|
| Status |
Public on Dec 01, 2020 |
| Title |
WT_1 |
| Sample type |
SRA |
| |
|
| Source name |
fruit pericarp
|
| Organism |
Solanum lycopersicum |
| Characteristics |
development stage: 38 dpa
tissue: fruit pericarp
genotype/variation: wild type
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA were isolated using SDS-phenol extraction method, from fruits pericarp which were frozen in liquid nitrogen immediately after harvest.
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 GA Pipeline v1.5 software used for basecalling.
Raw sequence reads were filtered for adaptor sequence, unknown base more than 10% and low-quaility reads, and filtered clean reads were then mapped to tomato whole genome using SOAPaligner/SOAP2 software.
Genome_build: ITAG, the International Tomato Annotation Group release version 2.5
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample .
|
| |
|
| Submission date |
Sep 05, 2018 |
| Last update date |
Dec 02, 2020 |
| Contact name |
Yuying Wang |
| E-mail(s) |
41783425@qq.com
|
| Organization name |
Institute of botany, the chinese academy of sciences
|
| Street address |
No.20 Nanxincun, Xiangshan
|
| City |
Beijing |
| ZIP/Postal code |
100093 |
| Country |
China |
| |
|
| Platform ID |
GPL16345 |
| Series (2) |
| GSE119493 |
RNA sequencing Reveals the Differentially Expressed Genes between Wild-type and SlDof1-RNAi Fruits |
| GSE119565 |
Regulatory network of SlDof1 in fruit ripening |
|
| Relations |
| BioSample |
SAMN09976771 |
| SRA |
SRX4643684 |
