Panoramic Parvovirus Strain Discovery Data Chain

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ParvoDB ID PV018090 GenBank Accession DQ000495
Subfamily Parvovirinae Genus Bocaparvovirus
Species Bocaparvovirus primate1 Sequence Length 5217
Definition Human bocavirus isolate st1, complete genome. Submission Date 2005-04-06
Strain Name st1 Sampling Date
Sampling Country None Location None
Submitted By Allander,T., Tammi,M.T., Eriksson,M., Bjerkner,A., Tiveljung Lindell,A. and Andersson,B. Submitting Institution Center for Genomics and Bioinformatics, Karolinska Institutet, Berzelius Vag 35, Stockholm SE-171 77, Sweden
Original Host None Sample Type nasopharyngeal aspirates
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 0.9% NaCl Diluting nasopharyngeal aspirates during the sampling process. 16118271 View Related Publication
2 2% human blood donor serum in molecular-biology-grade water Dissolving the pellet obtained after ultracentrifugation.
3 Ultrafree-MC, Millipore Filtering the dissolved pellet through a 0.22-μm spin filter.
4 Millex GV/HV, Millipore Filtering Pool 2 using 0.22-μm or 0.45-μm disk filters.
5 DNase I (100 units, Stratagene) Depleting contaminating nucleic acids from the samples.
6 QIAamp Blood Mini Kit (Qiagen, Hilden, Germany) Extracting DNA from the samples.
7 TRIzol LS reagent (Invitrogen) Extracting RNA from the samples.
8 RNase-free water with 1 mM DTT Dissolving the final RNA pellet.
9 Recombinant RNase inhibitor (Promega; 4 units) Preventing RNA degradation during extraction.
10 FR26RV-N primer Random PCR amplification of extracted DNA and RNA.
11 EcoPol buffer (10x, New England Biolabs) Buffer for the PCR reaction involving extracted DNA.
12 dNTP mixture (each at 10 mM) Nucleotide source for PCR reaction.
13 3'-5' exo- Klenow DNA polymerase (New England Biolabs) Enzyme for PCR amplification.
14 SuperScript II reverse transcriptase (Invitrogen) Reverse transcription of RNA to cDNA.
15 First-Strand buffer (5x, Invitrogen) Buffer for reverse transcription reaction.
16 GeneAmp PCR buffer II (Applied Biosystems) Buffer for subsequent PCR reactions.
17 AmpliTaq Gold DNA polymerase (Applied Biosystems) DNA polymerase for PCR amplification.
18 QIAquick PCR Purification Kit (Qiagen) Purifying PCR amplification products.
19 EcoRV Digesting amplification primers from PCR products.
20 QIAquick Gel Extraction Kit (Qiagen) Extracting specific PCR product fragments from agarose gel.
21 Zero Blunt PCR Cloning Kit (Invitrogen) Ligation of purified PCR products to vector and transformation into E. coli.
22 Luria-Bertani agar plates with kanamycin Selecting transformed E. coli colonies.
23 Templiphi (Amersham Biosciences) Rolling circle amplification for producing sequencing templates.
24 DYEnamic ET Dye Terminator Cycle Sequencing reagents (Amersham Biosciences) Sequencing of DNA templates.
25 188F primer Forward primer specific for Human Bocavirus (HBoV) detection by PCR.
26 542R primer Reverse primer specific for Human Bocavirus (HBoV) detection by PCR.