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Sample GSM745572 Query DataSets for GSM745572
Status Public on Oct 03, 2011
Title cotyledon_Tendral_WMVinfected_7dpi_rep3
Sample type RNA
 
Source name cotyledon,Tendral,WMVinfected,7dpi
Organism Cucumis melo
Characteristics tissue: cotyledon
genotype: Tendral
physiological condition: WMV infected
days post-inoculation: 7
Treatment protocol The viral isolate used in this study was WMV-M116, kindly provided by Dr. Moriones (Estación Experimental “La Mayora”-CSIC, Málaga, Spain). Mechanical inoculations were carried out using standard procedures. Dehydrated viral inoculum was first revived by mechanical inoculation of squash fully-expanded cotyledons. Systemically infected squash leaves were harvested after 15 days post-inoculation (dpi) and used as inoculum source for melons. Squash leaves were ground in a sterile mortar in the presence of inoculation buffer (0.2 M phosphate buffer pH 8.0, 0.1 % v/v β-mercaptoethanol, 0.03 g/mL active charcoal) and, then, carborundum (0.037 mm diameter) dusted 7 days old melon cotyledons were rubbed with this infectious mixture. Control non-infected melon cotyledons were rubbed using only inoculation buffer (mock-inoculated controls).
Growth protocol Germination of melon seeds was carried out in Petri dishes for 48 h at 25 ºC. After germination, seeds were sown in 0.5 L pots and kept in growth chambers (MLR-351H from Sanyo) with 16 h light/25 ºC and 8 h dark/18 ºC for about three weeks.
Extracted molecule total RNA
Extraction protocol Cotyledon samples were independently frozen in liquid N2 and stored at -80 ºC. RNA extracts were prepared from these samples using Tri-Reagent (Sigma Chemical Co., St. Louis, MO, USA) following the manufacturer´s instructions. To eliminate traces of genomic DNA, total RNA was incubated with DNAse I (New England Biolabs, London, UK) 10 min at 37 ºC. Then, reaction volume was adjusted to 100 µl and the aqueous phase extracted with phenol:chloroform:isoamilalcohol (125:24:1). Total RNA was precipitated with 10 % (v/v) NaCl 3M and 2.5 v of absolute ethanol by centrifugation (12.000 g, 20 min, 4º C).
Label Cy3
Label protocol Labeling was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.
 
Hybridization protocol Hybridization was performed by NimbleGen Systems Inc., Madison, WI, USA following their standard operating protocol. See www.nimblegen.com.
Scan protocol Scanning was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.
Data processing Data were normalised using the normalisation algorithm RMA with the package oligo version 1.8.2 (Carvalho et al. 2007, Biostatistics 8 (2): 485-499) written in R (R Development Core Team, http://www.R-project.org).
 
Submission date Jun 20, 2011
Last update date Oct 03, 2011
Contact name Daniel Gonzalez-Ibeas
E-mail(s) agr030@cebas.csic.es
Organization name CEBAS-CSIC
Department Biologia Estres y Patologia Vegetal
Lab Patologia Vegetal
Street address Campus de Espinardo s/n
City Espinardo
State/province Murcia
ZIP/Postal code 30100
Country Spain
 
Platform ID GPL13748
Series (1)
GSE30111 Recessive resistance to Watermelon mosaic virus in melon is associated with a defense response as revealed by microarray analysis
Relations
Reanalyzed by GSM761296

Data table header descriptions
ID_REF
VALUE RMA-normalized

Data table
ID_REF VALUE
c15d_01-A04-M13R_c 10.12589047
c15d_01-A05-M13R_c 13.87954409
c15d_01-A06-M13R_c 11.95407374
c15d_01-A08-M13R_c 11.68957257
c15d_01-B01-M13R_c 9.310422753
c15d_01-B06-M13R_c 11.33670889
c15d_01-B08-M13R_c 12.11559686
c15d_01-C01-M13R_c 4.272304687
c15d_01-C10-M13R_c 11.83561278
c15d_01-C11-M13R_c 9.876600783
c15d_01-D10-M13R_c 7.864005199
c15d_01-E02-M13R_c 7.905468771
c15d_01-E08-M13R_c 4.562299685
c15d_01-F01-M13R_c 10.61742213
c15d_01-F02-M13R_c 10.99769916
c15d_01-F03-M13R_c 13.50868744
c15d_01-F06-M13R_c 11.8523162
c15d_01-G03-M13R_c 5.395866402
c15d_01-G05-M13R_c 8.261075114
c15d_01-G06-M13R_c 13.50909451

Total number of rows: 17443

Table truncated, full table size 480 Kbytes.




Supplementary file Size Download File type/resource
GSM745572.pair.gz 1.1 Mb (ftp)(http) PAIR
Processed data included within Sample table

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