|
| Status |
Public on Apr 01, 2024 |
| Title |
Evereste_mock 6hpi_R2 |
| Sample type |
SRA |
| |
|
| Source name |
leaf
|
| Organism |
Malus domestica |
| Characteristics |
tissue: leaf
genotype: Evereste
treatment: water 0.01% Silwet
|
| Treatment protocol |
Inoculation was performed by vaccum infiltration as described in Dugé de Bernonville et al., 2012. Briefly the top young leaves of each shoot were infiltrated by dipping the shoot itself into the bacterial suspension or mock. Plants were then cultivated under the growth conditions
|
| Growth protocol |
Plants were grated on MM106 roostock and grown in individual potss under greenhouse conditions (natural photoperiod supplemented with artificial light if needed, 17°C night and 20–23°C day)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was harvested using NucleoSpin RNA Plant (Macherey Nagel)
Libraries were generated using the Illumina mRNA Stranded protocol
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
The sequenced reads (ranging from 21.5 to 60 million read pairs per sample) were mapped on the reference transcriptional units from GDDH13 v1.1 using Salmon software (Patro et al., 2017)
Identification of differentially expressed genes (DEGs) was performed with EdgeR, including a Benjamini–Hochberg procedure to control the false discovery rate (FDR) (Love et al., 2014)
Assembly: MJAX00000000.1
Supplementary files format and content: tab-delimited file include raw counts values for each sample, logCPM and log2ratios for each comparison
|
| |
|
| Submission date |
Mar 26, 2024 |
| Last update date |
Apr 23, 2024 |
| Contact name |
Matthieu Gaucher |
| E-mail(s) |
[email protected]
|
| Organization name |
INRAE
|
| Department |
SPE
|
| Lab |
IRHS
|
| Street address |
42 rue Georges Morel
|
| City |
Beaucouzé |
| ZIP/Postal code |
49071 |
| Country |
France |
| |
|
| Platform ID |
GPL29987 |
| Series (1) |
| GSE262535 |
Modulation of apple leaf trancriptome by Erwinia amylovora infection in Evereste (resistant) and MM106 (susceptible) genotypes |
|
| Relations |
| BioSample |
SAMN40622400 |
| SRA |
SRX24068232 |
