|
| Status |
Public on Nov 25, 2013 |
| Title |
ATR1D, rep3 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
spider mites fed Arabidopsis line atr1D
|
| Organism |
Tetranychus urticae |
| Characteristics |
developmental stage: adult
gender: female
treatment: Arabidopsis line atr1D
|
| Treatment protocol |
Adult female spider mites were transferred to the three Arabidopsis lines (Col-0, qKo, atr1D) or bean, and after 24 hours, the gene expression levels were analyzed.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from about 100 adult female spider mites using RNeasy Mini Kit (Qiagen) following manufacturer's instructions.
|
| 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 |
spider mites fed Arabidopsis line Col-0
|
| Organism |
Tetranychus urticae |
| Characteristics |
developmental stage: adult
gender: female
treatment: Arabidopsis line Col-0
|
| Treatment protocol |
Adult female spider mites were transferred to the three Arabidopsis lines (Col-0, qKo, atr1D) or bean, and after 24 hours, the gene expression levels were analyzed.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from about 100 adult female spider mites using RNeasy Mini Kit (Qiagen) following manufacturer's instructions.
|
| 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 cRNAs 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 |
Replicate 3 of 4, atr1D vs. Col-0
The Arabidopsis line has previously been characterized: The Arabidopsis ATR1 Myb transcription factor controls indolic glucosinolate homeostasis. Celenza JL, Quiel JA, Smolen GA, Merrikh H, Silvestro AR, Normanly J, Bender J. Plant Physiol. 2005 Jan;137(1):253-62. PMID 15579661.
|
| 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).
Two-color data processed using limma with the following parameters:
Background correction: normexp with offset=50
Within array normalization: loess
Between array normalization: Aquantile
|
| |
|
| Submission date |
Jul 10, 2013 |
| Last update date |
Nov 26, 2013 |
| 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) |
| GSE48771 |
Spider mite responses to feeding on Col-0, myb28 myb29 cyp79b2 cyp79b3, and atr1D Arabidopsis plants |
|
