 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Aug 11, 2021 |
| Title |
W-VA-2 |
| Sample type |
SRA |
| |
|
| Source name |
Mycelium sample
|
| Organism |
Aspergillus niger |
| Characteristics |
strain: N402
treatment: 2h incubation on vanillic acid
genotype: cspA1
|
| Growth protocol |
Strains were grown at 30 °C in Minimal Medium (MM) or Compete Medium (CM) prepared as described previously. All liquid cultures were incubated in the rotary shaker at 250 rpm. In transfer experiment, freshly harvested spores were pre-grown for 16h in CM with 2% (w/v) glucose. The mycelium was then harvested by filtration over sterile cheesecloth, washed with MM andwas transferred to 50 mL MM with 0.02 % (w/v) aromatic compound. After 2h of incubation, the mycelium was harvested by vacuum filtration, dried between two sheets of paper and frozen in liquid nitrogen. The culture filtrate was harvested, centrifuged and frozen. All samples were stored in -20°C until being processed.
|
| 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 quantity and quality was checked with a RNA6000 Nano Assay using the Agilent 2100 Bioanalyser (Agilent Technologies, Santa Clara, CA, USA).
RNA libraries were prepared for sequencing using standard Illumina protocols.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Data processing |
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and removed for low-quality sequence, then mapped to Aspergillus niger NRRL3 whole genome using Bowtie2 (Langmead B et al., Genome Biology, 2009) and HISAT software (Kim D, Langmead B and Salzberg SL, Nature Methods, 2015).
“Fragments per kilobase of exon model per million mapped reads” (FPKM) was calculated using RSEM tool (Li B & Dewey CN, BMC bioinformatics, 2011).
Genome_build: Aspergillus niger NRRL3 (http://genome.jgi.doe.gov/Aspni_NRRL3_1)
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample
|
| |
|
| Submission date |
Jul 21, 2020 |
| Last update date |
Aug 11, 2021 |
| 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 |
GPL25519 |
| Series (1) |
| GSE154865 |
Identification of three enzymes of the vanillin and vanillic acid metabolic pathway in the filamentous fungi Aspergillus niger |
|
| Relations |
| BioSample |
SAMN15594452 |
| SRA |
SRX8785876 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4681735_W-VA-2.gene.FPKM.txt.gz |
164.9 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
|
|
|
|
 |
