Journal: BioMed Research International

Article Title: Construction and Preliminary Characterization Analysis of Wuzhishan Miniature Pig Bacterial Artificial Chromosome Library with Approximately 8-Fold Genome Equivalent Coverage

doi: 10.1155/2013/587493

Figure Lengend Snippet: Characterization of digested BAC vector and PFGE size fractionation of digested HMW by Hind III. (a) Characterization of digested vector by electrophoresis; M: 1 kb DNA ladder; 1: BAC vector digested by Hind III; 2: BAC vector digested by B am H I and X ho I; (b) initial PFGE size fractionation of partially digested HMW; M: Lamda Ladder PFG Marker; 1, 5, 10, 15, 20, and 50 U/ μ gDNA, respectively; (c) second-size selection PFGE, used to eliminate smaller DNA molecules; M: Lamda Ladder PFG Marker; 100–200 kb, 200–300 kb, 300–400 kb, respectively; (d) quantification of Wuzhishan miniature pig genomic DNA.1: 100–200 kb DNA; 2: 200–300 kb DNA; 3: 300–400 kb DNA.

Article Snippet: After establishing the minimal amount of restriction enzyme required for complete digestion of the vector in a series of test reactions, the vector DNA was digested with an appropriate amount of Hind III restriction endonuclease (New England Biolabs) and treated with alkaline phosphatase (CIAP) for dephosphorylation [ ].

Techniques: Plasmid Preparation, Fractionation, Electrophoresis, Marker, Selection

Journal: BioMed Research International

Article Title: Construction and Preliminary Characterization Analysis of Wuzhishan Miniature Pig Bacterial Artificial Chromosome Library with Approximately 8-Fold Genome Equivalent Coverage

doi: 10.1155/2013/587493

Figure Lengend Snippet: Summary of the Wuzhishan miniature pig BAC library.

Article Snippet: After establishing the minimal amount of restriction enzyme required for complete digestion of the vector in a series of test reactions, the vector DNA was digested with an appropriate amount of Hind III restriction endonuclease (New England Biolabs) and treated with alkaline phosphatase (CIAP) for dephosphorylation [ ].

Techniques: Clone Assay

Journal: Science Advances

Article Title: Concordance of hydrogen peroxide–induced 8-oxo-guanine patterns with two cancer mutation signatures of upper GI tract tumors

doi: 10.1126/sciadv.abn3815

Figure Lengend Snippet: ( A ) Outline of the CD-seq and enzymatic cleavage methods used to map oxidized thymines at single-base resolution. ( B ) Base resolution view of oxidized thymines along the human NOD1 and CFAP77 genes. Orange and lavender segments represent the divergent read pairs. Green arrows indicate single-base gaps matching the excised oxidized DNA base. ( C ) Heatmaps and metagene profiles of permanganate-oxidized thymines along human genes. DNA from untreated cells produced very few divergent read pairs, and the data could not be used in similar displays. Different cleavage enzymes, Endo III or NEIL1, or a combination of the two was used.

Article Snippet: DNA base damage was evaluated by treatment with Endo III (NEB) and/or NEIL1 (OriGene, Rockville, MD) DNA glycosylases, followed by Endo IV and S1 treatment, and then observed on a 1% agarose gel.

Techniques: Produced

Journal: Science Advances

Article Title: Concordance of hydrogen peroxide–induced 8-oxo-guanine patterns with two cancer mutation signatures of upper GI tract tumors

doi: 10.1126/sciadv.abn3815

Figure Lengend Snippet: ( A ) Trinucleotide sequence specificity. Forty-eight trinucleotide contexts were analyzed, but the gapped reads occurred chiefly at trinucleotides with central thymine. Different enzymes (Endo III and NEIL1 in combination and alone) were used to excise the oxidized bases. ( B ) Sequence context of thymine oxidation by permanganate using logo plot analysis. Position 11 represents the permanganate-oxidized thymine base. At each base position, the height of each letter represents the relative frequency of that nucleic acid base. Note the enrichment of A or C 3′ to the thymine.

Article Snippet: DNA base damage was evaluated by treatment with Endo III (NEB) and/or NEIL1 (OriGene, Rockville, MD) DNA glycosylases, followed by Endo IV and S1 treatment, and then observed on a 1% agarose gel.

Techniques: Sequencing

Journal: Frontiers in Immunology

Article Title: Genotoxic Mechanism of Action of TBBPA, TBBPS and Selected Bromophenols in Human Peripheral Blood Mononuclear Cells

doi: 10.3389/fimmu.2022.869741

Figure Lengend Snippet: Oxidative damage to pyrimidines in DNA. Oxidative damage to DNA pyrimidines in human PBMCs treated with TBBPA, TBBPS, 2,4,6-TBP and PBP at the concentrations of 0.01 µg/mL, 0.1 µg/mL and 1 µg/mL for 24 h. DNA damage was measured as the percentage of DNA in the comet tail using the enzyme endo III and the alkaline version of the comet assay. The mean ± SD was calculated for 3 experiments (3 blood donors). Statistically different from negative control at *P<0.05. Statistical analysis was conducted using one-way ANOVA and a posteriori Tukey test.

Article Snippet: Endonuclease III and human 8-oxoguanine DNA glycosylase were bought in New England BioLabs (USA).

Techniques: Single Cell Gel Electrophoresis, Negative Control