|
| Status |
Public on Jan 15, 2021 |
| Title |
Trametes versicolor BRFM1218 4w-3 |
| Sample type |
SRA |
| |
|
| Source name |
Trametes versicolor BRFM1218 4w
|
| Organism |
Trametes versicolor |
| Characteristics |
strain: BRFM1218
age of culture: 4 weeks
|
| Growth protocol |
Mycelium of Trametes versicolor BRFM1218 and Trametes versicolor 1956-1252 (NIBIO collection) were grown on 4% malt agar medium and harvested after 2 and 4 weeks of incubation.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted and purified from triplicate cultures using the RNeasy Plant Mini Kit
cDNA libraries were prepared for sequencing using standard Illumina protocols by Beckman Coulter Genomics
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
This sample is from 4 weeks old Trametes versicolor BRFM1218 mycelium. It is the third of three biological replicates used in this experiment.
|
| Data processing |
Illumina software was used by Beckman Coulter Genomics to generate fastq raw data files
Reads were aligned to Trametes versicolor (https://mycocosm.jgi.doe.gov/Trave1/Trave1.home.html) reference transcripts using CLC Genomics Workbench 7.5.1 and Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated.
Genome_build: Trametes versicolor (https://mycocosm.jgi.doe.gov/Trave1/Trave1.home.html)
Supplementary_files_format_and_content: tab-delimited text files include unique aligned reads, total aligned reads and RPKM values for each sample
|
| |
|
| Submission date |
Jul 09, 2020 |
| Last update date |
Jan 16, 2021 |
| Contact name |
Annegret Kohler |
| E-mail(s) |
annegret.kohler@inrae.fr
|
| Phone |
+33 (0)383 394072
|
| Organization name |
INRAE
|
| Department |
UMR 1136
|
| Lab |
Interactions Arbres/Micro-organismes
|
| Street address |
Centre INRAE Grand Est Nancy
|
| City |
Champenoux |
| ZIP/Postal code |
54280 |
| Country |
France |
| |
|
| Platform ID |
GPL21933 |
| Series (1) |
| GSE154077 |
Gene expression analysis of two strains of Trametes versicolor |
|
| Relations |
| BioSample |
SAMN15491710 |
| SRA |
SRX8698142 |
