|
| Status |
Public on Dec 09, 2018 |
| Title |
R3A45 |
| Sample type |
SRA |
| |
|
| Source name |
Fungal mycelium
|
| Organism |
Aspergillus fumigatus A1163 |
| Characteristics |
tissue: Fungal mycelium
cultivation condition: Fungus alone
time point: 45 min
|
| Treatment protocol |
10^9 untreated or heat-inactivated Pseudomonas cells were added to pre-cultivated A. fumigatus.
|
| Growth protocol |
10^8/ml Aspergillus fumigatus conidia were inoculated in 100 ml AMM medium and pre-cultivated for 12 h at 37° C in shaking conditions (200 rpm). Total mycelium was filtered, washed, and then transferred into 100 ml of fresh AMM.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using the RNeasy Plant Mini Kit (Qiagen) according to the manufacturer instructions.
Enrichment of mRNA by poly(A) attached to magnetic beads and subsequent cDNA library construction (performed by LGC Genomics Berlin).
100 bp paired-end read.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
processed data file: counts.csv
|
| Data processing |
Basecalls performed using CASAVA.
Reads were trimmed with btrim.
Trimmed reads were mapped to the reference genome with tophat1.
Mapped reads were counted using htseq-count.
Genome_build: Aspergillus_fumigatusa1163
Supplementary_files_format_and_content: counts.csv: Comma-delimited text file includes counts for each gene per sample.
|
| |
|
| Submission date |
Nov 09, 2018 |
| Last update date |
Dec 09, 2018 |
| Contact name |
Vito Valiante |
| E-mail(s) |
vito.valiante@leibniz-hki.de
|
| Organization name |
Leibniz-Institute for Natural Product Research and Infection Biology
|
| Department |
Leibniz Research Group - Biobricks of Microbial Natural Product Syntheses
|
| Street address |
Beutenbergstrasse 11A
|
| City |
Jena |
| ZIP/Postal code |
07745 |
| Country |
Germany |
| |
|
| Platform ID |
GPL25791 |
| Series (1) |
| GSE122391 |
Transcriptomics analysis of Aspergillus fumigatus co-cultivated with Pseudomonas aeruginosa |
|
| Relations |
| BioSample |
SAMN10406681 |
| SRA |
SRX5000009 |
