|
| Status |
Public on Jan 22, 2019 |
| Title |
wtR1_mRNA_Seq_rep2 |
| Sample type |
SRA |
| |
|
| Source name |
mature leaves
|
| Organism |
Solanum lycopersicum |
| Characteristics |
genotype: T1 of the regenerated wild type wtR0
tissue: mature leaves
|
| Growth protocol |
Tomato plants were grown in soil in a growth room with the condition of 14/10 h and 25/20 °C for day/night.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from wtR1, 2A and 2B by Trizol Reagent (Ambion) using the same leaf material as for the DNA extraction.
The library construct and deep sequencing were then performed at the Core Facility of Genomics in Shanghai Center for Plant Stress Biology.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
mRNA-Seq: The reads were aligned to the tomato genome using TopHat2 with "--b2-very-sensitive" option. The ITAG2.4 annotation gff3 file was supplied as the “-G” option to TopHat2.
genome build: tomato genome build 2.50 (SL2.50)
processed data files format and content: For mRA_Seq: The FPKM values were calculated via cuffdiff from Cufflinks suite of tools.
|
| |
|
| Submission date |
Aug 04, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Jian-Kang Zhu |
| E-mail(s) |
zhu132@purdue.edu
|
| Organization name |
Purdue University
|
| Department |
Department of Horticulture and Landscape Architecture
|
| Street address |
625 Agriculture Mall Dr.
|
| City |
West Lafayette |
| State/province |
IN |
| ZIP/Postal code |
47907 |
| Country |
USA |
| |
|
| Platform ID |
GPL19694 |
| Series (1) |
| GSE102273 |
Critical function of DNA methyltransferase 1 in tomato development and regulation of the DNA methylome and transcriptome |
|
| Relations |
| BioSample |
SAMN07450767 |
| SRA |
SRX3062717 |
