Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Transcription profiling of Atlantic salmon fed with a low, medium or high histidine diet

ABSTRACT: Atlantic salmon at their 2nd year in sea were fed with a low, medium or high histidine diet (L, M, and H, respectively) for several months. Samples were taken at three time points, after the first, second and third period, and a number of fishes were assigned to a new feed group following a crossover experimental design. The feeding experiment was carried out in duplicates in cages in sea water. A number of 6 fishes of each nutritional group and from each replicate were sampled at each time point, and weight, length and cataract development were monitored of the sampled fish and an additional number of fishes (18-34). Fish developed cataracts with different severity in response to dietary histidine levels. Lens N-acetylhistidine contents reflected the dietary histidine levels and were negatively correlated to cataract scores. This experiment contains four dietary groups of fish, named LM, HM, LLL and MMM.
LM: Low histidine diet in the first period, Medium histidine diet in the second period
HM: High first, Medium second period
LLL: Low diet in all three periods
MMM: Medium diet in all three periods
In the analysis LM and HM is compared for early effects, while LLL vs MMM is compared for stable long time effects. Each feeding period is roughly a month each. Each dietary group contains 11 biological replicates. The RNA samples were labelled and hybridised to two channel 16K cGRASP salmonid arrays using a common reference design. The common reference was made from a pool of all samples.

ORGANISM(S): Salmon salar

SUBMITTER: Christiane Trösse

PROVIDER: E-TABM-678 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Project description:Recently we had discovered a solid cord like structure at the limbus of human eyes, termed as the Limbal Epithelial Crypt (LEC). It arises from the undersurface of the interpalisade rete ridges and extends towards the conjunctiva over the conjunctival stroma. Anatomical and immunohistochemical studies have shown it to be potentially a Stem Cell Niche. To confirm this hypothesis we conducted comparative gene expression profile of LEC with pathway and Geneontology studies in comparison with other ocular surface epithelial regions such as cornea, limbus, LEC stroma and conjunctiva. Frozen tissue blocks of corneoscleral buttons dissected from cadaver eyes were cryosectioned. These tissue sections from different ocular surface regions were laser microdissected. Extracted RNA was amplified & hybridized to 30,000k Human spotted cDNA microarray chips. Raw data obtained with Genepix Pro6 software was filtered, normalized & analysed on BASE & Jexpresspro software. Unpaired T-Test, Significance Analysis of Microarrays were performed on the data. Database for Annotation, Visualisation, and Integrated Discovery (DAVID) (http://www.DAVID.niaid.nih.gov) and Ingenuity Pathway Analysis (IPA) was used to determine the enriched GO terms and pathways in the differentially expressed genes. Quantitative gene expression analysis (qPCR) and immunohistochemistry was performed on the genes of interest. Statistical analysis for real time PCR was performed on SPSS16 to determine the normalised expression of gene of interest on ocular surface regions. Samples were prepared from five human ocular surface epithelial regions such as Cornea, Limbus, LEC, LEC Stroma, Conjunctiva. There were four replicates in each groups except Cornea and Conjunctiva with 3 each. The Standard Probe (SP) was prepared from mixing equal amount of Corneal and conjunctival epithelial RNA followed by ethanol precipitation. Samples were labelled with Cy5 dye and Standard Probe with Cy3 Dye. These were mixed in equal amount to prepare hybrid probes which were then hybridised to microarray slide.

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Transcription profiling of Atlantic salmon fed with a low, medium or high histidine diet

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