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Saccharomyces cerevisiae mutant strain with R1158 strain background: Fold change after doxycycline treatment

ABSTRACT: To understand the extent that Heat shock protein 90 (Hsp90) regulated its target proteins at the transcription level, transcriptomic change was profiled in yeast cells upon Hsp90 compromising. We genetically modified the R1158 strain (resulting genotype of mutant strain: TETp-HSC82 hsp82Δ arg4Δ lys5Δ car2Δ::URA3) and then reduced the Hsp90 amount with doxycycline treatment. Fold change of mRNA from untreated to treated cells indicated the transcriptomic change. Totally, we identified 1104 genes mis-regulated with a fold change of no less than 1.5 (P <0.05) upon Hsp90 compromising.

ORGANISM(S): Saccharomyces cerevisiae

PROVIDER: GSE56186 | GEO | 2014/03/26

SECONDARY ACCESSION(S): PRJNA242663

REPOSITORIES: GEO

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Saccharomyces cerevisiae mutant strain with R1158 strain background: Fold change after doxycycline treatment

Project description:To understand the extent that Heat shock protein 90 (Hsp90) regulated its target proteins at the transcription level, transcriptomic change was profiled in yeast cells upon Hsp90 compromising. We genetically modified the R1158 strain (resulting genotype of mutant strain: TETp-HSC82 hsp82Δ arg4Δ lys5Δ car2Δ::URA3) and then reduced the Hsp90 amount with doxycycline treatment. Fold change of mRNA from untreated to treated cells indicated the transcriptomic change. Totally, we identified 1104 genes mis-regulated with a fold change of no less than 1.5 (P <0.05) upon Hsp90 compromising. Two-condition experiment, treated vs. untreated cells. Biological duplicates, independently grown and harvested. Technical triplicates for RNA isolation.

2014-03-26 | E-GEOD-56186 | biostudies-arrayexpress

Expression data from rat vocal fold at different periods after vocal fold injury

Project description:Expression data from rat vocal fold at different periods after vocal fold injury

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Expression data from rat vocal fold at different periods after vocal fold injury (miRNA)

Project description:Expression data from rat vocal fold at different periods after vocal fold injury (miRNA)

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Transcriptome Comparison of phoU Homologies: Genes Deletion strain and the Parent Strain in stationary phase (10 h)

Project description:Purpose: To compare the transcriptome changes in phoU1(serp0956) or phoU2(serp0316)deletion strain with the parent strain SE1457 in stationary phase (10 h). Methods: Total RNA was isolated and sequenced from the phoU1 deletion strain, phoU2 deletion strain and the parent strain SE1457 in stationary phase (10 h) in triplicate using an illumina high-seq 2500. Raw data was analyzed using TopHat. Genes were considered changed which performed fold-change>=1.5 and FDR<=0.05. Changed genes were then filtered to reveal the downstream targets of phoU1 or phoU2. Results: The expression of 2 genes were significantly decreased and no genes was significantly increased in expression level due to the loss of phoU1 expression.The expression of 279 genes were significantly decreased and 716 genes were significantly increased in expression level due to the loss of phoU2 expression.

2017-10-03 | GSE97656 | GEO

Transcriptome Comparison of phoU Homologies Genes Deletion strain and the Parent Strain in log-phase (6 h).

Project description:Purpose: To compare the transcriptome changes in phoU1(serp0956) or phoU2(serp0316)deletion strain with the parent strain SE1457 in log-phase (6 h) Methods: Total RNA was isolated and sequenced from the phoU1 deletion strain, phoU2 deletion strain and the parent strain SE1457 in log-phase (6 h) in triplicate using an illumina high-seq 2500. Raw data was analyzed using TopHat. Genes were considered changed which performed fold-change>=1.5 and FDR<=0.05. Changed genes were then filtered to reveal the downstream targets of phoU1 or phoU2 in log-phase (6 h). Results: The expression of 23 genes were significantly decreased and 69 genes was significantly increased in expression level due to the loss of phoU1 expression.The expression of 474 genes were significantly decreased and 471 genes were significantly increased in expression level due to the loss of phoU2 expression.

2017-10-03 | GSE97400 | GEO

Transcriptome analysis of the ΔYGP1 strain compared to its parental strain

Project description:We sought to understand the change in the global gene expression profile of the ΔYGP1 strain in comparison with the BGL-6_Kl parental strain. The transcriptome analysis revealed the change in expression of genes involved in cell wall structure, biogenesis, and integrity that might contribute to the improvement of the BGL display efficiency phenotype.

2021-05-01 | GSE173680 | GEO

Auxin regulates functional gene groups in a fold-specific manner in Arabidopsis root

Project description:Auxin plays a pivotal role in virtually every aspect of plant morphogenesis. It simultaneously orchestrates a wide variety of processes, including cell wall biogenesis, transition through the cell cycle, and metabolism of a wide range of chemical substances, among others. The coordination principles for such complex regulation in a cell at a system level are poorly understood. Here, we apply a whole-genome approach to estimate the coherence of the auxin-regulated transcriptional response in gene groups, united by a certain biological process, molecular function or cell component, based on the fold change of the expression level. The corresponding analysis of RNA-Seq data for Arabidopsis roots treated with auxin for 6 h revealed that the intervals for the fold change of gene expression levels are quite narrow for many functional gene groups. The fold-specific manner of auxin response in most of these groups was confirmed using independent microarray data. To predict the mechanisms underlying such a coordinated expression, we performed motif enrichment analysis, which revealed TBX1-3, SBX, REG and TCP/site 2 as the candidates associated with fold-specific responses to auxin.

2017-06-01 | GSE97258 | GEO

RNA-seq of patient-derived melanoma cells depleted for GLI1 and SOX2

Project description:We report the RNA-seq of melanoma cells depleted for SOX2 and GLI1. Three pairs of total RNAs from each condition were generated for library preparations and subsequent RNA-seq. All samples had over 50 million reads with over 93% of the reads mapping to the human genome (obtained from the UCSC Genome Browser assembly ID:hg19). Using differential expression analysis (fold change (FC)>1.5, false discovery rate (FDR)<0.1 as standard cut-offs), we identified 1104 entities commonly altered in both SOX2- and GLI1-knocked down cells. We grouped genes into enrichment clusters revealed by DAVID functional annotation tool (https://david.ncifcrf.gov/).

2020-10-06 | GSE159049 | GEO

Regenerating zebrafish fin fold vs. uncut control

Project description:Teleost fish have the remarkable ability to regenerate their body parts including heart, spinal cord, and the caudal fin, while many higher vertebrates including us humans have only a limited ability. To facilitate molecular and genetic approaches for regeneration, we previously established an assay using the fin fold of early stage larvae, which regenerate their caudal fin folds as in adult regeneration. Here, we performed transcriptional profiling of regenerating larval fin folds and identified genes with differential expression during regeneration. Gene expression profiling of zebrafish larval fin-fold regeneration was performed by comparing amputated fin fold and uncut control. Keywords: Stress response, injury response. Two time points, 18-24 hours post amputation (hpa) and 48 hpa, of regenerating fin fold were analyzed. We performed one replicate per each time point. For microarray expression profiling, total RNA was extracted from regenerating and uncut caudal fin folds of AB strain larvae. Tail tissues of 16-24 hpa, 48 hpa, and uncut siblings of the respective stages including 3-5 posterior somite segments were collected on ice. Total RNA was extracted by using TRIzol reagent (Invitrogen, Carlsbad, California, United States) according to the manufacturerâs instruction. The quantity and quality of total RNA were assessed by absorbance at 260 nm and 280 nm and by gel electrophoresis. Approx. 9 Î¼g of total RNA was recovered from ~250 tail tissues at 16-24 hpa or uncut control tissues; and approx. 5 Î¼g, from ~130 tail tissues at 48 hpa or uncut control tissues. Probes for microarray analysis were labeled with cy3 (amputated fin fold at 16-24 hpa and uncut control at 48 hpa) or cy5 (uncut control at 16-24 hpa and amputated fin fold at 48 hpa), and used for hybridization.

2010-05-19 | E-GEOD-11391 | biostudies-arrayexpress

RNA sequence (RNA-seq) profiling of Syn6.5 consolidation strain

Project description:The Sc2.0 project is building a eukaryotic synthetic genome from scratch. A major milestone has been achieved with all individual Sc2.0 chromosomes assembled. Here, we describe consolidation of multiple synthetic chromosomes using advanced endoreduplication intercrossing with tRNA expression cassettes to generate a strain with 6.5 synthetic chromosomes. The 3D chromosome organization and transcript isoform profiles were evaluated using Hi-C and long-read direct RNA sequencing. We developed CRISPR Directed Biallelic URA3-assisted Genome Scan, or “CRISPR D-BUGS”, to map phenotypic variants caused by specific designer modifications, known as “bugs”. We first fine-mapped a bug in synthetic chromosome II (synII), and then discovered a combinatorial interaction associated with synIII and synX, revealing an unexpected genetic interaction that links transcriptional regulation, inositol metabolism and tRNASerCGA abundance. Finally, to expedite consolidation, we employed chromosome substitution to incorporate the largest chromosome (synIV), thereby consolidating >50% of the Sc2.0 genome in one strain.

2023-10-02 | GSE244061 | GEO

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