Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Hela Mitotic Selection - gene expression time series in early G1 phase of the human cell cycle

ABSTRACT: HeLa mitotic cells were collected using a mitotic shakeoff apparatus to study gene expression in early G1 phase of the human cell cycle. This set includes microarray data from two shake-off experiments : shake 1 (0h-14h) which was conducted over 14 hours and RNA samples collected every 2 hrs, and shake 2 (0min-120min) which was conducted over 2 hours and samples collected every 15 minutes. Total RNA was prepared using ULTRASPEC RNA isolation system, and Reference RNA was extracted from asynchronously growing HeLa cells using TRIzol. For cDNA synthesis and microarray hybridization, refer to Whitfield ML. et al., Mol Biol Cell, 2002. 13(6): p. 1977-2000. Groups of assays that are related as part of a time series. Age: g1 progression after mitotic shake-off Replicate: two biological replicates (shake1 and shake2) Keywords: time_series_design Computed

ORGANISM(S): Homo sapiens

SUBMITTER: Michael Whitfield

PROVIDER: E-GEOD-12473 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Identification of G1-regulated genes in normally cycling human cells.

Beyrouthy Maroun J MJ Alexander Karen E KE Baldwin Amy A Whitfield Michael L ML Bass Hank W HW McGee Dan D Hurt Myra M MM

PloS one 20081215 12

<h4>Background</h4>Obtaining synchronous cell populations is essential for cell-cycle studies. Methods such as serum withdrawal or use of drugs which block cells at specific points in the cell cycle alter cellular events upon re-entry into the cell cycle. Regulatory events occurring in early G1 phase of a new cell cycle could have been overlooked.<h4>Methodology and findings</h4>We used a robotic mitotic shake-off apparatus to select cells in late mitosis for genome-wide gene expression studies. ...[more]

PMID: 19079774

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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.

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Dataset Information

Hela Mitotic Selection - gene expression time series in early G1 phase of the human cell cycle

Publications

Identification of G1-regulated genes in normally cycling human cells.

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