|
| Status |
Public on Sep 13, 2018 |
| Title |
MpChi_180min_B |
| Sample type |
SRA |
| |
|
| Source name |
cell suspension
|
| Organism |
Nicotiana tabacum |
| Characteristics |
genotype: BY-2
treatment: MpChi
time: 180min
|
| Treatment protocol |
Cell suspensions (3 – 5 days-old) were transferred to 12-well plates (2.5 mL/well) and kept at room temperature with gentle rocking for at least 2 h. Cells were treated with 10 nM NAG6, 100 nM MpChi, 10 nM NAG6 + 100 nM MpChi or H2O (Mock treatment). Mixtures of elicitors and proteins were kept at room temperature for at least 10 minutes before addition to plant cells. Samples were harvested immediately before the start of the experiment (Time 0, untreated cells) and at four time points after the treatment (15 min, 60 min, 120 min and 180 min). The experiment was performed in triplicate.
|
| Growth protocol |
Nicotiana tabacum BY-2 cells were maintained in liquid Murashige and Skoog medium (supplemented with 30 g/L sucrose, 1 mg/L 2,4-Dichlorophenoxyacetic acid, 0.1 mg/L kinetin and 1X Gamborg’s vitamins) in the dark at 27oC and 100 rpm. Cells were subcultured weekly.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from Nicotiana tabacum cells using the Trizol reagent protocol
poly(A) RNA was isolated from 1000 ng total RNA and used to prepare non-stranded Illumina RNA-seq libraries. Following library preparation, quality control and quantification were performed using a 2100 Bioanalyzer instrument (Agilent) and the Quant-iT PicoGreen dsDNA Reagent (Invitrogen), respectively.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
MPCHI047
|
| Data processing |
Illumina Casava version 1.8 was used for basecalling
Quality assessment of the sequencing reads was performed using the FastQC version 0.11.5
Trimmomatic version 0.36 was used to identify and discard reads containing Illumina adapter sequences
Quality-filtered reads were mapped to 69,500 cDNA sequences of the Nicotiana tabacum K326 v4.5 reference using HiSat2 version 2.0.5
featureCounts version 1.5.2 was used to count reads that mapped to each one of the 69,500 sequences
Genome_build: K326 v4.5
Supplementary_files_format_and_content: tab-delimited text file including read counts per gene for each sample
|
| |
|
| Submission date |
Mar 18, 2018 |
| Last update date |
Sep 13, 2018 |
| Contact name |
Paulo Teixeira |
| E-mail(s) |
paulojt@usp.br
|
| Phone |
+551934294344
|
| Organization name |
University of São Paulo (ESALQ/USP)
|
| Department |
Biology
|
| Street address |
Av. Pádua Dias, 11
|
| City |
Piracicaba |
| State/province |
SP |
| ZIP/Postal code |
13418-900 |
| Country |
Brazil |
| |
|
| Platform ID |
GPL22345 |
| Series (1) |
| GSE111980 |
RNA-seq of Nicotiana tabacum BY-2 cells treated with the chitin oligomer NAG6 and with the Moniliophthora perniciosa effector MpChi |
|
| Relations |
| BioSample |
SAMN08729527 |
| SRA |
SRX3808589 |
