Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Saccharomyces cerevisiae transcriptome analysis of conditional yjr141w-psd mutant compared to control strain

ABSTRACT: The experiment investigates the consequences of Yjr141w downregulation on gene expression in yeast. The essential protein Yjr141w was depleted from cells using a tagged variant (Yjr141w-psd). The photo-sensitive degron (psd) module initiates degradation of the tag and its associated protein upon blue-light exposure. Altogether, we compared samples of the control yeast strain (ESM356-1) grown in darkness (3 arrays) and grown exposed to blue-light (wavelength 465 nm; light-flux 30 µmol m-2 s-1) with the Yjr141w-psd strain (YAL81) grown in darkness and grown exposed to blue-light.

INSTRUMENT(S): Affymetrix GeneChip Scanner 3000 7G

ORGANISM(S): Saccharomyces cerevisiae

SUBMITTER: Christof Taxis

PROVIDER: E-MTAB-5022 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Publications

Proteasome Activity Is Influenced by the HECT_2 Protein Ipa1 in Budding Yeast.

Lutz Anne P AP Schladebeck Sarah S Renicke Christian C Spadaccini Roberta R Mösch Hans-Ulrich HU Taxis Christof C

Genetics 20180308 1

The ubiquitin-proteasome system (UPS) controls cellular functions by maintenance of a functional proteome and degradation of key regulatory proteins. Central to the UPS is the proteasome that adjusts the abundance of numerous proteins, thereby safeguarding their activity or initiating regulatory events. Here, we demonstrate that the essential <i>Saccharomyces cerevisiae</i> protein Yjr141w/Ipa1 (Important for cleavage and PolyAdenylation) belongs to the HECT_2 (homologous to E6-AP carboxyl termi ...[more]

PMID: 29519818

Similar Datasets

Light-regulated genes in Cryptococcus neoformans

Project description:Light is a universal environmental signal perceived by many organisms, including the fungi in which light regulates both common and unique biological processes depending on the species. We conducted a whole-genome microarray analysis on the basidiomycete fungus Cryptococcus neoformans to identify light-regulated genes. Two-condition experiment, cells grown in complete darkness or exposed to white light. Six biological replicates independently grown and harvested. One replicate per array.

2010-04-23 | E-GEOD-21484 | biostudies-arrayexpress

Transcriptional response of Arabidopsis seedlings to light

Project description:We report the transcriptomic response of Arabidopsis thaliana seedlings grown in continuous white light, darkness or darkness and 1 hour of red light

2022-03-09 | GSE181167 | GEO

Changs in Histone 3 Lysine 9 Acetylation (H3K9ac) in Arabidopsis seedlings in response to light

Project description:We report the changes in H3K9ac in Arabidopsis thaliana seedlings grown in continuous white light, darkness or darkness and 1 hour of red light

2022-03-09 | GSE181432 | GEO

Decoupling behavioral and transcriptional responses to color in an eyeless cnidarian

Project description:We utilized the eyeless sea anemone, Nematostella vectensis, to quantify gene expression differences between different colors of light (red, green, blue) and in constant darkness through comparisons of 96 transcriptomes

2019-06-12 | GSE132526 | GEO

Blue light inhibition of tuberization

Project description:A tuberization inhibitor has long been postulated, but not yet found. We found that blue light inhibits tuberization in Norland, a day-neutral variety of Solanum tuberosum L. Tissue-cultured plants formed tubers within 8 weeks under continuous darkness, and white, red, or far-red light. Preliminary experiments indicated that a one- or two-day exposure to blue light after 3-4 weeks of dark treatment will inhibit tuber formation in ‘Norland’ plants. Using this system and expression profiling, we may be able to identify candidate tuberization inhibitors. 'Norland' plants (subcultured from existing cultures and grown for two weeks under continuous 100 umol/m2-s white fluorescent light) were placed in tuber-inducing media containing 6% sucrose, vitamins, MS salts, and kinetin (2.5 mg/L). Tubes containing plants were wrapped in two layers of aluminum foil. After 3 weeks and 2 days, half of the tubes were exposed to 6-7 umol/m2-s blue light. The other half of the tubes were left in darkness (controls). After 2 days, all plants were harvested and frozen in liquid nitrogen. Plants exposed to blue light were harvested under blue light. Control plants were harvested under < 2 umol/m2-s light conditions. All plant transfers were done at 1700 (5 PM) to avoid possible complications due to circadian effects. Experiments were performed four times, from subculture to harvest. RNA was extracted from stem and leaf tissue of plants using the Qiagen RNeasy Plant Mini kit. Extracted RNA was then converted to dsDNA using the Invitrogen protocol and reagents for double stranded cDNA synthesis. The resulting dsDNA was in vitro transcribed into amplified RNA using the Ambion procedure and reagents for in vitro transcription. cDNA was purified using Qiagen MinElute columns and protocol. Amplified RNA was purified using Ambion columns or Qiagen RNeasy columns and the Ambion protocol, and quantified using RiboGreen dye fluorometry. Keywords: Direct comparison

2008-02-13 | GSE10491 | GEO

Pseudomonas syringae pv. tomato DC3000 exploits light signals to optimize virulence and colonization of leaves

Project description:To explore the effect of light perception on Pseudomonas syringae pv. tomato DC3000 at a global level, we carried out microarray hybridization experiments. We hybridize custom-designed microarrays (Agilent Technologies) with probes isolated from PsPto after a 10 min treatment with either 20 μE/m2s blue light, 20 μE/m2s red light, 70 μE/m2s white light, or cells kept in the darkness.

2018-10-01 | GSE101783 | GEO

Photomorphogenesis of Arabidopsis seedlings is accompanied by complex alternative splicing alterations

Project description:We analyzed transcriptome-wide gene expression and AS changes in etiolated Arabidopsis seedlings exposed to red, blue, and white light. Our study revealed that different types of light signals trigger rapid AS responses of numerous genes, including splicing factors and other functional groups. Among these candidates was RRC1, which was previously shown to function in PHYB signaling. The light signaling phenotype of an rrc1 mutant could only be complemented with the splicing variant being up-regulated upon light exposure, indicating a self-reinforcing circuit. Finally, we provide evidence that light-regulated AS can occur in a phytochrome-independent manner and is closely intertwined with the plantâ??s energy status. Analysis of alternative splicing patterns of dark-grown Arabidopsis seedlings exposed for 1 or 6 hours to white, blue, or red light, or kept in darkness; all samples in duplicates

2016-10-23 | E-GEOD-70575 | biostudies-arrayexpress

blue200micE_vs_blue20micE

Project description:Series of 6 repetitions of hybridization of treatment (blue200micE) and control (blue20micE) each. Comparison of plants grown for 48 hours at 200µE blue light versus plants exposed for 48 hours at 20µE to blue light. E. Lopez, unpublished Keywords: repeat sample

2005-01-01 | GSE1179 | GEO

atmyc2_cop1_mutant_light_ABA_treatment

Project description:Although many regulatory components of light signaling have been functionally characterized, only a few of them have been reported to cross talk with other signaling cascades. In this study, we have analyzed the expression profiles of Arabidopsis genes in wild-type, atmyc2 mutant, cop1-6 mutant, and atmyc2 cop1-6 double mutant seedlings grown under constant dark, constant blue-light, and constant blue-light along with abscisic acid (ABA) to illustrate the interplay of negative regulators, AtMYC2 and COP1, in light and ABA signaling Keywords: Light and abscisic acid treatment Expression data for wild-type, atmyc2, cop1-6, and atmyc2 cop1-6 seedlings under constant dark, blue-light and blue-light along with abscisic acid Ten-day-old Arabidopsis (wild-type, atmyc2 mutant, cop1-6 mutant, and atmyc2 cop1-6 double mutant) seedlings grown under constant dark, constant blue-light (35 µmol/sec/m2), and constant blue-light along with ABA (0.5 µm) were used for RNA extraction and hybridization on Affymetrix microarrays. Two biological replicates of each sample were used for microarray analysis.

2009-12-31 | E-GEOD-8955 | biostudies-arrayexpress

Analyses of genes regulated by the N-terminal photolyase homology region (CNT1/PHR) of CRY1 by RNA-seq

Project description:Total RNA was extracted from samples including 35S::CNT1-NLS-YFP;cry1 and 35S::CNT1-G283E-NLS-YFP;cry1 seedlings grown in continuous blue light and subjected to high throughput sequencing. Previous studies reported that the C-terminal domain of CRY1 regulates hypocotyl elongation and blue light-regulated genes. This study reveals that CNT1 overexpression also regulates blue light-regulated genes, supporting the role of CNT1 in hypocotyl elongation at transcriptomic level.

2016-07-25 | GSE59763 | 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