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| Status |
Public on Jan 31, 2017 |
| Title |
D8_control_0h_rep 3 |
| Sample type |
SRA |
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| Source name |
D8_control_0h
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| Organism |
Cucumis sativus |
| Characteristics |
line: D8
treatment: control
time: 0 h
tissue: leaves
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| Treatment protocol |
Powdery mildew conidia were collected from naturally-infected cucumber plants in the greenhouse. A spore suspension at 10e6 spores per ml was made by soaking heavily infected leaves in tap water (containing 0.01% Tween-20 as surfactant). Inoculation was performed at the 3rd true-leaf stage by spraying the spore suspension evenly on the surface of the seedlings. After inoculation, the plants were maintained in a controlled growth chamber at 25 °C day/20 °C night with a 16-/8-h (light/dark) photoperiod.
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| Growth protocol |
Normal growth
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using RNAiso Plus Total RNA extraction reagent (Cat#9109, TAKARA)和RNeasy Mini Kit(Cat#74106，Qiagen）following the manufacturer’s instructions and checked for a RIN number to inspect RNA integrity by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).Qualified total RNA was further purified by RNeasy micro kit (Cat#74004, QIAGEN, GmBH, Germany) and RNase-Free DNase Set (Cat#79254, QIAGEN, GmBH, Germany).
RNA libraries were prepared for sequencing using standard Illumina protocols
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
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| Data processing |
An index of the reference genome was built using Bowtie v0.12.8
single-end clean reads were aligned to the reference genome using TopHat v2.0.9
Cufflinks v2.1.1 was used to count the read numbers mapped to each gene
To identify most differentially expressed genes, we ranked genes according to their size and sequencing coverage normalized FPKM (fragments per kilo base of exon per million). The log2 fold changes of gene FPKM between two genotypes were tested statistically to determine whether an individual gene expression was altered significantly or not.
Genome_build: cucumber 9930 V2 database (http://www.icugi.org/cgi-bin/ICuGI/index.cgi)
Supplementary_files_format_and_content: tab-delimited text file includes FPKM values for each Sample
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| Submission date |
May 09, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Xuewen Xu |
| E-mail(s) |
596620842@qq.com
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| Organization name |
Yangzhou University
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| Street address |
48 wenhui east road
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| City |
Yangzhou |
| State/province |
Jiangsu |
| ZIP/Postal code |
225009 |
| Country |
China |
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| Platform ID |
GPL20825 |
| Series (1) |
| GSE81234 |
Identification of candidate regulators of powdery mildew resistance in cucumber using comparative RNA-sequencing based transcriptome analysis |
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| Relations |
| BioSample |
SAMN04962348 |
| SRA |
SRX1750610 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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