|
| Status |
Public on Feb 09, 2024 |
| Title |
Dark-4h-GMUCT-3 |
| Sample type |
SRA |
| |
|
| Source name |
Leaf
|
| Organism |
Solanum lycopersicum |
| Characteristics |
tissue: Leaf
genotype: HeinZ 1706
treatment: Dark-4h-GMUCT-3
|
| Treatment protocol |
25℃ 12h light/ 12-h dark
|
| Growth protocol |
25℃ 12h light/ 12-h dark, and leaves were harvest at 4 weeks of age
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Leaf tissue was ground with a mortar and pestle. RNA was extracted with a RNA isolation kit (Bioer Technology, Cat. BSC65S1).
RNA-seq libraries were prepared with paired-end and 150 nt ; GMUCT was prepared with Single-end and 50 nt
|
| |
|
| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
uncapped and cleaved transcripts
|
| Data processing |
GMUCT reads were trimmed to remove the adapter sequences using cutadapt with default parameter
RNA-Seq reads (150-nucleotide paired-end sequences) were trimmed to remove the adapter sequences using cutadapt with default parameter
Trimmed reads were aligned to the Tomato genome (SL4.0) using STAR (version 2.4.2a with parameters “—outFilterMultimapNmax 10 –outFilterMismatchNmax 10 –outFilterMismatchNoverLmax 0.10”); for small RNAs, the reads were also aligned to full-length mature mRNAs of all Tomato protein-coding genes using STAR as above.
The gene expression leves of protein coding genes were normalized by RPM.
HTSeq was used to calculate the raw reads mapping to given genes in strand-specific manner.
Assembly: Slycopersicum_691_SL4.0.fa
Supplementary files format and content: txt files, count
Library strategy: GMUCT
|
| |
|
| Submission date |
Feb 11, 2023 |
| Last update date |
Feb 09, 2024 |
| Contact name |
Pengfei Xu |
| E-mail(s) |
xupengfei2022@sjtu.edu.cn
|
| Phone |
15527845498
|
| Organization name |
Shanghai Jiao Tong University
|
| Street address |
800 Dongchuan
|
| City |
Shanghai |
| State/province |
Shanghai |
| ZIP/Postal code |
200032 |
| Country |
China |
| |
|
| Platform ID |
GPL16345 |
| Series (1) |
| GSE225098 |
Circadian regulation of genes contributed by rapid RNA turnover in tomato |
|
| Relations |
| BioSample |
SAMN33260446 |
| SRA |
SRX19338767 |
