BYxwild_40
Ontology highlight
ABSTRACT:
ORGANISM(S): Saccharomyces cerevisiae
PROVIDER: GSE37 | GEO | 2002/05/01
SECONDARY ACCESSION(S): PRJNA84871
REPOSITORIES: GEO
Similar Datasets
Project description:Expression analysis of BY4716(isogenic to S288c) and a wild isolate collected by R. Mortimer. Each strain was grown in culture 6 independent times and RNA from each culture was isolated. Each of these RNA samples was subjected to a dye-swap pair of arrays (except the "RM11" sample, which only got one array). All arrays used the same pool of reference BY4716 sample. In sample titles, "BY" alone signifies the reference sample and all other strings represent independent cultures. All sample titles are of the form S1-S2. S1 indicates the sample whose signal was read as channel 1 (Cy5 labeling, fluorescence at 635 nm) and S2 as channel 2 (Cy3, 532 nm). Keywords: repeat sample
2002-05-01 | GSE38 | GEO
Project description:Haploid segregants from a cross between the yeast strains BY4716 and RM11-1a as in Brem et al. 2002 and Yvert et al. 2003. This series contains all GSE617 samples (re-submitted for convenience), plus 27 additional segregants assayed with the same protocol and the same reference sample as GSE617. Keywords: other
2005-01-20 | GSE1990 | GEO
Project description:human bronchial smooth muscle cells were growth arrested. One group was stimulated with 10ng/mL of IL-1beta, TNF-alfa, and gamma IFN for 20 hours. For every cDNA sample, 2 dyeflipped slides were hybridized (these have the same date in the titles). All cy3 (channel 2) measurements were normalized to the dye coupling control before a ratio of the values was taken. Keywords: parallel sample
2004-04-09 | GSE1288 | GEO
Project description:In this study, we found that kinase-dead IKKM-NM-1 knockin (KAL) mice. develop spontaneous lung squamous cell carcinomas (SCCs) associated with IKKM-NM-1 downregulation and marked pulmonary inflammation.KKM-NM-1 downregulation dysregulates the expression of multiple oncogenes and tumor suppressors in K5+ lung epithelial cells. The mutant macrophages increase inflammatory responses and oxidative stress to promote DNA damage in IKKM-NM-1-mutant K5+ lung epithelial cells, which further dysregulate the levels of multiple oncogenes, tumor suppressors, and stem cell genes, thereby promoting the IKKM-NM-1lowK5+p63hi cell transition to tumor cells in L-IkkM-NM-1KA/KA lungs. To further investigate the underlying mechanisms by which the lung SCC development, we generated two cell lines, named as S1 and S2 individually, which were derived from KAL lung SCC. The S1 cells express high level of Sca1 and exhibit tumorigenic phenotype, while the S2 cells express low level of Sca1 and exhibit less tumorigenic phenotype. The aim of this microarray assay is to identify differentially expressed genes between S1 and S2 cells, which may highlight the important genes or pathways involved in inflammation-associated lung SCC carcinogenesis. There were two cell lines were used to perform Gene chip assay with Affymetrix. The two cell lines, named as S1 and S2 individually, were derived from KAL lung SCC. The S1 cells express high level of Sca1 and exhibit tumorigenic phenotype, while the S2 cells express low level of Sca1 and exhibit less tumorigenic phenotype.
2015-01-27 | E-GEOD-65291 | biostudies-arrayexpress
Project description:Dynamical response to oxygen downshift under fermentation conditions was tested by taking sample before (S1) and after (S2, S3 and S4) the oxygen downshift. The dynamical changes relevant for ongoing research on physiology were applied.
2008-07-08 | GSE12006 | GEO
Project description:We profiled the time-dependent expression levels of a set of 95 genomically characterized haploid yeast segregants in response to rapamycin. They were derived from two genetically diverse parental yeast strains, BY4716 and RM11. Both parental strains have been sequenced. Our goal is to capture widespread transcriptional changes over time, and to leverage on both the temporal and genetic variations to construct regulatory networks.
2011-11-03 | E-MTAB-412 | biostudies-arrayexpress
Project description:DNA methylation profiling in epiRIL344 BC1-S1 to BC1-S6 aerial part (epiRIL344_BC1-S1 - epiRIL344_BC1-S2 - epiRIL344_BC1-S3 - epiRIL344_BC1-S4 - epiRIL344_BC1-S5 - epiRIL344_BC1-S6) Keywords: Genome binding/occupancy profiling by genome tiling array
2012-09-03 | GSE37285 | GEO
Project description:Background & Aims: Hepatocellular carcinoma (HCC) is the second most lethal cancer due to lack of effective therapies. Although promising, HCC molecular classification, which enriches potential responders to specific therapies, has not yet been assessed in clinical trials of anti-HCC drugs. We aimed to overcome these challenges by developing clinicopathological surrogate indices of HCC molecular classification. Methods: HCC classification defined in our previous transcriptome meta-analysis (S1, S2, and S3 subclasses) was implemented in an FDA-approved diagnostic platform (Elements assay, NanoString). Ninety-six HCC tumors (training set) were assayed to develop molecular subclass-predictive indices based on clinicopathological features, which were independently validated in 99 HCC tumors (validation set). Molecular deregulations associated with the histopathological features were determined by pathway analysis. Sample sizes for HCC clinical trials enriched with specific molecular subclasses were determined. Results: HCC subclass-predictive indices were: steatohepatitic (SH)-HCC variant and immune cell infiltrate for S1 subclass, macrotrabecular/compact pattern, lack of pseudoglandular pattern, and high serum alpha-fetoprotein (>400 ng/mL) for S2 subclass, and microtrabecular pattern, lack of SH-HCC and clear cell variants, and lower histological grade for S3 subclass. Macrotrabecular/compact pattern, a predictor of S2 subclass, was associated with activation of therapeutically targetable oncogene YAP and stemness markers EPCAM/KRT19. BMP4 was associated with pseudoglandular pattern. Subclass-predictive indices-based patient enrichment reduced clinical trial sample sizes from 121, 184, and 53 to 30, 43, and 22 for S1, S2, and S3 subclass-targeting therapies, respectively. Conclusions: HCC molecular subclasses can be enriched by clinicopathological indices tightly associated with deregulation of therapeutically targetable molecular pathways.
2015-06-17 | GSE59548 | GEO
Project description:Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of leaf color at different development stages. The goals of this study are to compare anthocyanin biosynthesis, chlorophyll metabolism and chloroplast organization transcriptome profiling (RNA-seq) to microarray and quantitative reverse transcription polymerase chain reaction (qRT–PCR) methods and to evaluate protocols for optimal high-throughput data analysis Methods: Leaf mRNA profiles of 12 RNA sequencing libraries (S1, S2, S3_S, and S3_C) were generated by deep sequencing, in triplicate, using an Illumina HiSeq 4000 system. After removing reads of low quality, those that remained were mapped to the reference genome (ftp://ftp.ensemblgenomes.org/pub/release-38/plants/genbank/brassica_oleracea/) using the HISAT package, allowing for a maximum of two mismatches and multiple alignments per read (up to 20 by default). qRT–PCR validation was performed using SYBR Green assays Results: Using an optimized data analysis workflow, we mapped about 571.74 million sequence reads per sample to the the reference genome (ftp://ftp.ensemblgenomes.org/pub/release-38/plants/genbank/brassica_oleracea/) and identified 99, 391, 74, and 543 DEGs were detected in pairwise comparison (S2 vs. S1, S3_S vs. S2, S3_C vs. S2, and S3_S vs. S3_C, respectively). The DEGs were associated with ‘photosynthesis’and other pathways in the Kyoto Encyclopedia of Genes and Genomes database; DEGs related to chloroplast organization were identified in the Gene Ontology analysis. The DEGs identified by RNA sequencing were confirmed by qRT-PCR analysis, indicating that the data were reliable. These findings provide information that can be useful for investigating the molecular basis for leaf variegation in ornamental kale and other plants. Conclusions: The results presented here reveal changes in the transcriptome profile of a bicolor leaf kale. DEGs related to anthocyanin biosynthesis, chlorophyll metabolism and chloroplast organization were detected. These results demonstrate that leaf color at different stages of development is influenced by anthocyanin biosynthesis, chloroplast and pigment metabolism, providing a foundation for investigating the molecular basis for bicolor leaf in ornamental kale and other plants.
2021-03-27 | GSE115279 | GEO
Project description:Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of leaf color at different development stages. The goals of this study are to compare chlorophyll metabolism and chloroplast organization transcriptome profiling (RNA-seq) to microarray and quantitative reverse transcription polymerase chain reaction (qRT–PCR) methods and to evaluate protocols for optimal high-throughput data analysis Methods: leaf mRNA profiles of 12 RNA sequencing libraries (S1, S2, S3_S, and S3_C) were generated by deep sequencing, in triplicate, using an Illumina HiSeq 4000 system. After removing reads of low quality, those that remained were mapped to the reference genome (ftp://ftp.ensemblgenomes.org/pub/release-38/plants/genbank/brassica_oleracea/) using the HISAT package, allowing for a maximum of two mismatches and multiple alignments per read (up to 20 by default). qRT–PCR validation was performed using SYBR Green assays Results: Using an optimized data analysis workflow, we mapped about 571.74 million sequence reads per sample to the the reference genome (ftp://ftp.ensemblgenomes.org/pub/release-38/plants/genbank/brassica_oleracea/) and identified 1028, 4323, 428, and 1033 DEGs were detected in pairwise comparison (S2 vs. S1, S3_S vs. S2, S3_S vs. S2, and S3_S vs. S3_C, respectively). The DEGs were associated with ‘photosynthesis’, ‘carbon fixation in photosynthetic organisms’, ‘porphyrin and chlorophyll metabolism’ and other pathways in the Kyoto Encyclopedia of Genes and Genomes database; DEGs related to chloroplast organization were identified in the Gene Ontology analysis. The DEGs identified by RNA sequencing were confirmed by qRT-PCR analysis, indicating that the data were reliable. These findings provide information that can be useful for investigating the molecular basis for leaf variegation in ornamental kale and other plants. Conclusions: The results presented here reveal changes in the transcriptome profile of a variegated leaf kale. DEGs related to chlorophyll metabolism and chloroplast organization were detected. These results demonstrate that leaf color at different stages of development is influenced by chloroplast and pigment metabolism, providing a foundation for investigating the molecular basis for leaf variegation in ornamental kale and other plants.
2021-03-27 | GSE112493 | GEO