|
| Status |
Public on Jun 03, 2015 |
| Title |
akuB_S.4b |
| Sample type |
SRA |
| |
|
| Source name |
fungal cells
|
| Organism |
Aspergillus fumigatus |
| Characteristics |
strain: strain CEA17
mutant: akuB knock-out mutant
treatment: siamycin
time point: 4
|
| Treatment protocol |
After 16 hours incubation (37 °C, 200 rpm shaking), 0,1 mg / L Caspofungin and / or 1 mg / L Siamycin was added to the media and samples collected 4 hours after induction
|
| Growth protocol |
10^6 spores / ml were inoculated in AMM media supplemented with Glucose (1% w/v), MgSO4 (1% w/v), and Hunter’s trace elements
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was prepared using the RNeasy Plant Mini kit (Qiagen, Germany) according to the manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols; 50 bp single end
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
Strain CEA17 (deletion of the gene Afu2g02620 in the CEA10 background)
|
| Data processing |
FASTQ files were receiven from GATC, Konstanz, Germany
Mapping of read pairs using TopHat (v1.4.1; --GTF GTF from CADRE; -maxintronlength 4000, -g 1)
Read counting using R-package easyRNASeq, annotation from BioMart (fungi_mart_19)
Normalisation using R-package DESeq
Genome_build: Aspergillus fumigatusa1163 A1163 (CADRE)
Supplementary_files_format_and_content: comma seperated values (csv) with the normalised read counts
|
| |
|
| Submission date |
Mar 06, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Robert Altwasser |
| Organization name |
Max-Delbrück-centrum
|
| Department |
AG Di Virgilio
|
| Street address |
Robert-Rössle-Str. 10
|
| City |
Berlin |
| ZIP/Postal code |
13125 |
| Country |
Germany |
| |
|
| Platform ID |
GPL18295 |
| Series (1) |
| GSE55663 |
Hitting the caspofungin salvage pathway of human-pathogenic fungi with the novel lasso peptide humidimycin (MDN-0010) |
|
| Relations |
| BioSample |
SAMN02676243 |
| SRA |
SRX482120 |
