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Sample GSM1128686 Query DataSets for GSM1128686
Status Public on Apr 24, 2013
Title Uninjured VHb leaves positioned above herbivory exposure 2
Sample type RNA
 
Channel 1
Source name Control treatment, VHb A leaf
Organism Populus tremula x Populus tremuloides
Characteristics line: V617/45, generated via Agrobacterium mediated gene transfer using pBVHb
tissue: leaf
leaf type: above leaf, LPI 7
plant number: 43
treatment: none
Treatment protocol The saplings of wt and VHb lines grown 1.5 months under standard greenhouse conditions were used in the experiments. In the herbivory treatment, one larvae of Conistra vaccinii L. (Lepidoptera: Noctuidae) was placed on the leaf inside the veil cloth bag for 24 hours, which after samples were collected to liquid nitrogen.
Growth protocol The lines were multiplicated on liquid MS medium (full strength of C10H12FeN2NaO8; half strength of other micro and macro nutrients; 2.22 μM BA and 2.85 μM IAA) in RITA® temporary immersion containers (Vitropic, Saint-Mathieu-de-Tréviers, France) under 16:8 h light/dark photoperiod (110-130 μmol m-2s-1) at 22 ºC. Saplings were rooted on MS without plant growth regulators, acclimated in the Botanical Gardens of the University of Oulu (65°03'N, 25°27'E), and potted to limed and fertilised soil, and grown under standard greenhouse conditions.
Extracted molecule total RNA
Extraction protocol The total RNA was extracted as described by Jaakola et al. (Mol. Biotechnol. 19 (2001) 201-203) except for the first centrifugation step which was omitted.
Label Cy5
Label protocol The SuperScript III reverse transcriptase (Invitrogen, Carlsbad, CA, USA) was used to synthesize cDNAs in accordance with the manufacturer's instructions and the instructions of the 3DNA Array 50 Expression Array Detection Kit For Microarrays (Genisphere Inc, Hatfield, PA, USA).
 
Channel 2
Source name Herbivory treatment, VHb A leaf
Organism Populus tremula x Populus tremuloides
Characteristics line: V617/45, generated via Agrobacterium mediated gene transfer using pBVHb
tissue: leaf
leaf type: above leaf, LPI 6
plant number: 49
treatment: herbivore (chestnut moth larvae)
Treatment protocol The saplings of wt and VHb lines grown 1.5 months under standard greenhouse conditions were used in the experiments. In the herbivory treatment, one larvae of Conistra vaccinii L. (Lepidoptera: Noctuidae) was placed on the leaf inside the veil cloth bag for 24 hours, which after samples were collected to liquid nitrogen.
Growth protocol The lines were multiplicated on liquid MS medium (full strength of C10H12FeN2NaO8; half strength of other micro and macro nutrients; 2.22 μM BA and 2.85 μM IAA) in RITA® temporary immersion containers (Vitropic, Saint-Mathieu-de-Tréviers, France) under 16:8 h light/dark photoperiod (110-130 μmol m-2s-1) at 22 ºC. Saplings were rooted on MS without plant growth regulators, acclimated in the Botanical Gardens of the University of Oulu (65°03'N, 25°27'E), and potted to limed and fertilised soil, and grown under standard greenhouse conditions.
Extracted molecule total RNA
Extraction protocol The total RNA was extracted as described by Jaakola et al. (Mol. Biotechnol. 19 (2001) 201-203) except for the first centrifugation step which was omitted.
Label Cy3
Label protocol The SuperScript III reverse transcriptase (Invitrogen, Carlsbad, CA, USA) was used to synthesize cDNAs in accordance with the manufacturer's instructions and the instructions of the 3DNA Array 50 Expression Array Detection Kit For Microarrays (Genisphere Inc, Hatfield, PA, USA).
 
 
Hybridization protocol Hybridizations and post-washings were conducted following the instructions of 3DNA Array 50 Expression Array Detection Kit (Genisphere Inc).
Scan protocol Slides were scanned at 633 nm and 543 nm at 98 % laser power, at a resolution of 10 µm with varying PMT values with ScanArray® Gx PLUS (Microarray Scanner, PerkinElmer, Waltham, MA, USA). The fixed-circle method was used in the quantification of spots, and the total-algorithm in the normalization was conducted with the ScanArray Express software (PerkinElmer).
Description VHb_A_rep2
Replicate 2.
Data processing The statistical processing of the data was conducted separately on the two lines and different leaf samples by using identical procedures. The low quality spots were downweighted; these included spots with the sum of median pixel intensities less than 300 and spots having the feature pixel intensity less than 55 % above one standard deviation of the background pixel intensity in both wavelengths. The data was normalized by using print-tip loess within and Aquantile (Aq) between array normalizations.
 
Submission date Apr 23, 2013
Last update date Apr 24, 2013
Contact name Suvi Tuulia Sutela
E-mail(s) suvi.sutela@oulu.fi
Organization name University of Oulu
Department Biology
Street address P.O. Box 3000
City Oulu
ZIP/Postal code 90014
Country Finland
 
Platform ID GPL17056
Series (1)
GSE46331 24-hour herbivory exposure of VHb-expressing Populus tremula x Populus tremuloides

Data table header descriptions
ID_REF
VALUE Print-tip loess and Aq-normalized log2 ratios (Cy5/Cy3) calculated using limma

Data table
ID_REF VALUE
1 null
2 -0.415037499
3 -0.822661198
4 -0.524844609
5 -0.110580577
6 -0.497709546
7 null
8 -0.194338122
9 -0.284958182
10 -0.216484652
11 -0.192645078
12 -0.137503524
13 -0.752072487
14 -0.236425897
15 null
16 -0.476438044
17 -0.368257283
18 -0.436863862
19 -1.099535674
20 -0.996977442

Total number of rows: 25392

Table truncated, full table size 439 Kbytes.




Supplementary file Size Download File type/resource
GSM1128686_VHb_A_rep2_52.gpr.gz 950.1 Kb (ftp)(http) GPR
Processed data included within Sample table

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