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Sample GSM4962701 Query DataSets for GSM4962701
Status Public on Dec 04, 2021
Title Fg349-MS2-WT-RNA_1
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 NDPS25
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 SAMN17025175
SRA SRX9648523

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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