Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Homeostatic Adjustment and Metabolic Remodeling in Glucose-limited Yeast Cultures Time Course 1

ABSTRACT: Time course of batch growth. Reference (channel 1) was a culture grown in MD medium with 2.4 g/L glucose, with 5 slpm air-flow, stirring at 400 rpm and a constant 300C temperature, dilution 0.25 volumes/hour. The experimental (channel 2) time course samples were grown in batch for the indicated time. The "Low-D chemostat vs. High-D chemostat" hybridization's channel 2 sample was grown in a chemostat, with a dilution rate of 0.05 volumes/hour; it is most similar to the time course samples taken between 8 and 9 hours. Groups of assays that are related as part of a time series. FactorCategory: Elapsed Time; name: Elapsed Time; Measurement: time(absolute) 0 h; name: 45181_Elapsed Time; Measurement: time(absolute) 8.5 h; name: 38150_Elapsed Time; Measurement: time(absolute) 8.75 h; name: 38151_Elapsed Time; Measurement: time(absolute) 9 h; name: 38152_Elapsed Time; Measurement: time(absolute) 9.25 h; name: 38153_Elapsed Time; Measurement: time(absolute) 7.25 h; name: 38145_Elapsed Time; Measurement: time(absolute) 9.5 h; name: 38154_Elapsed Time; Measurement: time(absolute) 7.5 h; name: 38146_Elapsed Time; Measurement: time(absolute) 9.75 h; name: 38155_Elapsed Time; Measurement: time(absolute) 7.75 h; name: 38147_Elapsed Time; Measurement: time(absolute) 10 h; name: 38156_Elapsed Time; Measurement: time(absolute) 8 h; name: 38148_Elapsed Time; Measurement: time(absolute) 8.25 h; name: 38149_Elapsed Time FactorCategory: Growth Condition; name: Growth Condition; Growth Condition: chemostat dilution control; name: 45181_Growth Condition; Growth Condition: batch; name: 38150_Growth Condition; Growth Condition: batch; name: 38151_Growth Condition; Growth Condition: batch; name: 38152_Growth Condition; Growth Condition: batch; name: 38153_Growth Condition; Growth Condition: batch; name: 38145_Growth Condition; Growth Condition: batch; name: 38154_Growth Condition; Growth Condition: batch; name: 38146_Growth Condition; Growth Condition: batch; name: 38155_Growth Condition; Growth Condition: batch; name: 38147_Growth Condition; Growth Condition: batch; name: 38156_Growth Condition; Growth Condition: batch; name: 38148_Growth Condition; Growth Condition: batch; name: 38149_Growth Condition Computed

ORGANISM(S): Saccharomyces cerevisiae

SUBMITTER: Matt Brauer

PROVIDER: E-GEOD-3205 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Homeostatic adjustment and metabolic remodeling in glucose-limited yeast cultures.

Brauer Matthew J MJ Saldanha Alok J AJ Dolinski Kara K Botstein David D

Molecular biology of the cell 20050309 5

We studied the physiological response to glucose limitation in batch and steady-state (chemostat) cultures of Saccharomyces cerevisiae by following global patterns of gene expression. Glucose-limited batch cultures of yeast go through two sequential exponential growth phases, beginning with a largely fermentative phase, followed by an essentially completely aerobic use of residual glucose and evolved ethanol. Judging from the patterns of gene expression, the state of the cells growing at steady ...[more]

PMID: 15758028

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Project description:Summary: Breast cancer cell lines have been used widely to investigate breast cancer pathobiology and new therapies. Breast cancer is a molecularly heterogeneous disease, and it is important to understand how well and which cell lines best model that diversity. In particular, microarray studies have identified molecular subtypes (luminal A, luminal B, ERBB2-associated, basal-like and normal-like) with characteristic gene-expression patterns and underlying DNA copy number alterations (CNAs). Here, we studied a collection of breast cancer cell lines to catalog molecular profiles and to assess their relation to breast cancer subtypes. Whole-genome DNA microarrays were used to profile gene expression and CNAs in a collection of 52 widely-used breast cancer cell lines, and comparisons were made to existing profiles of primary breast tumors. Hierarchical clustering was used to identify gene-expression subtypes, and Gene Set Enrichment Analysis (GSEA) to discover biological features of those subtypes. Genomic and transcriptional profiles were integrated to discover within high-amplitude CNAs candidate cancer genes with coordinately altered gene copy number and expression. Transcriptional profiling of breast cancer cell lines identified one luminal and two basal-like (A and B) subtypes. Luminal lines displayed an estrogen receptor (ER) signature and resembled luminal-A/B tumors, basal-A lines were associated with ETS-pathway and BRCA1 signatures and resembled basal-like tumors, and basal-B lines displayed mesenchymal and stem-cell characteristics. Compared to tumors, cell lines exhibited similar patterns of CNA, but an overall higher complexity of CNA (genetically simple luminal-A tumors were not represented), and only partial conservation of subtype-specific CNAs. We identified 80 high-level DNA amplifications and 13 presumptive homozygous deletions, and the resident genes with concomitantly altered gene-expression, highlighting known and novel candidate breast cancer genes. Overall, breast cancer cell lines were genetically more complex than tumors, but retained expression patterns with relevance to the luminal-basal subtype distinction. The compendium of molecular profiles defines cell lines suitable for investigations of subtype-specific pathobiology, biomarkers and therapies, and provides a resource for discovery of new breast cancer genes. HEEBO oligonucleotide microarrays from the Stanford Functional Genomics Facility were used to perform gene expression profiling of 50 human breast epithelial cell lines, in comparison to a universal RNA reference. Expression data were analyzed by hierarchical clustering to identify subgroups, and gene set enrichment analysis to identify subgroup-specific gene pathways.

Dataset Information

Homeostatic Adjustment and Metabolic Remodeling in Glucose-limited Yeast Cultures Time Course 1

Publications

Homeostatic adjustment and metabolic remodeling in glucose-limited yeast cultures.

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