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Sample GSM2634194 Query DataSets for GSM2634194
Status Public on Aug 21, 2017
Title R002 developing seeds, 10-11 days after flower opening
Sample type RNA
 
Source name Arabidopsis thaliana recombinant inbred line R002 developing seeds, 10-11 days after flower opening
Organism Arabidopsis thaliana
Characteristics tissue: developing seeds
genotype: Recombinant inbred line R002
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 R002, 10-11 days after flower opening
A_R002
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 6.69166
244902_at 5.31609
244903_at 7.673107
244904_at 6.087073
244905_at 4.447912
244906_at 7.798099
244907_at 4.425675
244908_at 3.519012
244909_at 4.856415
244910_s_at 3.743064
244911_at 3.193085
244912_at 8.511017
244913_at 5.865778
244914_at 3.335715
244915_s_at 5.045163
244916_at 4.385036
244917_at 4.071249
244918_at 3.76411
244919_at 5.42487
244920_s_at 6.065541

Total number of rows: 22810

Table truncated, full table size 424 Kbytes.




Supplementary file Size Download File type/resource
GSM2634194_A_R002_20110914.CEL.gz 3.3 Mb (ftp)(http) CEL
Processed data included within Sample table

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