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Sample GSM2634240 Query DataSets for GSM2634240
Status Public on Aug 21, 2017
Title R194 developing seeds, 10-11 days after flower opening
Sample type RNA
 
Source name Arabidopsis thaliana recombinant inbred line R194 developing seeds, 10-11 days after flower opening
Organism Arabidopsis thaliana
Characteristics tissue: developing seeds
genotype: Recombinant inbred line R194
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 R194, 10-11 days after flower opening
A_R194
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 6.458468
244902_at 5.353808
244903_at 7.807388
244904_at 6.049954
244905_at 4.322973
244906_at 7.849791
244907_at 4.2114
244908_at 3.947889
244909_at 5.497312
244910_s_at 3.827957
244911_at 3.528544
244912_at 7.925529
244913_at 5.789857
244914_at 3.372347
244915_s_at 4.994647
244916_at 4.30374
244917_at 4.301205
244918_at 3.81762
244919_at 5.381178
244920_s_at 6.348418

Total number of rows: 22810

Table truncated, full table size 424 Kbytes.




Supplementary file Size Download File type/resource
GSM2634240_A_R194_20110916.CEL.gz 3.3 Mb (ftp)(http) CEL
Processed data included within Sample table

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