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Sample GSM2634193 Query DataSets for GSM2634193
Status Public on Aug 21, 2017
Title Q226 developing seeds, 10-11 days after flower opening
Sample type RNA
 
Source name Arabidopsis thaliana recombinant inbred line Q226 developing seeds, 10-11 days after flower opening
Organism Arabidopsis thaliana
Characteristics tissue: developing seeds
genotype: Recombinant inbred line Q226
Stage: 10-11 days after flower opening
Treatment protocol Siliques of plants were harvested ten or eleven days after flower opening and immediately frozen in liquid nitrogen. Eight siliques each from six different plants were pooled for each of the recombinant inbred lines. The siliques were dissected and only the seeds were used for RNA extraction. For each of the recombinant inbred lines one sample was prepared.
Growth protocol A. thaliana seeds of 116 recombinant inbred lines were sown in pots with substrate 1 (Klasmann‐Deilmann GmbH, Geeste, Germany) and grown after stratification for 3 days at 4°C in long‐day conditions (16 h light at 20°C and 70% relative humidity/8 h dark at 16°C and 60% relative humidity). Light intensity during the light phase amounted to approximately 250 µE m−2 s−1. At least six plants per accession were grown.
Extracted molecule total RNA
Extraction protocol RNA was isolated from 200 mg samples of seeds. After grinding for 45 s at 27 Hz with Mixer Mill MM400 (Retsch GmbH, Haan, Germany) the samples were mixed with 0.7 ml extraction buffer (1 M Tris-HCl (pH 9.0), 1% (v/v) SDS, 10 mM EDTA (pH 8.0), 0.5% (v/v) β-mercaptoethanol in DEPC-H2O (0.1% (v/v)) and subsequently with 0.7 ml of phenol/chloroform/isoamyl alcohol (25:24:1). After centrifugation for 10 min, the aqueous phases were extracted once more with phenol/chloroform/isoamyl alcohol and then with chloroform. After adding 0.1 volume of 3 M sodium acetate (pH 5.4) and 2.5 volumes of 96% ethanol the samples were kept for 45 min at -80°C and then centrifuged for 5 min. The resulting RNA pellets were dissolved in 0.4-0.5 ml of DEPC-H2O (0.1% (v/v) and after centrifugation the supernatants were mixed with 1 volume of 4 M LiCl. After an overnight incubation on ice, RNA pellets were collected by centrifugation, washed in 1 ml each of 2 M LiCl, 96% and 70% ethanol, dried and dissolved in ribonuclase-free water. All centrifugation steps were carried out at 14,000 rpm and 4°C. Purification of RNA samples was achieved with RNeasy columns (Qiagen) and the peqGOLD OptiPure reagent (Peqlab Biotechnologie GmbH, Erlangen, Germany) according to manufacturer’s instructions.
Label Biotin
Label protocol Labeling was performed by ATLAS Biolabs GmbH, Berlin Germany (Affymetrix authorised service provider)
 
Hybridization protocol Hybridisation was performed by ATLAS Biolabs GmbH, Berlin Germany (Affymetrix authorised service provider)
Scan protocol Scanning was performed by ATLAS Biolabs GmbH, Berlin Germany (Affymetrix authorised service provider)
Description Gene expression data, developing seeds of Arabidopsis thaliana recombinant inbred line Q226, 10-11 days after flower opening
A_Q226
Data processing The raw hybridisation intensity data files (‘CEL’ files) were directly imported into the RMAExpress 1.0.5 program (Irizarry et al. 2003) in order to carry out background correction, quantile normalisation and the transformation to log2 values with the normalisation approach robust multi-array average.
 
Submission date May 22, 2017
Last update date Jan 23, 2018
Contact name Renate Hanna Schmidt
E-mail(s) schmidtr@ipk-gatersleben.de
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
 
Platform ID GPL198
Series (1)
GSE99150 eQTL analysis - Extracting genotype information of recombinant inbred lines from transcript profiles established with high-density oligonucleotide arrays

Data table header descriptions
ID_REF
VALUE RMAExpress 1.0.5 log2 values

Data table
ID_REF VALUE
244901_at 6.219245
244902_at 5.414877
244903_at 8.496484
244904_at 6.265456
244905_at 4.114732
244906_at 7.226501
244907_at 4.031822
244908_at 3.981367
244909_at 6.014261
244910_s_at 3.644645
244911_at 3.448899
244912_at 8.057828
244913_at 5.693681
244914_at 3.299998
244915_s_at 5.000023
244916_at 4.150128
244917_at 4.051576
244918_at 3.653845
244919_at 5.350603
244920_s_at 6.189282

Total number of rows: 22810

Table truncated, full table size 424 Kbytes.




Supplementary file Size Download File type/resource
GSM2634193_A_Q226_20110915.CEL.gz 3.4 Mb (ftp)(http) CEL
Processed data included within Sample table

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