|
| Status |
Public on Feb 14, 2017 |
| Title |
48h flooded and infected replicate3 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
Root_48h flooded and infected
|
| Organism |
Persea americana |
| Characteristics |
tissue: root
rootstock: Dusa
time-point: 48 hours
|
| Treatment protocol |
Split into one of four groups: control, flooded, infected, combination treatment
|
| Growth protocol |
Plants were grown under greenhouse conditions in 2l containers in soil-perlite mix (1:1)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA extracted using phenol chloroform extraction
|
| Label |
Cy5
|
| Label protocol |
4-6ug of RNA was transcribed into single stranded cDNA priming with random nonamer and oligo(dt) primers, using the Superscript III Reverse transcriptase. Samples labelled with Cy5 and References with Cy3 (CyDye Post-Labelling Reactive Dye Pack, GE Healthcare Life Sciences)
|
| |
|
| Channel 2 |
| Source name |
pooled reference
|
| Organism |
Persea americana |
| Characteristics |
tissue: root
rootstock: Dusa
reference type: Reference pool (0h, 8h, 22h, 48h, 96h, 7d)
|
| Treatment protocol |
Split into one of four groups: control, flooded, infected, combination treatment
|
| Growth protocol |
Plants were grown under greenhouse conditions in 2l containers in soil-perlite mix (1:1)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA extracted using phenol chloroform extraction
|
| Label |
Cy3
|
| Label protocol |
4-6ug of RNA was transcribed into single stranded cDNA priming with random nonamer and oligo(dt) primers, using the Superscript III Reverse transcriptase. Samples labelled with Cy5 and References with Cy3 (CyDye Post-Labelling Reactive Dye Pack, GE Healthcare Life Sciences)
|
| |
|
| |
| Hybridization protocol |
Hybridization was carried out according to the two-colour microarray-based gene expression analysis protocol (Agilent)
|
| Scan protocol |
Microarray slides were scanned using the Axon GenePix 400B scanner (Molecular devices)
|
| Description |
Biological replicate 3 of 3:48h flooded and infected
|
| Data processing |
Axon GenePix6.0 software was used for image analysis. Normalization and statistical analysis was carried out in the R environment
|
| |
|
| Submission date |
May 10, 2016 |
| Last update date |
Feb 14, 2017 |
| Contact name |
Bianca Reeksting |
| E-mail(s) |
bjreeksting@gmail.com
|
| Organization name |
University of Pretoria
|
| Department |
Department of Genetics
|
| Street address |
117 Lunnon Road
|
| City |
Pretoria |
| ZIP/Postal code |
0002 |
| Country |
South Africa |
| |
|
| Platform ID |
GPL21856 |
| Series (1) |
| GSE81297 |
Transcriptome response of avocado roots subjected to flooding and infection by the oomycete Phytophthora cinnamomi |
|
