Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

High-Resolution DNA Binding Specificity Analysis of Yeast Transcription Factors

ABSTRACT: We used microarrays to detail the global program of gene expression underlying rRNA processing gene regulation during heat shock. PBF1 is YBL054W (TOD6) and PBF2 is YER088C (DOT6).

ORGANISM(S): Schizosaccharomyces pombe Saccharomyces cerevisiae

PROVIDER: GSE13684 | GEO | 2009/01/15

SECONDARY ACCESSION(S): PRJNA110437

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

Transcription profiling of yeast wild type BY4741, single deletion mutants delta-pbf1, delta-pbf2 and double mutant delta-pbf1 delta-pbf2 before and after heat shock

Project description:We used microarrays to detail the global program of gene expression underlying rRNA processing gene regulation during heat shock. PBF1 is YBL054W (TOD6) and PBF2 is YER088C (DOT6). Experiment Overall Design: S. cerevisiae cells were grown @ 25 ÂºC to O.D. 600 of 0.3~04, in triplicate. Half of the cells were collected at T0 and half of the cells were subjected to 25 ÂºC-->37 ÂºC heat shock and cells were collected after 20 min, as samples T20. Total RNAs were collected and used to perform expression microarray analysis on Affymetrix Yeast Array 2.0 platform. The changes of gene expression upon heat shock were analyzed for four strains, wild type BY4741, single deletion mutants delta-pbf1, delta-pbf2 and double mutant delta-pbf1 delta-pbf2.

2009-01-25 | E-GEOD-13684 | biostudies-arrayexpress

High-resolution DNA-binding specificity analysis of yeast transcription factors.

Project description: Not available

| S-EPMC2665775 | biostudies-literature

Genetic and Epigenetic Determinants Establish a Continuum of Hsf1 Occupancy and Activity Across the Yeast Genome

Project description:We performed ChIP-seq of Hsf1 under non heat shock, 5-minute heat shock and 120 minute heat shock conditions. We used the conditional chemical genetics approach known as “anchor away” (AA) to rapidly inactivate Hsf1. We coupled Hsf1-AA to and nascent RNA seq (NAC)-seq to define the genes whose expression depends on Hsf1 during heat shock.

2018-07-26 | GSE117653 | GEO

Yeast linker histone HHO1p effect on transcription before and after heat shock

Project description:DNA array expression analysis comparing RNA transcripts in wild type and hho1 strains before and after a heat-shock from 25 to 37 degrees. Keywords: expression, heat shock

2008-07-01 | GSE9095 | GEO

Heat shock stimulates genomic instability and phenotypic variations in yeast

Project description:Yeast Saccharomyces cerevisiae has been widely used as a model system for studying genomic instability. In this study, heat-shock-induced genomic alterations were explored in the heterozygous diploid yeast strain JSC25-1. In combination of the whole-genome microarray, the patterns of chromosomal instability induced by heat shock could also be explored at a whole genome level. Using this system, we found heat-shock treatment resulted in hundreds-fold higher rate of genomic alterations, including aneuploidy and loss of heterozygosity (LOH).

2020-05-18 | GSE150711 | GEO

Nucleosome positioning under perturbation conditions in yeast

Project description:We report nucleosome poisitioning under pertubation conditions such as heat shock, CHD1 deletion, and SET2 deletion

2014-10-23 | GSE56095 | GEO

Measuring the dependence of the yeast heat shock response on intracellular pH and translation during stress

Project description:S. cerevisiae cells acidify when they experience stressful temperatures. In addition, newly-translated proteins are thought to misfold, triggering the heat shock response. To determine whether heat-shock associated acidification and translation state are important for the cellular response, we manipulated intracellular pH, blocked translation, heat shocked cells, and sequenced the transcriptome.

2020-06-30 | GSE152916 | GEO

Yeast HSF1 vs hsf1-ba1

Project description:Upon heat shock, Hsf1 protein is extensively phosphorylated, however, this modification is inhibited by an hsf1-bal mutation. To get genome-wide effect of the hyperphosphorylation on Hsf1-regulated transcription, the heat-induced gene expression profiles in HSF1 and hsf1-bal cells were compared. Keywords: stress response

2005-09-27 | GSE3361 | GEO

A disease-linked lncRNA mutation in RNase MRP inhibits ribosome synthesis [yeast]

Project description:Mutations in the human RMRP gene cause Cartilage Hair Hypoplasia (CHH), an autosomal recessive disorder characterized by skeletal abnormalities and impaired T-cell activation. RMRP encodes a non-coding RNA, which forms the core of the RNase MRP ribonucleoprotein complex. In budding yeast, RMRP cleaves a specific site in the pre-ribosomal RNA (pre-rRNA) during ribosome synthesis. CRISPR-mediated disruption of RMRP in human cells lines caused growth arrest, with pre-rRNA accumulation. Here, we analyzed disease-relevant primary cells, showing that mutations in RMRP impair mouse T cell activation and delay pre-rRNA processing. Analysis of pre-rRNA processing in patient-derived human fibroblasts with CHH-linked mutations showed a similar pattern of processing delay. Human cells engineered with the most common CHH mutation (70AG in RMRP) show specifically impaired pre-rRNA processing, resulting in reduced mature rRNA and a reduced ratio of cytosolic to mitochondrial ribosomes. Moreover, the 70AG mutation caused a reduction in intact RNase MRP complexes. Together, these results indicate that CHH is a ribosomopathy, and the first human disorder of rRNA processing to be described.

2021-03-29 | GSE171020 | GEO

Nucleosome positioning under perturbation conditions in yeast

Project description:We report nucleosome poisitioning under pertubation conditions such as heat shock, CHD1 deletion, and SET2 deletion Mono-nucleosome DNA was prepared from wild type strain under normal or heat shock conditions, or CHD1 or SET2 deletion strain. The mono-nucleosome DNA was mapped.

2014-10-23 | E-GEOD-56095 | 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