|
| Status |
Public on Sep 28, 2017 |
| Title |
Ca 24h-1 |
| Sample type |
SRA |
| |
|
| Source name |
fruit
|
| Organism |
Solanum lycopersicum |
| Characteristics |
tissue: fruit
developmental stage: mature green stage
treatment: injected with CaCl2, and harvested at 24 hours after injection
|
| Treatment protocol |
CaCl2 and H2O were injected in the mature green tomato fruit, and havested at 0h, 8h, and 24h after injeciton
|
| Growth protocol |
Tomato plants (S. lycopersicum cv ‘microtom’) were grown in greenhouse at 28 °C and 16 h/8 h (light/dark).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted using the RNeasy plant mini kit (Qiagen); on-column DNase digestion with the RNase-Free DNase set (Qiagen) was performed to remove contaminating DNA
Illumina TruSeq RNA sample preparation kit
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
injected with CaCl2, and harvested at 24 hours after injection
|
| Data processing |
The paired-end raw reads were filtered with Illumina Pipeline (CASAVA) v1.8.2 with the default parameter.
The raw reads after filtered were separately aligned to the Solanum lycopersicum (ITAG 2.3) genome and CDS with RNA-Seq analysis algorithm included in the CLC Genomics Workbench 7.0.4 (CLC bio, Boston, USA) using the default parameters.
Genome_build: SL 2.4
Supplementary_files_format_and_content: xls, rpkm value
|
| |
|
| Submission date |
Sep 28, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Tianbao Yang |
| E-mail(s) |
tianbao.yang@ars.usda.gov
|
| Phone |
301-504-6635
|
| Organization name |
USDA-ARS
|
| Department |
BARC
|
| Lab |
Fruit Quality Lab
|
| Street address |
10300 BALTIMORE AVENUE
|
| City |
beltsville |
| State/province |
MD |
| ZIP/Postal code |
20705 |
| Country |
USA |
| |
|
| Platform ID |
GPL16345 |
| Series (1) |
| GSE73520 |
Calcium treatment can delay tomato (Solanum lycopersicum L.) fruit senescence |
|
| Relations |
| SRA |
SRX1293156 |
| BioSample |
SAMN04121949 |
