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| Status |
Public on Feb 28, 2024 |
| Title |
qT1_5DPI_A |
| Sample type |
SRA |
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| Source name |
leaf
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| Organism |
Malus domestica |
| Characteristics |
tissue: leaf
genotype: Pool of F064, F117, F207 and F244 genotypes
treatment: Venturia inaequalis strain EU-B04
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| Treatment protocol |
Plants received water treatment two days before scab inoculation, and sampling for RNAseq analysis occurred on non inoculated plants at day of inoculation with the EU-B04 strain of Venturia inaequalis (0DPI) and on inoculated plant 5 days post inoculation (5DPI). For the scab inoculation, monoconidial suspensions were prepared from diseased dry leaves at a concentration of 2.5 × 10exp5 conidia.ml−1 and sprayed on grafted trees, incubated thereafter 2 days at 17°C under a plastic sheet to maintain a high humidity, according to the conditions described by Caffier et al. (2010).
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| 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)
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| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was harvested using NucleoSpin RNA Plant (Macherey Nagel)
Libraries were generated using the Illumina mRNA Stranded protocol
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
raw_counts.sf
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| Data processing |
The sequenced reads (ranging from 29.3 to 41 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: GDDH13v1.1
Supplementary files format and content: tab-delimited file include raw counts values for each sample, logCPM and log2ratios of the 16 comparisons
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| Submission date |
Dec 15, 2023 |
| Last update date |
Feb 28, 2024 |
| Contact name |
Laure Perchepied |
| E-mail(s) |
[email protected]
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| Organization name |
INRAE
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| Lab |
IRHS
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| Street address |
42 rue Georges Morel
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| City |
Beaucouzé |
| ZIP/Postal code |
49071 |
| Country |
France |
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| Platform ID |
GPL29987 |
| Series (1) |
| GSE250309 |
Modulation of apple leaf transcriptome by QTLs and infection by Venturia inaequalis |
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| Relations |
| BioSample |
SAMN38858689 |
| SRA |
SRX22904690 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM7977356_qT1_5DPI_A.sf.gz |
703.3 Kb |
(ftp)(http) |
SF |
SRA Run Selector |
| Raw data are available in SRA |
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