|
| Status |
Public on Dec 25, 2018 |
| Title |
sl_local_w2_3 |
| Sample type |
SRA |
| |
|
| Source name |
leaves
|
| Organism |
Solanum lycopersicum |
| Characteristics |
replicate: 3
tissue: 2h wounded leaves
cultivar: Castlemart
|
| Treatment protocol |
Three to four weeks old plants with 3-4 true leaves were used for wound treatment. For the wound-elicitation, the lower 1st and 2nd true leaves were crushed with a hemostat to cross the midrib of all leaflets.
|
| Growth protocol |
Tomato was grown on Jiffy-7 peat pot (Hummert International, Earth City, MO) in a growth chamber under 16 h light (6:00 to 22:00, 200 μmol m-2 s-1)/ 8 h dark cycle at 28ºC.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA from the leaf tissues were extracted with RNeasy Plant Mini Kit (Qiagen, Germantown, MD, USA).
The purified total RNA was used to construct a library for 100-bp paired-end sequencing following the Illumina protocol.
TruSeq Stranded Total RNA Library Prep Kit was used for library preparation.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Adaptor sequences were trimmed from the sequence reads. Adaptor sequences is for TrueSeq-3.
The RNA-seq reads to the genome through TopHat with the options (-I 500 -g 1; otherwise with default). Transcript levels of annotated genes were determined and shown as FPKM (Fragments Per Kilobase per Million fragments mapped) calculated with Cufflinks
Genome_build: The reference genome sequences and gene annotation of Solanum lycopersicum (ITAG2.4) and Solanum pennellii (Spenn_v2.0) were retrieved from Sol Genomics Network
Supplementary_files_format_and_content: The "Processed data_RNA-expression" contains the RNA expression (FPKM value) of annotated genes in the samples listed above.
|
| |
|
| Submission date |
Jan 12, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Ming-Jung Liu |
| E-mail(s) |
mjliu@gate.sinica.edu.tw
|
| Organization name |
Academia sinica
|
| Street address |
128 Sec. 2, Academia Rd, Nankang
|
| City |
Taipei |
| ZIP/Postal code |
11529 |
| Country |
Taiwan |
| |
|
| Platform ID |
GPL19694 |
| Series (1) |
| GSE93556 |
Regulatory divergence controlling wound-responsive gene expression in domesticated and wild tomatoes |
|
| Relations |
| BioSample |
SAMN06220427 |
| SRA |
SRX2488239 |
