Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

33 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Transcription start site mapping of Saccharomyces cerevisiae grown in YPD media using the nAnTi-iCAGE protocol

ABSTRACT: We used nAnT-iCAGE – unbiased single-nucleotide resolution method for genome-wide transcription start site (TSS) capture, to produce libraries from Saccharomyces cerevisiae total RNA. Our goal was to investigate S. cerevisiae core-promoters and assess the rules of transcription initiation in BY4741 strain grown in YPD media.

INSTRUMENT(S): Illumina MiSeq

ORGANISM(S): Saccharomyces cerevisiae S288c

SUBMITTER: Nevena Cvetesic

PROVIDER: E-MTAB-7465 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

SLIC-CAGE (Super-Low Input Carrier-CAGE) development: comparison with Saccharomyces cerevisiae nAnTi-CAGE and nanoCAGE libraries and validation of SLIC-CAGE on Mus musculus total RNA

Project description:We developed SLIC-CAGE (Super-Low Input Carrier-CAGE) approach to capture 5'end of RNA polymerase II transcripts from as little as 5-10 ng of total RNA. The dramatic increase in sensitivity compared to existing CAGE methods is achieved by specially designed, selectively degradable carrier RNA. We tested SLIC-CAGE on Saccharomyces cerevisiae (BY4741 strain) and produced libraries from 1-100 ng of total cellular RNA. We also produced S. cerevisiae nAnT-iCAGE libraries as the current gold-standard CAGE libraries using the recommended 5 micrograms of total cellular RNA to assess the quality of SLIC-CAGE libraries produces with up to 1000-fold less material. We provide a direct comparison between SLIC-CAGE and the latest nanoCAGE protocol (libraries created using S. cerevisiae total RNA) and show that SLIC-CAGE produces unbiased libraries of higher complexity and quality than nanoCAGE. Finally, we provide SLIC-CAGE libraries on mouse embryonic stem cells (E14) using 5-100 ng of total cellular RNA as starting material.

2018-10-25 | E-MTAB-6519 | biostudies-arrayexpress

CAGE experiment of S. Cerevisiae strain CEN.PK113-7D in four different chemostat conditions

Project description:The CAGE experiment was performed in four different chemostat conditions to assess if and how much the Transcription start site landscape changes in the industrial relevant S. Cerevisiae strain CEN.PK113-7D in different conditions. CAGE was also used to obtain accurate TSS annotations for each expressed gene.

2019-01-03 | E-MTAB-6650 | biostudies-arrayexpress

SLIC-CAGE (Super-Low Input Carrier-CAGE) application on mouse primordial germ cells isolated from embryonic day E11.5

2018-10-25 | E-MTAB-7056 | biostudies-arrayexpress

CAGE sequencing of iPSC and Human dermal fibroblasts

Project description:CAGE sequencing of iPSC and Human dermal fibroblasts, total RNA and fractionated into nuclear, cytoplasmic and chromatin fractions.

2021-04-28 | E-MTAB-10384 | biostudies-arrayexpress

Transcription profiling by array of Saccharomyces cerevisiae strain VL3 with or without the the co-inoculation of a second yeast species, Pichia kluyveri (PKKR1).

Project description:Replicate cultres of Saccharomyces cerevisiae strain VL3 (a commercial wine strain) were inititaed with and without the the co-inoculation of a second yeast species, Pichia kluyveri (PKKR1). In addition replicate cultures of Pichia kluyveri were initiated. The media for all cultures was sterile Sauvignon blanc grape juice. Triplicates of each treatment were destructively harvested at days 2, 9 and 16 of fermentation and RNA extracted. RNA from S. cerevisiae could not be preferentially extracted from co-ferments. P. kluyveri genome has not been sequenced and so homology to S. cerevisiae probes on the array could not be accurately estimated. We extracted RNA from the P. kluyveri single ferments and hybridised them to the S. cerevisiae arrays to control for this. These species diverged over 100 MYA, and we did not observe abundant homology by way of cross hybridisation. The mean probe intensity for P. kluyveri cDNA was 17-fold lower than for S. cerevisiae, but some probes reported reasonable signal. The intensity distribution of these probes fit a log-normal distribution (P<0.01). 97% of the distribution fell below one-thirtieth of the S. cerevisiae maximum intensity: the remaining 3%, comprising 429 probes, potentially have reasonable homology to P. kluyveri cDNA and we removed these from all analyses. Please see associated additional file 'removePKKR1.r' R code to achieve this.

2012-09-01 | E-MTAB-1235 | biostudies-arrayexpress

RNA-seq of hydroxy-acid producing strains of Crabtree-negative Saccharomyces cerevisiae

Project description:Differential gene expression analysis of five different strains of Crabtree-negative Saccharomyces cerevisiae that lack pyruvate decarboxylase activity. The three different acids studied were lactic, malic, and 3-hydroxypropionic acid.

2019-03-01 | E-MTAB-7600 | biostudies-arrayexpress

RNAseq of yeast cells sampled during the lag (10% glucose consumption), mid-exponential (75% glucose consumed) and post-exponential phases (>99% glucose consumed)

Project description:The aim of the study was to identify regulatory elements of promoters associated with glucose-dependent gene expression profiles. For the transcriptome analysis an overnight culture of log-phase S. cerevisiae CEN.PK-113-7D grown in Delft medium was inoculated into a 500mL Delft medium at a starting OD of 0.03We carried out biological triplicate sampling from a 1 ltr BioStat Q bioreactor at 30 degrees with 800rpm agitation, with controlled aeration and pH maintained at 6 using 2M NaOH.

2019-04-01 | E-MTAB-7657 | biostudies-arrayexpress

Proteomic Analysis of Protein Methylation in the Yeast Saccharomyces cerevisiae

Project description:Protein methylation catalyzed by SAM-dependent methyltransferase represents a major PTM involved in important biological processes. Because methylation can occur on nitrogen, oxygen and sulfur centers and multiple methylation states exist on the nitrogen centers, methylproteome remains poorly documented. Here we present the methylation by isotope labeled SAM (MILS) strategy for a highly-confident analysis of the methylproteome of the SAM-auxotrophic Saccharomyces cerevisiae based on the online multidimensional μHPLC/MS/MS technology. We identified 117 methylated proteins, containing 182 methylation events associated with 174 methylation sites. About 90% of these methylation events were previously unknown. Our results indicated, 1) over 6% of the yeast proteome are methylated, 2) the amino acid residue preference of protein methylation follows the order Lys >> Arg > Asp > Glu ≈ Gln ≈ Asp > His > Cys, 3) the methylation state on nitrogen center is largely exclusive, and 4) the methylated proteins are located mainly in nucleus/ribosome associated with translation/transcription and DNA/RNA processing. Our dataset is the most comprehensive methylproteome known-to-date of all living organisms, and should significantly contribute to the field of protein methylation and related research.

2020-01-27 | PXD000606 | Pride

Redox control of the cAMP/PKA pathway during protein misfolding stress

Project description:Protein aggregation is the abnormal association of misfolded proteins into larger, often insoluble structures that can be toxic during ageing and in protein aggregation-associated diseases. This RNA-seq study in Saccharomyces cerevisiae investigated the role of Tsa1, which is a member of the highly conserved 2-Cys peroxiredoxin (Prx) enzyme family, on protein aggregation.

2021-04-19 | E-MTAB-9355 | biostudies-arrayexpress

Antibiotic-induced Alternations in Gut Microflora are Associated with the Suppression of Immune-related Pathways in Grass Carp

Project description:Because antibiotics have been widely used to prevent severe losses due to infectious fishery diseases, the liberal application and overuse of antibiotics has led to the spread and evolution of bacterial resistance, food safety hazards, and environmental issues. The use of some antibiotics, including florfenicol and enrofloxacin, is allowed in aquaculture in China. Accordingly, to better address the concerns and questions associated with the impact of administered enrofloxacin and florfenicol to grass carp, here we investigated the immune response, bacterial diversity, and transcriptome of the intestine of C. idella treated with these oral antibiotics. The aim of this study was to provide an in-depth evaluation of the antibiotic-induced patterns and dynamics of the microbiota grass carp and the potential mechanism involved.

2022-08-08 | E-MTAB-12057 | biostudies-arrayexpress

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