|
| Status |
Public on Jan 13, 2023 |
| Title |
In-vitro Z.tritici strain Zt114, replicate 3 |
| Sample type |
SRA |
| |
|
| Source name |
in-vitro fungal culture
|
| Organism |
Zymoseptoria tritici |
| Characteristics |
strain: Zt14
in-vitro growth phase: log phase growth
in-vitro medium: Culture medium: YPD broth
|
| Treatment protocol |
Sampling at log phase in vitro or at stated days post infection in-planta
|
| Growth protocol |
in-vitro broth culture or in-planta wheat infections as described above
|
| Extracted molecule |
total RNA |
| Extraction protocol |
TRIzol (Invitrogen)
Illumina 100bp paired-end reads
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
Zt114_invitro_3
|
| Data processing |
Reads mapped using HiSat2 (v2.0.5)
Mapped reads counted using Subread FeatureCounts (v1.6.2)
Assembly: pangenome assembly: Pangenome_Zt_17I_IPO323_v3.fasta ; annotation: annotation_pangenomveV3_2.gtf (bespoke for this paper, data archived and included here)
Supplementary files format and content: FeatureCount gene counts: ztriticiPangenomePlantaCounts.txt
|
| |
|
| Submission date |
Jan 04, 2023 |
| Last update date |
Jan 13, 2023 |
| Contact name |
Daniel Smith |
| E-mail(s) |
dan.smith@rothamsted.ac.uk
|
| Organization name |
Rothamsted Research
|
| Department |
IDE
|
| Street address |
West Common
|
| City |
Harpenden |
| State/province |
Hertfordshire |
| ZIP/Postal code |
AL5 2JQ |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL33003 |
| Series (1) |
| GSE222164 |
Combined pangenomics and transcriptomics reveals core and redundant virulence processes in a rapidly evolving fungal plant pathogen |
|
| Relations |
| BioSample |
SAMN32578823 |
| SRA |
SRX18930153 |
