Beef

Development of the BoviAnalyser cDNA Bovine Microarray

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Abstract

DNA microarrays are powerful tools to analyze the expression pattern of thousands of genes simultaneously in response to treatments, during tissue differentiation or related to differences in traits such as marbling or disease resistance. We developed a bovine cDNA microarray, BoviAnalyser, containing 11,088 genes spotted in duplicate. A set of 10,608 ESTs was selected from MARC 1-4 libraries to include: 1) all the known genes, 2) unknown, putative or hypothetical genes expressed in muscle, liver or adipose. Functional assignments for these clones were compared to the human by BLASTx to add putative IDs to unknown genes. The selected set included 4484 known genes, 1170 hypothetical proteins, 497 unknown and 4364 not assigned genes. A database of human genes expressed in muscle, liver and adipose was used to evaluate the percentage of human genes are present on the microarray. The BoviAnalyser contains 66.37%, 71.02% and 67.34% of the human genes expressed in muscle, liver and adipose. The 12,000 cDNA clones were rearrayed from the MARC libraries 1- 4 into 125 96- well plates. Two clones per plate were randomly sequenced to evaluate the consistency of the data. A total of 12 clones (5.5%) had sequence mismatches been excluded from the set. This new library was used to isolate plasmids containing the cDNA, amplify, purify and prepare the cDNAs to be spotted. The boviAnalyser also contain a set of 18 controls including negatives (blank, spotting solution and spiking), 10 spiking (A. thaliana), B-actin, GAPDH, combined 15 low, 15 average, 15 high expressed and the 45 combined spotted on every subgrid. A small array containing 192 triplicate genes was spotted to standardize the protocols for post processing the slides, probe synthesis, labeling, hybridization and scanning of the slides. Based on our evaluation, we would conclude that MARC libraries are a good source of ESTs for microarray production. The selected set allows the evaluation of changes in gene expression in different bovine tissues including muscle, liver and adipose. The BoviAnalyser is a bovine microarray suitable to be used to analyze molecular mechanisms controlling cell proliferation, differentiation in response to different treatments or variation in economic traits such as marbling and disease resistance.

Keywords: ASL R1877

How to Cite:

Rosa, A. J., Ren, G. & Reecy, J. M., (2004) “Development of the BoviAnalyser cDNA Bovine Microarray”, Iowa State University Animal Industry Report 1(1). doi: https://doi.org/10.31274/ans_air-180814-592