|
| Status |
Public on May 17, 2024 |
| Title |
ref_a |
| Sample type |
SRA |
| |
|
| Source name |
Mycelium sample
|
| Organism |
Aspergillus niger |
| Characteristics |
tissue: Mycelium sample
cell line: N593 delta-kusA (reference strain)
cell type: Mycelium sample
genotype: N593 delta-kusA (cspA1, pyrG-, kusA::amdS)
treatment: grown on maltose for 2 hour
|
| Growth protocol |
The strains were pre-grown in complete medium containing 2% (w/v) fructose for 16h. The mycelium was harvested and washed with minimal medium (MM) , and then was transferred to 50 ml MM (pH 6) with 25 mM maltose. After 2h of incubation, the mycelium was harvested and frozen in liquid nitrogen.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted from grinded mycelia and were single-end sequenced using Illumina HiSeqTM 2000 platform .
Purification of mRNA, synthesis of cDNA library and sequencing were conducted at the BGI Tech Solutions Co., Ltd. (Hong Kong, China).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Clean reads were then mapped to the genome of Aspergillus niger NRRL3 (http://genome.jgi.doe.gov/Aspni_NRRL3_1) using Bowtie2 and HISAT. The gene expression level was measured as Fragments Per Kilobase of transcript per Million mapped reads or FPKM.
Assembly: Aspergillus niger NRRL3 (http://genome.jgi.doe.gov/Aspni_NRRL3_1)
Supplementary files format and content: table-delimited text file including FPKM values
|
| |
|
| Submission date |
Feb 29, 2024 |
| Last update date |
May 17, 2024 |
| 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 |
GPL21721 |
| Series (1) |
| GSE260627 |
Compare transcriptome profile of reference strain and mutant of HapX during A.niger grown on maltose |
|
| Relations |
| BioSample |
SAMN40208943 |
| SRA |
SRX23801373 |
