Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Genome-wide midrange transcription profiles reveal expression level relationships in human tissue specification - GeneNote

ABSTRACT: PolyA+ RNA samples from the twelve healthy human tissues were purchased from Clontech (Palo Alto, CA). Each RNA sample is typically composed of a pool of 10-25 individuals. The expression intensity of mRNA was assayed across five microarrays (Affymetrix GeneChips U95A–E). Please note GeneNote is now retired: https://genecards.weizmann.ac.il/cgi-bin/genenote/home_page.pl. This dataset is part of the TransQST collection.

ORGANISM(S): Homo sapiens

SUBMITTER: Orit Shmueli

PROVIDER: E-GEOD-803 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Genome-wide midrange transcription profiles reveal expression level relationships in human tissue specification.

Yanai Itai I Benjamin Hila H Shmoish Michael M Chalifa-Caspi Vered V Shklar Maxim M Ophir Ron R Bar-Even Arren A Horn-Saban Shirley S Safran Marilyn M Domany Eytan E Lancet Doron D Shmueli Orit O

Bioinformatics (Oxford, England) 20040923 5

<h4>Motivation</h4>Genes are often characterized dichotomously as either housekeeping or single-tissue specific. We conjectured that crucial functional information resides in genes with midrange profiles of expression.<h4>Results</h4>To obtain such novel information genome-wide, we have determined the mRNA expression levels for one of the largest hitherto analyzed set of 62 839 probesets in 12 representative normal human tissues. Indeed, when using a newly defined graded tissue specificity index ...[more]

PMID: 15388519

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Project description:The Infectious Hematopoietic Necrosic Virus (IHNV) DNA vaccine is based on the viral glycoprotein gene (G gene) and induces a non-specific anti-viral immune response and long-term specific immunity against IHNV in salmonid fishes. This study characterized gene expression responses associated with the early anti-viral response. Homozygous rainbow trout were injected intra-muscularly (I.M.) with vector DNA or the IHNV DNA vaccine. Gene expression at the I.M. site was evaluated using a 16,000 feature salmon cDNA microarray. Eighty different transcripts were significantly modulated in the vector DNA group while 910 transcripts were modulated in the IHNV DNA vaccinated group relative to control group. Quantitative reverse transcriptase PCR was used to examine expression of selected genes at the I.M. site and in other secondary tissues. In the localized response (I.M. site), the magnitudes of gene expression changes were higher in the vaccinate group relative to the vector DNA group for the majority of genes analyzed. At secondary systemic sites (e.g. gill, kidney and spleen) evaluated with RT-PCR of specific genes, the main difference was the up-regulation of the type I IFN-related genes in only the IHNV DNA vaccinated group. Keywords: disease vaccine response Gene expression at the site of I.M injection was evaluated 7 days post-injection in clonal rainbow trout. Gene expression was compared across three treatments, with replicate clonal rainbow trout individuals (Hot Creek strain) within each treatment. Treatments included injection with 1X PBS (control group), plasmid vector only (without IHNV G gene; hereafter referred to as vector group), and the pIHNV vaccine (vaccine group). Three clonal individuals from the control, three individuals from the vector group, and four individuals from the vaccine group were labeled with Cy3 and used for individual hybridizations to ten slides, comparing hybridization of each individual to a major reference RNA pool. The major reference pool consisted of three unhandled clonal rainbow trout and constituted a pool of RNA from the anterior kidney, spleen, liver and muscle and was labelled with Cy5. Total RNA was extracted from samples, amplified, and hybridized to 16,000 feature Atlantic salmon cDNA arrays developed by the Genomic Research for Atlantic Salmon project. Differential expression was compared among control, vector, and vaccine groups.

Dataset Information

Genome-wide midrange transcription profiles reveal expression level relationships in human tissue specification - GeneNote

Publications

Genome-wide midrange transcription profiles reveal expression level relationships in human tissue specification.

Similar Datasets

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