|
Status |
Public on Dec 01, 2020 |
Title |
WT_3 |
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 |
SAMN09976773 |
SRA |
SRX4643686 |