Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Saccharomyces cerevisiae

ABSTRACT: Genome-wide mapping of transcription start sites in a ∆set2 strain

PROVIDER: PRJNA265047 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR1631656_1.fastq.gz	Fastqsanger.gz
	SRR1631656_2.fastq.gz	Fastqsanger.gz
	SRR1631657_1.fastq.gz	Fastqsanger.gz
	SRR1631657_2.fastq.gz	Fastqsanger.gz
	SRR1631658_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 8

Similar Datasets

Cryptic Transcription in a set2∆ in Saccharomyces cerevisiae

2008-10-31 | GSE13310 | GEO

Saccharomyces cerevisiae

Project description:Comparison of alternative decapping enzymes to map transcription start sites genome-wide

| PRJNA298055 | ENA

Genome-wide mapping of transcription start sites in a ∆set2 strain

Project description:Here we quantified the transcription start site usage in a WT strain (BY4741) and a ∆set2 strain associated with the appearence of cryptic transcription start sites.

2015-01-14 | GSE62735 | GEO

Saccharomyces cerevisiae

Project description:set2, set2sir4 transcription profiles

| PRJNA95887 | ENA

Saccharomyces cerevisiae

Project description:Genome-wide mapping of the binding sites of transcription factor Cst6p in Saccharomyces cerevisiae

| PRJNA306490 | ENA

Saccharomyces cerevisiae

Project description:In vitro transcription start sites (TSSs) determined by 5'-RACE

| PRJNA361496 | ENA

Saccharomyces cerevisiae

Project description:GENOME WIDE IMPACT OF SSL2 MUTANTS ON TRANSCRIPTION START SITE USAGE

| PRJNA610641 | ENA

Cryptic Transcription in a set2â in Saccharomyces cerevisiae

Project description:In cells lacking the histone methyltransferase Set2, initiation of RNA polymerase II transcription occurs inappropriately within the protein-coding regions of genes, rather than being restricted to the proximal promoter. Here, we mapped the transcripts produced in an S. cerevisiae strain lacking Set2, and applied rigorous statistical methods to identify sites of cryptic transcription at high resolution. Wild type (BY4741) and set2â (BY4741) strains were grown at 30Â°C in YPD (1% yeast extract, 2% peptone, 2% dextrose) to an OD600 of 0.6-0.8. For each of the three replicates, Total RNA was extracted by acid-phenol method (Xiao et al. 2003). Double-stranded cDNA was prepared using an Invitrogen SuperScriptâ¢ (Cat No. 11917-010) primed with Oligo(dt) and random hexamers. For each replicate, the wt and set2â cDNA were independetly fluorescently labeled and comparatively hybridized to high-resolution 385K Saccharomyces cerevisiae CGH arrays (2005-08-16_SCER_WG_CGH) with Tm-normalized probes. In one of the replicates, assignment of the fluorescent label was reversed.

2010-05-17 | E-GEOD-13310 | biostudies-arrayexpress

Chd1 chromatin remodelers maintain nucleosome organization and repress cryptic transcription

Project description:Proper chromatin organization is essential for defining transcription units and maintaining genomic integrity in eukaryotes. Mutations affecting the chromatin structure can lead to increased cryptic transcription and genomic instability. In this study we found that deletion of the Schizosaccharomyces pombe Chd1-type chromatin remodelers, hrp1 and hrp3, causes strong, genome-wide accumulation of antisense transcripts, while the amount of coding mRNA transcripts is mostly unaffected. Nucleosome mapping revealed a specific role for Chd1-remodelers in the positioning of nucleosomes in gene coding regions. While the arrangement of nucleosomes in promoter regions was similar to WT, nucleosome organization within coding regions was remarkably irregular in hrp1∆hrp3∆ strain. We extended our analysis to other mutations associated with enhanced cryptic transcription activity, such as set2∆, alp13∆, and FACT complex subunit pob3∆. While nucleosomes were severely depleted in the pob3∆ strain, nucleosome positioning was less affected. In sharp contrast, nucleosome organization in the alp13∆ and set2∆ strains was indistinguishable from WT. These data indicate multiple mechanisms in the repression of cryptic promoter activity in eukaryotic cells. Genome-wide profiling of H3K9/K14 acetylation Genome-wide expression analysis of either Alp13-, Set2-, Hrp3 or Hrp1 and Hrp3-deficient cells Genome-wide expression analysis of either Hrp1, Hrp3, or Hrp1 and Hrp3-deficient cells Nucleosome mapping experiments

2012-09-15 | GSE40872 | GEO

Saccharomyces cerevisiae 3' poly(A) site mapping

Project description:The use of alternative polyadenylation sites is common and affects the post-transcriptional fate of mRNA, including its stability, localization, and translation. Here we present a method for genome-wide and strand-specific mapping of poly(A) sites and quantification of RNA levels at unprecedented efficiency by using an on-cluster dark T-fill procedure on the Illumina sequencing platform. Our method outperforms former protocols in quality and throughput, and reveals new insights into polyadenylation in Saccharomyces cerevisiae.

2013-01-10 | GSE40110 | 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