|
| Status |
Public on Aug 31, 2022 |
| Title |
6WB24_A |
| Sample type |
SRA |
| |
|
| Source name |
Aspergillus niger N593 delta-kusA
|
| Organism |
Aspergillus niger |
| Characteristics |
genotype: galE/ladB
medium: 1xMM +1% wheat bran
time point: 24 hr
|
| Treatment protocol |
The pre-cultures containing 250 ml CM with 2% D-fructose in 1 L Erlenmeyer flasks were inoculated with 106 spores/ml and incubated for 16 h. Subsequently, the mycelia were harvested by filtration on sterile cheesecloth, washed with MM and ~0.5 g (dry weight) was transferred to 250 ml Erlenmeyer flasks containing 50 ml MM supplemented with 1% WB or 1% SBP. All cultures were performed in triplicate. After 2, 8 and 24 h of incubation, the mycelia were harvested by vacuum filtration, dried between tissue paper and frozen in liquid nitrogen.
|
| Growth protocol |
The strains were grown at 30°C using Minimal Medium (MM, pH 6) or Complete Medium (CM, pH 6) with the appropriate carbon source. When required, media of auxotrophic strains were supplemented with 1.22 g/L uridine. All liquid cultures were incubated in an orbital shaker at 250 rpm and 30°C.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Total RNA was extracted from ground mycelial samples using TRIzol® reagent (Invitrogen) and purified with the NucleoSpin® RNA Clean-up Kit (Macherey-Nagel), while contaminant gDNA was removed by rDNase treatment directly on the silica membrane. The RNA quality and quantity were analysed with a RNA6000 Nano Assay using the Agilent 2100 Bioanalyzer (Agilent Technologies).
For RNA‐Seq, The TruSeq stranded mRNA (cat#20020594) was used to generate cDNA library for illumina NextSeq550 platform according to the manufacturer protocol. Single-read sequencing of the cDNA libraries with a read length of 150 was performed with NextSeq 550 Sequencing System using NextSeq 500/550 High Output v2 kit 150 cycles (cat#20024907).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
NextSeq 550 |
| |
|
| Data processing |
Data quality was assessed with fastqc (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
Read-trimming was conducted using bbduk (http://jgi.doe.gov/data-and-tools/bb-tools/).
Reads were aligned to the A. niger NRRL 3 genome (Aguilar‐Pontes et al., 2018) using STAR (https://github.com/alexdobin/STAR).
BAM file outputs were mapped to genes using htseq‐count (Anders et al., 2015) using default settings.
Genome_build: Aspergillus niger NRRL 3 genome (Aguilar‐Pontes et al., 2018)
Supplementary_files_format_and_content: .txt files represent number of raw read counts mapping to each gene
|
| |
|
| Submission date |
Feb 08, 2022 |
| Last update date |
Aug 31, 2022 |
| Contact name |
Ronald de vries |
| E-mail(s) |
fungalphysiology@gmail.com
|
| Phone |
+31(0)30-2122600
|
| Organization name |
westerdijkinstitute
|
| Street address |
Uppsalalaan 8
|
| City |
Utrecht |
| State/province |
Utrecht |
| ZIP/Postal code |
3584 CT |
| Country |
Netherlands |
| |
|
| Platform ID |
GPL31925 |
| Series (1) |
| GSE196397 |
Metabolic engineering reveals the relative importance of different sugar catabolic pathways during growth of Aspergillus niger on plant biomass |
|
| Relations |
| BioSample |
SAMN25761412 |
| SRA |
SRX14109292 |
