|
| Status |
Public on Apr 01, 2023 |
| Title |
P2P2_106 |
| Sample type |
SRA |
| |
|
| Source name |
I. batatas 3rd leaves, 1 h IbPep1 treatment
|
| Organism |
Ipomoea batatas |
| Characteristics |
tissue: 3rd leave
genotype: Ipomoea batatas Lam.; cultivar Tainong 57
treatment: IbPep2
|
| Treatment protocol |
Sweet potatoe leaves were treated for 1 h with IbHypSysIV, IbPep1 or water (control)
|
| Growth protocol |
Sweet potato scions (Ipomoea batatas Lam.; cultivar Tainong 57) were grown in phytochambers under long day conditions (16 h light : 8 h dark) at 28 °C (day) and 25°C (night) in 70% relative humidity for 3 weeks
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted according to 1 using TRIzol Reagent (Invitrogen, USA). 1 Meents, A. K. et al. Volatile DMNT systemically induces jasmonate-independent direct anti-herbivore defense in leaves of sweet potato (Ipomoea batatas) plants. Scientific Reports 9, doi:10.1038/s41598-019-53946-0 (2019).
Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendationsies for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
P2P2_106
|
| Data processing |
Raw reads were trimmed by in-house scripts.
Assembly: The clean reads were mapped onto Ipomoea trifida reference genome (http://sweetpotato.uga.edu/), using HISAT2 V2.0.5 with default parameter. HTSeq V0.6.1 software was used with the union mode to count read numbers mapped of genes for each sample.
Supplementary files format and content: Data matrix with read counts for further analysis with DESeq2 V1.22.2
|
| |
|
| Submission date |
Mar 15, 2023 |
| Last update date |
Apr 01, 2023 |
| Contact name |
Axel Mithöfer |
| E-mail(s) |
amithoefer@ice.mpg.de
|
| Organization name |
Max-Planck-Institute for Chemical Ecology
|
| Department |
Plant Defense Physiology
|
| Street address |
Hans-Knöll-Straße 8
|
| City |
Jena |
| State/province |
Thuringia |
| ZIP/Postal code |
07745 |
| Country |
Germany |
| |
|
| Platform ID |
GPL30016 |
| Series (1) |
| GSE227409 |
Identification of a DAMP receptor and its cognate peptide ligand in sweet potato (Ipomoea batatas) |
|
| Relations |
| BioSample |
SAMN33770222 |
| SRA |
SRX19681801 |
