|
| Status |
Public on Jan 01, 2018 |
| Title |
ow_2DPAe_rep2 RNA-seq |
| Sample type |
SRA |
| |
|
| Source name |
ovary wall/pericarp of 2DPAe (emasculated) fruit
|
| Organism |
Solanum lycopersicum |
| Characteristics |
cultivar: Moneymaker
tissue: ovary wall/pericarp
Stage: 2DPA (emasculated at -2DPA)
|
| Treatment protocol |
No treatment
|
| Growth protocol |
the tomato plants were grown in greenhouse on soil
|
| Extracted molecule |
total RNA |
| Extraction protocol |
the fruits of different stages were collected and the ovule and ovary wall were dissected under microscope. The total RNA was extracted using TRIZOL reagent (Invitrogen Cat#15596026).
Strand-specific RNA-Seq libraries generated from samples above were constructed using dUTP method (Parkhomchuk et al., 2009) and sequenced on Illumina Hiseq 2500.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
R10_rep2
|
| Data processing |
The RNA-seq reads were aligned to the tomato genome (ITAG2.4) using tophat-2.0.11 (Trapnell et al., 2009) with anchor length more than 8nt for spliced alignments. Only uniquely mapped reads were retained for subsequent analysis.
Genome_build: ITAG2.4
Supplementary_files_format_and_content: bigWig
|
| |
|
| Submission date |
Nov 09, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Xia Cui |
| E-mail(s) |
cuixia@caas.cn
|
| Organization name |
Chinese Academy of Agricultural Sciences
|
| Street address |
12 Zhongguancun Nandajie
|
| City |
Beijing |
| ZIP/Postal code |
100081 |
| Country |
China |
| |
|
| Platform ID |
GPL19694 |
| Series (1) |
| GSE74827 |
Spatial-temporal order of regulation in tomato early fruit development |
|
| Relations |
| BioSample |
SAMN04252588 |
| SRA |
SRX1425148 |
