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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Yarrowia lipolytica biolipid production during D-stat setup. [Part 1]

ABSTRACT: First part of the time-course transcriptomic profilling of the oleaginous yeast Yarrowia lipolytica, obtained during a controlled decellerostat (D-stat) setup. A nitrogen limitation was applied during the course of the D-stat to initiate and control de novo biolipid synthesis. Yarrowia lipolytica Agilent microarray, one-color staining. Each time sample was spotted in triplicate. A reference condition was spotted in quadruplicate, based on a RNA pool from three samples obtained during the biomass production phase.

ORGANISM(S): Yarrowia lipolytica

SUBMITTER: Nicolas Morin

PROVIDER: E-GEOD-35445 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Yarrowia lipolytica biolipid production during D-stat setup. [Part 2]

Project description:Second part of the time-course transcriptomic profilling of the oleaginous yeast Yarrowia lipolytica, obtained during a controlled decellerostat (D-stat) setup. A nitrogen limitation was applied during the course of the D-stat to initiate and control de novo biolipid synthesis. Yarrowia lipolytica Agilent microarray, one-color staining. Each time sample was spotted in triplicate (except for sample 26, for which a technical replicate of replicate r1 was performed).

2015-01-01 | E-GEOD-35446 | biostudies-arrayexpress

Yarrowia lipolytica biolipid production during D-stat setup.

Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

2015-01-01 | E-GEOD-35447 | biostudies-arrayexpress

The pyruvate-tricarboxylic acid cycle node: a focal point of virulence control in the enteric pathogen Yersinia pseudotuberculosis

Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

2014-09-17 | E-GEOD-54547 | biostudies-arrayexpress

Dynamics of two oscillation phenotypes in S. cerevisiae [4hr]

Project description:Genetic and environmental factors influence the phenotype of an organism. Time is rarely considered when studying changes in cellular phenotype. Time-resolved microarray data revealed genome-wide transcriptional changes in cells oscillating with ~2 and ~4 h periods. We mapped the global patterns of transcriptional oscillations into a 3-dimensional map to represent different cellular phenotypes of oscillation period. This map shows the dynamic nature of transcripts through time and concentration space, and that they are ordered and coupled to each other. Although cells differed in oscillation periods, transcripts involved in certain processes were conserved in a deterministic way. This ordered timing of biological process may allow cells to grow energetically efficient. Decreased glucose levels in the media were found to increase the redox cycles of yeast strain CEN.PK113-7D. Glucose may have acted as signaling molecules for timing longer catabolic processes in the cell population. As oscillation period lengthened, the peak to trough ratio of transcripts increased and the percent of cells in the unbudded (G0/G1) phase of the cell cycle increased. Gene transcripts appear to be coordinated with metabolic functions and the cell cycle. High-resolution samples over time were collected for CEN.PK113-7D oscillating with 4 hour period.

2012-04-16 | E-GEOD-30052 | biostudies-arrayexpress

Dynamics of two oscillation phenotypes in S. cerevisiae [2hr]

2012-04-16 | E-GEOD-30051 | biostudies-arrayexpress

Dynamics of two oscillation phenotypes in S. cerevisiae reveal a network of genome-wide transcriptional and cell cycle oscillators.

Project description:This SuperSeries is composed of the following subset Series: GSE30051: Dynamics of two oscillation phenotypes in S. cerevisiae[2hr] GSE30052: Dynamics of two oscillation phenotypes in S. cerevisiae[4hr]. Refer to individual Series

2012-04-16 | E-GEOD-30053 | biostudies-arrayexpress

The pyruvate-tricarboxylic acid cycle node: a focal point of virulence control in the enteric pathogen Yersinia pseudotuberculosis [csrA mutant]

Project description:Whole transcriptome assessment of the Yersinia pseudotuberculosis strain YPIII. The Y. pseudotuberculosis csrA regulon was determined in Yersinia minimal minimum developed for the study. CsrA is a key regulator coordinating virulence and metabolism. Y. pseudotuberculosis YPIII or the isogenic csrA mutant strain were cultivated at 25M-BM-0C under aeration on a rotary shaker. First pre-cultures were grown in a 1:1 mixture of HAMM-bM-^@M-^Ys F-12 Nutrient Mixture (Invitrogen, Carlsbad, US) and liquid DMEM medium (Biochrom, Berlin, DE). Second pre-cultures and main cultures were grown in a Yersinia minimal medium (YMM). The analysis comprised three biological replicates for each strain. In addition, samples, taken at three different time points of the exponential growth phase, were used to validate constant expression during the cultivation. Total RNA was extracted using SV Total RNA Isolation System (Promega). The samples were treated with RNase-free DNase (Roche Applied Science) and the quality of the RNA was confirmed by the lack of PCR amplification of the hns gene and by using an Agilent 2100 Bioanalyzer.

2014-09-17 | E-GEOD-54545 | biostudies-arrayexpress

The pyruvate-tricarboxylic acid cycle node: a focal point of virulence control in the enteric pathogen Yersinia pseudotuberculosis [crp mutant]

Project description:Whole transcriptome assessment of the Yersinia pseudotuberculosis strain YPIII. The Y. pseudotuberculosis crp regulon was determined in Yersinia minimal minimum developed for the study. Crp is a key regulator coordinating virulence and metabolism. Y. pseudotuberculosis YPIII or the isogenic crp mutant strain were cultivated at 25M-BM-0C under aeration on a rotary shaker. First pre-cultures were grown in a 1:1 mixture of HAMM-bM-^@M-^Ys F-12 Nutrient Mixture (Invitrogen, Carlsbad, US) and liquid DMEM medium (Biochrom, Berlin, DE). Second pre-cultures and main cultures were grown in a Yersinia minimal medium (YMM). The analysis comprised three biological replicates for each strain. In addition, samples, taken at three different time points of the exponential growth phase, were used to validate constant expression during the cultivation. Total RNA was extracted using SV Total RNA Isolation System (Promega). The samples were treated with RNase-free DNase (Roche Applied Science) and the quality of the RNA was confirmed by the lack of PCR amplification of the hns gene and by using an Agilent 2100 Bioanalyzer.

2014-09-17 | E-GEOD-54544 | biostudies-arrayexpress

The pyruvate-tricarboxylic acid cycle node: a focal point of virulence control in the enteric pathogen Yersinia pseudotuberculosis [rovA mutant]

Project description:Whole transcriptome assessment of the Yersinia pseudotuberculosis strain YPIII. The Y. pseudotuberculosis rovA regulon was determined in Yersinia minimal minimum developed for the study. RovA is a key regulator for Yersinia virulence. Y. pseudotuberculosis YPIII or the isogenic rovA mutant strain were cultivated at 25M-BM-0C under aeration on a rotary shaker. First pre-cultures were grown in a 1:1 mixture of HAMM-bM-^@M-^Ys F-12 Nutrient Mixture (Invitrogen, Carlsbad, US) and liquid DMEM medium (Biochrom, Berlin, DE). Second pre-cultures and main cultures were grown in a Yersinia minimal medium (YMM). The analysis comprised three biological replicates for each strain. In addition, samples, taken at three different time points of the exponential growth phase, were used to validate constant expression during the cultivation. Total RNA was extracted using SV Total RNA Isolation System (Promega). The samples were treated with RNase-free DNase (Roche Applied Science) and the quality of the RNA was confirmed by the lack of PCR amplification of the hns gene and by using an Agilent 2100 Bioanalyzer.

2014-09-17 | E-GEOD-54546 | biostudies-arrayexpress

RNA-seq of the prototrophic non-hyphal smooth-33 mutant (FKP514) and its prototrophic control strain (FKP391)

Project description:FKP503 is a non-hyphal mutant strain (smooth-33) that was obtained from multiple passages of its parental strain FKP355. FKP355 and FKP503 are leucine auxotrophic strains: for further investigation prototropic strains FKP391 and FKP514 were constructed. To compare transcriptomic changes, FKP391 and FKP514 were cultured in chemostats under conditions stimulating lipid accumulation (nitrogen restriction).

2018-11-26 | E-MTAB-7400 | biostudies-arrayexpress

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