Panoramic Parvovirus Strain Discovery Data Chain

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ParvoDB ID PV012723 GenBank Accession OR800006
Subfamily Parvovirinae Genus Erythroparvovirus
Species Erythroparvovirus primate1 Sequence Length 5266
Definition MAG: Human parvovirus B19 isolate SEN/H3A_UCAD-SHC0712/2019 genomic sequence. Submission Date 2023-10-16
Strain Name SEN/H3A_UCAD-SHC0712/2019 Sampling Date 2019-06-26
Sampling Country Senegal Location Senegal
Submitted By Levine,Z.C., Sene,A., Mkandawire,W., Deme,A.B., Ndiaye,T., Sy,M., Gaye,A., Diedhiou,Y., Mbaye,A.M., Ndiaye,I., Gomis,J., Ndiop,M., Sene,D., Faye Paye,M., Macinnis,B., Schaffner,S.F., Park,D.J., Badiane,A.S., Colubri,A., Ndiaye,M., Sy,N., Sabeti,P., Ndiaye,D. and Siddle,K.J. Submitting Institution Infectious Diseases, Broad Institute, 75 Ames St, Cambridge, MA 02142, 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 RNAse I (Lucigen) or Ambion TURBO DNase To obtain purified DNA and RNA from total nucleic acids extracted from plasma. 37662407 View Related Publication
2 Nextera XT (Illumina) and UD index primers (IDT/Illumina) For preparing libraries from cDNA for unbiased RNA sequencing.
3 AMPure XP (Agilent) Library purification for unbiased RNA sequencing and 16S sequencing library preparation.
4 Power SYBR Green PCR MasterMix (Thermo Fisher) For performing qPCR for total bacterial load and pan-Borrelia detection.
5 Q5 high fidelity polymerase (NEB) For amplification in 16S sequencing library preparation and IGS sequencing nested-PCR.
6 BioAnalyzer (Agilent) Visualization of 16S sequencing libraries.
7 Mindray BC 20s Automated blood count with differential.
8 HemoCue 201/301 To measure blood glucose levels.
9 HemoCue Glucose 201 To measure hemoglobin levels.
10 BioAnalyzer TapeStation For checking quality of IGS sequencing amplified product.
11 Inactivated buffer (Qiagen AVL) For plasma sample inactivation.
12 fancyimpute Python library (MICE algorithm) For imputation of missing values in the multivariate model development.
13 ProcartaPlex Panel (Invitrogen) and Simplex Kits For measuring cytokine and chemokine levels using the Luminex platform.
14 HemoCue Rapid diagnostics tests for malaria proteins upon patient enrollment.
15 Lucigen RNAse I Purify DNA and RNA from total nucleic acids for sequencing for unbiased RNA sequencing analysis.
16 Qiagen QIAmp Viral Mini RNA Total nucleic acids extraction for sequencing.