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Transcriptomic and Proteomic Analysis of Saccharomyces cerevisiae with Secretion of Cellobiohydrolases

ABSTRACT: The aim of present study is to understand the impact of genetic engineering event, integration of ClCBH2 gene into yeast genome, as well as the subsequent biological process, such as expression and secretion of CBH2 protein. Further, the ‘dosage’ of genetic engineering event, the copy number inserted ClCBH2 gene, is also of particular interest. In parallel, the relationship between the copy number of ClCBH2 gene and the condition of yeast culture during CBH2 production, as well as the effect of these two factors towards yeast metabolism are investigated. Extensive transcriptomics analysis and comparison were conducted for three CBP yeast strains with different copy numbers of ClCBH2 gene, at two growth rates

ORGANISM(S): Saccharomyces cerevisiae

PROVIDER: GSE72413 | GEO | 2015/08/27

SECONDARY ACCESSION(S): PRJNA293996

REPOSITORIES: GEO

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Transcriptomic and Proteomic Analysis of Saccharomyces cerevisiae with Secretion of Cellobiohydrolases

Project description:The aim of present study is to understand the impact of genetic engineering event, integration of ClCBH2 gene into yeast genome, as well as the subsequent biological process, such as expression and secretion of CBH2 protein. Further, the ‘dosage’ of genetic engineering event, the copy number inserted ClCBH2 gene, is also of particular interest. In parallel, the relationship between the copy number of ClCBH2 gene and the condition of yeast culture during CBH2 production, as well as the effect of these two factors towards yeast metabolism are investigated. Extensive transcriptomics analysis and comparison were conducted for three CBP yeast strains with different copy numbers of ClCBH2 gene, at two growth rates A twenty-four array study using total RNA recovered from three CBP yeast strains with different copy numbers of ClCBH2 gene, at two growth rates

2015-08-27 | E-GEOD-72413 | biostudies-arrayexpress

Metabolomics of mice inoculated with human stool (part III).

Project description:Mice were inoculated with human stool samples from donors in a high gene copy number group or low gene copy number group. After several weeks, cecal contents were collected and frozen at -80. Aliquots were made on dry ice and then stored at -80 until shipment on dry ice. Analysis of short chain fatty acids (SCFA) of cecal content was performed.

2017-06-19 | ST000747 | MetabolomicsWorkbench

Quantitative proteomic analyses of budding yeast cells harboring an additional chromosome

Project description:Phenotypic variability is a hallmark of diseases involving chromosome gains and losses, such as Down Syndrome and cancer. Allelic variances have been thought to be the sole cause of this heterogeneity. Here, we systematically examine the consequences of gaining and losing single or multiple chromosomes to show that the aneuploid state causes non-genetic phenotypic variability. Yeast cell populations harboring the same defined aneuploidy exhibit heterogeneity in cell cycle progression and response to environmental perturbations, which we show to be partly due to gene copy number imbalances. Thus, subtle changes in gene expression severely impact the robustness of biological networks and cause alternate behaviors when they occur at a large scale. Because trisomic mice also exhibit variable phenotypes, we further propose that non-genetic individuality is a universal characteristic of the aneuploid state that could contribute to variability in presentation and treatment responses of diseases caused by aneuploidy.

2017-04-10 | PXD006009 | Pride

Array-CGH and Next-generation sequencing of duplication CNVs reveals that most are tandem and some disrupt genes at breakpoints

Project description:Interpreting the genomic and phenotypic consequences of copy number variation (CNV) is essential to understand the etiology of genetic disorders. Whereas deletion CNVs obviously lead to haploinsufficiency, duplications may cause disease through triplosensitivity, gene disruption, or gene fusion at breakpoints. The mutational spectrum of duplications has been studied at certain loci and in some cases these copy number gains are complex chromosome rearrangements involving triplications and/or inversions. However, the organization of clinically relevant duplications throughout the genome has not been investigated on a large scale. Here, we fine mapped 184 germline duplications (14.7 kb-25.3 Mb; median 532 kb) ascertained from individuals referred for diagnostic cytogenetics testing. We performed next-generation sequencing (NGS) and whole-genome sequencing (WGS) to sequence 130 breakpoints from 112 subjects with 119 CNVs and found that most (83%) were tandem duplications in direct orientation. The remainder were triplications embedded within duplications (8.4%), adjacent duplications (4.2%), insertional translocations (2.5%), or other complex rearrangements (1.7%). In addition, we predicted six in-frame fusion genes at sequenced duplication breakpoints. Four gene fusions were formed by tandem duplications, one by two interconnected duplications, and one by duplication inserted at another locus. These novel fusion genes could be related to clinical phenotypes and warrant further study. Though most duplications are positioned head-to-tail adjacent to the original locus, those that are inverted, triplicated, or inserted can disrupt or fuse genes in a manner that may not be predicted by conventional copy number analysis. Thus, interpreting the genetic consequences of duplication CNVs requires breakpoint-level analysis.

2014-10-25 | GSE62657 | GEO

AUD Biomarkers Study (Proteomic and Genomic Analysis of Biospecimens)

Project description:Study purpose: to explore the entire spectrum of proteomic and genomic changes (amongst others) involved in diseases and in healthy/control populations. The Study is designed to discover biomarkers, develop and validate diagnostic assays, instruments and therapeutics as well as other medical research. Specifically, researchers may analyze proteins, RNA, DNA copy number changes, including large and small (1,000-100,000 kb) scale rearrangements, transcription profiles, epigenetic modifications, sequence variation, and sequence in both diseased tissue and case-matched germline DNA from Subjects.

| 62369 | ecrin-mdr-crc

Microarray-CGH of wine yeast strains

Project description:Gene copy number comparison between similar wine yeast strains of Saccharomyces cerevisiae from different geographic origins.

2010-02-14 | GSE16941 | GEO

Genome-wide localisation map of ScRad9-9Myc overexpressed in pYX142 grown in SC (synthetic complete medium) along with BCS and BPS copper/iron chelators

Project description:This experiment was performed in order to assess the specificity of Rad9 binding to S. cerevisiae genome. In another ChIP-chip experiment in SC BCS BPS growth conditions we have found Rad9 present to a significant number of genomic loci and wanted to examine how specific this localisation is. For that we inserted Rad9 gene in the high copy plasmid pYX142 and transformed it in BJ5457 rad9delta yeast cells. Cells were grown under the same conditions and ChIP-chip was performed. By this experiment we aimed to examine quantitavely and qualitatively the Rad9-targets when Rad9 is overexpressed and to compare the findings with previous experiments of ours.

2014-11-01 | E-MTAB-2200 | biostudies-arrayexpress

Gene trapping in the Asian malaria vector, Anopheles stephensi

Project description:A piggyBac transposon-based gene trap element was transformed into the Asian malaria vector, Anopheles stephensi, and remobilized using the jumpstarter approach using genetic crosses. Individuals that displayed a gene trap remobilization event were then photodocumented and their RNA and DNA complements were extracted. The DNA compelement was used to determine the genomic insertion site, while the RNA was used to determine the transcript coverage of the genes into which the transposons inserted. In nearly half of the cases, insertion was identified to fall within introns present in the 5'-UTR of transcripts- which are not indicated in the current ab initio models for Anopheles stephensi. The ability to utilize next generation RNA-Seq elucidated the functionality of the gene trap elements that inserted outside of the ab initio gene models, providing clear evidence that not only was the gene trap element working properly, but that it also had a bias towards 5'-end insertion, in particular, 5'-UTR intronic insertion. RNA from 200 pooled individually-extracted An. stephensi that demonstrated a gene trap remobilizable event.

2016-03-01 | E-GEOD-78771 | biostudies-arrayexpress

Ty Copy Number Control

Project description:Evolution of transposable element copy number control in yeast

| PRJEB33725 | ENA

Comparative genomic hybridization by array of mouse embryonic stem cells with giant piggyBac transposons stably inserted

Project description:Detection of copy-number gain of the ES cells with giant piggyBac transposons stably inserted in the genome using Agilent regional high density comparative genomic array with average probe spacing 130 bp. Extracts were made from equal amounts of human lymphoma cell line DNA mixed with mouse ES samples and control (wild type AB2.2) DNA in order to produce a baseline for normalisation for the array copy number detection.

2010-09-01 | E-MEXP-2788 | biostudies-arrayexpress

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