|
| Status |
Public on Dec 04, 2021 |
| Title |
Fg349-MS2-WT-RNA_3 |
| Sample type |
SRA |
| |
|
| Source name |
F. graminearum CBS185.32 wild-type
|
| Organism |
Fusarium graminearum |
| Characteristics |
strain: CBS185.32
genotype/variation: wild type
|
| Growth protocol |
Fusarium graminearum CBS185.32 was grown for three days in modified liquid MS (glucose was substituted with sucrose).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Mycelia were harvested by filtering, rinsed twice with sterile deionized water, and flash frozen in liquid nitrogen. One milliliter of TRIzolTM Reagent (Thermo Fischer Scientific) was added to 200 mg of mycelium before grinding for 1.5 min at 30 Hz using a TissueLyzer (Qiagen). Total RNA was then extracted using a previously published protocol (Hallen et al., 2007).
The NEBNext Ultra Directional RNA Library Prep Kit for Illumina (cat. # E7420L New England BioLabs) was used to prepare all RNA-seq libraries, following the manufacturer’s instructions. Sequencing was performed by the GenomEast platform, a member of the ‘France Génomique’ consortium (ANR-10-INBS-0009). Samples were run in 9-plex on an Illumina HiSeq 4000 in paired mode, 2x50 bp.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
NDPS27
|
| Data processing |
Sequenced reads were mapped to Fusarium graminearum CBS185.32 genome (FungiDB v44) using STAR-2.5.1b with parameters --alignIntronMax 10000 --alignMatesGapMax 10000 --quantMode GeneCounts
Genome_build: Fusarium graminearum CBS185.32 genome (FungiDB v44)
Supplementary_files_format_and_content: The matrix table (tab-delimited text file) with raw values for all features.
|
| |
|
| Submission date |
Dec 08, 2020 |
| Last update date |
Dec 04, 2021 |
| Contact name |
Adeline SIMON |
| Organization name |
INRAE
|
| Lab |
BIOGER
|
| Street address |
22 place de l'agronomie
|
| City |
Palaiseau |
| ZIP/Postal code |
91120 |
| Country |
France |
| |
|
| Platform ID |
GPL24502 |
| Series (1) |
| GSE162839 |
Gene expression profile in MS medium for the phytopathogenic fungus Fusarium graminearum |
|
| Relations |
| BioSample |
SAMN17025173 |
| SRA |
SRX9648525 |
