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Series GSE38109 Query DataSets for GSE38109
Status Public on May 22, 2012
Title Natural variation in Arabidopsis thaliana transcriptomes
Organism Arabidopsis thaliana
Experiment type Expression profiling by genome tiling array
Summary 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.
 
Overall design 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.
 
Contributor(s) Hollister J, Smith LM, Guo Y, Ott F, Weigel D, Gaut B
Citation(s) 21252301
Submission date May 22, 2012
Last update date May 09, 2017
Contact name Felix Ott
Organization name Max Planck Institute for Developmental Biology
Street address Spemannstr. 35-39
City Tuebingen
ZIP/Postal code 72076
Country Germany
 
Platforms (1)
GPL10977 [At35b_MR] Affymetrix Arabidopsis Tiling 1.0R Array
Samples (3)
GSM934755 LS_001_bA
GSM934756 LS_001_bB
GSM934757 LS_001_bC
This SubSeries is part of SuperSeries:
GSE38113 Transposable elements and small RNAs contribute to gene expression divergence between Arabidopsis thaliana and Arabidopsis lyrata
Relations
BioProject PRJNA167306

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE38109_RAW.tar 72.9 Mb (http)(custom) TAR (of CEL)
GSE38109_tilingRMA_LS_001_COL0_flowers_16deg_TAIR8.txt.gz 372.4 Kb (ftp)(http) TXT
Processed data are available on Series record

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