Panoramic Parvovirus Strain Discovery Data Chain

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ParvoDB ID PV010896 GenBank Accession JX179279
Subfamily Parvovirinae Genus Bocaparvovirus
Species Bocaparvovirus primate1 Sequence Length 495
Definition Human bocavirus 1 isolate BO/85 capsid protein gene, partial cds. Submission Date 2012-06-14
Strain Name BO/85 Sampling Date 1985
Sampling Country United Kingdom Location United Kingdom
Submitted By Kapusinszky,B., Minor,E., Minor,D., Minor,P. and Delwart,E.L. Submitting Institution Molecular Virology, University of California at San Francisco, Blood Systems Research Institute, 270 Masonic Avenue, San Francisco, CA 94118, USA
Original Host Homo sapiens Sample Type stool 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 virus culture medium without fetal bovine serum Holds the stool samples after swabbing for later analysis. 22875894 View Related Publication
2 zirconia/silica beads (RPI, Mount Prospect, IL) Assists in nucleic acid extraction by mixing with stool suspensions.
3 RNA minikit (Qiagen, Valencia, CA) Used for the total extraction of nucleic acids from stool suspensions.
4 RiboLock RNase Inhibitor (Fermentas Inc.) Added to nucleic acids to prevent RNA degradation.
5 random nanomer, oligo(dT) (Eurofins MWG Operon), or specific primers (IDT, Coralville, IA) Used in the reverse transcription step for RNA viruses.
6 SuperScript buffer (Invitrogen, Carlsbad, CA) Part of the reaction mixture for reverse transcription.
7 100 mM dithiothreitol Part of the reaction mixture for reverse transcription.
8 10 mM dNTP Part of the reaction mixture for reverse transcription.
9 SuperScript III reverse transcriptase (Invitrogen, Carlsbad, CA) Enzyme used to synthesize cDNA from RNA.
10 RiboLock RNase inhibitor Prevent RNA degradation during reverse transcription.
11 REDTaq mix (Sigma) Enzyme mix used for PCR amplification.
12 NEBTaq (New England BioLabs) Enzyme used for PCR amplification.
13 Ex Taq (TaKaRa Bio Inc., Shiga, Japan) Enzyme used for PCR amplification.
14 PlatinumTaq DNA polymerase (Invitrogen, Carlsbad, CA) Enzyme used for PCR amplification.
15 ethidium bromide Used for visualization of PCR products in agarose gel electrophoresis.
16 QIAquick kit (Qiagen, Valencia, CA) Used for purification of PCR amplicons.
17 ExoSAP-IT (USB Corp., Cleveland, OH) Used for cleaning up fragments less than 100 bp before sequencing.