Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Gene expression profiles of whole blood incubated with live meningococci

ABSTRACT: Blood from two donors was incubated for timepoints up to 24 hours in the presence and absence of live meningococci. The donors are labelled NP and SW. 'SWB' refers to blood that was incubated with meningococci; 'Unstim' refers to control blood incubated in the absence of meningococci. Duplicate arrays were prepared for the majority of timepoints ('a' and 'b'), except where the array of of poor quality and not used in the analysis. We infected heparinised whole blood from two healthy donors (adult volunteers) with 108 live meningococci, serogroup B, type MC58, as previously described.8 Blood was incubated at 37°C for 0, 1, 3, 6, 12, and 24 h. At every timepoint we removed a sample and harvested the plasma by centrifugation (1200 g, 10 min). We gathered the remaining blood into RNA stabilisation fluid. Uninfected control blood was obtained for every timepoint. An all pairs experiment design type is where all labeled extracts are compared to every other labeled extract. Using regression correlation

ORGANISM(S): Homo sapiens

SUBMITTER: Cheryl Hemingway

PROVIDER: E-GEOD-3934 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Role of interleukin 6 in myocardial dysfunction of meningococcal septic shock.

Pathan Nazima N Pathan Nazima N Hemingway Cheryl A CA Alizadeh Ash A AA Stephens Alick C AC Boldrick Jennifer C JC Oragui Emmanuelle E EE McCabe Colm C Welch Steven B SB Whitney Adeline A O'Gara Peter P Nadel Simon S Relman David A DA Harding Sian E SE Levin Michael M

Lancet (London, England) 20040101 9404

<h4>Background</h4>Myocardial failure has a central role in the complex pathophysiology of septic shock and contributes to organ failure and death. During the sepsis-induced inflammatory process, specific factors are released that depress myocardial contractile function. We aimed to identify these mediators of myocardial depression in meningococcal septic shock.<h4>Methods</h4>We combined gene-expression profiling with protein and cellular methods to identify a serum factor causing cardiac dysfu ...[more]

PMID: 14738793

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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

Gene expression profiles of whole blood incubated with live meningococci

Publications

Role of interleukin 6 in myocardial dysfunction of meningococcal septic shock.

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