|
| Status |
Public on May 03, 2017 |
| Title |
NK_in_HD |
| Sample type |
SRA |
| |
|
| Source name |
NK virus infected isolate
|
| Organism |
Aspergillus fumigatus |
| Characteristics |
tissue: Fungal mycelia
|
| Treatment protocol |
No special treatment
|
| Growth protocol |
All A. fumigatus strains of interest were inoculated onto 25 ml of solid Aspergillus Complete Media (ACM) from 50% glycerol stocks which were kept at -20 °C.Plates were incubated at 37°C for 5 days and spores were harvested with 15 ml of sterile distilled water. Spore suspensions were used to inoculate 500 ml of ACM broth. Inoculated bottles were incubated at 37°C with shaking at 130 rpm. After 5 days, mycelia were harvested.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNAs were extracted using Trizol and small RNAs were isolated using PEG8000 precipitation.
Libraries were constructed using Scriptminer kit with high definition Illumina adapters.
|
| |
|
| Library strategy |
ncRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Adapter removal step was conducted using the UEA sRNA workbench [Stocks et al, 2012]. The 3' adapter sequence was identified using the first 6 nt. Adapter guessing strategy was also used to double check the adapter removal procedure.
Quality checks including size class distribution, nucleotide composition analysis, complexity analysis and Jaccard similarity were done before genome matching.
Reads were mapped full length, no mis-matches or gaps allowed to the host Aspergillus fumigatus genome and also viral genomes using PatMan [Prueffer et al, 2008]
Differentially expressed virus-derived small RNAs were determined and mapped to the fungal genome to identify the potential targets.
The miRNAs were identified using the miRCat and miRprof tool within the UEA workbench.
The sRNA loci were identfied using CoLIde [Mohorianu et al, 2013]
Genome_build: A_fumigatus_Af293 genome version_s03_m04_r22
Supplementary_files_format_and_content: csv file containing the sRNA expression levels.
|
| |
|
| Submission date |
Sep 23, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Irina Mohorianu |
| E-mail(s) |
[email protected]
|
| Organization name |
University of Oxford
|
| Department |
Medical Sciences Division
|
| Lab |
Oxford Vaccine Group
|
| Street address |
Headington
|
| City |
Oxford |
| ZIP/Postal code |
OX3 7LE |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL18295 |
| Series (1) |
| GSE61680 |
Small RNA profiles of three different mycovirus-infected Aspergillus fumigatus isolates, created using Illumina high definition adapters |
|
| Relations |
| BioSample |
SAMN03076218 |
| SRA |
SRX708798 |
