|
| Status |
Public on Mar 27, 2017 |
| Title |
E. coli 3 hours 2 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
E. coli injected, whole organism
|
| Organism |
Tetranychus urticae |
| Characteristics |
age: adult
gender: female
injection: 3 hours post injection of E. coli
|
| Treatment protocol |
Mites were injected with 1OD of bacteria.
|
| Growth protocol |
Mite strains 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 300 injected adult female mites in four replicates.
|
| Label |
cy5
|
| Label protocol |
Using the Agilent Low Input Quick Amp Labeling Kit (version 6.5 Agilent Technologies), Cy3- and Cy5-labeled cRNA was generated using 100 ng of total RNA as starting material (excluding RNA-spike in controls).
|
| |
|
| Channel 2 |
| Source name |
LB-buffer injected, whole organism
|
| Organism |
Tetranychus urticae |
| Characteristics |
age: adult
gender: female
injection: LB buffer
|
| Treatment protocol |
Mites were injected with 1OD of bacteria.
|
| Growth protocol |
Mite strains 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 300 injected adult female mites in four replicates.
|
| Label |
cy3
|
| Label protocol |
Using the Agilent Low Input Quick Amp Labeling Kit (version 6.5 Agilent Technologies), Cy3- and Cy5-labeled cRNA was generated using 100 ng of total RNA as starting material (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 subsequently washed using the Gene Expression Wash Buffer Kit (Agilent Technologies)
|
| Scan protocol |
After standard Agilent washing procedures, hybridized arrays were scanned using an Agilent Microarray High Resolution Scanner.
|
| Description |
Replication 2 out of 4, 3 hours post injection of E. coli
|
| Data processing |
Data was extracted and normalized using Agilent Feature Extraction Software (GE2_107_Sep09 protocol). The data output files were subsequently transferred to limma (Smyth, 2004) for further statistical analysis. After background corrections, within- and between-array normalizations, significant differential expression was identified using cut-offs of log2FC and BH FDR-corrected p-value at 1 and 0.05, respectively. Within the linear modelling of the data, intra-spot correlations were incorporated (Smyth & Altman, 2013).
|
| |
|
| Submission date |
Dec 15, 2014 |
| Last update date |
Mar 28, 2017 |
| 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) |
| GSE64199 |
Transcriptomic responses in the spider mite Tetranychus urticae to bacterial infection |
|
