|
| Status |
Public on Jun 23, 2014 |
| Title |
AC-Pink rep1 |
| Sample type |
SRA |
| |
|
| Source name |
Tomato fruits
|
| Organism |
Solanum lycopersicum |
| Characteristics |
type: Wild type
strain: Ailsa Craig cultivar
age: 45 DAP
|
| Treatment protocol |
The harvested fruits were sliced and immediately frozen in liquid nitrogen and stored at -80°C.
|
| Growth protocol |
Plants were grown in a glasshouse under 16-h light at 26°C and 8-h dark at 20°C conditions, and the fruits were harvested at 35 and 45 DAP.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
The frozen fruits were powdered with moter and pestle. Total RNA samples were prepared from fruits of wild type, a FUL1/FUL2 suppressed line (TF18) and rin mutant at 35 DAP (G stage) and 45 DAP (P-stage) by SDS-phenol extraction and following elimination of polysaccharides with 2-botoxyethanol. The RNAs were further purified with the RNeasy Plus Kit (Qiagen). The quality of the RNAs was confirmed using a 2100 Bioanalyzer (Agilent).
RNA libraries were prepared for sequencing using standard Illumina protocols.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Illumina CASAVA software (ver.1.8.1) was used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to the predicted protein-coding sequences (CDS) of tomato genes provided the International Tomato Annotation Group (ITAG, version2; available at http://solgenomics.net/organism/Solanum_lycopersicum/genome) using bowtie2 with parameters -q -p 4.
Reads Per Kilobase of exon per Million mapped reads (RPKM) were calculated for all tomato predicted genes.
Genome_build: ITAG2_cds
Supplementary_files_format_and_content: A tab-delimited text file includes RPKM values for each sample.
|
| |
|
| Submission date |
Jul 27, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Yasuhiro Ito |
| E-mail(s) |
yasuito@affrc.go.jp
|
| Organization name |
National Food Research Institute
|
| Department |
Food Biotechnology Division
|
| Lab |
Metabolic Regulation Laboratory
|
| Street address |
2-1-12 Kannondai
|
| City |
Tsukuba |
| State/province |
Ibaraki |
| ZIP/Postal code |
305-8642 |
| Country |
Japan |
| |
|
| Platform ID |
GPL16345 |
| Series (1) |
| GSE49289 |
Transcriptome profiling of tomato fruits of a FRUITFULL-suppressed line and rin mutant by next generation RNA sequencing |
|
| Relations |
| BioSample |
SAMN02296624 |
| SRA |
SRX328378 |
