|
| Status |
Public on Oct 09, 2018 |
| Title |
MAT1_2_WT1 |
| Sample type |
SRA |
| |
|
| Source name |
control mating-type MAT1-2
|
| Organism |
Aspergillus fumigatus |
| Characteristics |
strain: Af293
mating-type: MAT1-2
genotype: wild-type
tissue: mycelium
|
| Treatment protocol |
mycelia were separated from culture broth by filtration, washed, and snap frozen in liquid nitrogen
|
| Growth protocol |
liquid cultures were inoculated with fungal conidia and allowed to grow overnight before shifting the formed mycelia to inducing, xylose-containing culture media
|
| Extracted molecule |
total RNA |
| Extraction protocol |
nucleic acids from frozen and ground mycelia were extraced with the TRIzole reagent, cleaned, and DNase I digested to be followed by RNA purification
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
replicate1
|
| Data processing |
Sequencing in 50 bp single reads was performed on the Genome Sequencer Illumina HiSeq2000, and trimming to eliminate contaminating adapter sequences was carried out using Trimmomatic, version 0.36. The number of total raw and trimmed reads per sample ranged from 19.1 to 29.5 Mio and 18.0 to 28.1 Mio, respectively, with mapping percentages reaching at least 96% throughout all samples (minimum 96.0%, maximum 97.6%) upon alignment to the annotated reference genome sequences of the A. fumigatus A1163 [MAT1-1] and Af293 [MAT1-2] isolates using the most recent version 2.1.0 of HISAT2. The resulting read count data were then analysed for differential expression by comparison between sample and control (AfS146 and AfS147 compared to D141 and Af293, respectively) by means of the DESeq2 software package (v1.20.0).
|
| |
|
| Submission date |
Apr 19, 2018 |
| Last update date |
Oct 09, 2018 |
| Contact name |
Sven Krappmann |
| E-mail(s) |
[email protected]
|
| Organization name |
FAU Erlangen-Nuernberg
|
| Department |
Institute for Microbiology
|
| Street address |
Wasserturmstr. 3/5
|
| City |
Erlangen |
| ZIP/Postal code |
91054 |
| Country |
Germany |
| |
|
| Platform ID |
GPL18295 |
| Series (1) |
| GSE113404 |
Monitoring the mating-type-driven transcriptomes of Aspergillus fumigatus |
|
| Relations |
| BioSample |
SAMN08957072 |
| SRA |
SRX3974085 |
