|
| Status |
Public on Sep 01, 2012 |
| Title |
Bemisia tabaci adults fed on PAP Purple plants for 6hr vs wild type- Replicate1- dye swap |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
Bemisia tabaci adults fed on wild type plants for 6hr
|
| Organism |
Bemisia tabaci |
| Characteristics |
developmental status: adult
feeding: fed on wild type plants for 6hr
|
| Treatment protocol |
Feeding B.tabaci adults on PAP Purple transgenic plants for 6hr compared to wild type.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
TRIZOL
|
| Label |
Cy5
|
| Label protocol |
Cy3 and cy5 stnadard aminoallyl labeling
|
| |
|
| Channel 2 |
| Source name |
Bemisia tabaci adults fed on PAP Purple plants for 6hr
|
| Organism |
Bemisia tabaci |
| Characteristics |
developmental status: adult
feeding: fed on PAP Purple plants for 6hr
|
| Treatment protocol |
Feeding B.tabaci adults on PAP Purple transgenic plants for 6hr compared to wild type.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
TRIZOL
|
| Label |
Cy3
|
| Label protocol |
Cy3 and cy5 stnadard aminoallyl labeling
|
| |
|
| |
| Hybridization protocol |
The labeled cDNAs were purified by QIAquick PCR purification kit (QIAGEN) and mixed in 20XSSC with 20µg poly(A) and 0.15% v/v SDS and then hybridized to the microarray in a 65° C water bath for 16-18hr. The slides were washed for 2 minutes in each of the following solutions: 1.14 X SSC with 0.0285% SDS, then 1.14 X SSC, 0.228 X SSC and 0.057 X SSC. Next, the slides were dried at 1000 X g for 5 in a table-top centrifuge.
|
| Scan protocol |
Agilent automatic scanner (Agilent Technologies, Santa Clara, CA, USA).
|
| Description |
Hyb16
|
| Data processing |
ScanArray Express - Microarray Analysis System, version3 was used for data acquisition. (Perkin Elmer LAS, Inc, 2004)
The fluorescence intensity of the spots was quantified using the ScanArray software (Waltham, MA, USA). Statistical analysis was performed using the Limma (Linear Models for Microarray Data) package from the Bioconductor project (http://www.bioconductor.org). The gpr files (raw data) were read into limma using the function "read.maimages". Probes with flag values less than -74 were filtered out. Local background subtraction and lowess normalization were applied within arrays and a quantile normalization between arrays. Standard quality control was performed using the plot functions of Limma. The statistical analysis was performed using an approach called linear models for designed microarray experiments. We estimated the fold-changes and standard errors by fitting a linear model for each gene and applying empirical Bayes smoothing to the standard errors. FDR (false discovery rate) was used to correct for multiple comparisons. A 1.5-fold cut-off was considered as a filtering criterion for identifying B. tabaci ESTs that are significantly up- or down-regulated during short-term feeding (6 h) on PAP versus WT plants.
|
| |
|
| Submission date |
Aug 22, 2011 |
| Last update date |
Sep 01, 2012 |
| Contact name |
Michal Alon |
| E-mail(s) |
[email protected]
|
| Phone |
972-8-9489365
|
| Fax |
972-8-9466768
|
| Organization name |
Hebrew University of Jerusalem
|
| Department |
Department of Entomology
|
| Lab |
Dr. Shai Morin
|
| Street address |
Herzel St.
|
| City |
Rehovot |
| ZIP/Postal code |
76100 |
| Country |
Israel |
| |
|
| Platform ID |
GPL9003 |
| Series (1) |
| GSE31569 |
Insights into the transcriptomics of polyphagy: Bemisia tabaci adaptability to phenylpropanoids involves coordinated expression of defense and metabolic genes |
|
