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Status |
Public on Feb 29, 2016 |
Title |
WT-5 |
Sample type |
RNA |
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Source name |
Arabidopsis thaliana 96-hours old etiolated hypocotyls, wild type
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Organism |
Arabidopsis thaliana |
Characteristics |
ecotype: Columbia genotype: wild-type
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Treatment protocol |
Arabidopsis thaliana (Columbia ecotype): wild type/atpme3-1 loss-of-function mutant
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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.
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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) .
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Label |
Cy3
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Label protocol |
Labeling was performed following NimbleGen One-color labeling kit instructions (Roche)
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Hybridization protocol |
Hybridization was performed overnight at 42°C using a 4-position NimbleGen hybridization system 4
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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.
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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.
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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).
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Submission date |
Nov 24, 2015 |
Last update date |
Feb 29, 2016 |
Contact name |
Alain Mareck |
E-mail(s) |
alain.mareck@univ-rouen.fr
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Organization name |
université de rouen Haute Normandie
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Department |
departement de biologie glycobiologie et matrice extracellulaire végétale
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Street address |
2 rue tenieres
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City |
Mont-Saint-Aignan |
ZIP/Postal code |
76821 |
Country |
France |
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Platform ID |
GPL13697 |
Series (1) |
GSE75326 |
Expression analysis of Arabidopsis thaliana mutant atpme3-1 |
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