Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Cj1223c Mutant vs. Overexpressed, Time Course

ABSTRACT: The Cj1223c gene was cloned downstream of a strong promoter into the replicating plasmid pRY108, and was highly expressed in the wild type Campylobacter jejuni 81-176 strain (overexpressed). The Cj1223c gene was knocked out by allelic replacement in the 81-176 strain background (mutant). This mutant also carried an empty pRY108 vector. The Cj1223c overexpressing strain and the mutant were grown overnight in liquid broth, supplemented with kanamycin. The following morning, both cultures were diluted back to O.D.600=0.100, and allowed to continue to grow, shaking. At various time intervals (2, 6, 10, and 24 hours), samples of each culture were removed, combined with 1/10 stop solution, and the bacteria pelleted for RNA preparation. An all pairs experiment design type is where all labeled extracts are compared to every other labeled extract. Computed

ORGANISM(S): Campylobacter jejuni

SUBMITTER: Joanna Mackichan

PROVIDER: E-GEOD-3198 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

The Campylobacter jejuni dccRS two-component system is required for optimal in vivo colonization but is dispensable for in vitro growth.

MacKichan Joanna K JK Gaynor Erin C EC Chang Christopher C Cawthraw Shaun S Newell Diane G DG Miller Jeff F JF Falkow Stanley S

Molecular microbiology 20041201 5

A Campylobacter jejuni two-component signal transduction system (TCSTS), designated dccR-dccS (diminished capacity to colonize; Cj1223c-Cj1222c), has been found to be important for in vivo colonization but dispensable for in vitro growth. A DeltadccR response regulator mutant generated using the virulent strain 81-176 background exhibited significantly reduced colonization of immunocompetent limited flora (I-LF) mice, severe combined immunodeficient limited flora (SCID-LF) mice, and 1-day-old ch ...[more]

PMID: 15554967

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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

Cj1223c Mutant vs. Overexpressed, Time Course

Publications

The Campylobacter jejuni dccRS two-component system is required for optimal in vivo colonization but is dispensable for in vitro growth.

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