|
| Status |
Public on Feb 09, 2024 |
| Title |
CME_R1 |
| Sample type |
SRA |
| |
|
| Source name |
leaf
|
| Organism |
Malus domestica |
| Characteristics |
tissue: leaf
genotype: Golden delicious
treatment: formulated cutin monomer extract
|
| Treatment protocol |
CME and FB were sprayed to runoff on entire plants with a spray gun. Plants received two treatments four days apart, and sampling for RNAseq analysis occurred 3 days after the second treatment
|
| Growth protocol |
Plants were grown in individual pots (8 x 5.5 x 7 cm) 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 23 to 44.6 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 DESeq2, including a Benjamini–Hochberg procedure to control the false discovery rate (FDR) (Love et al., 2014)
Assembly: GDDH13 v1.1
Supplementary files format and content: tab-delimited file include raw counts values for each sample, logCPM and log2ratios of the CME/FB comparison
|
| |
|
| Submission date |
Oct 17, 2023 |
| Last update date |
Feb 09, 2024 |
| Contact name |
Matthieu Gaucher |
| E-mail(s) |
matthieu.gaucher@inrae.fr
|
| 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) |
| GSE245564 |
Modulation of apple leaf trancriptome by tomato cutin monomer extract |
|
| Relations |
| BioSample |
SAMN37858286 |
| SRA |
SRX22116600 |
