|
| Status |
Public on Jul 27, 2013 |
| Title |
Pinneaple replica 4 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
Meristems of juvenile Pineapple sweet orange (C. sinensis (L.)
|
| Organism |
Citrus sinensis |
| Characteristics |
developmental stage: juvenile
|
| Treatment protocol |
Wild type plants of two different developmental stages (juvenile and adult) were compared
|
| Growth protocol |
Plants were growth in a temperature-controlled (18°C night and 26ºC day) greenhouse.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from meristems using RNeasy Plant Mini Kit (Qiagen, Hilden, Germany)
|
| Label |
Cy5
|
| Label protocol |
RNA was labelled following an indirect method (Randolph and Waggoner, 1997). Reverse transcription, cDNA purification, dye coupling and fluorescent cDNA purification was accomplished as described by Forment et al. (2005), except that total RNA (40 ug) was used instead of poly(A)+ RNA.
|
| |
|
| Channel 2 |
| Source name |
Meristems of adult Pineapple sweet orange (C. sinensis (L.)
|
| Organism |
Citrus sinensis |
| Characteristics |
developmental stage: adult
|
| Treatment protocol |
Wild type plants of two different developmental stages (juvenile and adult) were compared
|
| Growth protocol |
Plants were growth in a temperature-controlled (18°C night and 26ºC day) greenhouse.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from meristems using RNeasy Plant Mini Kit (Qiagen, Hilden, Germany)
|
| Label |
Cy3
|
| Label protocol |
RNA was labelled following an indirect method (Randolph and Waggoner, 1997). Reverse transcription, cDNA purification, dye coupling and fluorescent cDNA purification was accomplished as described by Forment et al. (2005), except that total RNA (40 ug) was used instead of poly(A)+ RNA.
|
| |
|
| |
| Hybridization protocol |
Microarray hybridisation and washing were performed as described by Martinez-Godoy et al. (2008).
|
| Scan protocol |
Hybridized microarray slides were scanned at 532-nm for the Cy3 and 635-nm for the Cy5 dyes, with a GenePix 4000B scanner (Axon Molecular Devices, Sunnyvale CA), at 10-nm resolution and 100% laser power.
|
| Description |
Meristems of juvenile Pineapple sweet orange (C. sinensis (L.) , labeled with Cy3, compared to meristems of adult Pineapple sweet orange (C. sinensis (L.) , labeled with Cy5; replica 4
|
| Data processing |
The data were global median normalized using GenePix Pro 6.0 (Axon Molecular Devices) and LOWESS correction was applied using the Acuity 4.0 software (Axon Molecular Devices). Spots with a net intensity in both channels below twofold the mean background intensity were considered low-signal spots and removed. To detect differentially expressed genes, data were analyzed with the Significance Analysis of Microarray package (Tusher et al. 2001) using two-class unpaired comparison.
|
| |
|
| Submission date |
Aug 01, 2012 |
| Last update date |
Jul 28, 2013 |
| Contact name |
Gema Ancillo |
| E-mail(s) |
[email protected]
|
| Phone |
00 34 96 3424000
|
| Fax |
00 34 96 3424001
|
| URL |
http://www.ivia.es
|
| Organization name |
Instituto Valenciano de Investigaciones Agrarias (IVIA)
|
| Department |
Protección Vegetal y Biotecnología
|
| Lab |
III-N-8
|
| Street address |
Ctr. Moncada-Naquera Km 4.5
|
| City |
Moncada |
| State/province |
Valencia |
| ZIP/Postal code |
46113 |
| Country |
Spain |
| |
|
| Platform ID |
GPL15839 |
| Series (1) |
| GSE39799 |
Identification of transcription factors potentially involved in the juvenile to adult phase transition in Pineapple sweet orange (C. sinensis (L.) |
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