Panoramic Parvovirus Strain Discovery Data Chain
| ParvoDB ID | PV012097 | GenBank Accession | MK139243 |
| Subfamily | Parvovirinae | Genus | Dependoparvovirus |
| Species | Dependoparvovirus primate1 | Sequence Length | 4679 |
| Definition | Adeno-associated virus isolate CHC129_AAV.FL.linear, complete genome. | Submission Date | 2018-10-29 |
| Strain Name | CHC129_AAV.FL.linear | Sampling Date | 1997-04-01 |
| Sampling Country | France | Location | France |
| Submitted By | La Bella,T., Imbeaud,S., Peneau,C., Mami,I., Datta,S., Bayard,Q., Caruso,S., Hirsch,T.Z., Calderaro,J., Morcrette,G., Guettier,C., Paradis,V., Amaddeo,G., Laurent,A., Possenti,L., Chiche,L., Bouliac-Sage,P., Blanc,J.-F., Letouze,E., Nault,J.-C. and Zucman-Rossi,J. | Submitting Institution | Functional Genomics of Solid Tumors, INSERM U1162, 27 rue Juliette Dodu, Paris 75010, France |
| Original Host | Homo sapiens | Sample Type | tissue samples |
| Standardized Host Name | Homo sapiens | Host Tax Rank | species |
| Standardized Host Class | Mammalia | Standardized Host Order | Primates |
| Environmental Origin | - N/A - | Reagent Origin | - N/A - |
| Number | Reagent/Consumables | Purpose | PMID/Url | Reference |
|---|---|---|---|---|
| 1 | Fluidigm 96.96 dynamic arrays | Quantitative RT-PCR (qRT-PCR) for detecting viral DNA. | 31375600 | View Related Publication |
| 2 | BioMark Real-Time PCR system | Quantitative RT-PCR (qRT-PCR) for detecting viral DNA. | ||
| 3 | TaqMan probe sets | Designing specific primers for PCR analysis. | ||
| 4 | Genomic DNA | Source material for screening viral DNA using qRT-PCR. | ||
| 5 | 120-mer primers | Recognizing AAV genotypes 1-13 for viral capture of genomic DNA. | ||
| 6 | Burrows-Wheeler Aligner | Mapping viral reads to reference sequences. | ||
| 7 | Samtools | Extracting read pairs aligned on the virus. | ||
| 8 | Custom reference genome | Including human chromosomes and virus sequences for alignment. | ||
| 9 | Bedtools multicov utility | Calculating read coverage in genomic bins. | ||
| 10 | Integrative Genomics Viewer | Validating viral insertions by visual inspection. | ||
| 11 | Illumina TruSeq Stranded mRNA kit | RNA sequencing by enriching poly(A)+ RNA. | ||
| 12 | HiSeq2000 sequencer | Generating RNA-seq data. | ||
| 13 | TopHat2 | Aligning RNA-seq reads. | ||
| 14 | Cufflinks | Reconstructing chimeric RNA sequences. | ||
| 15 | ElemeNT | Predicting transcription start sites (TSS). | ||
| 16 | Alamut Visual software | Identifying splicing signals on chimeric DNA sequences. | ||
| 17 | ATGpr | Identifying translation initiation sites. | ||
| 18 | Poly(A) Signal Miner | Identifying PolyA sites. | ||
| 19 | DNAse/TaqMan-based assay | Detecting AAV episomal forms. | ||
| 20 | Glycerol | Used in the episomal detection assay. | ||
| 21 | Dimethyl sulfoxide | Used in the episomal detection assay. | ||
| 22 | ExoSAP-IT (Applied Biosystem) | Purifying PCR products for Sanger sequencing. | ||
| 23 | QuikChange Lightning site-directed mutagenesis kit (Agilent) | Introducing point mutations in viral polyA signal. | ||
| 24 | Lipofectamine 3000 (Life Technologies) | Transfecting HepG2 cells. | ||
| 25 | pmirGLO plasmid (Promega) | Cloning constructs for luciferase assays. | ||
| 26 | Dual-luciferase reporter assay system | Measuring luciferase activity post-transfection. | ||
| 27 | GraphPad Prism | Performing statistical analysis. |