|
| Status |
Public on Dec 31, 2020 |
| Title |
rl-fr_rep2 |
| Sample type |
SRA |
| |
|
| Source name |
cucumber 649
|
| Organism |
Cucumis sativus |
| Characteristics |
tissue: Female bud
geographic location: China:Harbin
cultivar: Southern China type
genotype: round leaf (rl)
|
| Treatment protocol |
No treatment
|
| Growth protocol |
All plants were grown in the greenhouse of Xiangyang farm of Northeast Agricultural University, Harbin, China. Pest and water management was carried out according to standard practices.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
The total RNA was extracted using the Trizol reagent (Invitrogen, USA) according to the manufacturer’s instructions. Dried RNA samples were dissolved in diethylpyrocarbonate treated H2O, then used for cDNA synthesis by using RevertAidTM First Strand cDNA Synthesis Kit (MBI Fermentas, Canada).
RNA libraries were prepared for sequencing using Illumina HiSeq 2000
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Illumina Casava1.7 software used for basecalling.
Raw reads were first subject to 3’ adapter removal and quality filtering (Q > 17 and length >= 25 bp). Clean reads were mapped to the cucumber genome sequence using Hisat. Read counts of each gene were summarized by the HTSeq-count. Lowly expressed genes were removed
Genome_build: v2i
Supplementary_files_format_and_content: Tab-delimited text file include RPM (Reads per Million) values
|
| |
|
| Submission date |
Jan 08, 2018 |
| Last update date |
Dec 31, 2020 |
| Contact name |
Renyi Liu |
| E-mail(s) |
[email protected]
|
| Phone |
02157078228
|
| Organization name |
Shanghai Center for Plant Stress Biology
|
| Department |
Bioinformatics
|
| Street address |
3888 Chenhua Road
|
| City |
Shanghai |
| State/province |
Shanghai |
| ZIP/Postal code |
201602 |
| Country |
China |
| |
|
| Platform ID |
GPL16310 |
| Series (1) |
| GSE108865 |
CsPID is required for lateral organ organogenesis and development in cucumber |
|
| Relations |
| BioSample |
SAMN08326587 |
| SRA |
SRX3540825 |
