susceptibility to EPS This study is a part of a convergent functional genomic approach that plans to integrate the data presented here with: data from gene expression analysis of neuroblastoma cell line under treatment with risperidone; and data from gene expression analysis of peripheral blood from first psychotic patients treated with risperidone. Gene expression was assessed by microarray (Affymetrix GeneChip® Arrays MG 430 PM) in mice treated with risperidone 1mg/kg for three consecutive days

2015-04-09 | E-GEOD-67723 | biostudies-arrayexpress

Expression data SK-N-SH cells treated with risperidone

Project description:We performed a pharmacotranscriptomic analysis of a human neuroblastoma cell line (SK-N-SH) exposed to risperidone to identify molecular mechanisms involved in the cellular response to risperidone and thus identify candidate genes for pharmacogenetic studies. This study is a part of a convergent functional genomic approach that plans to integrate the data presented here with: data from gene expression analysis of experimental animal brain under treatment with risperidone; and data from gene expression analysis of peripheral blood from first psychotic patients treated with risperidone. Gene expression was assessed by microarray (Human Genome U219 Array) in cells treated with risperidone 10 ÂµM at 6, 24 and 48 h

2012-03-22 | E-GEOD-36678 | biostudies-arrayexpress

Global gene expression profiles of the reticulate mutants cue1-6 and lcd1-1 compared to the wild type (Col-0)

Project description:This experiment aims at the identification of commonly differentially regulated genes in leaves of cue1-6 and lcd1-1 compared to the wild type. Although different genes are knocked out in both mutants, these defects result in a common reticulate leaf phenotype. Hence the overlap of differentially regulated genes might provide information as to the mechanistic background leading to metabolic and/or developmental constraints.

2023-04-01 | E-MTAB-2846 | biostudies-arrayexpress

Expression data from myelo-dendritic progenitors as well as from mature myeloid and dendritic cells

Project description:Dendritic cells (DCs) are essential regulators of immune responses; however, transcriptional mechanisms establishing DC lineage commitment are poorly defined. Here we report that the PU.1 transcription factor induces specific remodeling of the higher-order chromatin structure at the Interferon Regulatory Factor-8 (Irf8) gene to initiate DC fate choice. Generation of an Irf8 reporter mouse enabled us to pinpoint an initial progenitor stage at which DCs separate from other myeloid lineages in the bone marrow. In the absence of Irf8, this progenitor undergoes DC-to-neutrophil reprogramming, indicating that DC commitment requires an active, Irf8-dependent escape from alternative myeloid lineage potential. Mechanistically, myeloid Irf8 expression depends on high PU.1 levels, resulting in local chromosomal looping and activation of a lineage- and developmental stage-specific cis-enhancer. These data delineate PU.1 as a concentration-dependent rheostat of myeloid lineage selection by controlling long-distance contacts between regulatory elements, and suggest that specific higher-order chromatin remodeling at the Irf8 gene determines DC differentiation. Mature macrophages, Granulocytes and DCs were isolated from wildtype mouse spleens for successive RNA extraction and hybridization on Affymetrix microarrays. 3 different pools, each consisting of splenic cells from 5 mice were prepared. Cell populations were isolated by flow cytometry. MDPs were isolated from Wildtype and IRF8 deficient bonemarrow by flowcytometry, again creating 3 biological replicates, each consisting of pooled cells from 5 mice. Differential gene expression between wildtype and IRF8 deficient MDPs was subgrouped into macrophage, granuloctic and DC signatures, derived from expression data of these cell populations.

2013-04-27 | E-GEOD-45467 | biostudies-arrayexpress

Microarray of reconstructed epidermis from skin models made with cells from African and Caucasian Skin type

Project description:The aim of this study was to analyze the in vitro biological epidermal processes occurring in reconstructed skins using cells from breast skin of African and Caucasian skin type color. A exploration of mRNA expression levels in the epidermis of reconstructed skin was undertaken to elucidate the differential in vitro functions of keratinocytes. The reconstruction of skin models was made with keratinocytes and fibroblasts from four different donors per skin type and experiments were conducted in triplicate for each donor. At the end of culture, the epidermis from reconstructed skin was manually separated from the dermal equivalent part in order to analyse gene expression in keratinocytes only. RNA samples were labelled with biotin and hybridation was performed on Affymetrix Human Genome U133 + PM Array Plates.

2020-08-10 | E-MTAB-9433 | biostudies-arrayexpress

High REDOX RESONSIVE TRANSCRIPTION FACTOR1 levels result in accumulation of reactive oxygen species in Arabidopsis thaliana shoots and roots [mature leaves]

Project description:Redox Responsive Transcription Factor1 (RRTF1) in Arabidopsis is rapidly and transiently upregulated by H202, as well as biotic and abiotic induced redox signals. Inactivation of RRTF1 restricts and overexpression promotes reactive oxygen species (ROS) accumulation in response to stress. Overexpressor (oe) lines are impaired in root and shoot development, light sensitive and susceptible to Alternaria brassicae infection. These symptoms are diminished by the beneficial root endophyte Piriformospora indica which reduces ROS accumulation locally in roots and systemically in shoots, and by antioxidants and ROS inhibitors which scavenge ROS. More than 850 stress-, redox-, ROS regulated-, ROS scavenging-, defense-, cell death- and senescence-related genes are regulated by RRTF1, ~ 30% of them have ROS related functions. Bioinformatic analyses and in vitro DNA binding assays demonstrate that RRTF1 binds to GCC-box and GCC-box like sequences in the promoter of RRTF1-responsive genes. Upregulation of RRTF1 by stress stimuli as well as H2O2 requires WRKY18/40/60. RRTF1 is co-regulated with the phylogenetically related RAP2.6, which contains GCC-box like sequene in its promoter, but RAP2.6 oe lines do not accumulate higher ROS levels. RRTF1 stimulates systemic ROS accumulation in distal non-stressed leaves. We conclude that the highly conserved RRTF1 rapidly, transiently and systemically induce ROS accumulation in response to ROS and ROS-producing abiotic and biotic stress signals. Necrotrophs stimulate RRTF1 expression, while symbiotic interactions of Arabidopsis with (hemi)-biotrophs and P. indica do not affect or repress RRTF1 expression. Mature leaves of 5 weeks-old Col-0 wild type and RRTF1-overexpressor Arabidopsis (called oe18), which were grown on soil under short-day condition at 20˚C, were subjected to RNA extraction and Affymetrix microarray analysis. Three biological independent experiments for both Col-0 and oe18 were performed.

2015-04-23 | E-GEOD-64853 | biostudies-arrayexpress

Haeusler LL_HL shift A. thaliana

Project description:Wild-type (Col-0) and mutant plants (adg1-1, tpt-2, adg1-1/tpt-2) were grown for 28 days under low light conditions and were then transferred to HL. Leaf samples for transcriptional profiling were taken at time 0 (before transfer to high light) and 4 hours and 48 hours (2 days) after transfer to high light.

2014-02-01 | E-MEXP-3791 | biostudies-arrayexpress

RNA-seq of murine Vg4+CD27-CD44+ and Vg4-CD27-CD44+ gamma delta from the lymph nodes of retinoic acid receptor deficient mice and littermate controls

Project description:The aim of this experiment was to decipher the role of retinoic acid receptor (RAR) on interleukin(IL)-17-producing gamma delta (gdT17) T cells. Therefore we generated mice where RAR activity is defective specifically in cells expressing the transcription factor RORgt, which is constitutively on in gdT17 cells. From these mice and their littermate controls we FACS-sorted the two major gdT17 populations from the lymph node (Vg4+ and Vg4-) and subjected them to RNA-seq.

2024-01-01 | E-MTAB-8554 | biostudies-arrayexpress

Autophagy_deficiency_pancreas

Project description:Transcriptional profiling analysis was performed on RNA from pancreatic tissue sections derived from autophagy deficient male mice at 4 and 18 weeks of age. Results were compared to littermate controls. Study groups contained RNA from pancreatic tissue sections of 1 control mouse and of 3 autophagy deficient mice for each timepoint.

2015-04-07 | E-MTAB-2635 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

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