|
| Status |
Public on Apr 30, 2014 |
| Title |
cyano4 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
London-CYANO, whole organism
|
| Organism |
Tetranychus urticae |
| Characteristics |
age: adult
gender: female
host: London-CYANO
|
| Growth protocol |
Both the London and London-CYANO 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 (London, London-CYANO)
|
| Label |
cy5
|
| Label protocol |
100 ng of total RNA (+ RNA-spike in control) was used to generate Cy3- or Cy5-labeled cRNAs, using the Agilent Low Input Quick Amp Labeling Kit (version 6.5 Agilent Technologies)
|
| |
|
| Channel 2 |
| Source name |
London, whole organism
|
| Organism |
Tetranychus urticae |
| Characteristics |
age: adult
gender: female
host: London
|
| Growth protocol |
Both the London and London-CYANO 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 (London, London-CYANO)
|
| Label |
cy3
|
| Label protocol |
100 ng of total RNA (+ RNA-spike in control) was used to generate Cy3- or Cy5-labeled cRNAs, using the Agilent Low Input Quick Amp Labeling Kit (version 6.5 Agilent Technologies)
|
| |
|
| |
| 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 (also provided by Agilent Technologies)
|
| Scan protocol |
Hybridized arrays were scanned using an Agilent Microarray High Resolution Scanner.
|
| Description |
Replicate 4 of 4, London-CYANO vs London
|
| Data processing |
Data were extracted and normalized using Agilent Feature Extraction Software 10.5 with default parameter settings for gene expression two-color microarrays (GE2_107_Sep09). The data was transferred to GeneSpring GX 11.0 software (Agilent Technologies) for further statistical analysis. Probes were flag filtered (only probes that had flag-value “present” in 50% of all replicates were retained) and linked to T. urticae genes using the “Create New Gene-Level Experiment” option. Differentially expressed genes were identified by a Student’s t test with the cut off of Fold Change (FC) and corrected P-value (Benjamini-Hochberg correction) at 2 and 0.05, respectively.
|
| |
|
| Submission date |
Aug 23, 2013 |
| Last update date |
Apr 30, 2014 |
| Contact name |
Wannes Dermauw |
| E-mail(s) |
wannes.dermauw@ugent.be
|
| Phone |
003292646192
|
| Organization name |
University Ghent
|
| Department |
Crop Protection
|
| Lab |
Agrozoology
|
| Street address |
Coupure Links 653
|
| City |
Ghent |
| ZIP/Postal code |
9000 |
| Country |
Belgium |
| |
|
| Platform ID |
GPL16890 |
| Series (1) |
| GSE50162 |
Genome wide gene-expression analysis of the spider mite Tetranychus urticae after long term host transfer from acyanogenic Phaseolus vulgaris cv. 'Prelude' bean plants to cyanogenic Phaseolus lunatus cv. '8078' bean plants |
|
