Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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MicroRNA expression profiling of human colorectal cancer cell lines: HRT-18 vs. Caco-2

ABSTRACT: MicroRNAs regulate the biological aggressiveness of colorectal cancer (CRC) cells and might serve as potential prognostic factors and therapeutic targets. In this study, we therefore globally profiled microRNAs associated with aggressive growth in CRC cells, in an attempt to identify novel prognostic biomarkers in CRC patients. In detail, two different CRC cell lines (Caco-2 and HRT-18) with completely different growth rates and different E-cadherin expression were profiled for differences in more than 1000 human microRNAs by using microarray technology. Two-condition experiment, HRT-18 vs. Caco-2. Biological replicates: 3, independently grown and harvested. On each array, one BR of HRT-18 cells was directly compared to one BR of Caco-2 cells (serving as reference sample). All hybridizations were repeated with reversed dye assignment (dye-swap) as technical replicates.

ORGANISM(S): Homo sapiens

SUBMITTER: Michael Karbiener

PROVIDER: E-GEOD-53095 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Project description:a salmonid microarray was used to characterize environmentally-regulated shifts in gene expression between ocean and river habitats in gill and liver tissues of wild migrating adult Pacific sockeye salmon (Oncorhynchus nerka). To correlate gene expression with survival, non-lethal biopsy sampling of gill tissue and microarray-based profiling was combined with biotelemetry and genetic stock identification so that transcriptomic profiles could be compared between fish reaching spawning grounds and presumed mortalities. Fish were captured fish at two marine sampling sites, one within Johnstone Strait (JS), BC. Canada and one within Juan De Fuca Strait (JDFS), BC Canada. Ocean sites were contrasted to fish sampled within the Fraser River at Whonnock (W), BC, Canada. Gill and liver tissues were dissected at each of these sites. Non-lethal biopsy sampling was performed on migrating sockeye salmon intercepted within the Fraser River at Mission, BC, Canada and genetically-based stock ID was used to determine the stock-specific spawning grounds for each fish, giving an intended end-point of migration for each of the stocks investigated in this study.Gene expression levels were determined by comparing the amount of mRNA transcript in the experimental samples relative to a reference sample. A total of 123 microarrays were used to generate the dataset, corresponding to individual hybridizations of both gill and liver samples collected from JS (gill n=14; liver n=15), JDFS (gill n=15; liver n=13), W (gill n=11; liver n=10), and biopsy sampled gill tissue collected at Mission (n=45).Total RNA was amplified (1 round) with MessageAmpTMII-96 kit (Ambion, TX, USA), and reverse transcribed to cDNA before labelling with ALEXA dyes using the Invitrogen Indirect Labelling Kit. The reference contained the combined aRNA of all individuals used in the experiment, excluding bioposy sampled fish. Individual samples were labelled with Alexa 555 and the reference control with Alexa 647, and no dye swaps were perfromed.

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MicroRNA expression profiling of human colorectal cancer cell lines: HRT-18 vs. Caco-2

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