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| Status |
Public on Jun 26, 2020 |
| Title |
R2793 |
| Sample type |
SRA |
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| Source name |
mycelial biomass
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| Organism |
Aspergillus niger |
| Characteristics |
strain: AB4.1deltapclA
genotype: deltakexB
percentage of maximum biomass: 90percent
biological replicate: 1
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| Growth protocol |
Controlled batch cultivations for A. niger strains N402 and the ΔkexB strain were performed in 6.6L BioFlo bioreactors (New Brunswick Scientific), as previously described (Jørgensen et al., 2010). A batch of 21 L MM containing 0.75% D-glucose was made by adding 1 L filter-sterilized (0.2 µm pore) glucose (15.75% w/v) solution to a freshly autoclaved volume of 20 L MM (no carbon source) as described above. Allowing 1 day of dissolving and a check for contamination, 5 L MM 0.75% glucose was added to each bioreactor directly after autoclaving. Temperature, acidity and stir speed were set to and kept at 30°C, pH 3 and 250 rpm, respectively. The pH was controlled by addition of titrants (2M NaOH and 1M HCl). Sparger aeration of 1 L/min was left on to allow oxygen saturation of the medium prior to inoculation. Next, aeration was set to headspace only and 1.5 mL 10% w/v Yeast Extract was added to the medium to promote homogeneous germination for the to-be-added spores. Subsequently, a total of 5x109 (106 sp/mL) spores were added to the medium using a concentrated spore solution. Germination time of approximately 4-5h was maintained, preceding the addition of polypropyleneglycol P2000 anti-foam agent, increasing agitation to 750 rpm and changing aeration from headspace to sparger only (1 L/min). Oxygen, base and acid consumption were monitored and samples were taken at regular intervals to obtain biomass, culture filtrate and microscopy samples. Biomass was harvested by applying a vacuum over Whatman™ Glass Microfiber Filter (GF/C™) (diameter 47 mm, CAT No.1822-047, Buckinghamshire, UK). Samples were all quickly frozen in liquid nitrogen prior to storage at -80°C. Biomass accumulation through time was gravimetrically determined by lyophilizing designated samples from the corresponding broth culture mass.
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| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was isolated from mycelial biomass samples obtained from batch cultivated A. niger strains N402 and the ΔkexB strain, using TRIzol (Invitrogen). RNA was purified afterwards with NucleoSpin RNA Clean-up kit (Macherey-Nagel) with DNase treatment. Concentration and quality of the RNA was determined using a NanoDrop 2000 spectrophotometer (Thermo Scientific) and by gel-electrophoresis, respectively
RNA libraries were prepared for sequencing using standard Illumina protocols
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
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| Data processing |
Filtered reads were mapped to the NRRL3 transcriptome annotation version 20140311 using Salmon v.0.14.1
Differential gene expression was assessed via pairwise comparisons using DESeq2 v1.24.0 using the design ~ mutation
Supplementary_files_format_and_content: tab-delimited text files include read values for each gene in each Sample
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| Submission date |
Jun 02, 2020 |
| Last update date |
Jun 27, 2020 |
| Contact name |
Tim Marijn van Leeuwe |
| Organization name |
Leiden University
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| Street address |
Sylviusweg 72
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| City |
Leiden |
| ZIP/Postal code |
2333BE |
| Country |
Netherlands |
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| Platform ID |
GPL25519 |
| Series (1) |
| GSE151618 |
Deletion of the Aspergillus niger pro-protein processing protease gene kexB results in a pH-dependent morphological transition during submerged cultivations and increases cell wall chitin content |
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| Relations |
| BioSample |
SAMN15081182 |
| SRA |
SRX8453249 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4586710_R2793.tsv.gz |
214.4 Kb |
(ftp)(http) |
TSV |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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