|
| Status |
Public on Apr 13, 2020 |
| Title |
WT rep2 |
| Sample type |
SRA |
| |
|
| Source name |
Ailsa Craig
|
| Organism |
Solanum lycopersicum |
| Characteristics |
developmental stage: At 37 days after anthesis (dpa)
tissue: Pericarp
genotype: wild type (WT)
|
| Growth protocol |
Wild-type tomato and transgenic lines in the Ailsa-Craig background were grown in a greenhouse at 23°C under 16 h light and 8 h dark condition.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Pericarp tissues were collected, immediately frozen in liquid nitrogen, and total RNA was extracted using Trizol reagent kit. mRNA Seq Kit (Illumina) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Data processing |
Illumina Casava1.7 software used for basecalling.
Raw reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to the tomato reference genome (version SL3.0) using HISAT2.2.4 with "-rna-strandness RF" and other parameters set as a default.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: Tomato reference genome (version SL3.0)
Supplementary_files_format_and_content: tab-delimited excel files include RPKM values for each Sample
|
| |
|
| Submission date |
Dec 30, 2019 |
| Last update date |
Apr 13, 2020 |
| Contact name |
Li Zhiwei |
| E-mail(s) |
lizhiwei@scbg.ac.cn
|
| Phone |
18825179606
|
| Organization name |
South China Botanical Garden, Chinese Academy of Sciences
|
| Lab |
Key Laboratory of Plant Resources Conservation and Sustainable Utilization
|
| Street address |
No.723,Xingke Road
|
| City |
Guangzhou |
| ZIP/Postal code |
518000 |
| Country |
China |
| |
|
| Platform ID |
GPL25655 |
| Series (2) |
| GSE142713 |
Histone demethylase SlJMJ6 promotes fruit ripening by removing H3K27 methylation of ripening-related genes in tomato [RNA-Seq] |
| GSE142714 |
Histone demethylase SlJMJ6 promotes fruit ripening by removing H3K27 methylation of ripening-related genes in tomato |
|
| Relations |
| BioSample |
SAMN13698532 |
| SRA |
SRX7477123 |
