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Sample GSM3767590 Query DataSets for GSM3767590
Status Public on Apr 10, 2020
Title leaf_slug_0h_rep4
Sample type RNA
 
Source name leaf, slug damaged, 0h
Organism Solanum dulcamara
Characteristics tissue: leaf
treatment: slug damaged, 0h
location: Siethen
Treatment protocol The tip of leaf 10 from the apex was fitted with a clip cage to prevent the consumption of the whole leaf in the feeding treatments. Clip cages were left empty or received one adult GFS to initiate feeding exposure for 24 h.This exposure to slugs, that are mostly active at night, includes both locomotion mucus application and feeding. We did not assess when the slugs were actually feeding, but plants in the slug treatments showed substantial feeding damage (estimated by eye, > 1 cm2).
Growth protocol Solanum dulcamara plants were grown from seeds in a greenhouse at a 16 h photoperiod with minimum temperatures of 20/17°C (day/night) and a photon irradiance ~280 µmol m-2 s-1
Extracted molecule total RNA
Extraction protocol The total leaf area that was covered by the clip cage was collected for analyses of gene expression. Total RNA extraction and purification were performed on ground fresh leaf material using the RNeasy® Plant Mini kit (Qiagen) and DNAse I (Fermentas, RNAse-free) following the manufacturer’s instructions. Quality and quantity of the RNA were estimated using a NanoDrop 1000 device (Thermo Fisher Scientific, Waltham, MA, USA) and 1.5 % agarose gel electrophoresis. Equal quantities of total RNA from the four plants of a single plant population at each time point were pooled, resulting in four total RNA samples per treatment (control or induced).
Label Cy3
Label protocol Fluorescent cyanine 3-CTP-labelled cRNA was generated using the Low Input QuickAmp Labeling Kit (Agilent Technologies) using oligo-dT primer following the manufacture’s protocol.
 
Hybridization protocol 600 ng of the cRNA were hybridised using the Agilent Gene Expression Hybridisation Kit (Agilent Technologies) following the manufacturer’s protocol at 65°C for 17 h.
Scan protocol Fluorescence signals were detected by the SureScan Microarray Scanner (Agilent Technologies) at a resolution of 3 micron per pixel.
Description SS1
Data processing Microarray data were analysed using the “limma” software packages from Bioconductor in “R” (R Core Team, 2015; Ritchie et al., 2015). The uploaded data were background-corrected using the “normexp” method and normalized between microarrays using the “quantile” method and Log2-transformed.All raw data were background-corrected and normalized across all arrays.
 
Submission date May 14, 2019
Last update date Apr 11, 2020
Contact name Onno Wouter Calf
E-mail(s) owcalf@gmail.com
Organization name Radboud University
Department Molecular Interaction Ecology
Street address Heyendaalseweg 135
City Nijmegen
ZIP/Postal code 6525 AJ
Country Netherlands
 
Platform ID GPL23228
Series (1)
GSE131208 Slug feeding triggers dynamicmetabolomic and transcriptomic responses leading to induced resistance in Solanum dulcamara

Data table header descriptions
ID_REF
VALUE Quantile-normalized and log2-transformed signal intensities

Data table
ID_REF VALUE
1 7.558413
2 4.036081
3 3.731204
4 4.240711
5 4.159786
6 7.38895
7 8.335804
8 7.550017
9 7.44914
10 4.41567
11 9.257164
12 9.022885
13 4.703845
14 5.940289
15 8.587656
16 7.735337
17 5.605448
18 4.278371
19 5.729167
20 5.558867

Total number of rows: 62970

Table truncated, full table size 904 Kbytes.




Supplementary file Size Download File type/resource
GSM3767590_SS1.txt.gz 11.1 Mb (ftp)(http) TXT
Processed data included within Sample table

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