|
| Status |
Public on May 11, 2022 |
| Title |
Leaves infiltrated with X. citri 24 hpi, replicate3 |
| Sample type |
SRA |
| |
|
| Source name |
leaves
|
| Organism |
Citrus sinensis |
| Characteristics |
tissue: leaves
cultivar: Natal
infection: XC infection 24 hpi
|
| Treatment protocol |
Plant leaves of similar size and age were infiltrated with water suspensions of Xc or Xa (OD600nm = 0.1), or water as control
|
| Growth protocol |
Citrus plants were grown under green-house conditions
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Infiltrated leaf sectors collected at 24 and 48 h post inoculation were frozen in liquid nitrogen and total RNA was extracted from three independent leaves using Trizol reagent.
The RNA samples were treated with DNase I to remove traces of DNA and subjected to HISEQ2500 Illumina sequencing at the LaCTAD facility of the State University of Campinas, Brazil
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
Sample_XC_24_3
H2O_x_XC24.txt
|
| Data processing |
The expression value of each transcript (FPKM) was calculated using RSEM according to Mortazavi et al. (2008)
Assembly: Reads of each sample (28.000.000 on average) were aligned with the Citrus sinensis transcripts of the Phytozome database using the RSEM program (Li and Dewey, 2011)
Supplementary files format and content: RPKMs
|
| |
|
| Submission date |
May 08, 2022 |
| Last update date |
May 11, 2022 |
| Contact name |
Celso Eduardo Benedetti |
| E-mail(s) |
celso.benedetti@lnbio.cnpem.br
|
| Phone |
55-19-35121111
|
| Organization name |
Laboratorio Nacional de Biociencias
|
| Street address |
R. Giuseppe Maximo Scolfaro 10000
|
| City |
Campinas |
| State/province |
SP |
| ZIP/Postal code |
13083-970 |
| Country |
Brazil |
| |
|
| Platform ID |
GPL21082 |
| Series (1) |
| GSE202469 |
Transcriptional profiling of sweet orange leaves infected with Xanthomonas citri and Xanthomonas aurantifolii pathotype C |
|
| Relations |
| BioSample |
SAMN28156088 |
| SRA |
SRX15206559 |
