|
| Status |
Public on Apr 15, 2016 |
| Title |
Akita3 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
Akita
|
| Organism |
Tetranychus urticae |
| Characteristics |
life stage: adult
gender: female
|
| Growth protocol |
Both the susceptible and resistant mite strain were maintained in climatically controlled rooms at 26 °C, 60% RH and 16:8 h light:dark photoperiod
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA samples were isolated using the RNeasy minikit (Qiagen) and were subsequently treated with DNase (Turbo DNA-free kit, Ambion). RNA was extracted from 100-120 young adult female mites in four replicates from each strain.
|
| Label |
cy5
|
| Label protocol |
Using the Agilent Low Input Quick Amp Labeling Kit (version 6.5 Agilent Technologies), Cy3- or Cy5-labeled cRNA was generated using 100 ng of total RNA (excluding RNA-spike in controls).
|
| |
|
| Channel 2 |
| Source name |
Reference
|
| Organism |
Tetranychus urticae |
| Characteristics |
life stage: adult
gender: female
|
| Growth protocol |
Both the susceptible and resistant mite strain were maintained in climatically controlled rooms at 26 °C, 60% RH and 16:8 h light:dark photoperiod
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA samples were isolated using the RNeasy minikit (Qiagen) and were subsequently treated with DNase (Turbo DNA-free kit, Ambion). RNA was extracted from 100-120 young adult female mites in four replicates from each strain.
|
| Label |
cy3
|
| Label protocol |
Using the Agilent Low Input Quick Amp Labeling Kit (version 6.5 Agilent Technologies), Cy3- or Cy5-labeled cRNA was generated using 100 ng of total RNA (excluding RNA-spike in controls).
|
| |
|
| |
| Hybridization protocol |
Cy3- and Cy5-labeled cRNA were pooled and hybridized using the Gene Expression Hybridization Kit (Agilent Technologies) for 17h in a rotating hybridization oven at 20 r.p.m. and 65 °C; Slides were washed using the Gene Expression Wash Buffer Kit (Agilent Technologies)
|
| Scan protocol |
Hybridized arrays were scanned using an Agilent Microarray High Resolution Scanner.
|
| Description |
Replication 3 out of 4, Akita vs Reference
|
| Data processing |
Data were extracted and normalized using Agilent Feature Extraction Software 10.5 with default parameter settings for GE two-color microarrays (GE2_107_Sep09). The data was transferred to limma (Smyth, 2005) for further statistical analysis. After background corrections, within- and between-array normalizations, differential expression was identified by a cut off of Fold Change and corrected p-value (Benjamini-Hochberg correction) at 2 and 0.05, respectively.
|
| |
|
| Submission date |
Mar 13, 2015 |
| Last update date |
Apr 16, 2016 |
| Contact name |
Nicky Wybouw |
| Organization name |
University of Ghent
|
| Department |
Department of Crop Protection
|
| Street address |
Coupure Links 653
|
| City |
Gent |
| ZIP/Postal code |
9000 |
| Country |
Belgium |
| |
|
| Platform ID |
GPL16890 |
| Series (1) |
| GSE62915 |
Cyenopyrafen resistance in the two-spotted spider mite Tetranychus urticae |
|
