|
| Status |
Public on May 01, 2024 |
| Title |
LM1Tr, fungal biomass, low-melanin necromass, rep1 |
| Sample type |
SRA |
| |
|
| Source name |
RUT-C30
|
| Organism |
Trichoderma reesei |
| Characteristics |
strain: RUT-C30
time: 7 days
treatment: Low-melanin necromass
|
| Treatment protocol |
Three treatments were used: 1. Highley’s medium supplemented with 1% (w/v) glucose, 2. Highley’s medium with 0.45% (w/v) low-melanin necromass, 3. Highley’s medium with 0.45% high-melanin necromass
|
| Growth protocol |
Trichoderma reesei was routinely maintained on malt extract agar plates.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted using TRIzol and PureLink RNA mini kit
NEBNext Ultra II RNA Library Prep kit
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Data processing |
Raw data were processed with Collection of Hierarchical UMII-RIS Pipelines (CHURP; v0.2.2; Baller et al., 2019).
Kallisto v0.48.0 (Bray et al., 2016) was used to build the index and quantify transcripts
DESeq2 v1.42.0 (Love et al., 2014) was used to perfom differential gene expression analysis
Assembly: Trichoderma_reesei_rut_c_30_gca_000513815.TrireRUTC30_1.cdna.all.fa.gz
Supplementary files format and content: csv files containing raw counts for each sample
|
| |
|
| Submission date |
Apr 09, 2024 |
| Last update date |
May 01, 2024 |
| Contact name |
Jonathan Schilling |
| E-mail(s) |
schillin@umn.edu
|
| Organization name |
University of Minnesota
|
| Department |
Plant and Microbial Biology
|
| Lab |
Schilling lab
|
| Street address |
1445 Gortner Avenue
|
| City |
Saint Paul |
| State/province |
Minnesota |
| ZIP/Postal code |
55108 |
| Country |
USA |
| |
|
| Platform ID |
GPL34370 |
| Series (1) |
| GSE263516 |
Melanization of fungal necromass drives the upregulation of multiple chitinase, protease, and laccase genes when being degraded by Trichoderma reesei |
|
| Relations |
| BioSample |
SAMN40891600 |
| SRA |
SRX24195045 |
