|
| Status |
Public on Jan 01, 2015 |
| Title |
Uncover small RNAs in citrus somatic embryogenesis |
| Organism |
Citrus sinensis |
| Experiment type |
Non-coding RNA profiling by high throughput sequencing
Other
|
| Summary |
To uncover the involvement of miRNAs and siRNAs in somatic embryogenesis of the perennial woody crop citrus, we carried out high-throughput (Illumina) sequencing (HTS) of sRNAs and RNA degradome tags in non-embryogenic and embryogenic tissue of Valencia sweet orange. A total of 191 stem-loop structures were identified, emanating 50 known and 45 novel miRNAs, 130 miniature inverted-repeat transposable elements (MITEs) derived small interfering RNAs (siRNAs) and 94 other siRNAs. Combining with the result of degradome sequencing, a total of 235 phased siRNAs (phasiRNAs), and 195 cleaved target genes were identified for miRNAs/siRNAs.
|
| |
|
| Overall design |
Small RNA and degradome libraries of nonembryogenic callus (NEC), embryogenic callus (EC) and embryogenic callus exposed to somatic embryo induction for 1, 2, 3, 4 weeks (E1-4) of Valencia sweet orange (Citrus sinensis) were sequenced by Illumina platform, one biological replicates
|
| |
|
| Contributor(s) |
Wu X, Guo W |
| Citation(s) |
25615015 |
| Submission date |
Dec 06, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Xiaomeng Wu |
| E-mail(s) |
xm_wu@outlook.com
|
| Phone |
3107454227
|
| Organization name |
HuaZhong Agricultural University
|
| Department |
College of Horticulture & Forestry Sciences
|
| Lab |
Horticultural Plant Biology
|
| Street address |
Shizishan No.1
|
| City |
Wuhan |
| State/province |
Hubei |
| ZIP/Postal code |
430070 |
| Country |
China |
| |
|
| Platforms (1) |
| GPL17145 |
Illumina HiSeq 2000 (Citrus sinensis) |
|
| Samples (6)
|
|
| Relations |
| BioProject |
PRJNA230788 |
| SRA |
SRP033558 |
Less...
More...