Journal: Cell Reports Methods

Article Title: MASTR-seq enables multiplexed analysis of short tandem repeats with sequencing

doi: 10.1016/j.crmeth.2026.101341

Figure Lengend Snippet: Schematic of MASTR-seq procedure Day 1: (Step 1) Samples are dissociated to single-cell suspension, and cells are lysed. RNA and protein are digested by RNase A and proteinase K, respectively. DNA is subsequently purified by commercial HMW gDNA extraction kit or phenol:chloroform:isoamyl alcohol (PCIA, 25:24:1)-based method. (Step 2) HMW genomic DNA quality control assays are performed using Nanodrop for DNA quality, Qubit for quantifying DNA concentration, and gel electrophoresis for DNA integrity. Day 2: crRNA/tracrRNA annealing and Cas9 RNP assembling are completed (not shown in this schematic) before (step 3) HMW DNA dephosphorylation, (step 4) Cas9-mediated RNP cleavage, and (step 5) dA-tailing. (Step 6) The quality of Cas9-mediated RNP cleavage efficiency is assessed by PCR amplification of the target region using flanking primers. (Step 7) Cas9-RNP-cleaved products are purified from salts using sodium acetate-ethanol precipitation. Days 2–3: (step 8) target DNA fragments are precisely size-selected using BluePippin. Day 4: (step 9) samples are barcoded in a PCR-free manner and pooled for multiplexing using nanopore native barcodes. (Step 10) Adapters are ligated onto the multiplexed DNA. Days 4–6: (step 11) DNA is loaded onto the Nanopore flow cell and sequenced for 48 h (Step 12) Raw data are processed by basecalling, aligning and demultiplexing sequentially using Dorado. Custom computational tools are employed for the analyses of single-allele DNA methylation and STR tract length. See also .

Article Snippet: In applications with 5 × 10 6 cultured cell numbers or 20 mg clinical sample, we can obtain HMW DNA using commercial kits (NEB #T3060S/3050S) and consistently achieve >20 μg high-quality HMW DNA ( ).

Techniques: Single Cell, Suspension, Purification, Extraction, Control, Concentration Assay, Nucleic Acid Electrophoresis, De-Phosphorylation Assay, Amplification, Ethanol Precipitation, Multiplexing, DNA Methylation Assay

Journal: Scientific Reports

Article Title: Comparative evaluation of commercial DNA isolation approaches for nanopore-only bacterial genome assembly and plasmid recovery

doi: 10.1038/s41598-024-78066-2

Figure Lengend Snippet: Influence of commercial DNA extraction kits; ZymoBIOMICS™ DNA Miniprep Kit (ZM, Blue), Nanobind CBB Big DNA Kit (NB, orange), Fire Monkey High Molecular Weight (HMW) DNA Extraction Kit (FM, grey) and MagNaPure 96 system (RO, yellow) on DNA concentration (ng µL –1 ) ( a ) and DNA purity in ratio of A260/280 ( b ) and A260/230 ( c ) of eight pathogenic bacteria. Hatched green lines in ( b ) and ( c ) indicate recommended intervals. The values show the mean ± S.E. of three independent replicates and different letters indicate significantly difference between treatments according Duncan’s multiple range test ( p <0.05).

Article Snippet: In this work, we initiated our investigation by an evaluation of three commercial DNA extraction kits: (1) ZM: ZymoBIOMICS™ DNA Miniprep Kit (D4300, Zymo Research, USA), (2) NB: Nanobind CBB Big DNA Kit (Circulomics, USA), (3) FM: Fire Monkey High Molecular Weight (HMW) DNA Extraction Kit (Revolugen, UK), and (4) RO: one robot-based extraction system (MagNaPure 96 system; Roche, Switzerland).

Techniques: DNA Extraction, Molecular Weight, Concentration Assay, Bacteria

Journal: Scientific Reports

Article Title: Comparative evaluation of commercial DNA isolation approaches for nanopore-only bacterial genome assembly and plasmid recovery

doi: 10.1038/s41598-024-78066-2

Figure Lengend Snippet: Genome assembly statistics for all sequencing reads of eight pathogenic bacteria extracted by four different benchmark DNA extraction kits; ZymoBIOMICS™ DNA miniprep kit (ZM), nanobind CBB Big DNA Kit (NB), Fire Monkey High Molecular Weight (HMW) DNA extraction kit (FM) and MagNaPure 96 system (RO). The best assembly statistics from three independent replicates are shown. C, chromosome (chromosome contig); and P, plasmid (plasmid contig).

Article Snippet: In this work, we initiated our investigation by an evaluation of three commercial DNA extraction kits: (1) ZM: ZymoBIOMICS™ DNA Miniprep Kit (D4300, Zymo Research, USA), (2) NB: Nanobind CBB Big DNA Kit (Circulomics, USA), (3) FM: Fire Monkey High Molecular Weight (HMW) DNA Extraction Kit (Revolugen, UK), and (4) RO: one robot-based extraction system (MagNaPure 96 system; Roche, Switzerland).

Techniques: Sequencing, Bacteria, DNA Extraction, Molecular Weight, Plasmid Preparation

Journal: Scientific Reports

Article Title: Comparative evaluation of commercial DNA isolation approaches for nanopore-only bacterial genome assembly and plasmid recovery

doi: 10.1038/s41598-024-78066-2

Figure Lengend Snippet: Influence of genome coverage on raw read length, number of contigs, percentage of completeness and contig N50 of Enterococcus faecium (Efa, a), Streptococcus agalactiae (Sag, b), Streptococcus suis (Ssu, c), and Staphylococcus aureus (Sau, d) extracted by ZymoBIOMICS™ DNA Miniprep Kit (ZM, blue), Nanobind CBB Big DNA Kit (NB, orange), Fire Monkey High Molecular Weight (HMW) DNA Extraction Kit (FM, grey) and MagNaPure 96 system (RO, yellow). Panels without any dots represent exclusions due to lack of coverage to subsample at this depth.

Article Snippet: In this work, we initiated our investigation by an evaluation of three commercial DNA extraction kits: (1) ZM: ZymoBIOMICS™ DNA Miniprep Kit (D4300, Zymo Research, USA), (2) NB: Nanobind CBB Big DNA Kit (Circulomics, USA), (3) FM: Fire Monkey High Molecular Weight (HMW) DNA Extraction Kit (Revolugen, UK), and (4) RO: one robot-based extraction system (MagNaPure 96 system; Roche, Switzerland).

Techniques: Molecular Weight, DNA Extraction

Journal: Scientific Reports

Article Title: Comparative evaluation of commercial DNA isolation approaches for nanopore-only bacterial genome assembly and plasmid recovery

doi: 10.1038/s41598-024-78066-2

Figure Lengend Snippet: Influence of genome coverage on raw read length, number of contigs, contig N50 , and percentage of completeness of Acinetobacter baumannii (Aba, a), Klebsiella pneumoniae (Kpn, b), Pseudomonas aeruginosa (Psu, c), and Salmonella sp. group D (Sgd, d) extracted by ZymoBIOMICS™ DNA Miniprep Kit (ZM, blue), Nanobind CBB Big DNA Kit (NB, orange), Fire Monkey High Molecular Weight (HMW) DNA Extraction Kit (FM, grey) and MagNaPure 96 system (RO, yellow).

Article Snippet: In this work, we initiated our investigation by an evaluation of three commercial DNA extraction kits: (1) ZM: ZymoBIOMICS™ DNA Miniprep Kit (D4300, Zymo Research, USA), (2) NB: Nanobind CBB Big DNA Kit (Circulomics, USA), (3) FM: Fire Monkey High Molecular Weight (HMW) DNA Extraction Kit (Revolugen, UK), and (4) RO: one robot-based extraction system (MagNaPure 96 system; Roche, Switzerland).

Techniques: Molecular Weight, DNA Extraction

Journal: Scientific Reports

Article Title: Comparative evaluation of commercial DNA isolation approaches for nanopore-only bacterial genome assembly and plasmid recovery

doi: 10.1038/s41598-024-78066-2

Figure Lengend Snippet: Influence of genome coverages on percentage of plasmid coverage and circularization (N, non-circular plasmid; Y, circular plasmid) of Enterococcus faecium (Efa, a), Staphylococcus aureus (Sau, b), Acinetobacter baumannii (Aba, c), Klebsiella pneumoniae (Kpn, d), and Salmonella sp. group D (Sgd, e) extracted by ZymoBIOMICS™ DNA Miniprep Kit (ZM, blue), Nanobind CBB Big DNA Kit (NB, orange), Fire Monkey High Molecular Weight (HMW) DNA Extraction Kit (FM, grey) and MagNaPure 96 system (RO, yellow). The percentage of plasmid coverage was calculated by comparing the length of the recovered plasmid to that of the hybrid-reference plasmid.

Article Snippet: In this work, we initiated our investigation by an evaluation of three commercial DNA extraction kits: (1) ZM: ZymoBIOMICS™ DNA Miniprep Kit (D4300, Zymo Research, USA), (2) NB: Nanobind CBB Big DNA Kit (Circulomics, USA), (3) FM: Fire Monkey High Molecular Weight (HMW) DNA Extraction Kit (Revolugen, UK), and (4) RO: one robot-based extraction system (MagNaPure 96 system; Roche, Switzerland).

Techniques: Plasmid Preparation, Molecular Weight, DNA Extraction

Journal: Scientific Reports

Article Title: Comparative evaluation of commercial DNA isolation approaches for nanopore-only bacterial genome assembly and plasmid recovery

doi: 10.1038/s41598-024-78066-2

Figure Lengend Snippet: Summary of DNA isolation kit features used in this study.

Article Snippet: In this work, we initiated our investigation by an evaluation of three commercial DNA extraction kits: (1) ZM: ZymoBIOMICS™ DNA Miniprep Kit (D4300, Zymo Research, USA), (2) NB: Nanobind CBB Big DNA Kit (Circulomics, USA), (3) FM: Fire Monkey High Molecular Weight (HMW) DNA Extraction Kit (Revolugen, UK), and (4) RO: one robot-based extraction system (MagNaPure 96 system; Roche, Switzerland).

Techniques: DNA Extraction, Extraction