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Sample GSM2136473 Query DataSets for GSM2136473
Status Public on Apr 01, 2019
Title InfWS-1
Sample type RNA
 
Source name Arabidopsis thaliana WS infected
Organism Arabidopsis thaliana
Characteristics ecotype: Wassilewskija-0 (WS)
genotype/variation: wild type
infected with: 60 adults of Myzus persicae
Treatment protocol Three mature leaves of Col, WS or pme17 were infested with 60 adults of Myzus persicae during 24h, in a growth chamber at 23°C.
Growth protocol Leaves of Columbia-0 (Col), Wassilewskija (WS) and pme17 (KO mutant) were used, grown at 23°C in a Percival growth room during three weeks.
Extracted molecule total RNA
Extraction protocol Total RNA was extract according to Gehrig et al. 2000 and Verwoerd et al. 1989 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 (Université de Picardie Jules Verne, Amiens).
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 station
Scan protocol Slides were scanned using an Axon GenePix 4400 A scanner (Molecular Devices Corporation, Sunnyvale, CA, USA) piloted by GenePix pro software (Axon). Scanned images were then imported into NimbleScan software or DEVA software (NimbleGen Systems, Inc. Madison, WI, USA) for grid alignment and expression data analyses.
Description WS infected biological replicate 1 technical replicate 1
Data processing Raw data (.pair files) were normalized using intra-array (RMA background correction) and inter-array (quantile) normalizations using ANAIS software (Simon & Biot, 2010)
 
Submission date Apr 28, 2016
Last update date Apr 01, 2019
Contact name Christopher Wattier
Organization name Université de Picardie Jules Verne
Department Faculté des Sciences
Lab Centre de Ressources Régionales en Biologie Moléculaire
Street address 33 rue Saint Leu
City Amiens
State/province Somme
ZIP/Postal code 80000
Country France
 
Platform ID GPL21786
Series (1)
GSE80749 Transcript data affected by natural variation or PME17 mutation in Arabidopsis thaliana, infested or not with the aphid Myzus persicae

Data table header descriptions
ID_REF
VALUE normalized

Data table
ID_REF VALUE
Athal9P00000001 1425.19
Athal9P00000010 5651.63
Athal9P00000013 4149.07
Athal9P00000020 5099.91
Athal9P00000021 1812.66
Athal9P00000028 888.81
Athal9P00000034 1612.78
Athal9P00000039 983.10
Athal9P00000044 1502.28
Athal9P00000047 581.84
Athal9P00000050 171.55
Athal9P00000058 339.78
Athal9P00000062 1532.80
Athal9P00000065 3014.82
Athal9P00000073 2052.58
Athal9P00000080 309.59
Athal9P00000086 10676.71
Athal9P00000093 14270.33
Athal9P00000096 13884.39
Athal9P00000099 8236.26

Total number of rows: 137592

Table truncated, full table size 3205 Kbytes.




Supplementary file Size Download File type/resource
GSM2136473_IWS-1-grid.pair.gz 2.3 Mb (ftp)(http) PAIR
GSM2136473_IWS1_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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