|
| Status |
Public on Dec 22, 2024 |
| Title |
ETH04_IPO323_S18C_3 |
| Sample type |
SRA |
| |
|
| Source name |
Spores
|
| Organism |
Zymoseptoria tritici |
| Characteristics |
tissue: Spores
time: 15 hous
genotype: IPO323
treatment: GPL pH 7 18°C 15h
|
| Extracted molecule |
nuclear RNA |
| Extraction protocol |
The frozen samples were sent for RNA extraction and sequencing to Biomarker Technologies GmbH (BMKgene, Münster, Germany)
Ribosomal RNA was depleted by poly A enrichment, and DNA libraries were sequenced with Illumina NovaSeq 6000 at Novogene Europe
Libraries were prepared by Biomarker Technologies GmbH (BMKgene, Münster, Germany)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
Library name: Unknown_BW591-001U0060
|
| Data processing |
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Trimmomaticv0.35
Transcript abundances were quantified using Kallisto v0.46.1
Read counts were summarized using tximport v1.2.0
Read abundance normalization and differential gene expression analysis were performed with the R package DESeq2
Assembly: IPO323 reference strain (Goodwin et al. 2011) and annotations from Lapalu et al. 2023
Supplementary files format and content: tab-delimited txi.kallisto abundance counts for all samples
|
| |
|
| Submission date |
Dec 11, 2024 |
| Last update date |
Dec 22, 2024 |
| Contact name |
Cecile Lorrain |
| E-mail(s) |
[email protected]
|
| Organization name |
ETH Zurich
|
| Department |
Plant PAthology
|
| Lab |
Prof. Bruce McDonald
|
| Street address |
Universistätstrasse 2
|
| City |
Zurich |
| State/province |
Zurich |
| ZIP/Postal code |
8006 |
| Country |
Switzerland |
| |
|
| Platform ID |
GPL35186 |
| Series (1) |
| GSE284056 |
Responses to temperature shocks in Zymoseptoria tritici reveal specific transcriptional reprogramming and novel candidate genes for thermal adaptation |
|
| Relations |
| BioSample |
SAMN45698254 |
| SRA |
SRX27041837 |
