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Expression data from Regulatory T Cells either exposed to normal salt media or high salt media (+40mM NaCl)

ABSTRACT: Sodium Chloride Inhibits Suppressive Function of Foxp3+ Regulatory T Cells Given the functional changes observed secondary to exposure to high-salt we wanted to know what expression based changes were taking place in the regulatory T cell population that might help to explain the evidenced functional deficits.

ORGANISM(S): Homo sapiens

PROVIDER: GSE63327 | GEO | 2014/11/18

SECONDARY ACCESSION(S): PRJNA267688

REPOSITORIES: GEO

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Expression data from Regulatory T Cells either exposed to normal salt media or high salt media (+40mM NaCl)

Project description:Sodium Chloride Inhibits Suppressive Function of Foxp3+ Regulatory T Cells Given the functional changes observed secondary to exposure to high-salt we wanted to know what expression based changes were taking place in the regulatory T cell population that might help to explain the evidenced functional deficits. Regulatory T Cells (Tregs) were incubated either in the presence or absence of an additional 40mM NaCl for 3 days with anti-CD3/anti-CD28 to ascertain phenotypic and expression based changes in the cellular population.

2014-11-18 | E-GEOD-63327 | biostudies-arrayexpress

Genome-wide maps of EED binding genes in WT and JARID2 KO human embryonic stem cells (hESCs)

Project description:We wanted to know whether JARID2 KO in hESCs could affect EED occupancy on chromatin.

2021-06-10 | GSE149351 | GEO

RNA sequencing of rice root in salt stress condition (250mM NaCl treatment)

Project description:Soil salinity is a major production constrain for agricultural crops, especially in Oryza sativa (rice). Analyzing physiological effect and molecular mechanism under salt stress is key for developing stress-tolerant plants. Roots system has a major role in coping with the osmotic change impacted by salinity and few salt-stress-related transcriptome studies in rice have been previously reported. However, transcriptome data sets using rice roots grown in soil condition are more relevant for further applications, but have not yet been available. The present work analyzed rice root and shoot physiological characteristics in response to salt stress using 250 mM NaCl for different timepoints. Subsequently, we identified that 5 day treatment is critical timepoint for stress response in the specific experimental design. We then generated RNA-Seq-based transcriptome data set with rice roots treated with 250 mM NaCl for 5 days along with untreated controls in soil condition using rice japonica cultivar Chilbo. We identified 447 upregulated genes under salt stress with more than fourfold changes (p value < 0.05, FDR < 0.05) and used qRT-PCR for six genes to confirm their salt-dependent induction patterns. GO-enrichment analysis indicated that carbohydrate and amino-acid metabolic process are significantly affected by the salt stress. MapMan overview analysis indicated that secondary metabolite-related genes are induced under salt stress. Metabolites profiling analysis confirmed that phenolics and flavonoids accumulate in root under salt stress. We further constructed a functional network consisting of regulatory genes based on predicted protein–protein interactions, suggesting useful regulatory molecular network for future applications.

2021-06-15 | E-MTAB-10653 | biostudies-arrayexpress

Total RNA-seq revealed function of HBL1 lncRNA during cardiac differentiation from hiPSCs.

Project description:We reported loss of HBL1 lncRNA promoted cardiogenesis. Here we wanted to know the genomewide gene expression profiles caused by HBL1 KO during cardiac differentiation.

2021-06-10 | GSE149408 | GEO

Salt/NaCl stress in Desulfovibrio vulgaris Hildenborough

Project description:This set of microarray data was used to investigate the effects of D. vulgaris adaptation to excess NaCl. Keywords: stress response, one time point (the mid-log phase for both control and treated cells)

2010-04-11 | GSE14343 | GEO

Microarray on mouse soleus muscles from DMP1 Cre Mbtps1 knockout mice compared with littermate controls

Project description:Interestingly, the DMP1 cre Mbtps1 knockout mice do not demonstrate a noticeable bone phenotype despite gene expression changes. Only change was in bone stiffness. However, muscles from DMP1 cre Mbtps1 knockout mice did show a phenotype: changes in contractile force (increased); changes in myosin heavy chain expression, and an increase in myocyte regeneration evidenced by centralized nuclei in type I myosin heavy chain expressing cells. As a result, we wanted to know if these physiological changes were accompanied by changes in gene expression. We found that a number of genes were increased---including those associated with improved muscle performance and with activation of satellite cells, e.g., muscle stem cells. These changes in gene expression support our hypothesis which is that the bone (osteocytes) signal a change in muscle function via a cross-talk mechanism.

2015-12-29 | GSE69985 | GEO

The black truffle of Perigord responds to a temperature shift with an extensive reprogramming of its transcriptional activity

Project description:Taking advantage of the availability of the Tuber melanosporum genome sequence and a whole-genome microarray, we wanted to test the hypothesis that the transition from a growth temperature of 24-25°C to a cold one (4°C) is perceived by the filamentous fungus at the transcriptomic level and we wanted to identify and characterize the genes involved in this stress response.

2010-09-15 | GSE21626 | GEO

Response of Leptospirillum ferriphilum DSM14647 to elevated NaCl concentration

Project description:Leptospirillum ferriphilum is an important acidophilic ferrous iron-oxidizing species for bioleaching or biooxidation to win metals like copper or gold, respectively. L. ferriphilum is inhibited by elevated conentrations of chloride. In the present study, the type strain of L. ferriphilum (i.e. strain DSM 14647) by subcultivation in presence of increasing chloride concentrations was adapted to tolerate higher concentrations of NaCl. The adapted culture was grown in presence of 180 mM NaCl or and the non-adapted culture without NaCl, and both were harvested in the late exponential phase. Total RNA was isolated and checked for quality and integrity. For each of the two conditions three RNA preparations of high quality (integrity number above 7) were pooled. Ribosomal RNA was depleted. DNA libraries for paired-end sequencing on an Illumina MiSeq were generated with a TruSeq stranded mRNA library prep kit (Illumina). Among the genes up-regulated were those coding for proteins likely involved in intracellular pH regulation, response to reactive oxygen species, and Fe-S cluster biosynthesis. Among the genes down-regulated in presence of chloride were those related to lipopolysaccharide and peptidoglykane synthesis, and interestingly also those for (hydroxy) ectoine biosynthesis.

2022-03-31 | E-MTAB-11136 | biostudies-arrayexpress

A combinatorial Interplay Among the ACC Synthase Isoforms Regulates Ethylene Biosynthesis in Arabidopsis thaliana

Project description:ACC Synthase (ACS) is the key regulatory enzyme in the ethylene biosynthesis in plants. It catalyzes the conversion of s-adenosylmethionine (SAM) to 1-aminocyclopropane-1-carboxylic acid (ACC), the precursor of ethylene. Arabidopsis has nine ACS genes. The goal of the project is to inactivate each gene by insertional mutagenesis and amiRNA technology and eventually construct a null ACS mutant. We have been recently able to achieve this goal. Furthermore, we wanted to know how inactivation of individual ACS genes affects global gene expression. Keywords: ACS mutant comprrison; global gene expression.

2009-12-15 | GSE14496 | GEO

Salt (NaCl and KCl) Stress in Desulfovibrio vulgaris Hildenborough

Project description:Recent interest in the ability of Desulfovibrio vulgaris Hildenborough to reduce, and therefore contain, toxic and radioactive metal waste, has made all factors that affect its physiology of great interest. Increased salinity constitutes an important and frequent fluctuation faced by D. vulgaris in its natural habitat. Using data from microarray experiments, as well as other laboratory analyses, we used a systems approach to explore the effects of excess NaCl on D. vulgaris. This study demonstrates that import of osmoprotectants such as glycine betaine and ectoine constitute the primary mechanism used by D. vulgaris to counter hyper-ionic stress. Several efflux systems also were highly up-regulated, as was the ATP synthesis pathway. Increase in both RNA and DNA helicases suggested that salt stress had affected the stability of nucleic acid base pairing. An immediate response to salt stress included up-regulation of chemotaxis genes though flagellar biosynthesis was down-regulated. Other down-regulated systems included lactate uptake permeases and ABC transport systems. The extensive NaCl stress analysis was compared with microarray data from KCl stress and unlike many other bacteria, D. vulgaris responded similarly to the two stresses. Keywords: Comparison of cells treated with either NaCl (250 mM) or KCl (250 mM) to untreated cells at times of 0, 30, 60, 120, and 240 min.

2006-03-22 | GSE4447 | GEO

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