|
| Status |
Public on Sep 20, 2024 |
| Title |
Trametes versicolor colonised wood block single species control replicate 2 |
| Sample type |
SRA |
| |
|
| Source name |
Trametes versicolor TvFPH
|
| Organism |
Trametes versicolor |
| Characteristics |
tissue: Beechwood block
treatment: Control
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted using MoBIO Laboratories Inc Powersoil Total RNA Isolation Kit. 0.1 ng mRNA per sample was purified polyA separation using Dynabead kit (Ambion)
RNA libraries for RNA-seq were prepared using the SMARTer mRNA-Seq library prep kit following manufacturer's instructions
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
The raw fastq files were trimmed to remove Illumina adapter sequences using Cutadapt version 1.2.1 (Martin, 2011). The option “-O 3” was set, so the 3' end of any reads which matched the adapter sequence over at least 3 bp was trimmed off. The reads were further trimmed to remove low quality bases, using Sickle version 1.200 with a minimum window quality score of 20
R1/R2 read pairs were mapped to the reference sequences (T. versicolorv1 and H. sublateritium reference genomes available through the JGI mycocosm portal) using HISAT2 version 2.0.3beta
Differential transcripts between samples were calculated from reads alignment files using HTSeq count. All the differential gene expression analyses were performed in R environment using edgeR
Supplementary files format and content: Tab-delimited text file includes raw counts for each sample
|
| |
|
| Submission date |
Oct 11, 2023 |
| Last update date |
Sep 20, 2024 |
| Contact name |
Daniel Eastwood |
| E-mail(s) |
d.c.eastwood@swansea.ac.uk
|
| Organization name |
Swansea University
|
| Department |
Biosciences
|
| Street address |
Wallace Building Science, Swansea University, Singleton Park Campus
|
| City |
SWANSEA |
| State/province |
West Glamorgan |
| ZIP/Postal code |
SA2 8PP |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL24401 |
| Series (1) |
| GSE245088 |
Transcriptomic and proteomic analysis of Trametes versicolor interacting with a Hypholoma fasciculare mycelium foraging in soil |
|
| Relations |
| BioSample |
SAMN37778997 |
| SRA |
SRX22067206 |
