Saccharomyces cerevisiae
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA773207 | ENA |
REPOSITORIES: ENA
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Project description:Total RNA-seq analyses for the differentially expressed genes (DEGs) among WT (c42), Lin28 R192G hetero mut hESC (c26_5), and Lin28 R192G homo mut hESC (c38) To gain further molecular insight into the observed Lin28R192G mutation in human ESCs, we performed total RNA-sequencing (RNA-seq) analysis of the WT, Lin28 R192G hetero mut hESC, and Lin28 R192G homo mut hESC. The genes that are differentially expressed (DEGs) in Lin28 R192G hetero mut and Lin28 R192G homo mut hES compared to WT hESC.
2019-08-20 | GSE135994 | GEO
Project description:Long-term memory formation is attributed to experience-dependent gene expression. Dynamic changes in histone methylation status are essential for epigenetic regulation of memory consolidation-related genes. Here, we demonstrated that plant homeodomain finger protein 2 (PHF2) histone demethylase is upregulated in the mouse hippocampus during experience and plays an essential role in memory formation. QuantSeq analysis was performed to examine differential gene expression in the hippocampus of WT and PHF2 t/g mice. Transgenic mice were created by injecting the CMV-Flag-PHF2 vector into fertilized eggs from C57BL6 mice. Transgenic lines were established from 9 founders that were identified via PCR-based genotyping. Among the transgenic lines, mice with high PHF2 expressed brains were singled out for breeding. First, selected heterozygote males were bred with heterozygote females which produced homozygote, heterozygote and wild littermates. Since it is difficult to differentiate between hetero and homo mice with genotyping, we separated homo mice from hetero mice by breeding each of hetero and homo mice with wild type mice and confirming the genotypes of their offspring. In other words, hetero mice bred with wild type mice would have both wild type and hetero genotype of offspring, while homo mice bred with wild type mice would only have hetero genotype of offspring. Through this process, we particularly selected the homo mice and this transgenic line was used and maintained for this experiment.
2019-07-27 | GSE129148 | GEO
Project description:In Saccharomyces cerevisiae, the kinase Rio1 regulates rDNA transcription and segregation, pre-rRNA cleavage, and 40S ribosomal subunit maturation. Other roles are unknown. Human orthologue RIOK1; which is frequently overexpressed in malignancies, drives tumor growth and metastasis. Again, also RIOK1 biology is poorly understood. In this study, we charted the global activity of Rio1 in budding yeast. By producing and systems-integrating its protein-interaction, gene-transcription, and chromatin-binding maps we generated Rio1's multi-layered activity network, which controls protein synthesis and turnover, metabolism, growth, proliferation, and genetic stability. Rio1 regulates itself at the transcriptional level, and manages its network both directly and indirectly, via a battery of regulators and transcription factors, including Gcn4. We experimentally confirmed the network and show that Rio1 commands its downstream circuit depending on the growth conditions encountered. We also find that Rio1 and RIOK1 activities are functionally equivalent. Our data suggest that pathological RIOK1 expression may deregulate its network and fuel promiscuous transcription and ribosome production, uncontrolled metabolism, growth, proliferation, and chromosomal instability; well-known contributors to cancer initiation, maintenance and metastasis.
2020-11-23 | GSE107318 | GEO
Project description:Purpose: According to comparative transcriptomes data, the differentially expressed genes within these selected scrambled yeast strains can be digged out and further analyzed, seeking potential targets that were tuned drastically and might improve β-carotene production when modified. Methods: mRNA profiles of two Saccharomyces cerevisiae strains H0, S3 (each named as yJBH000 and yJBH012 in related manuscript) were generated in triplicate using illumina. Sequencing libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA) and index codes were added to each sample. The library preparations were sequenced on an Illumina Hiseq 4000 platform. 150 bp paired-end reads were generated as raw data. The read counts for each gene in the genome were summarized as processed data. Results: The yJBH012 had an obviously different pattern of global transcription as compared with the control yJBH000. The upregulation of 589 genes and down regulation of 236 genes were observed in this analysis.
2019-05-22 | GSE108580 | GEO
Project description:Raw expression values (CHP data) for transcriptional profiling of the response of Saccharomyces cerevisiae to challenges with various weak organic acids Keywords: response to weak organic acids
2007-02-27 | GSE5926 | GEO
Project description:Raw expression values (CHP data) for transcriptional profiling of the response of Saccharomyces cerevisiae to challenges with lactic acid at pH 3 and pH 5. Keywords: response to lactic acid
2008-07-30 | GSE10066 | GEO
Project description:Snapshots of pre-rRNA structural flexibility reveal eukaryotic 40S assembly dynamics at nucleotide resolution
| PRJNA230385 | ENA
Project description:Quantitative MS analysis of acetylation in yeast using SILAC labeling and MaxQuant. Download Index of Raw files first. We used quantitative mass spectrometry to analyze acetylation dynamics and stoichiometry in Saccharomyces cerevisiae. We found that acetylation accumulated in growth-arrested cells in a manner that depended on acetyl-CoA generation in distinct subcellular compartments. We used stable isotope labeling with amino acids in cell culture to quantify differences in protein, acetylation, and phosphorylation abundance by MS. Proteins from whole cell lysates were digested to peptides and acetylated peptides enriched using a polyclonal anti-acetyllysine antibody. Peptide fractions were analyzed by reversed-phase liquid chromatography coupled to high resolution liquid chromatography‐tandem mass spectrometry (LC-MS/MS) and raw MS data were computationally processed using MaxQuant.
2014-02-03 | PXD000507 | Pride