Browse
Submit Data
Databases
API
Help

Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

14 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Histone deacetylation at coding sequences adjusts transcription kinetics during Candida albicans morphogenesis [ChIP-seq]

ABSTRACT: The dataset contains ChIP-Seq data of the Set3 and Hos2 proteins in Candida albicans, assayed in two morphological phases (yeast and hypha). The Set3 and Hos2 proteins in the respective strains carry 9myc epitopes and ChIP was performed with an anti-myc antibody. Included samples are the following: 1 input and 1 ChIP sample of an untagged wild type strain as negative control assayed in the yeast phase, 1 input and 3 ChIP biological replicates of the Set3-9myc strain in the yeast phase, 1 input and 2 ChIP biological replicates of the Set3-9myc strain in the hypha phase, 1 input and 2 ChIP biological replicates of the Hos2-9myc strain in the yeast phase, 1 input and 2 ChIP biological replicates of the Hos2-9myc strain in the hypha phase, 1 input and 3 ChIP biological replicates of Set3-9myc in a set1delta/delta background in the yeast phase. ChIP-Seq was performed of Candida albicans strains in two morphological phases (yeast and hypha). Yeast-phase cells were grown to the exponential phase in YPD at 30C. Hyphal differentiation was induced by resuspending the cells in YPD+20% Fetal Calf Serum and a shift of the growth temperature to 37C. Induction was performed for 30 minutes. Cells were crosslinked with 1% formaldehyde for 15 minutes at room temperature.

ORGANISM(S): Candida albicans

SUBMITTER: Denes Hnisz

PROVIDER: E-GEOD-38425 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Histone deacetylation at coding sequences adjusts transcription kinetics during Candida albicans morphogenesis [ChIP-seq]

Project description:The dataset contains ChIP-Seq data of the Set3 and Hos2 proteins in Candida albicans, assayed in two morphological phases (yeast and hypha). The Set3 and Hos2 proteins in the respective strains carry 9myc epitopes and ChIP was performed with an anti-myc antibody. Included samples are the following: 1 input and 1 ChIP sample of an untagged wild type strain as negative control assayed in the yeast phase, 1 input and 3 ChIP biological replicates of the Set3-9myc strain in the yeast phase, 1 input and 2 ChIP biological replicates of the Set3-9myc strain in the hypha phase, 1 input and 2 ChIP biological replicates of the Hos2-9myc strain in the yeast phase, 1 input and 2 ChIP biological replicates of the Hos2-9myc strain in the hypha phase, 1 input and 3 ChIP biological replicates of Set3-9myc in a set1delta/delta background in the yeast phase.

2013-01-01 | GSE38425 | GEO

Histone deacetylation at coding sequences adjusts transcription kinetics during Candida albicans morphogenesis [RNA-seq]

Project description:Transcriptome analysis of wild type and set3-deficient Candida albicans cells in yeast and hyphal morphological phases RNA Sequencing was performed of wild type and set3-deficient Candida albicans strains in two morphological phases (yeast and hypha). Yeast-phase cells were grown to the exponential phase in YPD at 30oC. Hyphal differentiation was induced by resuspending the cells in YPD+20% Fetal Calf Serum and a shift of the growth temperature to 37oC. Induction was performed for 30 minutes. Three biological replicates of both genotypes in each morphological phases were analyzed.

2013-01-01 | E-GEOD-38426 | biostudies-arrayexpress

Fhl1 and lfh1 ChIP-chip

Project description:Fhl1-9myc ChIP-chip, YPD, OD600=0.8, 2 arrays with duplicate spotting of yeast intergenic regions. AND Ifh1-9myc ChIP-chip, cells grown in YPD, OD600=0.8, 2 arrays with duplicate spotting of yeast intergenic regions. Keywords = Fhl1 Keywords: other

2004-11-09 | GSE1930 | GEO

Fhl1 and lfh1 ChIP-chip

2010-06-05 | E-GEOD-1930 | biostudies-arrayexpress

FabR ChIP-chip on Salmonella enterica subsp. enterica serovar Typhimurium SL1344

Project description:FabR ChIP-chip on Salmonella enterica subsp. enterica serovar Typhimurium SL1344 using anti-Myc antibody against strain with chromosomally 9Myc-tagged FabR (IP samples) and wildtype strain (mock IP samples)

2014-12-31 | GSE52877 | GEO

Immunopurification results of cytoskeletal motor proteins in S. cerevisiae

Project description:The accompanying dataset is the result of a systematic study to identify the RNA cargoes associated with the cytoskeletal motor proteins of Saccharomyces cerevisiae. We immunopurified, via the use of integrated, C-terminal GFP and 9Myc tags, the five actomyosin motors, Myo1, Myo2, Myo3, Myo4, and Myo5; the kinesin-like proteins Kar3, Kip1, Kip2, Kip3, and Smy1; and the dynein, Dyn1, from S. cerevisiae. Cells were either treated with formaldehyde or with the small molecule latrunculin B. We used formaldehyde crosslinking to stabilize associations between motors proteins and interacting RNAs before IP. Yeast cells growing exponentially in rich medium were treated with formaldehyde, lysed and sonicated, then incubated with magnetic beads coupled to monoclonal antibodies against either 9Myc or GFP to isolate the tagged motor proteins along with any associated RNAs. After IP, the formaldehyde crosslinks were reversed and the enriched RNAs and RNAs purified from the corresponding total lysate were amplified and labeled respectively with Cy5 and Cy3, then jointly hybridized to custom-made, S. cerevisiae oligonucleotide microarrays (Hogan et al., PLoS Biology, 2008). Alternatively, the addition of a low concentration of latrunculin B (2 ug/ml) to live cells to partially solubilize the actin cytoskeleton allowed for successful IP of the motor proteins and associated mRNAs without the need for a chemical crosslinker. In both the case of latrunculin B and formaldehyde treatment, we also performed IPs in which the untagged parent yeast strains were processed for IP and microarray analysis in a manner identical to that of the tagged strains (labeled as mock). transcription profiling

2012-01-27 | E-GEOD-35343 | biostudies-arrayexpress

Saccharomyces cerevisiae

Project description:Chip-chip from budding yeast cells with Set3 complex

| PRJNA248460 | ENA

Chip-chip from budding yeast cells with Set3 complex

Project description:Chromatin immunoprecipitation of Set3 complex applied with tilling array chip ( ChIP on chip of either Set3-TAP or Snt1-TAP) analysis demonstrated that the genome-wide localization of Set3 complex in Saccharomyces cerevisiae

2014-12-31 | GSE57916 | GEO

Histone deacetylation at coding sequences adjusts transcription kinetics during Candida albicans morphogenesis [RNA-seq]

Project description:Transcriptome analysis of wild type and set3-deficient Candida albicans cells in yeast and hyphal morphological phases

2013-01-01 | GSE38426 | GEO

Chip-chip of Set3, of PolII, and of H3K4me2 from budding yeast cells

Project description:Chromatin immunoprecipitation of Set3, of PolII, and of H3K4me2, respectively, applied with tilling array chip (ChIP on chip of Set3, of PolII, and of H3K4me2, respectively) analysis demonstrated that a compared genomic occupancy of Set3, of PolII, and of H3K4me2 in Saccharomyces cerevisiae wild type cells compared anong those in Hst1 deleted, Hos2 deleted and Hst2 & Hos2 double deleted cells

2020-12-31 | GSE143665 | GEO

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