|
| Status |
Public on Jun 14, 2022 |
| Title |
TS_S3_replicate 2 |
| Sample type |
RNA |
| |
|
| Source name |
Thompson Seedless; seeds; pea size phase (BBCH 73-75; E-L 29); replicate 2
|
| Organism |
Vitis vinifera |
| Characteristics |
cultivar: Thompson Seedless
tissue: seeds
devepmental stage: pea size phase (BBCH 73-75; E-L 29)
|
| Treatment protocol |
Total transcriptome assays were performed on ovules and developing seeds derived from two seeded (Italia and Red globe) and two seedless (Thompson Seedless and Autumn Royal) table grape varieties. Four developing stages were considered: pre-bloom (BBCH 57-60; E-L 17), post-bloom (BBCH 65-68; E-L 19-25), pea size (BBCH 73-75; E-L 29) and veraison (BBCH 81; E-L 35) (Ref. A.A.V.V. 1997; Lorenz D.H. at al.1994)
|
| Growth protocol |
Seeded (Red Globe, Italia) and seedless (Autumn Royal, Thompson Seedless) table grapevine varieties were selected from a grape collection grown in the experimental field of the Research Centre Viticulture and Enology (CREA-VE) in Turi (BA) - South of Italy, under conventional vine management and without hormone treatments in the 2013-2014 seasons
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from 0.1 g of ovules or seeds collected at each experimental stage with Total RNA Isolation Mini Kit (Agilent Technologies). RNA integrity was assessed by automated gel electrophoresis on 2100 Bioanalyzer (Agilent Technologies).
|
| Label |
Cy3
|
| Label protocol |
The cDNA synthesis, labeling hybridization, and washing were performed according to the Agilent Microarray-Based Gene Expression Analysis Guide (6.9.1)
|
| |
|
| Hybridization protocol |
Hybridization was carried out in an Agilent custom microarray (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL26142) https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE126052containing 44K probes, corresponding to about 26k annotated genes plus EST and transcripts reported in the literature as candidate genes for important traits and QTLs available at NCBI databases (www.ncbi.nlm.nih.gov/gene/).
|
| Scan protocol |
Scanning and Feature Extraction was performed by using an Agilent Scanner following the settings and parameters indicated in the instruction manual
|
| Data processing |
A data-matrix was prepared selecting from each single sub-array outcome file the gProcessedSignalvalues, which are the raw fluorescence intensities of each probe.
|
| |
|
| Submission date |
Oct 29, 2021 |
| Last update date |
Jun 15, 2022 |
| Contact name |
Alessandra Amato |
| E-mail(s) |
alessandra.amato@univr.it
|
| Organization name |
University of Verona
|
| Street address |
strada le grazie 15
|
| City |
VR |
| ZIP/Postal code |
37134 |
| Country |
Italy |
| |
|
| Platform ID |
GPL30912 |
| Series (1) |
| GSE186838 |
Total transcriptome assays were performed on ovules and developing seeds derived from two seeded (Italia and Red globe) and two seedless (Thompson Seedless and Autumn Royal) table grape varieties |
|
