|
| Status |
Public on Dec 03, 2024 |
| Title |
Z-3-HAC_root_1h_2 |
| Sample type |
SRA |
| |
|
| Source name |
Roots, whole
|
| Organism |
Oryza sativa |
| Characteristics |
tissue: Roots, whole
Stage: 3 weeks after germination
cultivar: Kitaake
treatment: Z-3-HAC
time: 1h
|
| Treatment protocol |
As described in https://doi.org/10.1104/pp.15.00107
|
| Growth protocol |
As described in https://doi.org/10.1111/nph.18152
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Flash freezing + grinding in liquid nitrogen-cooled pestle and mortar + Qiagen RNEasy Plant Mini kit
Lexogen QuantSeq 3’ mRNA-Seq Library Prep Kit FWD
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
B2
|
| Data processing |
Trimming and adapter removal (Trimmomatic v 0.39; settings: 5 bp sliding window, trim if Phred < 20, discard if < 40 bp after trimming)
Alignment to rice genome (Rsubread v 2.6.4)
Read counting (Rsubread v 2.6.4)
Differential expression analysis (DESeq2 v 1.74.1)
Assembly: Os-Nipponbare-Reference-IRGSP-1.0
Supplementary files format and content: Count table, untransformed (in .csv format)
|
| |
|
| Submission date |
Dec 03, 2022 |
| Last update date |
Dec 03, 2024 |
| Contact name |
Willem Desmedt |
| E-mail(s) |
[email protected]
|
| Organization name |
Ghent University
|
| Department |
Plants and Crops
|
| Lab |
Applied Mycology and Phenomics
|
| Street address |
Valentin Vaerwyckweg 1
|
| City |
Ghent |
| ZIP/Postal code |
9000 |
| Country |
Belgium |
| |
|
| Platform ID |
GPL21087 |
| Series (1) |
| GSE220047 |
Transcriptome analysis of rice seedlings treated with Z-3-hexenyl acetate |
|
| Relations |
| BioSample |
SAMN32025916 |
| SRA |
SRX18480578 |
