Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Genomic copy number alterations as predictive markers of systemic recurrence in breast cancer

ABSTRACT: Array CGH containing 4,044 human bacterial artificial chromosome clones was used to assess copy number changes in 31 pairs of clinicopathologically well matched recurred / nonrecurred breast cancer tissues. Array CGH containing 4,044 human bacterial artificial chromosome clones was used to assess copy number changes in 31 pairs of clinicopathologically well matched recurred / nonrecurred breast cancer tissues.

ORGANISM(S): Homo sapiens

SUBMITTER: Ki-Tae Hwang

PROVIDER: E-GEOD-10128 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Publications

DNA copy number alterations and expression of relevant genes in triple-negative breast cancer.

Han Wonshik W Jung Eun-Mi EM Cho Jihyoung J Lee Jong Won JW Hwang Ki-Tae KT Yang Song-Ju SJ Kang Jason Jongho JJ Bae Ji-Yeon JY Jeon Yoon Kyung YK Park In-Ae IA Nicolau Monica M Jeffrey Stefanie S SS Noh Dong-Young DY

Genes, chromosomes & cancer 20080601 6

Triple-negative breast cancer (TNBC) is defined by a lack of expression of estrogen, progesterone, and HER2 receptors, and genetically most of them fall into the basal subgroup of breast cancer. The important issue of TNBC is poorer clinical outcome and absence of effective targeted therapy. In this study, we sought to identify DNA copy number alterations and expression of relevant genes characteristic of TNBC to discover potential therapeutic targets. Frozen tissues from 114 breast cancers were ...[more]

PMID: 18314908

Similar Datasets

Project description:Candida albicans and Candida dubliniensis are closely related species displaying differences in virulence and genome content, therefore providing potential opportunities to identify novel C. albicans virulence genes. C. albicans gene arrays were used for comparative analysis of global gene expression in the two species in reconstituted human oral epithelium (RHE). C. albicans (SC5314) showed upregulation of hypha-specific and virulence genes within 30 min postinoculation, coinciding with rapid induction of filamentation and increased RHE damage. C. dubliniensis (CD36) showed no detectable upregulation of hypha-specific genes, grew as yeast, and caused limited RHE damage. Several genes absent or highly divergent in C. dubliniensis were upregulated in C. albicans. One such gene, SFL2 (orf19.3969), encoding a putative heat shock factor, was deleted in C. albicans. ÎÎsfl2 cells failed to filament under a range of hypha-inducing conditions and exhibited greatly reduced RHE damage, reversed by reintroduction of SFL2 into the ÎÎsfl2 strain. Moreover, SFL2 overexpression in C. albicans triggered hyphal morphogenesis. Although SFL2 deletion had no apparent effect on host survival in the murine model of systemic infection, ÎÎsfl2 strain-infected kidney tissues contained only yeast cells. These results suggest a role for SFL2 in morphogenesis and an indirect role in C. albicans pathogenesis in epithelial tissues. Global gene expression in Candida albicans SC5314 or Candida dubliniensis CD36 on reconstituted human oral epithelium (RHE) 90 min postinoculation. Gene expression on RHE was compared to gene expression on polycarbonate filter (PCF; used as RHE support matrix) 90 min postinoculation. Performed in two biological replicates with reciprocal dye swaps for each biological replicate. Gene expression of Candida cells on RHE was normalized to gene expression in reference control (PCF); log2 ratios were calculated by dividing spot intensity of experimental by that of the reference control.

Project description:Nitrogen fixation is a highly energy-demanding process and highly regulated at multiple levels. The two major signals that regulate nitrogen fixation in most diazotrophs are oxygen and ammonia. In order to study the complex regulated mechanism and to highlight the complete nitrogen fixing system in genome level, here we present the transcriptional profiles of the nitrogen fixation genes of P.stutzeri A1501 in different growth conditions with a genome-wide DNA microarray. In this study, the three samples of "P.stutzeri A1501 treated with 0.1mM ammonia and 0.5% Oxygen tension","P.stutzeri A1501 treated with 0.1mM ammonia and 0.5% Oxygen tension-2" and "P.stutzeri A1501 treated with 0.1mM ammonia and 0.5% Oxygen tension-3" were three repeat experiments, while, the other three samples of "P.stutzeri A1501 treated with 20mM ammonia and 0.5% Oxygen tension-1", "P.stutzeri A1501 treated with 20mM ammonia and 0.5% Oxygen tension-2" and "P.stutzeri A1501 treated with 20mM ammonia and 0.5% Oxygen tension-3" were three repeat experiments. The gene expressions under these two growth phases were compared to investigate which genes' expression were effected by different ammonia concentrations. Keywords: nitrogen fixation, nitrogen repression P.stutzeri whole genome microarray, which was based on our sequenced strain A1501. The microarray used in this study featured 3988 of the 4145 ORFs identified in P.stutzeri strain A1501, because 157 ORFs were not on the microarray of the inability to amplify these products. ORFs were amplified with specific primer pairs (Invitrogen). To ensure that the elements of our array would detect specifically their corresponding genes and no others, the ORF coordinates fed into the primer program were circumscribed such that they would exclude regions of any ORF that contained significant similarity to any other ORF. Agarose gel electrophoresis was used to perform quality control on all PCR products. Oligonucleotides were removed from the PCR mix by PCR 96 cleanup plate (Millipore). DNA was resuspended in 12 Î¼l of spotting solution containing 50% dimethyl sulfoxide. PCR products were spotted onto gamma amino propylsilan coated GAPII slides (Corning) with a OmniGrid â¢ microarrayer (GeneMachines).The negative control genes were from the type III secretion system genes of shigella flexneri 2a and the commercial Arabidopsis genes (SpotReportâ¢ cDNA Array Validation System, Stratagene). The positive control genes were from the 16S rRNA of P.stutzeri A1501. We used Cy3-labeled genomic DNA and Cy5 dye-labeled cDNA, for hybridization. The cDNA was synthesized by reverse transcription of 5 Î¼g of total RNA. The labeled cDNA and genomic DNA samples were mixed and hybridized at 65â for 16 hours. Genomic DNA was used as a universal internal control for the quality of the microarray and also allowed for the comparison of results across multiple experiments. Each experiment was repeated three times from the beginning of inoculation.

Dataset Information

Genomic copy number alterations as predictive markers of systemic recurrence in breast cancer

Publications

DNA copy number alterations and expression of relevant genes in triple-negative breast cancer.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets