|
| Status |
Public on Mar 15, 2023 |
| Title |
RD2_W34 |
| Sample type |
SRA |
| |
|
| Source name |
leaf midrib
|
| Organism |
Citrus jambhiri |
| Characteristics |
tissue: leaf midrib
infection: CLas infection
treatment: Week 34
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using TRIzol® Reagent and purified using an RNeasy Mini Kit following the manufacturer’s protocol
Ribosomal RNA was removed from the total RNA using a Ribo-Zero rRNA removal kit for using plant seed/plant leaf following the manufacturer’s protocol. Subsequently, 50 ng of the purified RNA from each sample were used for library construction utilizing an Epicentre ScriptSeq v2 RNA-Seq library preparation kit according to the user’s guide.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Sequence reads were trimmed for adaptor sequence/low-quality sequence using fastp software
Trimmed sequence reads were mapped to mapped to Citrus clementina genome v1.0 (JGI) using HISAT2 software
StringTie was used to assemble transcripts of each sample, merge transcripts to get a consensus transcriptome assembly, and compute the abundance of transcripts for each sample
|
| |
|
| Submission date |
Oct 12, 2022 |
| Last update date |
Mar 15, 2023 |
| Contact name |
Xiaokang Zhuo |
| E-mail(s) |
zhuoxiaokang@ufl.edu
|
| Organization name |
University of Florida
|
| Department |
Citrus Research and Education Center
|
| Street address |
700 Experiment Station Rd
|
| City |
Lake Alfred |
| State/province |
Florida |
| ZIP/Postal code |
33850 |
| Country |
USA |
| |
|
| Platform ID |
GPL29550 |
| Series (1) |
| GSE215306 |
Role of long non-coding RNA in regulatory network response to ‘Candidatus Liberibacter asiaticus’ in citrus |
|
| Relations |
| BioSample |
SAMN31275103 |
| SRA |
SRX17882726 |
