|
Status |
Public on Dec 25, 2018 |
Title |
jai1_uw_2 |
Sample type |
SRA |
|
|
Source name |
leaves
|
Organism |
Solanum lycopersicum |
Characteristics |
replicate: 2 tissue: unwounded leaves cultivar: Castlemart genotype/variation: jai1 mutant
|
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 |
SAMN06220404 |
SRA |
SRX2488263 |