|
| Status |
Public on May 03, 2023 |
| Title |
amyR mutant_40h incubation on inulin [104627-001-004] |
| Sample type |
SRA |
| |
|
| Source name |
Mycelium sample
|
| Organism |
Aspergillus niger |
| Characteristics |
strain: amyR mutant
sampling time: 40h incubation on inulin
tissue: Mycelium
|
| Growth protocol |
10^3 conidia of A. niger control, ∆amyR, ∆inuR and ∆amyR∆inuR strains were inoculated and pre-grown between two sterile Polycarbonate Track Etched (PCTE) membrane layers (disc diameter 76 mm, PCTE 0.1 µm, PoreticsTM, GVS Filter Technology) on MM plates containing 1% soybean hulls as carbon source supplemented with 1.22 g/L uridine at 30°C. After two days, the polycarbonate membrane layers containing the fungal mycelia were transferred to MM plates containing 1% sucrose or 1% inulin supplemented with 1.22 g/L uridine and were grown at 30°C. Mycelia were collected after 40 h of growth and were frozen in liquid nitrogen and stored at -80°C.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted from grinded mycelia using TRIzol® reagent (Invitrogen, Breda, the Netherlands) and purified with NucleoSpin® RNA II Clean-up kit (Macherey-Nagel) with rDNase treatment. The RNA concentration and integrity was assessed using the Agilent Fragment Analyzer system. rRNA was depleted from total RNA using the rRNA depletion kit (Qiagen fast select).
Subsequently, samples were processed using the NEBNext Ultra II directional RNA library prep kit for Illumina®. Briefly, after fragmentation of the rRNA reduced RNA, a cDNA synthesis was performed. This was used for ligation with the sequencing adapters and PCR amplification of the resulting product. The quality and yield after sample preparation was measured with the Fragment Analyzer. The size of the resulting products was consistent with the expected size distribution (a broad peak between 300-500 bp). Clustering and DNA sequencing were performed using Illumina Novaseq6000 in line with manufacturer’s instructions at the concentration of 1.1nM of DNA.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Image analysis, base calling and the quality check were conducted using the Illumina data analysis pipeline RTAv3.4.4 and Bclfastqv2.20. The quality of raw reads was checked with FastQC v0.11.9 and Cutadapt v2.10 was used to remove low-quality and adapter of reads. Alignment of cleans reads was performed using STAR2 version v2.5.4b against the A. niger NRRL3. The aligned reads are stored in a sorted BAM format and indexed using Samtools v1.95. For the removal of PCR duplicates within the library Picard MarkDuplicates v2.23.66 was used. This tool uses UMI sequences (BAM tags) to determine which sequences are PCR duplicates and therefore should be removed. The deduplicated mapped reads are counted for each exonic feature in the reference GTF annotation using htseq-count v0.11.07.”. The normalized counts (FPKM) were generated with Cufflinks v2.2.1.
Assembly: Aspergillus niger NRRL3 (http://genome.jgi.doe.gov/Aspni_NRRL3_1)
Supplementary files format and content: tab-delimited text files include raw counts and FPKM values for each Sample
|
| |
|
| Submission date |
May 25, 2022 |
| Last update date |
May 03, 2023 |
| Contact name |
Ronald de Vries |
| E-mail(s) |
fungalphysiology@gmail.com
|
| Phone |
+ 31 (0)30 2122600
|
| Organization name |
Centre of fungal biodiversity
|
| Department |
fungal physiology
|
| Street address |
Uppsalalaan 8
|
| City |
Utrecht |
| ZIP/Postal code |
3584 CT |
| Country |
Netherlands |
| |
|
| Platform ID |
GPL32288 |
| Series (1) |
| GSE204768 |
Regulation of inulin and sucrose utilization by Aspergillus niger AmyR and InuR |
|
| Relations |
| BioSample |
SAMN28650068 |
| SRA |
SRX15448579 |
