Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Ultra high resolution array painting

ABSTRACT: Ultra high resolution breakpoint mapping using custom oligonucleotide arrays and array painting The two derivative chromosomes from 4 patients with balanced translocations were flow sorted, differentially labelled and hybridised to custom oligonucleotide arrays designed to cover the potential breakpoint region at high resolution. Single hybridisations with no replicates.

ORGANISM(S): Homo sapiens

SUBMITTER: Nigel Carter

PROVIDER: E-GEOD-4297 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Ultra-high resolution array painting facilitates breakpoint sequencing.

Gribble S M SM Kalaitzopoulos D D Burford D C DC Prigmore E E Selzer R R RR Ng B L BL Matthews N S W NS Porter K M KM Curley R R Lindsay S J SJ Baptista J J Richmond T A TA Carter N P NP

Journal of medical genetics 20060913 1

<h4>Objective</h4>To describe a considerably advanced method of array painting, which allows the rapid, ultra-high resolution mapping of translocation breakpoints such that rearrangement junction fragments can be amplified directly and sequenced.<h4>Method</h4>Ultra-high resolution array painting involves the hybridisation of probes generated by the amplification of small numbers of flow-sorted derivative chromosomes to oligonucleotide arrays designed to tile breakpoint regions at extremely high ...[more]

PMID: 16971479

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Project description:Although the evidence for a genetic predisposition to human essential hypertension is compelling, the genetic control of blood pressure (BP) is poorly understood. The Dahl salt-sensitive (S) rat is a model for studying the genetic component of BP. Using this model we previously reported the identification of 16 different genomic regions that contain one or more BP quantitative trait loci (QTLs). The proximal region of rat chromosome 1 contains multiple BP QTLs. Of these, we have localized the BP QTL1b region to a 13.5cM (20Mb) region. Interestingly, five additional independent studies in rats and four independent studies in humans have reported genetic linkage for BP control by regions homologous to QTL1b. To view the overall renal transcriptional topography of the positional candidate genes for this QTL, we sought a comparative gene expression profiling between a congenic strain containing QTL1b and control S rats by employing: (1) a saturated QTL1b interval specific oligonucleotide array, and (2) a whole genome cDNA microarray representing 20,465 unique genes that are positioned outside the QTL. Results indicated that 19 out of the 231 positional candidate genes for this QTL are differentially expressed between the two strains tested. Surprisingly, over 1,500 genes outside of QTL1b were differentially expressed between the two rat strains. Integrating the results from the two approaches revealed at least one complex network of transcriptional control initiated by the positional candidate Nr2f2. This network appears to account for the majority of gene expression differences occurring outside of the QTL interval. Further substitution mapping is currently underway to test the validity of each of these differentially expressed positional candidate genes. These results demonstrate the importance of using a saturated oligonucleotide array for identifying and prioritizing differentially expressed positional candidate genes of a BP QTL. Pairs of Cy5 and Cy3 labeled targets were co-hybridized onto either the oligonucleotide microarray or a custom TIGR rat cDNA array consisting of 26,401 probe elements representing 20,465 unique non-QTL1b genes. A âflip-dyeâ design was used as the experimental method of choice to account for potential dye-bias labeling effects. Seven âflip dyeâ normalized files are submitted for the oligonucleotide array and twelve individual hybridizations are submitted for the cDNA array.

Dataset Information

Ultra high resolution array painting

Publications

Ultra-high resolution array painting facilitates breakpoint sequencing.

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