NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM3506246 Query DataSets for GSM3506246
Status Public on Dec 11, 2018
Title leaf_control_L0_rep2
Sample type RNA
 
Source name leaf, undamaged control
Organism Solanum dulcamara
Characteristics genotype location: Friesland
treatment: undamaged control
tissue: L0 leaf
Treatment protocol The fifth fully developed was subjected to either Spodoptera exigua oviposition, received no eggs but feeding, received both egg deposition and feeding or remained untreated. Egg load ranged from 10 to 150 eggs and they were removed 3 d after oviposition. 12 neonate larvae per plant started feeding 12 hrs after egg removal on the previously egg-laden leaf or the corresponding leaf position of non-oviposited plants encaged in clip cages for 24 hrs. Then, this leaf and the corresponding leaf of unfed control- and egg-plants was cut at the petiole and immediately flash frozen in liquid nitrogen (L0-leaf).
Growth protocol Solanum dulcamara plants were grown from seeds in a greenhouse at a 16/8 h light/dark cycle and a photon irradiance between 190 - 250 µmol/ m s
Extracted molecule total RNA
Extraction protocol For each microarray sample, leaf material from three independent biological replicates was pooled. Leaf material was ground under liquid nitrogen and RNA was extracted with the NucleoSpin® RNA Plant kit (Macherey-Nagel GmbH & Co. KG) according to the manufacturer’s instructions using double the amount of RAP lysis buffer. RNA was DNase digested using TURBO DNA-free™ (AmbionTM) according to the manufacturer’s instructions.
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 Control_L0_F
Data processing Data were analyzed using the “limma” software packages from Bioconductor in “R” (R Core Team; 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. For the data-upload, all raw data were background-corrected and normalized across all arrays. In the publication, 1.5 fold the fluorescence value of the 90% percentile of non-labelled hairpin DNA probes (dark-corner spots) was set as limit of detection on each microarray. About 15% of the probes showed fluorescence values below this threshold in at least one microarray within each treatment group. These probes were considered non-expressed and removed from further analysis in the paper. Background-correction and normalization across arrays was then performed after removal of the non-expressed genes.
 
Submission date Dec 10, 2018
Last update date Dec 11, 2018
Contact name Daniel Geuss
E-mail(s) d.geuss@fu-berlin.de
Organization name Freie Universität Berlin
Department Biology
Lab Molecular Ecology
Street address Albrecht-Thaer-Weg 6
City Berlin
State/province Berlin
ZIP/Postal code 14195
Country Germany
 
Platform ID GPL23228
Series (2)
GSE123535 Oviposition by Spodoptera exigua on Solanum dulcamara alters the plant's response to herbivory and impairs larval performance [L0]
GSE123538 Oviposition by Spodoptera exigua on Solanum dulcamara alters the plant's response to herbivory and impairs larval performance

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

Data table
ID_REF VALUE
1 8.222342347
2 3.020526004
3 3.52748333
4 3.568595677
5 3.762664241
6 6.125629762
7 7.400435182
8 5.363041402
9 7.559616472
10 3.265231922
11 8.966235202
12 6.36686947
13 3.762664241
14 5.194348465
15 9.166450925
16 4.965305641
17 4.648060834
18 2.796590946
19 5.250695106
20 7.692833767

Total number of rows: 62970

Table truncated, full table size 1089 Kbytes.




Supplementary file Size Download File type/resource
GSM3506246_Control_L0_F.txt.gz 10.9 Mb (ftp)(http) TXT
Processed data included within Sample table

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap