Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Nucleosome position mapping by micrococcal nuclease analysis of S. cerevisiae cells in raffinose and galactose containing media

ABSTRACT: We analyed the nucleosome positions by using 2 concentrations of micrococcal nuclease of yeast strains that were grown in raffinose and galactose containing media (synthetic complete).

ORGANISM(S): Saccharomyces cerevisiae

PROVIDER: GSE116337 | GEO | 2019/05/14

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

Nucleosome position mapping by micrococcal nuclease analysis of S. cerevisiae anchor-away Sth1, Swi2 and/of TBP cells in raffinose and galactose-rich media in rapamycin or DMSO

Project description:We analyed the nucleosome positions by using 2 concentrations of micrococcal nuclease on yeast strains that were grown in raffinose or galactose containing media (synthetic complete). Strains contained FRB-tags to Sth1, Swi2, Sth1 & Swi2 or Sth1 and TBP, where TBP was tagged on one of two alleles in a diploid strain. Cells were treated for 60 min either with 7.5 uM rapamycin or the same volume of DMSO.

2023-01-11 | GSE190737 | GEO

Nucleosome position mapping by micrococcal nuclease analysis in S. cerevisiae of Top1-AID/Top2-AID strains with auxin in galactose-rich media

Project description:We analyed the nucleosome positions by using 2 concentrations of micrococcal nuclease of haploid yeast strains that were grown in galactose containing synthetic complete media. Strains contained AID-tags at the endogeous TOP1 and TOP2 genes. One strain contained OsTIR1 and these cells were either untreated or treated for 60 min with 500 uM auxin.

2023-04-28 | GSE196945 | GEO

Nucleosome position mapping by micrococcal nuclease analysis of S. cerevisiae cells in raffinose and galactose containing media

Project description:Nucleosome position mapping by micrococcal nuclease analysis of S. cerevisiae cells in raffinose and galactose containing media

| PRJNA478208 | ENA

Transcription profiling of yeast after a shift from media containing raffinose to one containg galactose

Project description:expression profile from a shift from raffinose to galatose. This serves as a control expirement.

2009-09-19 | E-TABM-693 | biostudies-arrayexpress

Global transcriptomic analysis of the Raffinose Utilization in Lactobacillus salivarius Ren

Project description:This study was aimed to further illustrate the expression files of REN between glucose and raffinose in MRS broth. Transcriptomic analysis combined with mutants of the key genes based on homologous recombination technology indicated that galA1 gene cluster plays an important role in raffinose metabolism. Gene rafP and galA1 are responsible for raffinose transport and α-galactoside hydrolysis, followed by galactose hydrolysis by galKTE and sucrose hydrolysis by scrB. Lactobacillus salivarius Ren expanded the carbon utilization spectrum to adapt the fluctuating carbohydrate sources in the environment and shifted its carbohydrate metabolism to mixed-acid fermentation and then generated extra energy to bacterial growth when exposed to raffinose.

2021-12-31 | GSE174336 | GEO

Micrococcal nuclease sequencing analysis for nucleosome localization of mouse fetal liver erythroblasts

Project description:Nucleosomal DNA was prepared using Simple ChIP Enzymatic Chromatin IP Kit according to manufacturer’s instruction. Briefly, Nuclei were isolated from purified Ter119 negative or in vitro cultured erythroblasts. Cross-linked native chromatin was then digested with MNase into mononucleosomal DNA. Sequencing libraries were generated from nucleosomal DNA, and sequencing was carried out using the Illumina system according to the manufacturer’s specification. In this study, we purified chromatin from in vitro cultured mouse fetal liver erythroblasts on day 0, day 1, and day 2. The chromatins were digested by micrococcal nuclease to make mononucleosomal products, which were further analyzed by next generation sequencing analysis. We aim to determine the dynamic changes of nucleosome during terminal erythropoiesis.

2014-10-01 | E-GEOD-55825 | biostudies-arrayexpress

B. thetaiotaomicron before and after galactose addition to tryptone media

Project description:B. thetaiotaomicron was grown in a batch culture fermenter containing tryptone media. Galactose (final concentration 0.2%) was added at OD600 = 0.3. Samples were taken immediately before and 60 minutes after addition. Keywords: time course

2006-09-01 | GSE5275 | GEO

Micrococcal nuclease does not substantially bias nucleosome mapping.

Project description: Not available

| S-EPMC3314939 | biostudies-literature

Transcriptional profiling of Myceliophthora thermophila on galactose and metabolic engineering for improved galactose utilization

Project description:Transcriptional landscape of MyceliopTranscriptional profiling of Myceliophthora thermophila on galactose and metabolic engineering for improved galactose utilization thora thermophila responding to soluble starch and the role of regulator AmyR on polysaccharide degradation Efficient biological conversion of all sugars from lignocellulosic biomass is necessary for cost-effective production of biofuels and commodity chemicals. Galactose is the next most abundant sugar in many hemicelluloses and it will be important to capture this carbon for an efficient bioconversion process of plant biomass. Thermophilic fugus Myceliophthora thermophila has been used as cell factory to produce biochemicals directly from renewable polysaccharides. This study determined the transcriptomic profiles of M. thermophila responding to galactose and identified the gene involved in the oxido-reductive pathway for galactose degradation, of which hexokinase might be the rate-limiting enzyme in this thermophilic fungus. Galactokinase was necessary for high induction of galactose transporter and disruption of galK resulted in decreased galactose utilization. Both of galactokinase deletion and sugar transporter overexpression could further activate the oxido-reductive pathway and led to improved galactose utilization. In addition, disruption of the Leloir pathway brought about reduced tolerance to cell wall perturbation, oxidative stress and high osmolality. In order to accelerate galactose consumption, the third galactose-degradation pathway- De Ley-Doudoroff pathway was successfully integrated into M. thermophila and the consumption rate of galactose was increased by 57%. This study will be benefit for the rational design of fungal strains to produce biofuels and biochemical from plant biomass, especially, marine plant biomass with the abundant of galactose, such as red seaweed and molasses.

2021-02-05 | GSE165516 | GEO

Transcription profiling of wild type, GALT-deficient and GALT-deficient-revertant yeast grown on media with galactose or glucose

Project description:To better understand the pathophysiology of galactose-1-phosphate uridyltransferase (GALT) deficiency in humans, we studied the mechanisms by which a GALT-deficient yeast survived on galactose medium. Under normal conditions, GALT-deficient yeast cannot grow in medium that contains 0.2% galactose as the sole carbohydrate, a phenotype of Gal(-). We isolated revertants from a GALT-deficient yeast by direct selection for growth in galactose, a phenotype of Gal(+). Comparison of gene expression profiles among wild-type and revertant strains on galactose medium revealed that the revertant down-regulated genes encoding enzymes including galactokinase, galactose permease, and UDP-galactose-4-epimerase (the GAL regulon). By contrast, the revertant strain up-regulated the gene for UDP-glucose pyrophosphorylase, UGP1. There was reduced accumulation of galactose-1-phosphate in the galactose-grown revertant cells when compared to the GALT-deficient parent cells.

2008-04-10 | E-MEXP-1420 | 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