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Genomic DNA concentration series in Allele Specific Expression study

ABSTRACT: Genomic DNA of COl-0 and Van-0 were labeled using Bioprime randon labeling kit. Labelled products were hybridized to AtSNPtile1 at a total amount of 6ug, 9ug, 12ug, 15ug, and 18ug. This experiment is to test whether the overall target amount affect the log allele intensity ratio. Each genotype has 5 hybridizations each at 6ug, 9ug, 12ug, 15ug and 18ug. Single chanel. Total two genotypes (Col, Van). Total 10 samples.

ORGANISM(S): Arabidopsis thaliana

SUBMITTER: Justin Borevitz

PROVIDER: E-GEOD-16503 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Global analysis of allele-specific expression in Arabidopsis thaliana.

Zhang Xu X Borevitz Justin O JO

Genetics 20090527 4

Gene expression is a complex trait determined by various genetic and nongenetic factors. Among the genetic factors, allelic difference may play a critical role in gene regulation. In this study we globally dissected cis (allelic) and trans sources of genetic variation in F(1) hybrids between two Arabidopsis thaliana wild accessions, Columbia (Col) and Vancouver (Van), using a new high-density SNP-tiling array. This array tiles the whole genome with 35-bp resolution and interrogates 250,000 SNPs ...[more]

PMID: 19474198

Similar Datasets

Genomic DNA concentration series in Allele Specific Expression study

Project description:Genomic DNA of COl-0 and Van-0 were labeled using Bioprime randon labeling kit. Labelled products were hybridized to AtSNPtile1 at a total amount of 6ug, 9ug, 12ug, 15ug, and 18ug. This experiment is to test whether the overall target amount affect the log allele intensity ratio.

2009-08-15 | GSE16503 | GEO

Genomic DNA 1:1 mixtures in Allele Specific Expression study

Project description:Genomic DNA of Col-0 and Van-0 were mixed at 1:1 and labeled using Bioprime randon labeling kit. A total of 16ug labelled products were hybridized to AtSNPtile1. Used as the reference of equal allele expression. Col and Van genomic DNA were mixed at 1:1 with four biological replicates. Single chanel. Total 4 samples.

2009-08-15 | E-GEOD-16505 | biostudies-arrayexpress

Genomic DNA mixture series in Allele Specific Expression study

Project description:Genomic DNA of Col-0, Van-0 and their mixture at different proportion were labeled using Bioprime randon labeling kit. A total of 16ug labelled products were hybridized to AtSNPtile1. This experiment is to test whether the log allele intensity ratio efficiently detects the allelic variation within targets. Templates include four Col genomic DNA replicates, four Van genomic DNA replicates, three Col and Van 1:1 mixture replicates, and one of each 1:2, 1:3, 1:5, 2:1, 3:1, 5:1 Col and Van mixture. Single chanel. Total 17 samples.

2010-05-06 | E-GEOD-16504 | biostudies-arrayexpress

mRNA samples in Allele Specific Expression study

Project description:Col-0 and Van-0 total RNA were mixed at 1:1. Total RNA also extracted from F1 hybrid samples from Col x Van and Van x Col. PolyA RNA were purified and double-strand cDNA were synthesized, followed by bioprime random labeling. A total of 16ug labelled products were hybridized to AtSNPtile1. cis regulatory effect was identified as allele specific expression in F1 hybrids. Composite trans regulatory effect was detected as deviation between parental expression and F1 hybrids expression. Each sample type has four replicates. Single chanel. Three sample types (Col and Van RNA 1:1 mixture, Col x Van F1 hybrids, Van x Col F1 hybrids). Total 12 samples.

2010-05-06 | E-GEOD-16506 | biostudies-arrayexpress

Genomic DNA 1:1 mixtures in Allele Specific Expression study

2009-08-15 | GSE16505 | GEO

mRNA samples in Allele Specific Expression study

2009-08-15 | GSE16506 | GEO

Genomic DNA mixture series in Allele Specific Expression study

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Genomic hybridization of Col, Van and reciprocal hybrids

Project description:Genomic DNA of Col, Van and reciprocal hybrids, bioprime random labeling, and hybridization to AtTILE1 forward array. Study on genetic ploymorphic between arabidopsis thaliana accessions Col-0 and Van-0, and set the scale of F1 hybrid intensity for SFPs.

2008-11-18 | GSE13620 | GEO

Gene expression of Col, Van and reciprocal hybrids

Project description:Gene expression of Col, Van and reciprocal hybrids using double-stranded cDNA followed by bioprime random labeling, and hybridization to AtTILE1 forward array. Study on gene expression polymorphism between arabidopsis thaliana accessions Col-0 and Van-0. Study on the inheritance of gene expression in reciprocal hybrids. Keywords: cDNA hybridization

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CG Methylation of Col, Van and reciprocal hybrids using HpaII and MspI digestion

Project description:CG Methylation of Col, Van and reciprocal hybrids using HpaII and MspI digestion followed by bioprime random labeling, and hybridization to AtTILE1 forward array. Study on constitutive and ploymorphic CG methylation between arabidopsis thaliana accessions Col-0 and Van-0. Study on the inheritance of CG methylation in reciprocal hybrids. Keywords: genomic hybridization

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