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E-GEOD-38109 - Natural variation in Arabidopsis thaliana transcriptomes

Status
Released on 21 May 2012, last updated on 24 July 2012
Organism
Arabidopsis thaliana
Samples (3)
Array (1)
Protocols (7)
Description
A major effort is underway to study the natural variation within the model plant species, Arabidopsis thaliana. Much of this effort is focused on genome resequencing, however the translation of genotype to phenotype will be largely effected through variations within the transcriptomes at the sequence and expression levels. To examine the cross-talk between natural variation in genomes and transcriptomes, we have examined the transcriptomes of three divergent A. thaliana accessions using tiling arrays. Combined with genome resequencing efforts, we were able to adjust the tiling array datasets to account for polymorphisms between the accessions and therefore gain a more accurate comparison of the transcriptomes. The corrected results for the transcriptomes allowed us to correlate higher gene polymorphism with greater variation in transcript level among the accessions. Our results demonstrate the utility of combining genomic data with tiling arrays to assay non-reference accession transcriptomes. Wild type accessions Col-0 were grown on soil at 16°C with a 16 hour light period. Inflorescence tissue up to floral stage 14 was used for RNA extraction. Samples were collected 7-8 hours into the light period, with tissue from five plants pooled for each sample. RNA samples were converted into double stranded and hybridized to whole genome tiling arrays (Affymetrix Arabidopis Tiling1.0R®). Three biological replicates were performed for each accession.
Experiment type
transcription profiling by tiling array 
Contacts
Brandon Gaut, Detlef Weigel, Felix Ott, Jesse Hollister, Lisa M Smith, Ya-Long Guo
Citation
MIAME
PlatformsProtocolsVariablesProcessedRaw
Files
Investigation descriptionE-GEOD-38109.idf.txt
Sample and data relationshipE-GEOD-38109.sdrf.txt
Raw data (1)E-GEOD-38109.raw.1.zip
Array designA-GEOD-10977.adf.txt
Links