Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

CRAC of yeast RNA polymerase II in various thermosensitive strains at permissive and non-permissive temperature and anchor-away strains with the addition of rapamycin.

ABSTRACT: We obtained RNA polymerase II occupancy profile across the genome of S.cerevisiae in several strains, Wild type at 25 and 37 degrees C, RNA15-1 at 25 and 37 degrees C, anchor-away parental strain plus rapamycin, Reb1 anchor-away plus rapamycin, Rap1 anchor-away plus rapamycin, Nrd1-AID plus auxin, and nrd1-AID without auxin. This allowed us to compare polymerase profiles when these proteins are depleted from the nucleus.

ORGANISM(S): Saccharomyces cerevisiae

PROVIDER: GSE97913 | GEO | 2018/01/10

SECONDARY ACCESSION(S): PRJNA383311

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

CRAC of yeast RNA polymerase II in anchor-away and auxin-degron strains.

Project description:We obtained RNA polymerase II occupancy profiles across the genome of S.cerevisiae strains: Abf1 anchor-away cells after addition of rapamycin for different time points (including no addition of rapamycin) and Rap1-AID auxin-degron cells after addition of auxin for different time points (including no addition of auxin) . This allowed us to compare polymerase occupancy profiles when these proteins are depleted from the nucleus or degraded.

2018-12-20 | GSE114589 | GEO

High-resolution mapping of transcribing RNAPIII by CRAC upon depletion of Nrd1 [Experiment 2]

Project description:Here we report high-resolution analyses of transcribing RNAPIII in either a wild-type (WT) background or a Nrd1 auxin-inducible degron (AID) strain in which Nrd1 can be rapidly depleted upon addition of the auxin analogue Indole-3-acetic acid (IAA). Nrd1 functions together with Sen1 in transcription termination at RNAPII-dependent non-coding genes. Here we show that depletion of Nrd1 does not affect transcription termination at RNAPIII-dependent genes, indicating that Nrd1 is not an RNAPIII transcription termination factor.

2022-07-13 | GSE174699 | GEO

ChIP-seq of Mediator subunits in Mediator mutants and wild type yeast

Project description:Mediator subunits Med17 (Srb4) and Med15 (Gal11) were subjected to ChIP in wild type yeast, med18 (srb5), med20 (srb2), and med2 med3 med15 (triple mutant) yeast, all in kin28-anchor away yeast after 1 hr rapamycin treatment to evict Kin28 from the nucleus. This results in inactivation of Kin28, which reduces Mediator turnover at promoters and allows stronger Mediator ChIP signal at promoters. <br></br>Both Med17 and Med15 were tagged with myc and precipitated using the monoclonal antibody against c-myc. Please note that a specific control for rapamycin treatment was not performed in this experiment, as that has been well documented in the literature for this experiment, using what is called the anchor away method. The untagged sample is a control for non-specific immunoprecipitation.

2017-12-01 | E-MTAB-5824 | biostudies-arrayexpress

Low temperature and mTOR inhibition favor stem cell maintenance in human keratinocyte cultures [RNA-seq]

Project description:Purpose: Comparison of genes expression pattern in normal human epidermal keratinocytes (NHEKs) which were cultured at several specific temperatures or with rapamycin. Methods: Basically, NHEKs were cultured with irradiated 3T3J2 feeder cells in cFAD medium (Pr Green's method) for 1 week. NHEKs were cultured at 32, 35, 36, 37 and 38 degrees C from beginning to end of cell culture, respectively. Furthermore, 100 nM rapamycin-added cFAD medium and ed at 37 degrees C. 7days after cell cuture, NHEKs were harvested for RNAseq analysis. Results: The culture condition at 32 degrees C and 37 degrees C with rapamycin maintained human epidermal keratinocyte stem cells. Conclusions: mTORC1 inhibition via temperature changes favors ex vivo maintenance of human epidermal keratinocyte stem cells.

2023-05-29 | GSE199522 | GEO

Low temperature and mTOR inhibition favor stem cell maintenance in human keratinocyte cultures [miRNA-seq]

2023-05-29 | GSE198696 | GEO

Genome-wide mapping of yeast RNA polymerase II termination

Project description:Using a modification of the yeast anchor away and PAR-CLIP protocols, we have mapped the position of Pol II genome-wide in living yeast cells after depletion of components of either the polyadenylation (pA) or non-pA termination complexes. Depletion of Ysh1 from the nucleus does not lead to readthrough transcription. In contrast, depletion of the termination factor Nrd1 leads to widespread runaway elongation of non-pA transcripts. Depletion of Sen1 also leads to readthrough at non-pA terminators but in contrast to Nrd1 this readthrough appears less processive. Examination of PAR-CLIP sequencing data of Pol II after removal of different transcriptional termination factors.

2014-07-24 | E-GEOD-56435 | biostudies-arrayexpress

Genome-wide mapping of yeast RNA polymerase II termination

2014-07-24 | GSE56435 | GEO

Xrn1-sensitive lncRNAs are insensitive to Dbp2 nuclear depletion

Project description:To investigate whether the action of Dbp2 on Xrn1-sensitive lncRNAs depends on a nuclear or cytoplasmic localization, we used the anchor-away approach to deplete a Dbp2-FRB-GFP fusion from the nucleus upon rapamycin treatment.

2023-07-27 | GSE235551 | GEO

CRAC of yeast RNA polymerase II in anchor-away and auxin-degron strains.

Project description:CRAC of yeast RNA polymerase II in anchor-away and auxin-degron strains.

| PRJNA471852 | ENA

ncRNA termination in Saccharomyces cerevisiae

Project description:Nuclear depletion of the essential transcription termination factor Nrd1 in Saccharomyces cerevisiae was studied using a combination of RNA-Seq, ChIP-Seq of Pol II and PAR-CLIP of Nrd1. The drug rapamycin induces the formation of a ternary complex between a protein of interest, the drug and the small subunit of the ribosome (both proteins are genetically engineered). The small ribosome subunit is transported out of the nucleus. therefore the protein of interest can be depleted from nucleus upon treatment with rapamycin.

2013-11-14 | E-MTAB-1766 | 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