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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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

ABSTRACT: The RNA sequencing experiment was performed in four different chemostat conditions as control for a CAGE sequencing experiment performed in the same conditions using the industrial relevant S. Cerevisiae strain CEN.PK113-7D

INSTRUMENT(S): NextSeq 500

ORGANISM(S): Saccharomyces cerevisiae

SUBMITTER: Christoph Börlin

PROVIDER: E-MTAB-6722 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Saccharomyces cerevisiae displays a stable transcription start site landscape in multiple conditions.

Börlin Christoph S CS Cvetesic Nevena N Holland Petter P Bergenholm David D Siewers Verena V Lenhard Boris B Nielsen Jens J

FEMS yeast research 20190301 2

One of the fundamental processes that determine cellular fate is regulation of gene transcription. Understanding these regulatory processes is therefore essential for understanding cellular responses to changes in environmental conditions. At the core promoter, the regulatory region containing the transcription start site (TSS), all inputs regulating transcription are integrated. Here, we used Cap Analysis of Gene Expression (CAGE) to analyze the pattern of TSSs at four different environmental c ...[more]

PMID: 30590648

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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

ChIP-seq for Leu3 with addition of different levels of leucine, valine and isoleucine

Project description:In this experiment we wanted to see how the binding behavior of the S. Cerevisiae transcription factor Leu3, on of the main regulators of leucine biosynthesis, is affected by different availability of the branched chain amino acids. For this we grow the cells in shake flask under glucose limitation and treated them 2 hours before sampling. The cells were then cross-linked with formaldehyde and ChIP-seq was performed using the Oxford Nanopore MinIon.

2020-07-01 | E-MTAB-8820 | biostudies-arrayexpress

Chromatin immunoprecipitation to identify Ino80 binding sites in yeast following phosphate startvation

Project description:ChIP on CHIP analysis were performed to analyse the direct involvement of Ino80 in the regulation of the phosphate responsive and nucleotide metabolism genes upon phosphate starvation: We immunoprecipitated Ino80-bound chromatin fragments after formaldehyde crosslinking from cells grown in minimal medium (EMM) or minimal medium lacking phosphate and purified, amplified and probed the Ino80-associated DNA using oligonucleotide tiling arrays.

2009-12-14 | E-MEXP-2284 | biostudies-arrayexpress

Transcription profiling by array of condition dependent regulation of lipid metabolism in Saccharomyces cerevisiae

Project description:Investigation of lipid metabolism as a function of three experimental factors: 1) aerobicity (aerobic vs anaerobic, or 'A' vs 'O'), 2) nutrient limitation (carbon vs nitrogen limitation, or 'C' vs 'N'), 3) temperature (30C vs 15C, or 'T' vs 't') using a full factorial design.

2013-01-31 | E-MEXP-3704 | biostudies-arrayexpress

RNA-seq of Saccharomyces cerevisiae CEN.PK-113.5D (KiURA3) strain grown in different chemostat limitations

Project description:RNA-seq data of chemostat conditions was collected in triplicate to get accurate genome-wide transcript levels that could be integrated with ChIP data from transcription factor binding to understand transcriptional regulation.

2019-03-25 | E-MTAB-6657 | biostudies-arrayexpress

ChIP-exo data for 21 transcription factors of yeast metabolic gene regulation in four different chemostat conditions

Project description:Conditions: Nitrogen-, ethanol-, anaerobic glucose- and respiratory glucose-limited chemostats. S.cerevisiae, CEN.PK-113-5D. 9x-Myc or TAP tags on C-terminal on each of the endogenous TFs. KiURA3 integrated downstream of tag for selection

2019-03-25 | E-MTAB-6673 | 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

Engineering acetyl-CoA supply: Functional expression of a bacterial pyruvate-dehydrogenase complex in the cytosol of Saccharomyces cerevisiae

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2014-11-04 | E-GEOD-59814 | biostudies-arrayexpress

RNA-seq of high lipid producing Yarrowia lipolytica during nitrogen or carbon restriction

Project description:A DGA1 overexpressing strain was cultivated in chemostat conditions, in either nitrogen or carbon restriction.

2016-03-03 | E-MTAB-3837 | biostudies-arrayexpress

RNA-seq of high lipid producing Yarrowia lipolytica during nitrogen or carbon restriction (control strain)

Project description:A control strain (MTYL038) was cultivated in chemostat conditions, in either nitrogen or carbon restriction. Functions as negative control to E-MTAB-3837.

2017-06-06 | E-MTAB-5284 | biostudies-arrayexpress

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