Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Gene expression profile analysis of non small cell lung cancer in North East India

ABSTRACT: The objective of this study was to identify the genes differentially expressed in non small cell lung carcinoma associated with prevalent risk factor such as smoking and betel quid chewing in high-risk north eastern Indian population. The tumor biopsies and matched normal tissue from distant site were collected in RNA later, snap-frozen in liquid nitrogen and stored at -70°C until processed. Data of clinicopathologic parameters were obtained from patients’ clinical and pathologic report. Institutional human ethics committee approved the study. Total RNA was isolated from tumor biopsies and matched normal of five patients. Total RNA from normal tissue from three patients was pooled in one slide and normal tissue from another two patients was pooled in another slide. Individual slide were used for each tumor samples. Isolation Kit: RNeasy mini Kit (Qiagen) Scanner Used: AFFYMETRIX, 428 Array

ORGANISM(S): Homo sapiens

SUBMITTER: Rakhshan Ihsan

PROVIDER: E-GEOD-30118 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Project description:Simple cost-effective bacterins are the earliest and most successfully used commercial vaccines in fish. In particular, those prepared from Yersinia ruckeri have proven effective at controlling Enteric Red Mouth Disease (ERM) and yersiniosis in rainbow trout and Atlantic salmon, respectively. However, the emergence of outbreaks of ERM caused by atypical biotypes of Y. ruckeri and reports of vaccine failure resulting in mass mortality of hatchery Atlantic salmon has reinvigorated interest in vaccines against fish bacterial diseases. Therefore the objective of this study was to identify surrogates of protection against yersiniosis using cDNA microarray to characterise the response of host genes in the gills of unvaccinated and vaccinated Atlantic salmon challenged with Y. ruckeri. Differentially expressed genes were identified using two-way ANOVA and restricted to those with >2.5-fold change at P<0.05. Using cDNA microarray we identified the expression of 6 genes in response to infection and 4 genes associated with the protective host response to yersiniosis. Analysis by real-time PCR confirmed that three immunologically relevant genes, namely a cathelicidin (47-fold) and a C-type lectin (19-fold) increased in response to yersiniosis. Including collagenase (17-fold increase), an important tissue remodelling and repair enzyme, these genes represent 3 of 6 non-protective and/or pathological responses to yersiniosis. Genes associated with the protective host response included an immunoglobulin gene and a selenoprotein that showed significant fold changes (15-fold increases each), highlighting the importance of antibody-mediated protection against yersiniosis. These findings provide much needed knowledge of the host-pathogen interaction in response to bacterial infection and immunisation in fish. Significantly, we identified a transcriptional biosignature consisting of predominantly immune-relevant genes (14 up and 3 down-regulated) in the gills of Atlantic salmon after immersion vaccination and before bacterial challenge. This biosignature may be used as a surrogate of protection and therefore as a predictor of vaccine success against yersiniosis. 36 microarray slides representing 6 individual fish (biological replicates) at 0 h (pre-challenge), 8 h, and 72 h post-challenge from both vaccinated and unvaccinated fish. Two-colour array using sample cDNA labelled with Cy5 and a common reference aRNA labelled with Cy3 hybridized to each slide.

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Gene expression profile analysis of non small cell lung cancer in North East India

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