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Sample GSM2136480 Query DataSets for GSM2136480
Status Public on Apr 01, 2019
Title Col-3
Sample type RNA
 
Source name Arabidopsis thaliana COL control
Organism Arabidopsis thaliana
Characteristics ecotype: Columbia-0 (Col)
genotype/variation: wild type
infected with: none (control)
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 Col control biological replicate 2 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 1371.64
Athal9P00000010 6179.55
Athal9P00000013 4406.32
Athal9P00000020 5602.38
Athal9P00000021 1715.20
Athal9P00000028 1054.40
Athal9P00000034 1185.07
Athal9P00000039 824.32
Athal9P00000044 957.99
Athal9P00000047 361.26
Athal9P00000050 134.65
Athal9P00000058 180.64
Athal9P00000062 1447.78
Athal9P00000065 2101.14
Athal9P00000073 1901.42
Athal9P00000080 186.94
Athal9P00000086 7444.56
Athal9P00000093 10115.95
Athal9P00000096 11164.85
Athal9P00000099 5464.89

Total number of rows: 137592

Table truncated, full table size 3193 Kbytes.




Supplementary file Size Download File type/resource
GSM2136480_TCol2-grid.pair.gz 2.3 Mb (ftp)(http) PAIR
GSM2136480_TCol2_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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