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Sample GSM4681730 Query DataSets for GSM4681730
Status Public on Aug 11, 2021
Title W-CI-1
Sample type SRA
 
Source name Mycelium sample
Organism Aspergillus niger
Characteristics strain: N402
treatment: 2h incubation on cinnamic 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 SAMN15594457
SRA SRX8785871

Supplementary file Size Download File type/resource
GSM4681730_W-CI-1.gene.FPKM.txt.gz 169.1 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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