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Sample GSM1949706 Query DataSets for GSM1949706
Status Public on Feb 29, 2016
Title WT-3
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 third 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 10100.6148
AT1G01020_1 614.4097
AT1G01020_2 246.0055
AT1G01030_1 2477.7293
AT1G01040_1 11147.5446
AT1G01046_1 2116.5087
AT1G01050_1 14929.7370
AT1G01060_1 10816.3335
AT1G01060_3 149.4689
AT1G01070_1 7227.8516
AT1G01070_2 428.2677
AT1G01073_1 222.6201
AT1G01080_1 13319.0084
AT1G01080_2 12079.1199
AT1G01090_1 29733.5825
AT1G01100_1 14377.4179
AT1G01100_2 16125.0068
AT1G01100_3 20063.8832
AT1G01110_1 6538.2291
AT1G01110_2 6913.3028

Total number of rows: 37118

Table truncated, full table size 795 Kbytes.




Supplementary file Size Download File type/resource
GSM1949706_A05-WT3_532-grid.pair.gz 2.3 Mb (ftp)(http) PAIR
GSM1949706_A05-WT3_532-grid_RMA.calls.gz 410.7 Kb (ftp)(http) CALLS
GSM1949706_A05-WT3_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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