|
| Status |
Public on Oct 05, 2021 |
| Title |
DA6 |
| Sample type |
SRA |
| |
|
| Source name |
∆spfA (772) rep3
|
| Organism |
Aspergillus fumigatus |
| Characteristics |
strain: spfA knockout mutant
treatment: Untreated
genotype: {delta}akuB::pyrG+, {delta}spfA::six
|
| Treatment protocol |
No treatment
|
| Growth protocol |
Cultures containing 50 mL of liquid YG were inoculated with 1 x 106 conidia/mL and incubated for 16 h at 37°C and 200 rpm.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
biomass was grounded under liquid nitrogen and the RNA extracted using a Direct-zol RNA MiniPrep kit (Zymo Research).
Library preparation was performed using NEBNext Ultra II Directional RNA Library Prep kit for RNA-seq.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
NextSeq 550 |
| |
|
| Description |
Mutant lacking the spfA gene
|
| Data processing |
A poly(A) RNA-Seq was carried out in the Genomics, Epigenomics and Sequencing Core (GESC) at the University of Cincinnati using a NextSeq 550 system (Illumina). After adapter trimming and quality control, fastq files of each sample were merged before data analysis
Gene expression analysis was carried out using the A. fumigatus Af293 reference genome and annotation tracks from FungiDB (release 51) in CLC Genomics Workbench (QIAgen). Expression values were estimated as transcripts per million (TPM).
Differential expression for RNA-Seq was calculated between the control and mutant strains using TMM as the normalization method.
Downstream analysis was performed using FungiDB and FungiFun2
Genome_build: Af293
Supplementary_files_format_and_content: Matrix table with expression values in TPM, fold change (∆spfA vs Parental strain), statistical analysis and enrichment analysis for every gene and every sample
|
| |
|
| Submission date |
Jun 30, 2021 |
| Last update date |
Oct 05, 2021 |
| Contact name |
Jose Pedro Guirao Abad |
| Organization name |
University of Cincinnati
|
| Department |
Pathology and Laboratory Medicine
|
| Lab |
1152
|
| Street address |
231 Albert Sabin Way
|
| City |
CINCINNATI |
| State/province |
OH |
| ZIP/Postal code |
45267-0529 |
| Country |
USA |
| |
|
| Platform ID |
GPL30331 |
| Series (1) |
| GSE179173 |
Pleiotropic Effects of the P5-Type ATPase SpfA on Stress Response Networks Contribute to Virulence in the Pathogenic Mold Aspergillus fumigatus |
|
| Relations |
| BioSample |
SAMN19967805 |
| SRA |
SRX11312047 |
