|
| Status |
Public on May 20, 2023 |
| Title |
Thatcher, Infected, 7 days, (Tc+LR7), rep2 |
| Sample type |
SRA |
| |
|
| Source name |
flag leaf
|
| Organism |
Triticum aestivum |
| Characteristics |
tissue: flag leaf
genotype: Thatcher
treatment: Infected 7 days
|
| Treatment protocol |
For infection, rust urediniospores were applied at the beginning of anthesis
|
| Growth protocol |
Plants were grown in Sunshine Mix #8 with a 16 hour/8 hour 22°C/17°C day/night cycle.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using the Zymo Direct-zol RNA Miniprep kit (Infected samples) or the Monarch NEB Total RNA Miniprep kit (Mock samples)
cDNA libraries for infected samples were prepared using the TruSeq Stranded mRNA kit; cDNA libraries for mock samples were preparred using an Illumina Stranded mRNA, Ligation kit.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
ID300817B25
|
| Data processing |
Adaptor and quality trimming performed with fastp (Phred Score > 20, min read length > 50).
Quantification with Salmon in mapping-based mode
Differential gene expression analysis with DESeq2.
Assembly: IWGSC_RefSeqv2.1_HC_CDS_assembly
Supplementary files format and content: Transformed (vsd) transcript values from DESeq2 in tab-delimited format
|
| |
|
| Submission date |
May 15, 2023 |
| Last update date |
May 20, 2023 |
| Contact name |
Michele Loewen |
| Organization name |
National Research Council of Canada (NRC)
|
| Street address |
100 Sussex Drive
|
| City |
Ottawa |
| State/province |
Ontario |
| ZIP/Postal code |
K1A 0R6 |
| Country |
Canada |
| |
|
| Platform ID |
GPL18862 |
| Series (1) |
| GSE232575 |
Transcriptomic profiling of Triticum aestivum L. cv Thatcher at 0, 7 and 14 days post infection with Puccinia triticina TBDG (11-180-1) |
|
| Relations |
| BioSample |
SAMN35099556 |
| SRA |
SRX20358303 |
