|
| Status |
Public on Sep 20, 2019 |
| Title |
Tree_13_Control_T0 |
| Sample type |
SRA |
| |
|
| Source name |
RNA-seq
|
| Organism |
Citrus sinensis |
| Characteristics |
cultivar: Valencia
infected with: Liberibacter asiaticus
tissue: leaf midrib and petiole
tree number: 13
treatment: Control
treatment time: 0
|
| Treatment protocol |
Three group of infected trees each were established: control plants, plants treated with benzbromarone and plants treated with tolfenamic acid. RNA was obtained two months before treatment (T0) and 2 weeks after treatment (T2).
|
| Growth protocol |
‘Valencia’ sweet orange trees (Citrus sinensis [L.] Osbeck), ranging in age from twenty to thirty years old. Standard grove care and maintenance was performed in each grove throughout the field trials, which included irrigation, fertilization and pest management.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Fifty leaves were collected randomly from the canopy of each tree. Following collection, the midrib and petiole of each leaf was excised and immediately submerged in RNAlater. Prior to RNA extraction, the tissue samples were freeze (-80°C), dried and homogenized. 25 mg of each powdered leaf was used. Total RNA was extracted with Isolate II RNA Plant Kit (Bioline, Taunton, MA). RNA integration number (RIN) was measured using BioAnalyzer (Agilent Technologies) RNA 6000 Nano Kit.
TruSeq Stranded total RNA with Ribo-Zero Plan Kit (Illumina)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Alignment of reads to the Clementina genome with TopHat2 (Kim et al. 2013)
Count of gene expression with HTSEQ-count (Anders et al. 2015)
Genes with less than 10 reads collectively for all samples were discarded
Gene expression values were normalized using the TMM method (Robinson and Oshlack, 2010)
Batch effects were removed witrh ARSyNseq (Tarazona et al. 2011).
Genome_build: ncbi_gca_000493195_1_citrus_clementina_v1_0
Supplementary_files_format_and_content: csv, gene expression counts
|
| |
|
| Submission date |
Sep 19, 2019 |
| Last update date |
Sep 20, 2019 |
| Contact name |
Leandro Octavio Balzano |
| E-mail(s) |
leobalzano@gmail.com
|
| Phone |
+17869754422
|
| Organization name |
University of Florida
|
| Department |
Microbiology and Cell Science
|
| Lab |
Conesa Lab
|
| Street address |
2033 Mowry Road
|
| City |
Gainesville |
| State/province |
FL |
| ZIP/Postal code |
32608 |
| Country |
USA |
| |
|
| Platform ID |
GPL21082 |
| Series (1) |
| GSE137736 |
RNA-seq analysis of citrus leaf samples of treated and untreated trees infected with Liberibacter asiaticus |
|
| Relations |
| BioSample |
SAMN12788761 |
| SRA |
SRX6874271 |
