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| Status |
Public on Oct 06, 2015 |
| Title |
mpkA.1b-2 |
| Sample type |
SRA |
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| Source name |
fungal cells
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| Organism |
Aspergillus fumigatus |
| Characteristics |
strain: 1163
mutant: akuB, mpkA knock-out mutant
repeated run: repeated due to lack of reads
time point: 1h
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| Treatment protocol |
After 16 hours incubation (37 °C, 200 rpm shaking), 0,1 mg / L Caspofungin was added to the media and samples collected 30 min (T0.5), 1 hour (T1), 4 hours (T4), and 8 hours (T8) after induction
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| 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
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| 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
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
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| Description |
Deletion of the gene Afu4g13720 in the CEA17 background
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| Data processing |
FASTQ files were receiven from GATC, Konstanz, Germany
repeated runs concatenated
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
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| Submission date |
Mar 10, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Robert Altwasser |
| Organization name |
Max-Delbrück-centrum
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| Department |
AG Di Virgilio
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| Street address |
Robert-Rössle-Str. 10
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| City |
Berlin |
| ZIP/Postal code |
13125 |
| Country |
Germany |
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| Platform ID |
GPL18295 |
| Series (1) |
| GSE55743 |
Network Modelling using Transcription Sequence Data Reveals Novel MAPK Interactions Important for Drug Resistance |
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| Relations |
| BioSample |
SAMN02680036 |
| SRA |
SRX483803 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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