|
| Status |
Public on Feb 16, 2018 |
| Title |
Tomato_OX |
| Sample type |
SRA |
| |
|
| Source name |
fruit
|
| Organism |
Solanum lycopersicum |
| Characteristics |
developmental stage: red ripening
tissue: fruit
genotype: ALMT9 over-expression line
|
| Treatment protocol |
To collect fruit samples from red ripening stages, flowers were tagged when fully opened (anthesis) and fruits were harvested from 3 individual plants of each genotype at 49 days after flowering (DAF)
|
| Growth protocol |
Plant growth and cultivation was carried out according to commercial practices with a day/night temperature of 28/20°C. Plants were pruned so that fruits were on one vine per plant.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA libraries were prepared for sequencing using standard Illumina protocols
The fruits from CK and OX1 harvested at ripening stage were frozen in liquid nitrogen and kept at -80°C until use.. Total RNA was extracted using a ZP411-2 GREENspin RNA quick extraction kit (ZOMANBIO, Beijing), excluding polyphenols and polysaccharides from the sample according to the manufacturer’s instructions
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Illumina HiSeq 2500 used for RNA-seq
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to S. lycopersicum whole genome by Tophat
Reads Per Kilobase of exon model per Million mapped reads (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009.
Genome_build: Heizn1706
Supplementary_files_format_and_content: tab-delimited text files include the number of RPKM values of each gene for each Sample.
Identifiers in our processed data (e.g. Solyc04g024500.2 etc.) are searchable in SGN (Sol Genomics Network) (ftp://ftp.solgenomics.net/genomes/Solanum_lycopersicum/annotation/ITAG2.4_release/)
|
| |
|
| Submission date |
Nov 10, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
JIE YE |
| E-mail(s) |
yjstudents@163.com
|
| Organization name |
Huazhong Agricultural University
|
| Lab |
Key Laboratory of Horticultural Plant Biology, Ministry of Education
|
| Street address |
No. 1, Shizishan Road
|
| City |
Wuhan City |
| State/province |
Hubei Province |
| ZIP/Postal code |
430070 |
| Country |
China |
| |
|
| Platform ID |
GPL19694 |
| Series (1) |
| GSE89772 |
A naturally unique variation in Al-activated malate transporter 9 determines fruit malate in cultivated tomato |
|
| Relations |
| BioSample |
SAMN06013356 |
| SRA |
SRX2343046 |
