|
| Status |
Public on Apr 10, 2017 |
| Title |
M82 35 DPA rep2 |
| Sample type |
SRA |
| |
|
| Source name |
M82 35 DPA_fruit pericarps
|
| Organism |
Solanum lycopersicum |
| Characteristics |
cultivar background: M82
developmental stage: 35 DPA
genotype/variation: Wild Type
phentoype: red-fruited tomato
tissue: fruit pericarps
|
| Growth protocol |
Plants were grown in a greenhouse at at Pujiang experimental base, Shanghai Jiao Tong University, Shanghai, China.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted using RNAprep pure Plant Kit (Cat#DP441). Sequencing libraries were constructed using Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001).
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 used for basecalling.
Raw reads were screened by FASTX-Toolkit to remove adaptor sequences and low-quality regions. The remaining high-quality reads were mapped to tomato reference genome (ITAG2.3) using TopHat (version 2.0)
fragments per kilobase of exon per million fragments mapped (FPKM) calculated by Cufflinks (http://cufflinks.cbcb.umd.edu/).
Genome_build: Solanum lycopersicum reference genome (ITAG2.3); http://www.ncbi.nlm.nih.gov/assembly/GCF_000188115.2
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each sample in each pairwise comparison (the gene locus can be traceable in Sol Genomics Network (https://solgenomics.net/search/locus)
|
| |
|
| Submission date |
Oct 10, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Lei Gao |
| E-mail(s) |
glei1103@hotmail.com
|
| Organization name |
Shanghai Jiao Tong University
|
| Street address |
Dongchuan Road No. 800
|
| City |
Shanghai |
| ZIP/Postal code |
200240 |
| Country |
China |
| |
|
| Platform ID |
GPL16345 |
| Series (1) |
| GSE73908 |
Transcriptomic difference between the wild type red-fruited tomato and its yellow-fruited mutant |
|
| Relations |
| BioSample |
SAMN04159003 |
| SRA |
SRX1326489 |
