Project description:To improve our understanding of the organization and evolution of the wheat gene space, we established the first map of genes of the wheat chromosome 1BS by hybridizing the newly developed INRA GDEC Triticum aestivum NimbleGen 12x40k unigenes microarray (A-MEXP-2314) with 3D-pools of MTP BACs of from the 1BS physical map. By hybridizing the BAC pools with the wheat NimbleGen 40K unigenes chip we managed to map almost 1063 unigenes on the wheat chromosome 1BS BACs. By comparison with 454 sequences and Illumina survey sequence contigs from the sorted chromosome 1BS, we confirmed the assignation of 849 unigenes in individual BACs from the chromosome 1BS. This data allowed us to study the organization of the wheat gene space along chromosome 1BS. The sequences of the unigenes helped to perform synteny and evolutionary analyses of these unigenes. DNA from MTP clones were pooled into 3D manner: library of MTP clones was stored in 17 plates of 384 wells (24 columns x 16 rows); plate1 pool consist of mixture of DNA from all MTP clones situated in plate 1, Row A pool consist of mixture of DNA from all MTP clones situated in Rows A (from all 17 plates, etc). The set of positive plate, column and row pools for the unigene (represented in microarray) allow to detect the list of putative positive clones (clones from the intersection of positive pools, cleaned using information on physical intersection clones based on clone fingerprints). Hence, all 57 experiments (17 for plate pools, 24 for column pools, and 16 for row pools) have the same experimental factor.
Project description:To improve the resources for map-based cloning and sequencing of the wheat genome, we established a physical map of the wheat chromosome 1BL with a high density of markers by hybridizing the newly developed INRA GDEC Triticum aestivum NimbleGen 12x17k ISBP microarray (A-MEXP-2312) with BAC pools from the 1BL physical map. Then, we managed to map 3912 ISBP on the wheat chromosome 1BL BACs. The values in the 'Factor Value[individual]' column represent the BAC pool that have been hybridized on the array. For example, the assay 1 correspond to the hybridization of a bulk of all DNA BAC of the plate 1 of the MTP (Minimum Tilling path) BAC library of the chromosome 1BL.
Project description:BAC pool DNA hybridisation of barley to 44k Agilent microarrays. We have used two-channel Agilent expression microarrays to address thousands of gene sequences to individual BAC clones and contigs that form part of an emerging physical map of the large and unsequenced 5300 Mbp barley genome. By using two-colour processing, each array allows simultaneous co-hybridization of two independent BAC pools (SP), for which the data is analysed separately. As a general approach the method represents a cost-effective, highly parallel alternative to traditional gene-to-BAC addressing methods. By coupling the BAC address-data with gene-based genetic maps we were able to anchor thousands of BACs to the barley genetic map.
Project description:In this study 405 patients with unexplained mental retardation and 89 unaffected parents were analyzed for DNA copy-number changes using a tiling-resolution genomewide microarray containing 32,447 BACs. This series contains 367 slides from 315 individuals previously not reported, plus an additional 239 slides from 179 individuals previously reported in the series GSE3191. Keywords: array CGH
