Panoramic Parvovirus Strain Discovery Data Chain

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ParvoDB ID PV010556 GenBank Accession AY622947
Subfamily Parvovirinae Genus Tetraparvovirus
Species Tetraparvovirus primate1 Sequence Length 226
Definition Human parvovirus 4 genomic sequence. Submission Date 2004-04-06
Strain Name None Sampling Date
Sampling Country United States of America Location United States of America
Submitted By Jones,M.S. Jr., Kapoor,A. and Delwart,E. Submitting Institution Medicine, UCSF, 270 Masonic Ave, San Francisco, CA 94118, USA
Original Host Homo sapiens Sample Type plasma 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 Plasma Specimens for analysis from subjects screened for acute HIV infection found to be HIV negative. 15956568 View Related Publication
2 Ultrafree MC 0.22-μm filter (Millipore, Bedford, MA) Filtration of plasma samples.
3 DNase I (Roche Diagnostics, Mannheim, Germany) Removal of contaminating human DNA from plasma samples.
4 QIAamp Viral RNA Mini kit (QIAGEN, Valencia, CA) Purification of DNase I-resistant nucleic acids.
5 QIAamp DNA Blood Mini kit (QIAGEN, Valencia, CA) Alternative purification of DNase I-resistant nucleic acids.
6 SuperScript II RNase H reverse transcriptase (Invitrogen, Carlsbad, CA) First-strand cDNA synthesis from viral RNA.
7 Random hexamers (GIBCO, Gaithersburg, MD) Primer for first-strand cDNA synthesis.
8 RNase H (Invitrogen, Carlsbad, CA) Second-strand cDNA synthesis.
9 DNA polymerase I (Invitrogen, Carlsbad, CA) Continuation of second-strand cDNA synthesis.
10 Klenow fragment (exo-) (New England Biolabs, Beverly, MA) Generation of complementary strand for detecting viral DNA.
11 Restriction enzyme Csp6.I (Fermentas, Hanover, MD) Digestion of double-stranded DNA.
12 Hybridized oligonucleotides NBam24 and NCsp11 (80 pmol) Adaptors ligated to restricted DNA.
13 T4 DNA ligase (Invitrogen, Carlsbad, CA) Ligation of adaptors to restricted DNA.
14 Taq polymerase (Promega, Madison, WI) PCR amplification.
15 Polyacrylamide gel electrophoresis (PAGE) Analysis of DNase-SISPA-amplified DNA.
16 pGEM-T Easy Subcloning of purified DNA.
17 5' Rapid Amplification of cDNA Ends (RACE) kit (Invitrogen, Carlsbad, CA) Amplification and sequencing of the 5' end of the genome.
18 Deoxycytidine Addition of poly(C) tail to 3' end of amplification products.
19 Terminal deoxynucleotidyl transferase (Invitrogen, Carlsbad, CA) Addition of poly(C) tail to 3' end of amplification products.
20 QIAquick columns (QIAGEN) Purification of amplification products.