Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Genomic copy number alterations as predictive markers of neoadjuvant chemotherapy response in breast cancer

ABSTRACT: Array CGH containing 4,044 human bacterial artificial chromosome clones was used to assess different copy number changes between chemotherapy responsive and non-resposive breast cancer tissues. Array CGH containing 4,044 human bacterial artificial chromosome clones was used to assess different copy number changes between chemotherapy responsive and non-resposive breast cancer tissues.

ORGANISM(S): Homo sapiens

SUBMITTER: Eun-Mi Jeong

PROVIDER: E-GEOD-10129 | 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:We proposed that the frequency of EBV reactivation may be crucial for its pathogenic role and highly recurrent EBV reactivations exert a profound influence on genome instability. Recurrent reactivations were induced in the EBV-latently infected NPC cells (NA cells) by treating with 12-o-tetradecanoylphorbol-13-acetate (TPA) and sodium n-butyrate (SB) once per passage periodically. Genome-wild oligoarray-based comparative genomic hybridization (CGH) technology was applied to investigate the copy-number aberrations in response for different frequencies of EBV reactivation. The results showed that the NR15 cells, NA cells with the highest frequency (15 times) of reactivation, exhibit extensive genomic copy-number alterations (CNAs) mostly involving chromosome 3p, 3q, 8p, 8q, 9p and 9q, whereas limited number of CNAs were observed both in NR1 cells where only the initial reactivation take place and NP15 cells which were culture in parallel with NR15 cells without EBV-reactivation. We concluded that it is the highly recurrent reactivations of EBV, but neither just a primary reactivation nor EBV-latent infection, may intimately involve in carcinogenesis of nasopharyngeal epithelial cells with the progressive genome instabilities and the accumulation of genetic mutations. Experiment Overall Design: Samples of four sources were analyzed. The NP1 cells denoted the EBV-latently infected nasopharyngeal carcinoma cell lines, NA cells, with low-passage-number and mock-treated. The NR1 denoted the NA cells harboring one time of EBV reactivation. The NR15 cells denoted the NA cells harboring fifteen times of EBV reactivation. The NP15 cells denoted the NA cells cultured in parallel with NR15 (experienced 15 times of passages) without EBV-reactivation. Genomic DNAs extracted from NP15, NR1 and NR15 cells were used as experimental samples and subjected to Cy5-labeling reactions. Genomic DNAs extracted from NP1 cells were used as the common reference samples subjected to Cy3-labeling reactions. All three experiments were verified by dye-swap design where the targets labeling conditions were exchanged, NP1 labeled with Cy5, and NP15, NR1 or NR15 labeled with Cy3.

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 neoadjuvant chemotherapy response 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