|
| Status |
Public on Aug 14, 2015 |
| Title |
Ph_Ch rep1 |
| Sample type |
SRA |
| |
|
| Source name |
leaves
|
| Organism |
Cucumis sativus |
| Characteristics |
cultivar: Changchunmici
tissue: leaves
inoculant: Sphaerotheca fuliginea
|
| Treatment protocol |
Physcion, chrysophanol alone and in combination treatment were applied to the cucumber plants before inoculation at concentrations of 10 mg/L and the surfactant Tween 20 was added in the final dilutions at a concentration of 0.25 g/L, respectively, and solvent-treated (contained 0.5% DMSO and 0.25% Tween 20) plants were used as controls. Inoculated plants were sprayed with a fine mist of S. fuliginea spore suspension eight hours after treatment. After inoculation, plants were incubated at 25◦C and 70% relative humidity until sampling. The fourth leaves of cucumber plants were collected immediately 3 days post-inoculation (dpi) until Solvent-treated plants disease. Each treatment had two or three biological replicates.
|
| Growth protocol |
The treated seeds were placed in Petri dishes with filter paper at the bottom and two layers of gauze above. Seeds were incubated at 25◦C constant temperature for 24h. When the buds grew about 5mm long, then sown them in plastic pots containing sterilized soil (200 mm in diameter, ten plants per pot) in a growth chamber at 25◦C. When the fourth leaves were fully expanded, the plants were ready for compound treatment and conidium inoculation.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cucumber leaves were sampled, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 3 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 2000 |
| |
|
| Data processing |
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. All the downstream analyses were based on the clean data with high quality.
Index of the reference genome was built using Bowtie v2.0.6 and paired-end clean reads were aligned to the reference genome using TopHat v2.0.9.
RPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene, considering the effect of sequencing depth and gene length for the reads count at the same time (Mortazavi et al., 2008)
Genome_build: ftp://www.icugi.org/pub/genome/cucumber/Chinese_long/v2/cucumber_ChineseLong_v2_genome.fa.gz
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample
|
| |
|
| Submission date |
Aug 13, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Yanping Li |
| E-mail(s) |
[email protected]
|
| Organization name |
Novogene institue
|
| Street address |
No 38 Xueqing Road, Haidian Distric
|
| City |
Beijing |
| ZIP/Postal code |
100083 |
| Country |
China |
| |
|
| Platform ID |
GPL16310 |
| Series (1) |
| GSE72034 |
Next Generation Sequencing Facilitates Quantitative Analysis of Physcion and Chrysophanol on cucumber powdery mildew Transcriptomes |
|
| Relations |
| BioSample |
SAMN03988538 |
| SRA |
SRX1144383 |
