Transcription profiling of tomato shoots and roots from plants systemically infected by TSWV reveals organ-specific transcriptional responses
Hybridization: Root_TSWV/Root_mock |
| Hybridization protocol |
| Hybridization solution | |
|---|
| Solution concentration | |
|---|
| Blocking agent | |
|---|
| Wash procedure | |
|---|
| Labeled Target Quantity | 1.5 ug of Cy3- and Cy5-labelled cRNA |
|---|
| Hybridization Time | |
|---|
| Hybridization Volume | |
|---|
| Hybridization Temperature | |
|---|
| Hybridization Instrument | Agilent oven (G2545A) |
|---|
|
| Scan information |
| Scan hardware | Agilent DNA microarray scanner |
|---|
| scan software | N/A |
|---|
|
| Image analysis information |
| Software | ImaGene ver 5.5.4 |
|---|
| Analysis algorithm | 1) Images
Cy5 = Red Cy3 = Green
2) Grid Flexibility
Enforce grid constraints = yes
Local flexibility = 6.0 pixels
Flexibility = 75%
3) Quality Control
Empty spots = no
Poor spots = yes
Find negative spots = no
4) Measurements
Background buffer = 2.25
Background width = 5.0
Auto seqmentation = no
Signal low cutoff = 20%
Signal high cutoff = 100%
Background low cutoff = 0%
Background high cutoff = 88%
5) Poor Spot Parameters
Contamination of Background/Signal = no
Ignored pixels % = yes (setting = 69)
Open perimeter = no
Shape regularity = no
Area to perimeter = yes (setting = 0.6)
Off-set value = yes (setting = 17.5) |
|---|
|
| Normalization information |
| Normalization software | marray package under R |
|---|
| Normalization algorithm | Print-tip specific Lowess Normalization |
|---|
| Normalization strategy | Total Array |
|---|
|
