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Series GSE99150 Query DataSets for GSE99150
Status Public on Aug 21, 2017
Title eQTL analysis - Extracting genotype information of recombinant inbred lines from transcript profiles established with high-density oligonucleotide arrays
Organism Arabidopsis thaliana
Experiment type Expression profiling by array
Summary In order to identify eQTL in developing seeds of Arabidopsis thaliana 116 Arabidopsis thaliana recombinant inbred lines (C24/Col 0 and Col 0/C24, Törjék et al. 2006) were analysed.
Overall design Expression data of 116 recombinant inbred lines (C24/Col 0 and Col 0/C24) that were established for developing seeds of the same stage (10-11 days after flower opening) provided the basis for an eQTL analysis. For each line one biological replicate was evaluated. The data were also used to develop a sequence feature polymorphism map. A sequence-based approach identified features on the array that showed sequence polymorphisms between A. thaliana accessions Col 0 and C24. Hybridisation intensities were retrieved for all probe sets consisting of one or several probes that were polymorphic in C24 (VM probes) and at least three probes that revealed perfect matches to the Col 0 and C24 genomes (IM probes). The mean hybridisation intensity of all IM probes of a particular probe set was divided by that of each VM probe. For each of the polymorphic probes the resulting ratios of all RILs were compiled and sorted in ascending order before they were subjected to a sliding window analysis in order to identify SFP markers. The genotypes of the recombinant inbred lines were determined with the SFP markers and a linkage map of the Col 0/C24 and C24/Col 0 recombinant inbred populations was generated.
Data for the parental lines Col-0 and C24 are also available (GSE94762).
Contributor(s) Schmidt R, Boudichevskaia A
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Submission date May 22, 2017
Last update date Jul 25, 2021
Contact name Renate Hanna Schmidt
Phone +49 39482 5591
Organization name Leibniz Institute of Plant Genetics and Crop Plant Research (IPK)
Department Breeding Research
Lab Genome Plasticity
Street address Corrensstrasse 3
City Stadt Seeland
State/province Sachsen-Anhalt
ZIP/Postal code 06466
Country Germany
Platforms (1)
GPL198 [ATH1-121501] Affymetrix Arabidopsis ATH1 Genome Array
Samples (116)
GSM2634135 Q000 developing seeds, 10-11 days after flower opening
GSM2634136 Q002 developing seeds, 10-11 days after flower opening
GSM2634137 Q003 developing seeds, 10-11 days after flower opening
BioProject PRJNA387439

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
GSE99150_RAW.tar 382.8 Mb (http)(custom) TAR (of CEL)
Processed data included within Sample table

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