|
| Status |
Public on Apr 06, 2015 |
| Title |
Castel_Gala_field_autumn_rep1 [5_rep1_CGmay2009_F_BZ6] |
| Sample type |
RNA |
| |
|
| Source name |
'Castel Gala', harvested during autumn
|
| Organism |
Malus domestica |
| Characteristics |
genetic background: Castel Gala
genotype/variation: Wild-type
tissues developmental stage: Harvested while dormant (A stage sensu Fleckinger)
tissue: Bud
treatment: none
|
| Treatment protocol |
Harvested buds were exposed to low temperatures under controlled conditions.
|
| Growth protocol |
'Royal Gala' and 'Castel Gala' buds were harvested from a commercial orchard in 2009 and 2010
|
| Extracted molecule |
total RNA |
| Extraction protocol |
LiCl precipitation, improved from the pine tree isolation method (Chang et al., 1993) by Zeng and Yang (2002)
|
| Label |
Cy3
|
| Label protocol |
200ng of total RNAs were amplified using the Ambion messageAmp II (Ambion, Austin TX) following manufacturer's instructions. 5µg of each aRNAs were retrotranscribed with 400U of Superscript II reverse-transcriptase (Invitrogen Corp., Carlsbad, CA) and labelled with 1.5mmol of Cyanine-3 (Cy3) or Cyanine-5 (Cy5) (Interchim, France), then purified with NucleoSpin Gel and PCR Clean-up column kits (Macherey-Nagel, GmbH & Co. KG, Germany). Purified labeled cDNA were quantified using NanoDrop ND-1000 (Nanodrop Technologies, DE, USA). Labelled samples were combined as 30 pmol for each dye and co-hybridized.
|
| |
|
| Hybridization protocol |
The hybridization performed on a NimbleGen Hybridization System 4 (mix mode B) at 42° overnigth. Afterwards, the slide were washed, dried, and scanned.
|
| Scan protocol |
Slides were scanned at 532 and 635nm at 2 μm resolution and high sensitivity with a Roche-NimbleGen MS200. Pair-data files were extracted from the scanned images using DEVA 1.2.1 software (Roche).
|
| Description |
5_rep1_CGmay2009_F_BZ6
Frozen in the field
|
| Data processing |
Statistical analyses were performed using R version 2.14.1 (R Development Core Team, 2011) and the package LIMMA 3.10.1 (Smyth G.K., 2005) from the Bioconductor project. Data were normalized by the lowess method from LIMMA.
|
| |
|
| Submission date |
Jan 07, 2015 |
| Last update date |
Apr 06, 2015 |
| Contact name |
Diogo Denardi Porto |
| Organization name |
EMBRAPA
|
| Department |
Embrapa Semiárido
|
| Street address |
BR428 road, Km 152
|
| City |
Petrolina |
| State/province |
Pernambuco |
| ZIP/Postal code |
56302-970 |
| Country |
Brazil |
| |
|
| Platform ID |
GPL16374 |
| Series (1) |
| GSE64717 |
Microarray analysis of apple buds during dormancy |
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