|
| Status |
Public on Jul 10, 2021 |
| Title |
WT rep1 |
| Sample type |
SRA |
| |
|
| Source name |
WT_pericarp
|
| Organism |
Solanum lycopersicum |
| Characteristics |
background: Ailsa Craig
genotype/variation: WT
developmental stage: At 38 days after anthesis (dpa)
tissue: Pericarp
|
| 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 at the equatorial part of the fruit 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 NovaSeq 6000 |
| |
|
| 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.
Fragments Per Kilobase of exon per Megabase of library size (FPKM) 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 FPKM values for each Sample
|
| |
|
| Submission date |
Apr 12, 2020 |
| Last update date |
Jul 10, 2021 |
| Contact name |
Ding xiaochun |
| E-mail(s) |
dingxc111@scbg.ac.cn
|
| Organization name |
SOUTH CHINA BOTANICAL GARDEN
|
| Street address |
723 xingke road, tianhe district
|
| City |
guangzhou city |
| State/province |
guangdong |
| ZIP/Postal code |
510000 |
| Country |
China |
| |
|
| Platform ID |
GPL27957 |
| Series (2) |
| GSE148526 |
Histone demethylase SlJMJ7 Integrates DNA demethylation, ethylene signal and major ripening-related transcription factors in coordination of fruit ripening in tomato [RNA-seq] |
| GSE148527 |
Histone demethylase SlJMJ7 integrates DNA demethylation, ethylene signal and major ripening-related transcription factors in coordination of fruit ripening in tomato. |
|
| Relations |
| BioSample |
SAMN14588126 |
| SRA |
SRX8110027 |
