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Gene expression in whi3 and WHI3x4 in YPD and YPE

ABSTRACT: Measurement of the change in steady state mRNA level in cells with whi3 deletion or WHI3 overexpression relative to wildtype cells. In the overexpression experiment, WHI3 is moderately overexpressed by integrating four copies of WHI3 at its endogenous locus. This was performed in YEP glucose medium and YEP ethanol medium. Goal was to measure the effects of WHI3 on global gene expression at RNA level.

ORGANISM(S): Saccharomyces cerevisiae

PROVIDER: GSE51165 | GEO | 2013/09/26

SECONDARY ACCESSION(S): PRJNA221378

REPOSITORIES: GEO

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Gene expression in whi3 and WHI3x4 in YPD and YPE

Project description:Measurement of the change in steady state mRNA level in cells with whi3 deletion or WHI3 overexpression relative to wildtype cells. In the overexpression experiment, WHI3 is moderately overexpressed by integrating four copies of WHI3 at its endogenous locus. This was performed in YEP glucose medium and YEP ethanol medium. Goal was to measure the effects of WHI3 on global gene expression at RNA level. Two testing mutants whi3 vs WHI3, WHI3x4 vs WHI3 in two conditions YPD and YPE. Biological replicates: 2 whi3 in YPD, 2 WHI3x4 in YPD, 2 whi3 in YPE, 2 WHI3x4 in YPE.

2013-09-26 | E-GEOD-51165 | biostudies-arrayexpress

Transcriptomic analyses of a Cyberlindnera jadinii strain (NBRC0988) grown in glucose and xylose

Project description:Strand-specific RNA-seq libraries were constructed for two samples, including (I) wild-type strain NBRC0988 grown in YEP medium containing 2% w/v glucose;(II) wild-type strain NBRC0988 grown in YEP medium containing 2% w/v xylose. For preparation of RNA samples, NBRC0988 cells grown overnight were inoculated into 100 ml liquid Yeast Extract Peptone Dextrose (YEPD) medium with the initial inoculation amount of OD600= 0.1, and cultured for 15 hours at 30℃ and 250 rpm. The cells were collected by centrifugation at 6,000g for 5 minutes. After washing twice with phosphate buffer saline (PBS), they were inoculated into new 100 mL YEP medium containing 2% w/v glucose or xylose.After flask culturing at 30°C and 250 rpm for an additional 5 hours, the yeast cells were collected by centrifugation for total RNA isolation and Illumina RNA-seq library construction. Total RNA for samples were isolated using TRIzol reagent (Invitrogen, Grand Island, USA), then used for high-throughput RNA sequencing. The 150-nt paired-end strand-specific RNA-seq libraries (SS_lib_type RF) were generated commercially at Novogene Biotechnology Co. Ltd (Tianjin, China) by using Illumina’s novaseq 6000 platform (Illumina, San Diego, USA).

2022-12-11 | GSE220542 | GEO

Elutriation time course

Project description:Small G1 daughter yeast cells were isolated by centrifugal elutriation. They were then released into YEP ethanol, and followed through one cell cycle, with samples being taken every 30 minutes. This study is described in more detail in Spellman PT et al.(1998) Mol Biol Cell 9:3273-97 Keywords: time-course

2002-02-12 | GSE24 | GEO

A novel response to microtubule perturbation in meiosis

Project description:Cells were grown to saturation in YPD (YEP + 2% glucose) for 24 hours, diluted into YPA (YEP + 2% potassium acetate) at OD600= 0.3 and grown over night at 30C. Cells were washed with sterilized water the next day and re-suspended in SPII medium (0.3% potassium acetate, pH = 7.0) at OD600= 1.9 to induce sporulation. Cells were sporulated at room temperature or 30C as indicated. Sporulation medium containing benomyl was always prepared freshly on the day of the experiment following the directions in {Shonn, 2000 #90}. Briefly, DMSO (dimethyl sulfoxide, Sigma-Aldrich) or benomyl [Methyl 1-(butylcarbamoyl)-2-benzimidazolecarbamate, Sigma-Aldrich; 30 mg/ml stock in DMSO] was dissolved in near-boiling SPII medium to avoid precipitation. The medium was then allowed to slowly cool to 30C or room temperature. At the time of drug treatment, cells were filtered and immediately re-suspended in the medium containing benomyl or DMSO. Keywords = benomyl sporulation saccharomyces microtubule spindle checkpoint Keywords: ordered

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Transcription profiling of S. cerevisiae novel response to microtubule perturbation in meiosis

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Transcriptomic analyses of a Cyberlindnera jadinii strain (NBRC0988) grown in glycerol

Project description:A strand-specific RNA-seq library was constructed for a single sample, specifically the wild-type strain NBRC0988 grown in YEP medium supplemented with 2% w/v glycerol. To prepare the RNA sample, NBRC0988 cells grown overnight were inoculated into 100 mL of liquid Yeast Extract Peptone Dextrose (YEPD) medium, with an initial inoculation OD600 of 0.1. These cells were then cultured for 15 hours at 30°C and 250 rpm. Subsequently, the cells were collected by centrifugation at 6,000g for 5 minutes. After being washed twice with phosphate buffer saline (PBS), they were inoculated into fresh 100 mL of YEP medium containing 2% w/v glycerol. Following flask culturing at 30°C and 250 rpm for an additional 5 hours, the yeast cells were collected by centrifugation for total RNA isolation and Illumina RNA-seq library construction. Total RNA from the sample was isolated using the TRIzol reagent (Invitrogen, Grand Island, USA) and then utilized for high-throughput RNA sequencing. Commercially, the 150-nt paired-end strand-specific RNA-seq libraries (SS_lib_type RF) were generated by Novogene Biotechnology Co. Ltd (Tianjin, China) using the Illumina's Novaseq 6000 platform (Illumina, San Diego, USA).

2024-03-14 | GSE261259 | GEO

To identify novel targets of a zinc finger transcription factor, Mxr1p in Pichia pastoris cultured in medium containing ethanol

Project description:The role of transcription factor Mxr1p has so far been studied in methanol, amino acid and acetate metabolism. We have demonstrated a key role of Mxr1p in regulation of ethanol metabolism when cells are cultured in medium containing ethanol as sole carbon source. We employed RNA Seq to identify new targets of Mxr1p in medium containing ethanol.

2021-09-22 | GSE168677 | GEO

YPD to YPGal timecourse

Project description:Timecourse analyses (0 to 850 min) of exponentially growing BQS252 yeast after shift from YPD to YPGal galactose medium. Total RNA in vivo labeled by run-on, or cDNA labelling using random decamers included. Genomic DNA also examined. Keywords: other

2004-07-29 | E-GEOD-1002 | biostudies-arrayexpress

Chromatin based modeling of transcription rates identifies the contribution of different regulatory layers to steady-state mRNA levels

Project description:Messenger RNA levels in eukaryotes are balanced by two consecutive regulatory layers. Primary, transcriptional regulation at the level of chromatin and secondary, post-transcriptional regulation of the initial transcript in the cytoplasm. Each layer is individually studied in mechanistic detail, while integration of both processes is required to quantify the individual contribution to steady-state RNA levels. Here we show that chromatin features are sufficient to model transcription rate but with different sensitivities in dividing versus post mitotic cells. In both cases chromatin derived transcript levels explains over 80% of variance in measured RNA level enabling to separate transcription from different post-transcriptional processes. By further inclusion of measurements of mRNA half-life and micro RNA expression data we identify a low quantitative contribution of RNA decay by either micro RNA or general differential turnover to final mRNA levels. Together this establishes a chromatin based quantitative model for the contribution of transcriptional and posttranscriptional processes to steady-state levels of messenger RNA. H3K36me3 ChIP followed by deep sequencing // time-series of mRNA measurement on Affymetrix microarray platform following actinomycinD treatment. MmES Samples: mRNA measurement on Affymetrix microarray platform following thioU labeling and separation of fractions according to labeled (newly synthetised) and unlabeled (pre-existing) RNA.

2012-07-23 | E-GEOD-33252 | biostudies-arrayexpress

Transcriptome analysis of Arabidopis seedlings grown on MS medium with and without ethanol

Project description:To identify ethanol-induced genes, gene expression profile between arabidopis seedlings grown on MS medium with and without ethanol using the custom microarray (GPL22706) were analyzed.

2021-07-31 | GSE171036 | GEO

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