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Sample GSM1949708 Query DataSets for GSM1949708
Status Public on Feb 29, 2016
Title WT-5
Sample type RNA
 
Source name Arabidopsis thaliana 96-hours old etiolated hypocotyls, wild type
Organism Arabidopsis thaliana
Characteristics ecotype: Columbia
genotype: wild-type
Treatment protocol Arabidopsis thaliana (Columbia ecotype): wild type/atpme3-1 loss-of-function mutant
Growth protocol Etiolated 96-hour-old hypocotyls from wild type and atpme3-1 of Arabidopsis thaliana were used. Sterilized seeds were laid on 9 % agar, incubated for 3 days in the dark at 4°C, then transferred for 6 hours at 20°C in a phytotron with white light (200 µm.m-2.s-1). Finally, petri dishes were kept in the dark for 4 days.
Extracted molecule total RNA
Extraction protocol total RNA was extract using Ambion RNAqueous kit and DNA was removed using the Ambion TURBO-DNAfree kit. RNA was quantified using Nanodrop 1000 spectrophotometer (thermo scientific) and RNA quality was assessed using Eukaryote total RNA Standard Sensitivity chips on the Experion system (Biorad). All extract protocols were performed at the Centre de Ressources Régionales en Biologie Moléculaire 5Université de picardie Jules Verne, Amiens). RNA concentration was determined using Nanodrop 1000 and RNA quality was assessed using Eukaryote Total RNA standard Sensitivity on the Experion (Biorad) .
Label Cy3
Label protocol Labeling was performed following NimbleGen One-color labeling kit instructions (Roche)
 
Hybridization protocol Hybridization was performed overnight at 42°C using a 4-position NimbleGen hybridization system 4
Scan protocol Slides were scanned using an Axon GenePix 4400 A scanner (molecular Devices Corporatiion, Sunnyvale, CA, USA) piloted by GenePiix pro software (Axon). Scanned images were then imported into Nimblescan software (NimbleGen Systems, Inc. Madison, WI, USA) for grid alignment and expression data analyses.
Description This sample is of wild-type Arabidopsis thaliana. It is the fifth of six wild-type biological replicates used in this experiment. Each replicate was obtained separately from the others and each replicate represents about 300 hypocotyles.
Data processing Raw data (.par files) were normalized using intra-array (RMA background correction) and inter-array (quantile) normalizations using ANAIS software (Simon & Biot, 2010, ANAIS: Analysis of NimbleGen Arrays Interface. Bioinformatics 2010 Oct; 26(19):2468-9).
 
Submission date Nov 24, 2015
Last update date Feb 29, 2016
Contact name Alain Mareck
E-mail(s) alain.mareck@univ-rouen.fr
Organization name université de rouen Haute Normandie
Department departement de biologie glycobiologie et matrice extracellulaire végétale
Street address 2 rue tenieres
City Mont-Saint-Aignan
ZIP/Postal code 76821
Country France
 
Platform ID GPL13697
Series (1)
GSE75326 Expression analysis of Arabidopsis thaliana mutant atpme3-1

Data table header descriptions
ID_REF
VALUE RMA-normalized, averaged gene-level signal intensity

Data table
ID_REF VALUE
AT1G01010_1 8707.4882
AT1G01020_1 628.3861
AT1G01020_2 279.8661
AT1G01030_1 2369.3159
AT1G01040_1 10924.9501
AT1G01046_1 3085.4397
AT1G01050_1 14200.7773
AT1G01060_1 14656.5917
AT1G01060_3 221.9335
AT1G01070_1 7564.7693
AT1G01070_2 516.7835
AT1G01073_1 193.1932
AT1G01080_1 12734.9973
AT1G01080_2 11898.1358
AT1G01090_1 31283.1933
AT1G01100_1 11657.3434
AT1G01100_2 14126.1765
AT1G01100_3 18626.3649
AT1G01110_1 5885.4554
AT1G01110_2 7371.5355

Total number of rows: 37118

Table truncated, full table size 795 Kbytes.




Supplementary file Size Download File type/resource
GSM1949708_A09-WT5_532-grid.pair.gz 2.3 Mb (ftp)(http) PAIR
GSM1949708_A09-WT5_532-grid_RMA.calls.gz 408.9 Kb (ftp)(http) CALLS
GSM1949708_A09-WT5_532-grid_norm_RMA.pair.gz 2.3 Mb (ftp)(http) PAIR
Processed data included within Sample table
Processed data provided as supplementary file

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