|
| Status |
Public on Jan 24, 2019 |
| Title |
Center of S. sclerotiorum 1980 colony grown on Arabidopsis thaliana rep3 |
| Sample type |
SRA |
| |
|
| Source name |
15 to 30mm wide colony (about 2 days old)
|
| Organism |
Sclerotinia sclerotiorum |
| Characteristics |
strain: 1980
treatment: center
culture medium: Arabidopsis thaliana
|
| Treatment protocol |
S. sclerotiorum strain 1980 was subcultured on Potato Dextrose Agar plates at 22°C. For inoculations, a 5-mm wide agar plug containing actively growing S. sclerotiorum mycelium was placed at the center of a Petri dish or on the adaxial surface of leaves and plants. The border (ring of ~5mm wide) and center of colonies were collected with a scalpel and frozen in liquid nitrogen.
|
| Growth protocol |
Samples1-6: S. sclerotiorum was grown in liquid potato dextrose medium (P6685 - Sigma) for 4 days at 24°C under shaking at 180 rpm. Cultures were filtered using vacuum and a fritted glass column protected with a doubled miracloth membrane and ground in liquid nitrogen.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
The edge and center of developed mycelial colonies (15 to 30 mm diameter) was harvested and stored in liquid nitrogen. Samples were ground with metal beads (2.5 mm) in a Retschmill apparatus (24hertz for 2x1min) before solubilizing in 1mL Trizol reagent (ThermoFisher) and left for 5 min at RT. Chloroform (200 µL) was added and mixed thoroughly before incubating for 3 min at RT. After centrifugation at ~12,000g (4°C) for 15min, the upper aqueous phase was recovered and nucleic acids were precipitated by adding 2µL GlycoBlue (Ambion) and 500µL isopropanol (10 min at -20°C). After centrifugation at ~15,000g (4°C) for 15min, pellets were washed twice with 70% ethanol before drying and resuspended in RNAse-free water. To eliminate chloroform traces, water resuspended nucleic acids were further cleaned using an RNA extraction kit (Quiagen) following manufacturer’s instructions. Genomic DNA was removed by DNase treatment (TURBO DNase; Ambion) following manufacturer’s instructions. The quality and concentrations of RNAs preparations were assessed with an Agilent apparatus and chips (nano).
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
Sample 15
HDX33
|
| Data processing |
HiSeq control software 2.2.38 or 2.2.58, RTA 1.18.61.0 or RTA 1.18.64.0, Illumina Casava1.8.2 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to whole genomes using the RNA-seq analysis function of the CLC genomics software with default settings.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using the RNA-seq analysis function of the CLC genomics software with default settings.
Genome_build: S. sclerotiorum version 2.0: https://www.ncbi.nlm.nih.gov/genome/487?genome_assembly_id=290987
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample
|
| |
|
| Submission date |
Jun 24, 2018 |
| Last update date |
Oct 21, 2020 |
| Contact name |
Sylvain Raffaele |
| E-mail(s) |
[email protected]
|
| Organization name |
INRAE
|
| Lab |
LIPME
|
| Street address |
28 chemin de borde rouge
|
| City |
Castanet tolosan |
| ZIP/Postal code |
31320 |
| Country |
France |
| |
|
| Platform ID |
GPL20037 |
| Series (1) |
| GSE116194 |
Global transcriptome of Sclerotinia sclerotiorum during in vitro growth and Arabidopsis thaliana infection |
|
| Relations |
| Reanalyzed by |
GSM4845035 |
| BioSample |
SAMN09476755 |
| SRA |
SRX4289125 |
