|
| Status |
Public on Feb 08, 2017 |
| Title |
F3H_F3 |
| Sample type |
SRA |
| |
|
| Source name |
V. fordii_F. oxysporum_late stage_root
|
| Organism |
Vernicia fordii |
| Characteristics |
tissue: seedling; root
infected with: Fusarium oxysporum
pathogen infection stage: 3; late stage
|
| Treatment protocol |
Before inoculation, the plantlet was sterilized in a solution containing 75% ethanol for 1 min, and 0.5% sodium hypochlorite for 3 min, and then 90% ethanol for 30 sec, and followed by rinsing three times in sterile water. For inoculation, a spore concentration of 1×10^6 spores per mL, diluted with sterile distilled water, was used to inoculate the plants. Before inoculations, the plants were carefully removed from the soil, and the roots were rinsed with sterile water and then dipped for 30 min into the fungal inoculum. The plants were sampled at 2-15 dpi (days post inoculation). The root, peel and leaves were cut and immediately frozen in liquid nitrogen and stored at -80℃ until retrieved for RNA preparation.
|
| Growth protocol |
V. fordii and V. montana plantlets with two or three leaves and approximately 30 cm in height were used. All plantlet were kept under growth chamber conditions at 26℃ with 16-h light/8-h dark photoperiod.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from the plant roots and root-stem transition region using the EASYspin plant RNA mini kit (Aidlab, Beijing, China) QIAGEN RNeasy plant mini kit (QIAGEN, Valencia, CA). RNA integrity was confirmed using the UV-Vis Spectrophotometer Q5000 (Quawell, USA). All RNA samples displayed a 260/280 ratio greater than 2.0 and RNA integrity numbers (RIN) ≥8.0. mRNA was purified from 30 µg of total RNA using Sera-mag Magnetic Oligo(dT) Beads (Illumina) and fragmented into small pieces using divalent cations under elevated temperature.
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 |
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then assembly use Trinity
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009.
Genome_build: Trinity assembly
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ;Trinity assembly result
|
| |
|
| Submission date |
Apr 13, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Yicun Chen |
| E-mail(s) |
[email protected]
|
| Phone |
86-571-6332-7982
|
| Organization name |
Chinese Academy of Forestry
|
| Department |
Institute of Subtropical Forestry
|
| Street address |
Fuchun Street
|
| City |
Hangzhou |
| State/province |
Zhejiang |
| ZIP/Postal code |
311400 |
| Country |
China |
| |
|
| Platform ID |
GPL17722 |
| Series (1) |
| GSE80228 |
Comparative transcriptomics reveals the different gene expression pattern related to wilt disease resistance and susceptibility in biodiesel plants of Vernicia |
|
| Relations |
| BioSample |
SAMN04849303 |
| SRA |
SRX1701950 |
