Starting Material
Accepted starting material for INVIEW Virus
| Virus type |
Starting material |
| RNA virus |
- Type: rRNA depleted or total RNA
- Quantity: 100 ng per sample
- Concentration: min. 5 ng/µl
- Dissolved in: RNase-, DNase- and protease-free molecular grade water
|
| dsDNA virus |
- 100 ng ng gDNA Qubit quantified (up to 100µl / concentration > 1 ng/µl)(NanoDrop quantified > 200 ng recommended)
- cDNA can not be accepted as starting material
|
| AAV / ssDNA virus |
- We recommend to use 500µl - 1 ml cell culture supernatant for the ssDNA extraction
- Please send min. 20µl of your extracted ssDNA (Conc.: 0.1 ng/µl)
- If you need to send TNA extracted from material other than cell culture supernatant please contact us.
|
| Unknown virus / virus mixtures |
- We recommend to use 500µl - 1 ml cell culture supernatant for the total nucleic acid (TNA) extraction
- Please send min. 20µl of your extracted TNA (Conc.: 0.1 ng/µl)
- If you need to send TNA extracted from material other than cell culture supernatant please contact us.
|
Accepted starting material for DNA and/or RNA isolation
- Tissue
- Cells
- Blood
- Environmental samples
- Cell culture supernatant
Accepted starting material for Total Nucleic Acid Extraction
- Cell culture supernatant
- Cell banks
- Allontoic fluid (eggs)
- Virus seed stocks
- Additional materials (e.g bioreactor samples)
- Environmental samples on request
Please note that only S1-classified material is accepted for DNA / RNA isolation ordered online. More information about the current classification of biological material can be found here (TRBA 466). Please contact us for further information on isolating DNA / RNA from material classified as S2.
RNA virus
- RNA isolation – efficient isolation of RNA for uniform and less-biased coverage
- Ribosomal RNA (rRNA) depletion – optimised removal of rRNA from mRNA for commonly studied organisms
Please contact us to check the compatibility of your organism
DNA virus
- DNA isolation – efficient isolation of DNA for uniform and less-biased coverage
- Total nucleic acid extraction
Unknown virus / virus mixtures
- Total nucleic acid extraction
RNA virus
Strand-specific cDNA library. No Poly-A selection.
ds DNA virus
Standard genomic library
ssDNA virus
Library preparation using a proprietary protocol for ssDNA virus
Unknown virus / virus mixtures
Library preparation using a proprietary protocol for all virus classes
- Type: Illumina
- Run mode: 2 x 150 bp
- Output: 5 M read pairs (or multiples of 5M read pairs)
Genome variant detection (DNA / RNA virus)
• Mapping against one reference
• Detection of SNPs and InDels
• Annotation of detected SNPs and InDels (using dbSNP)
• Allocation of effects on protein level (using Ensembl)
Viral metagenomic analysis (Unkown virus / virus mixtures)
- Sequence data quality assessment and cleaning
- Removal of host* contaminated sequenced reads
- Screening for known viruses using curated complete virus genome database
- Taxonomy assignments and generating sample's virus profile
- Analysis reporting
*Available hosts: Human, Mouse, Rat, Green Monkey, Chicken, Chinese Hamster (CHO), Duck (other host organisms on request)
Genome variant detection
• Alignment file (bam)
• SNP and InDel tables including annotated variants and effects (vcf, tsv, bed)
• Comprehensive data analysis report
Viral metagenomic analysis (Unkown virus / virus mixtures)
- Sample wise tables of detected virus (TSV)
- Comprehensive data analysis report (HTML)
- 12 days for up to 192 samples for dsDNA viruses
- 15 days for up to 192 samples for RNA viruses
- 27 days for up to 24 samples for ssDNA virus, unknown viruses or virus mixtures (express service available)