|
| Status |
Public on Apr 03, 2024 |
| Title |
A. fumigatus Af293 peptone DFP and H2O2 1 |
| Sample type |
SRA |
| |
|
| Source name |
mycelium
|
| Organism |
Aspergillus fumigatus |
| Characteristics |
tissue: mycelium
genotype: Af293 reference strain
treatment: peptone DFP and H2O2
|
| Treatment protocol |
Mycelia from 4 × 100 mL of these exponential growth phase cultures were transferred into 12 × 100 mL fresh minimal broth containing 1.52 g/L KH2PO4, 0.52 g/L MgSO4 4H2O and 0.52 g/L KCl (pH 6.5) and 20 g/L glucose, 4 g/L casein peptone (glucose + peptone cultures) as carbon/energy source. These cultures were supplemented with either 0.1 v/v% Barratt’s trace element solution (“iron supplemented” cultures) or 0.1 v/v% iron free Barratt’s trace element solution and 1 mM deferiprone (“DFP treated” or “iron limited” cultures) as iron chelator. Cultures were incubated for 8 h at 37 °C and 220 rpm, then some of them were treated with 75 mM H2O2 and samples were taken for RNA isolation 1 h after oxidative stress treatment. The whole experiment was repeated with minimal broth containing only 4 g/L casein peptone (“peptone”) (instead of 20 g/L glucose and 4 g/L casein peptone).
|
| Growth protocol |
Barratt’s minimal broth (100 mL in 500 mL Erlenmeyer flask) supplemented with 5 g/L yeast extract and inoculated with 1x108 conidia was incubated in a rotary shaker at 37 °C, 220 rpm (approx. 3.7 Hz) for 17 h.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated from lyophilized samples with Trisol reagent.
RNA libraries for RNA-seq were prepared using TruSeq RNA Sample preparation kit (Illumina) following manufacturer's protocols.
RNA-seq (single read, 75 bp)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
The FastQC package (http://www.bioinformatics.babraham.ac.uk/projects/fastqc) was used for quality control.
Reads were aligned to the genome of A. fumigatus Af293 with hisat2 (version 2.1.0).
DESeq2 (version 1.24.0) (Love et al. 2014) was used to determine differentially expressed genes.
FeatureCounts 2.0.0, (Liao et al. 2014) was used to generate read counts and RPKM values.
Assembly: A_fumigatus_Af293_version_s03-m05-r17_chromosomes.fasta.gz (from from http://www.aspergillusgenome.org/download/sequence/A_fumigatus_Af293/current); A_fumigatus_Af293_version_s03-m05-r17_features_with_chromosome_sequences.gff.gz (from http://www.aspergillusgenome.org/download/gff/A_fumigatus_Af293)
Supplementary files format and content: excell file includes count and RPKM values for each Sample
|
| |
|
| Submission date |
Feb 23, 2024 |
| Last update date |
Apr 03, 2024 |
| Contact name |
Tamas Emri |
| E-mail(s) |
emri.tamas@science.unideb.hu
|
| Organization name |
University of Debrecen
|
| Street address |
Egyetem ter 1
|
| City |
Debrecen |
| ZIP/Postal code |
4032 |
| Country |
Hungary |
| |
|
| Platform ID |
GPL23268 |
| Series (1) |
| GSE256524 |
The oxidative stress response highly depends on glucose and iron availability in Aspergillus fumigatus |
|
| Relations |
| BioSample |
SAMN40092322 |
| SRA |
SRX23724996 |
