Unknown,Transcriptomics,Genomics,Proteomics

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Effect of NaCl on CDC1551 gene expression

ABSTRACT: Gene Expression profiling of M. tuberculosis CDC1551 treated with 0.25 M NaCl vs untreated samples. The dataset includes 5 biological replicates.

ORGANISM(S): Mycobacterium tuberculosis

SUBMITTER: David Russell

PROVIDER: E-MTAB-1374 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Project description:Inferring the heritability of gene expression is one of the main areas of the field of genetical genomics. With the possibility to treat the abundances of gene transcripts as a suite of quantitative traits, genetical genomics can make an extensive use of the microarray technology. Here we extended a major method for estimating the heritability of a quantitative trait, single parent-offspring regression, to assess the heritability of the expression of genes with two-channel microarrays. In a series of maternal parent-offspring pairs of Interior spruce (Picea glauca x engelmannii, our focus in the outer stem tissues is the expression of defense-related genes, the heritability of which can affect fitness and necessary for evolution by natural selection. Parent-offspring pairs of Interior spruce planted as a part of Tree Breeding and Improvement Program of the Forest Genetics Section, British Columbia Ministry of Forests and Range, Prince George, BC, Canada (http://www.for.gov.bc.ca/hre/forgen/interior/spruce.htm#1) were used. A total of 30 trees, comprising 15 parent-offpsring pairs were sampled. These include15 offsprings and 15 maternal parents (grafts), which were planted within ~ 1Km range west (122º 42’ 43’’W, 53º 45’41’’N) of the offsprings, hence grown in a relatively similar environment. The bark and the attached phloem were separated from inner layers in the mid-morning hours of June 25, 2008, flash-frozen in liquid nitrogen, and transferred into separate containers. A chain design was decided for gene expression profiling (a total of 45 slides) using the Treenomix third generation cDNA microarray platform (GEO accession #: GPL5423). Array350 kit (Genisphere, Hatfield, USA) was chosen for the microarray hybridizations. The slides were scanned with a ProScanArray scanner (PerkinElmer, Downers Grove, IL, USA), and the scanned TIF images were processed by ImaGene software (BioDiscovery, Inc., El Segundo, CA, USA) to quantify spot signals. Normalization was done between arrays using variance stabilizing (VSN) method for ratio based analysis of the expression data.

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Effect of NaCl on CDC1551 gene expression

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