|
| Status |
Public on Jun 13, 2017 |
| Title |
Vesuviano Sarno Rep2 |
| Sample type |
SRA |
| |
|
| Source name |
Fruit
|
| Organism |
Solanum lycopersicum |
| Characteristics |
developmental stage: Red ripe
cultivar: Vesuviano
location: Sarno
tissue: fruit
|
| Growth protocol |
Tomato plants were cultivated in standard conditions in field in two locations of the Campania region, Sarno (SA) and Acerra (NA).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from powdered fruit tomato samples following the protocol developed by Wang et al. (2009).
TruSeq RNA Sample Prep Kit v2
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 1000 |
| |
|
| Description |
processed data file: Vesuviano_Sarno_FPKM_All_Replicates.txt
|
| Data processing |
Basecalls performed using CASAVA, version 1.8.2
Quality control performed with RseQC, version 2.3.9
Read alignment with TopHat, version 2.0.6
Abundance estimation and differential expression analysis performed with Cufflinks, version 2.1.1, –multi-read-correct, –GTF-guide
Genome_build: S. lycopersicum version 2.40, San Marzano and Vesuviano genomes (Ercolano et al., 2014)
Supplementary_files_format_and_content: Tab-delimited text files include RPKM values for each Sample replicate
|
| |
|
| Submission date |
Nov 20, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Daniela D'Esposito |
| E-mail(s) |
danieladesposito@hotmail.it
|
| Organization name |
University of Naples Federico II
|
| Department |
Department of Agriculture
|
| Street address |
Via Università 100
|
| City |
Portici |
| ZIP/Postal code |
80055 |
| Country |
Italy |
| |
|
| Platform ID |
GPL21167 |
| Series (1) |
| GSE75273 |
Genomic response to environment affects tomato fruit organoleptic performance |
|
| Relations |
| BioSample |
SAMN04285071 |
| SRA |
SRX1441789 |
