|
| Status |
Public on Apr 30, 2011 |
| Title |
G. hirsutum water-inoculated |
| Sample type |
SRA |
| |
|
| Source name |
waterâinoculated cotton roots
|
| Organism |
Gossypium hirsutum |
| Characteristics |
tissue: roots
infection: water-inoculated cotton roots
|
| Treatment protocol |
Seedlings of each cotton variety with two fully expanded leaves were infected with the pathogen by root-dip inoculation into a suspension of fungal conidia for 5 min, and returned to the Hogland liquid medium for discrete post-inoculation time intervals. Control seedlings were inoculated with water.
|
| Growth protocol |
The sterilized seeds of each variety were put on pasteurized sands for germination. Seedlings were grown in a growth chamber at 25â 28°C and watered with Hogland culture liquid every 3 days for 15 days.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated from roots using a modified CTAB method with isopropanol instead of lithium chloride for RNA precipitation. The total RNAs from roots which were harvested at 12 and 24 hours after inoculation were pooled in an equal fraction ratio. Small RNA cloning was performed as described previously by Sunkar and Zhu ( 2004). Briefly, 0.5 M NaCl and 10% PEG8000 were used to precipitate and enrich RNAs with low molecular weight. After that, about 100 μg of low molecular weight RNA were processed by 15% denaturing polyacryl amide gel electrophoresis (PAGE). After gel electrophoresis, the small RNA fragments in the range of 10â32 nt were excised and eluted with 0.4 M NaCl overnight at 4°C. The RNA was dephosphorylated using alkaline phosphatase (New England Biolabs, Beijing China) and recovered by ethanol precipitation. The isolated small RNAs were then sequentially ligated to RNA/DNA chimeric oligonucleotide adapters, and were converted to DNA by RT-PCR. Finally, the DNA was sequenced by Solexa sequencing technology (BGI, Beijing China).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina Genome Analyzer |
| |
|
| Description |
genomic small RNAs
|
| Data processing |
For non-coding RNAs identification, clean reads were compared with rRNA, tRNA, snRNA, and snoRNA deposited in NCBI and Rfam database using the SOAP 2.0 program. Next, sequence tags were searched against the miRNA database, miRBase, in order to identify conserved miRNAs in cotton.
|
| |
|
| Submission date |
Mar 29, 2011 |
| Last update date |
Jun 11, 2013 |
| Contact name |
Zujun Yin |
| E-mail(s) |
[email protected]
|
| Phone |
86-0372-2562279
|
| Organization name |
Chinese Academy of Agricultural Sciences
|
| Department |
Cotton Research Institute
|
| Lab |
State Key Laboratory of Cotton Biology
|
| Street address |
38 Huanghe Dadao, Anyang 455000, Henan, China
|
| City |
Anyang |
| State/province |
Henan |
| ZIP/Postal code |
455000 |
| Country |
China |
| |
|
| Platform ID |
GPL9362 |
| Series (1) |
| GSE28236 |
Genome-wide profiling of miRNAs and other small non-coding RNAs in the Verticillium dahliae inoculated cotton roots |
|
| Relations |
| BioSample |
SAMN02198588 |
