Journal: Malaria Journal

Article Title: Detection of low-density Plasmodium falciparum infections using amplicon deep sequencing

doi: 10.1186/s12936-019-2856-1

Figure Lengend Snippet: Mock and natural infection sample composition. a Mock infection samples were constructed from mixtures of P. falciparum and human DNA to mimic the parasite DNA concentrations found in extracted low-density infections. b DNA from up to five clonal cultured parasite lines was combined to create each mock sample, leading to within-sample haplotype counts of one to four. c Natural infection samples were previously collected and extracted from a combination of symptomatic patients and asymptomatic carriers . Parasite densities were determined by blood smear

Article Snippet: These stock solutions were then diluted to the indicated concentrations in sequencing-grade water and 10 ng commercial human DNA (Promega Corp cat#G3041) was added to all samples.

Techniques: Infection, Construct, Cell Culture

Journal: Malaria Journal

Article Title: Detection of low-density Plasmodium falciparum infections using amplicon deep sequencing

doi: 10.1186/s12936-019-2856-1

Figure Lengend Snippet: Identification of haplotypes in mock samples. a Detection of known haplotypes within the mock samples was dependent on the haplotype concentration (copies/μl) within the DNA sample. 5 μl of DNA template were used in the first round PCR amplification step prior to sequencing. Error bars represent the binomial-estimated standard deviation. b Across all mock samples, 31% of identified haplotypes were erroneous, but these haplotypes were generally supported by fewer reads than correct haplotypes. The number of nucleotide (nt) errors per haplotype was calculated as the nucleotide distance between an observed haplotype and the closest expected haplotype within the sample

Article Snippet: These stock solutions were then diluted to the indicated concentrations in sequencing-grade water and 10 ng commercial human DNA (Promega Corp cat#G3041) was added to all samples.

Techniques: Concentration Assay, Amplification, Sequencing, Standard Deviation

Journal: Oncotarget

Article Title: Analysis of the 9p21.3 sequence associated with coronary artery disease reveals a tendency for duplication in a CAD patient

doi: 10.18632/oncotarget.24567

Figure Lengend Snippet: (A) A scheme of TAR cloning of the CAD region from DNA isolated from Promega genomic DNA by 9p21-1 TAR vector. h1A and h1B are targeting hooks for 9p21-1 TAR vector. h2A and h2B are targeting hooks for 9p21-2 TAR vector. (B) Southern analysis of the TAR/YAC isolates. Genomic DNA from three independent YAC clones was digested by NotI, separated by CHEF, and blot-hybridized with a 862 bp specific probe (positions on chromosome 9: 22084459-22085320 in human genome sequence; version hg19). The size of the predicted cloned material is ∼66.8 kb. (C) CHEF analysis of NotI-digested three BAC isolates (lanes 1, 2 correspond to BAC clones obtained from a YAC clone #1; lane 3 corresponds to a BAC obtained from a YAC clone #2). (D) HindIII digestion profiles of BACs from the C087 patient and normal individuals. Lane 1 corresponds to genomic DNA isolated from the A218 BAC clone of the C087 patient containing four 50 kb repeat units; Lanes 2 – 4 correspond to genomic DNA isolated from BAC clones of normal genomic DNA (Promega). M1 - CHEF DNA Size Lambda Ladder (BIO-RAD); M2 - Quick-Load 2-Log DNA Marker (BioLabs).

Article Snippet: Human DNA purified from blood cells of normal individuals was purchased from Promega (Cat. No. G3041).

Techniques: Cloning, Isolation, Plasmid Preparation, Clone Assay, Sequencing, Marker

Journal:

Article Title: Optimum conditions for selective isolation of genes from complex genomes by transformation-associated recombination cloning

doi:

Figure Lengend Snippet: Effect of shearing of genomic DNA on number of transformants obtained

Article Snippet: Commercial female genomic DNA (catalog number G1521; Promega) and human genomic DNA (catalog number G3041; Promega) were used for cloning the human HPRT gene.

Techniques: Transformation Assay

Journal:

Article Title: Optimum conditions for selective isolation of genes from complex genomes by transformation-associated recombination cloning

doi:

Figure Lengend Snippet: Physical characterization of YACs generated by an Alu-containing TAR cloning vector from human genomic DNA sheared to different size fragments. The pNKBAC39 vector containing Alu targeting hooks was used to generate mini-YAC libraries from high molecular weight genomic DNA (A), and DNA sheared to fragments of 50–150 kb (B), 50–200 kb (C) and 50–250 kb (D). Chromosome size DNA was isolated from yeast transformants, separated by CHEF gel electrophoresis, and blot-hybridized with an Alu probe for visualization of the linearized YAC DNA molecules. The molecular weight of each band was estimated by comparing it with the high molecular weight marker. Two hundred YACs were analyzed.

Article Snippet: Commercial female genomic DNA (catalog number G1521; Promega) and human genomic DNA (catalog number G3041; Promega) were used for cloning the human HPRT gene.

Techniques: Generated, Cloning, Plasmid Preparation, High Molecular Weight, Isolation, Nucleic Acid Electrophoresis, Molecular Weight, Marker

Journal:

Article Title: Optimum conditions for selective isolation of genes from complex genomes by transformation-associated recombination cloning

doi:

Figure Lengend Snippet: Effect of DNA concentration on yield of transformants during TAR cloning. Different amounts of human or mouse genomic DNA prepared in aqueous solutions with size fragments roughly between 50 and 200 kb were presented to yeast spheroplasts together with 1.0 µg of an Alu-containing TAR vector (pNKBAC39 or pVC-B1-B2) containing B1 and B2 mouse-specific repeats. Open and black circles represent experiments with human and mouse DNA, respectively. The y-axis represents the number of colonies per experiment.

Article Snippet: Commercial female genomic DNA (catalog number G1521; Promega) and human genomic DNA (catalog number G3041; Promega) were used for cloning the human HPRT gene.

Techniques: Concentration Assay, Cloning, Plasmid Preparation