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Sample GSM1009011 Query DataSets for GSM1009011
Status Public on Sep 26, 2012
Title non-infected resistant line R R0:0 65645802
Sample type RNA
 
Source name non-infected resistance line
Organism Solanum lycopersicum
Characteristics genotype: TYLCV resistant line R
infection: non-infected
tissue: whole plant
Treatment protocol Five days after LeHT1 silencing, groups of twenty silenced and twenty non-silenced plants of the same age were inoculated with TYLCV by caging plants with viruliferous whiteflies for a 3-day long inoculation access period, (approximately 30 insects per plant), in insect-proof wooden cages kept at 24-27 ºC in an insect-proof growth chamber.
Growth protocol Plants were grown in an insect-proof greenhouse kept at 18 ºC – 24 0C, with 8 h/16 h dark/light regimen.
Extracted molecule total RNA
Extraction protocol Total RNA was extracted using the RNeasy Mini kit (Qiagen Inc., Valencia, CA, USA) and the RNAprotect reagent (Qiagen) and DNA was removed by on-column DNase digestion with the RNase-Free DNase set (Qiagen).
Label Cy3
Label protocol Labeling was performed by NimbleGen Systems Inc., Reykjavik, Iceland, following their standard operating protocol. See www.nimblegen.com.
 
Hybridization protocol Hybridization was performed by NimbleGen Systems Inc. Reykjavik, Iceland following their standard operating protocol. See www.nimblegen.com.
Scan protocol Scanning was performed by NimbleGen Systems Inc., Reykjavik, Iceland, following their standard operating protocol. See www.nimblegen.com.
Data processing The raw data (.pair file) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), quantile normalization (Bolstad et al. Bioinformatics 19(2):185), and background correction as implemented in the NimbleScan software package, version 2.4.27 (Roche NimbleGen, Inc.).
 
Submission date Sep 25, 2012
Last update date Sep 26, 2012
Contact name Dagan Sade
Organization name Hebrew University of Jerusalem
Street address Hertzel
City Rehovot
ZIP/Postal code 76100
Country Israel
 
Platform ID GPL16103
Series (1)
GSE41135 Expression analysis of tomato plants TYLCV resistant, susceptible and resistant line silenced in the hexose transporter (LeHT1) gene before and 7 days after inoculation of tomato with Tomato yellow leaf curl virus (TYLCV).

Data table header descriptions
ID_REF
VALUE log-2 RMA-normalized, averaged gene-level signal intensity

Data table
ID_REF VALUE
SL1_00sc00002_2_1_1 8.84875
SL1_00sc00002_32_1_1 10.0232
SL1_00sc00002_4_1_1 7.58631
SL1_00sc00002_53_1_1 10.4741
SL1_00sc00002_63_1_1 8.13206
SL1_00sc00002_9_1_1 10.9954
SL1_00sc00010_1_1_1 6.34181
SL1_00sc00010_10_1_1 4.21723
SL1_00sc00010_11_1_1 6.45828
SL1_00sc00010_12_1_1 5.38336
SL1_00sc00010_13_1_1 5.61677
SL1_00sc00010_14_1_1 8.40956
SL1_00sc00010_15_1_1 5.28318
SL1_00sc00010_16_1_1 4.63052
SL1_00sc00010_17_1_1 3.66676
SL1_00sc00010_18_1_1 5.94205
SL1_00sc00010_19_1_1 7.23055
SL1_00sc00010_2_1_1 5.13258
SL1_00sc00010_20_1_1 4.57046
SL1_00sc00010_21_1_1 4.27798

Total number of rows: 33809

Table truncated, full table size 966 Kbytes.




Supplementary file Size Download File type/resource
GSM1009011_65645802_532.pair.gz 1.3 Mb (ftp)(http) PAIR
GSM1009011_65645802_532_norm_RMA.pair.gz 1.4 Mb (ftp)(http) PAIR
Processed data included within Sample table
Processed data provided as supplementary file

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