Structured Review

Toyobo kod fx neo dna polymerase
Kod Fx Neo Dna Polymerase, supplied by Toyobo, used in various techniques. Bioz Stars score: 99/100, based on 114 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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Average 99 stars, based on 114 article reviews
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kod fx neo dna polymerase - by Bioz Stars, 2020-01
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Clone Assay:

Article Title: A GFP-tagged version of the pseudorabies virus protein UL56 localizes to the Golgi and trans-Golgi network through a predicted C-terminal leucine-rich helix in transfected cells
Article Snippet: The PCR was performed using KOD FX Neo DNA polymerase (TOYOBO, Japan) according to the manufacturer’s instructions at a final 50 μL reaction volume containing 2× buffer (25 μL), forward primer (2.5 μL; 10 μM), reverse primer (2.5 μL; 10 μM), KOD FX Neo (1.25 μL; 1 unit/μL), dNTP (7.5 μL; 2 mM each), genomic DNA (~ 200 ng) and ddH2 O. .. The designated plasmids pAcGFP-UL56, p3 × Flag-UL56 or pCMV-HA-UL56 were constructed by cloning the UL56 PCR product into pAcGFP1-C1, p3 × Flag, or pCMV-HA at indicated restriction sites (Additional file : Table S1).

Article Title: Redox environment is an intracellular factor to operate distinct pathways for aggregation of Cu,Zn-superoxide dismutase in amyotrophic lateral sclerosis
Article Snippet: PLASMIDS, E. coli STRAINS AND PROTEIN EXPRESSION A vector, pET15b (Novagen), was used for the construction of plasmids expressing human SOD1 without any tags; a SalI site was first introduced between BamHI and Bpu1102I sites of pET15b, and cDNA of human SOD1 was then cloned between NcoI and SalI site. .. Mutations were introduced by an inverse PCR method using KOD-FX-neo DNA polymerase (TOYOBO), and all constructs used in this study were confirmed by DNA sequencing.

Article Title: Engineering a synthetic pathway for maleate in Escherichia coli
Article Snippet: Strains and plasmid construction E. coli NovaBlue competent cells (Novagen, Cambridge, MA, USA) were used for gene cloning. .. Polymerase chain reaction (PCR) was performed using the KOD FX Neo DNA polymerase (Toyobo, Osaka, Japan) and the appropriate primer pairs.

Article Title: Segmental and tandem chromosome duplications led to divergent evolution of the chalcone synthase gene family in Phalaenopsis orchids
Article Snippet: Paragraph title: Cloning and labelling of DNA probes for fluorescence in situ hybridization (FISH) mapping ... The CHS-containing DNA fragments were amplified by PCR, which was performed using 10 ng of genomic DNA, 1× PCR buffer, 0.4 mm of each dNTP, 0.3 μm each of forward and reverse primer, and 1.0 U of KOD FX Neo DNA polymerase (TOYOBO, Osaka, Japan) in a total reaction volume of 50 μL.

Article Title: Evaluation of ATM heterozygous mutations underlying individual differences in radiosensitivity using genome editing in human cultured cells
Article Snippet: .. PCR-based and Sanger sequencing genotyping of the neomycin-resistant clones PCR genotyping to screen for the ATM -edited hTERT-RPE1 cell clones was performed using extracted genomic DNA as a template and KOD-FX Neo DNA polymerase (TOYOBO) with three types of primer pair: the first primer pair consisted of ATM gene exon 11 forward Fp (5′-TCCTGCAGTATGCTGTTTGACTTTGGC-3′) and ATM gene exon 11 reverse Rp (5′-CTGTGAAGAATTGGAGGCACTTCTGTGC-3′) primers for detecting ATM gene exon 11; the second primer pair consisted of ATM gene exon 11 forward Fp and Neo r -reverse Np (5′-GCGGATCTGACGGTTCACTAAACCAGC-3′) primers for detecting the forward insertion of the drug-resistant gene cassette into ATM gene; and the third primer pair consisted of ATM gene exon 11 reverse Rp and Neo r -reverse Np primers for detecting the reversed insertion. ..

Amplification:

Article Title: Chitin-based barrier immunity and its loss predated mucus-colonization by indigenous gut microbiota
Article Snippet: .. Specimens were treated with 180 μL of 50 mM NaOH at 95 °C for 10 min, mixed with 20 μL of 1 M Tri-HCl (pH 8.0) and centrifuged at 12,500×g at RT for 10 min. Supernatants were collected for PCR amplification using KOD FX Neo DNA polymerase (Toyobo, Japan) and 16S universal primers: 27f (AGAGTTTGATCMTGGCTCAG) and 1492r (TACGGYTACCTTGTTACGACTT). .. Reaction products were assessed by agarose gel electrophoresis followed by SYBR safe staining (Thermo Fisher Scientific, USA).

Article Title: Impaired neuronal KCC2 function by biallelic SLC12A5 mutations in migrating focal seizures and severe developmental delay
Article Snippet: .. SLC12A5 coding exons were amplified by PCR using KOD FX Neo DNA polymerase (Toyobo), with amplified DNA as the template. .. DNA libraries were prepared by using the Nextera DNA Sample Preparation Kit (Illumina) and sequenced on the MiSeq (Illumina) with 150 bp paired-end reads.

Article Title: A GFP-tagged version of the pseudorabies virus protein UL56 localizes to the Golgi and trans-Golgi network through a predicted C-terminal leucine-rich helix in transfected cells
Article Snippet: Plasmid construction and transfection The UL56 gene was amplified by polymerase chain reaction (PCR) from the extracted viral genome with primers UL56 GFP F/R, UL56 Flag F/R or UL56 HA F/R, respectively (Additional file : Table S1). .. The PCR was performed using KOD FX Neo DNA polymerase (TOYOBO, Japan) according to the manufacturer’s instructions at a final 50 μL reaction volume containing 2× buffer (25 μL), forward primer (2.5 μL; 10 μM), reverse primer (2.5 μL; 10 μM), KOD FX Neo (1.25 μL; 1 unit/μL), dNTP (7.5 μL; 2 mM each), genomic DNA (~ 200 ng) and ddH2 O.

Article Title: Segmental and tandem chromosome duplications led to divergent evolution of the chalcone synthase gene family in Phalaenopsis orchids
Article Snippet: .. The CHS-containing DNA fragments were amplified by PCR, which was performed using 10 ng of genomic DNA, 1× PCR buffer, 0.4 mm of each dNTP, 0.3 μm each of forward and reverse primer, and 1.0 U of KOD FX Neo DNA polymerase (TOYOBO, Osaka, Japan) in a total reaction volume of 50 μL. .. The PCR step-down cycling conditions were as follows: 94 °C for 2 min; five cycles of 98 °C for 10 s and 70 °C for 3.5 min; five cycles of 98 °C for 10 s and 68 °C for 3.5 min; five cycles of 98 °C for 10 s and 65 °C for 3.5 min; 20 cycles of 98 °C for 10 s and 60 °C for 3.5 min; 68 °C for 7 min; and then 25° C for 10 s. The PCR products were then cloned into the pZeroback vector (TIANGEN Biotech, Beijing, China) and transformed into Escherichia coli DH5α.

Article Title: A low-frequency IL4R locus variant in Japanese patients with intravenous immunoglobulin therapy-unresponsive Kawasaki disease
Article Snippet: .. Candidate genetic regions were individually amplified with specific primers (Additional file : Table S1, S2), KOD FX neo DNA polymerase (Toyobo, Osaka, Japan), and 200 ng of pooled genome as a template. .. Amplified products were purified with Agencourt AMPure XP (Beckman Coulter, Brea, CA, USA) and shearing was performed by sonication.

Article Title: Overexpression of Tisochrysis lutea Akd1 identifies a key cold-induced alkenone desaturase enzyme
Article Snippet: .. The complete ORF encoding TOD-1 and -2 was amplified with the following primer pairs; eORF2F1 and eORF2aR1 for TOD-1 , and eORF2F1 and eORF2bR1 for TOD-2 using KOD FX Neo DNA polymerase (Toyobo). .. Expression of TOD-1 and -2 was investigated by quantitative real-time PCR (qRT-PCR) as follows: (1) Total RNA was extracted from the cells using Trizol (Invitrogen) and the RNeasy Plant Mini Kit (Qiagen); the extracted RNA was treated with the TurboDNase Kit (Ambion). (2) Using 1 μg of total RNA as the template, cDNA was synthesised using the poly-T20 primer and SuperScriptIII reverse transcriptase (Invitrogen) in a 20 μL reaction mixture. (3) To examine the expression of TOD-1 and -2 , qRT-PCR was performed using 5 ng of cDNA as a template on the Applied Biosystems StepOnePlus Real-Time PCR System (ThermoFisher Scientific) using RT-qPCR SYBR GREEN Reagents (GoTaq qPCR Master Mix, Promega).

Article Title: Dynamics of Sulfate-Reducing Bacteria Community Structure in Surface Sediment of a Seasonally Hypoxic Enclosed Bay
Article Snippet: Briefly, extracted DNA was subjected to the PCR amplification of bacterial dsrA regions using the universal primer sets DSR1Fmix (containing DSR1F, DSR1Fa, DSR1Fb, DSR1Fc, and DSR1Fd) ( , , ) and DSR1334R ( ). .. PCR was performed in a 30-μL reaction mixture using PCR buffer, 15 U of KOD FX Neo DNA polymerase (Toyobo, Osaka, Japan), 12 nmol of dNTP mix, 6 pmol of each primer, and 30 ng of extracted DNA.

Article Title: Evaluation of ATM heterozygous mutations underlying individual differences in radiosensitivity using genome editing in human cultured cells
Article Snippet: PCR-based and Sanger sequencing genotyping of the neomycin-resistant clones PCR genotyping to screen for the ATM -edited hTERT-RPE1 cell clones was performed using extracted genomic DNA as a template and KOD-FX Neo DNA polymerase (TOYOBO) with three types of primer pair: the first primer pair consisted of ATM gene exon 11 forward Fp (5′-TCCTGCAGTATGCTGTTTGACTTTGGC-3′) and ATM gene exon 11 reverse Rp (5′-CTGTGAAGAATTGGAGGCACTTCTGTGC-3′) primers for detecting ATM gene exon 11; the second primer pair consisted of ATM gene exon 11 forward Fp and Neo r -reverse Np (5′-GCGGATCTGACGGTTCACTAAACCAGC-3′) primers for detecting the forward insertion of the drug-resistant gene cassette into ATM gene; and the third primer pair consisted of ATM gene exon 11 reverse Rp and Neo r -reverse Np primers for detecting the reversed insertion. .. The wild-type-sized PCR products amplified with the third primer pair were directly sequenced using 3130 Genetic Analyzer (Applied Biosystems).

Article Title: Wild-type Cu/Zn-superoxide dismutase is misfolded in cerebrospinal fluid of sporadic amyotrophic lateral sclerosis
Article Snippet: .. Each of five exons in the SOD1 gene was amplified with PCR using KOD FX Neo DNA polymerase (TOYOBO). .. Primers used for amplification of the exons are summarized in Additional file : Table S1.

Synthesized:

Article Title: A GFP-tagged version of the pseudorabies virus protein UL56 localizes to the Golgi and trans-Golgi network through a predicted C-terminal leucine-rich helix in transfected cells
Article Snippet: The PCR was performed using KOD FX Neo DNA polymerase (TOYOBO, Japan) according to the manufacturer’s instructions at a final 50 μL reaction volume containing 2× buffer (25 μL), forward primer (2.5 μL; 10 μM), reverse primer (2.5 μL; 10 μM), KOD FX Neo (1.25 μL; 1 unit/μL), dNTP (7.5 μL; 2 mM each), genomic DNA (~ 200 ng) and ddH2 O. .. Complementary oligonucleotides used for constructing shorter UL56 truncations were synthesized and annealed to form a DNA duplex containing cohesive ends, and then cloned into Xho I and Hin dIII digested pAcGFP1-C1 (Additional file : Tables S2-S4).

Construct:

Article Title: A GFP-tagged version of the pseudorabies virus protein UL56 localizes to the Golgi and trans-Golgi network through a predicted C-terminal leucine-rich helix in transfected cells
Article Snippet: The PCR was performed using KOD FX Neo DNA polymerase (TOYOBO, Japan) according to the manufacturer’s instructions at a final 50 μL reaction volume containing 2× buffer (25 μL), forward primer (2.5 μL; 10 μM), reverse primer (2.5 μL; 10 μM), KOD FX Neo (1.25 μL; 1 unit/μL), dNTP (7.5 μL; 2 mM each), genomic DNA (~ 200 ng) and ddH2 O. .. The designated plasmids pAcGFP-UL56, p3 × Flag-UL56 or pCMV-HA-UL56 were constructed by cloning the UL56 PCR product into pAcGFP1-C1, p3 × Flag, or pCMV-HA at indicated restriction sites (Additional file : Table S1).

Article Title: Redox environment is an intracellular factor to operate distinct pathways for aggregation of Cu,Zn-superoxide dismutase in amyotrophic lateral sclerosis
Article Snippet: .. Mutations were introduced by an inverse PCR method using KOD-FX-neo DNA polymerase (TOYOBO), and all constructs used in this study were confirmed by DNA sequencing. .. Competent cells of E. coli , BL21(DE3; New England Biolabs) and SHuffleTM T7 Express lysY (New England Biolabs), were transformed with a plasmid.

Real-time Polymerase Chain Reaction:

Article Title: Overexpression of Tisochrysis lutea Akd1 identifies a key cold-induced alkenone desaturase enzyme
Article Snippet: The complete ORF encoding TOD-1 and -2 was amplified with the following primer pairs; eORF2F1 and eORF2aR1 for TOD-1 , and eORF2F1 and eORF2bR1 for TOD-2 using KOD FX Neo DNA polymerase (Toyobo). .. Expression of TOD-1 and -2 was investigated by quantitative real-time PCR (qRT-PCR) as follows: (1) Total RNA was extracted from the cells using Trizol (Invitrogen) and the RNeasy Plant Mini Kit (Qiagen); the extracted RNA was treated with the TurboDNase Kit (Ambion). (2) Using 1 μg of total RNA as the template, cDNA was synthesised using the poly-T20 primer and SuperScriptIII reverse transcriptase (Invitrogen) in a 20 μL reaction mixture. (3) To examine the expression of TOD-1 and -2 , qRT-PCR was performed using 5 ng of cDNA as a template on the Applied Biosystems StepOnePlus Real-Time PCR System (ThermoFisher Scientific) using RT-qPCR SYBR GREEN Reagents (GoTaq qPCR Master Mix, Promega).

Article Title: Masc‐induced dosage compensation in silkworm cultured cells
Article Snippet: PCR was performed using KOD FX‐neo DNA polymerase (TOYOBO, Osaka, Japan). .. Quantitative RT‐PCR (RT‐qPCR) of BmIMPM and rp49 was performed using a KAPA™ SYBR FAST qPCR kit (Kapa Biosystems, Wilmington, MA, USA), as previously described .

Expressing:

Article Title: Redox environment is an intracellular factor to operate distinct pathways for aggregation of Cu,Zn-superoxide dismutase in amyotrophic lateral sclerosis
Article Snippet: Paragraph title: PLASMIDS, E. coli STRAINS AND PROTEIN EXPRESSION ... Mutations were introduced by an inverse PCR method using KOD-FX-neo DNA polymerase (TOYOBO), and all constructs used in this study were confirmed by DNA sequencing.

Article Title: Overexpression of Tisochrysis lutea Akd1 identifies a key cold-induced alkenone desaturase enzyme
Article Snippet: Paragraph title: Expression analysis of TOD-1 and -2 ... The complete ORF encoding TOD-1 and -2 was amplified with the following primer pairs; eORF2F1 and eORF2aR1 for TOD-1 , and eORF2F1 and eORF2bR1 for TOD-2 using KOD FX Neo DNA polymerase (Toyobo).

Transformation Assay:

Article Title: Redox environment is an intracellular factor to operate distinct pathways for aggregation of Cu,Zn-superoxide dismutase in amyotrophic lateral sclerosis
Article Snippet: Mutations were introduced by an inverse PCR method using KOD-FX-neo DNA polymerase (TOYOBO), and all constructs used in this study were confirmed by DNA sequencing. .. Competent cells of E. coli , BL21(DE3; New England Biolabs) and SHuffleTM T7 Express lysY (New England Biolabs), were transformed with a plasmid.

Article Title: Segmental and tandem chromosome duplications led to divergent evolution of the chalcone synthase gene family in Phalaenopsis orchids
Article Snippet: The CHS-containing DNA fragments were amplified by PCR, which was performed using 10 ng of genomic DNA, 1× PCR buffer, 0.4 mm of each dNTP, 0.3 μm each of forward and reverse primer, and 1.0 U of KOD FX Neo DNA polymerase (TOYOBO, Osaka, Japan) in a total reaction volume of 50 μL. .. The PCR step-down cycling conditions were as follows: 94 °C for 2 min; five cycles of 98 °C for 10 s and 70 °C for 3.5 min; five cycles of 98 °C for 10 s and 68 °C for 3.5 min; five cycles of 98 °C for 10 s and 65 °C for 3.5 min; 20 cycles of 98 °C for 10 s and 60 °C for 3.5 min; 68 °C for 7 min; and then 25° C for 10 s. The PCR products were then cloned into the pZeroback vector (TIANGEN Biotech, Beijing, China) and transformed into Escherichia coli DH5α.

Derivative Assay:

Article Title: Segmental and tandem chromosome duplications led to divergent evolution of the chalcone synthase gene family in Phalaenopsis orchids
Article Snippet: Cloning and labelling of DNA probes for fluorescence in situ hybridization (FISH) mapping The cDNA sequences of CHS genes in P. aphrodite derived from the Orchidstra 2.0 database were first used as queries in a BLAST algorithm-based search of the assembled genomic shotgun sequences of P. aphrodite . .. The CHS-containing DNA fragments were amplified by PCR, which was performed using 10 ng of genomic DNA, 1× PCR buffer, 0.4 mm of each dNTP, 0.3 μm each of forward and reverse primer, and 1.0 U of KOD FX Neo DNA polymerase (TOYOBO, Osaka, Japan) in a total reaction volume of 50 μL.

Transfection:

Article Title: A GFP-tagged version of the pseudorabies virus protein UL56 localizes to the Golgi and trans-Golgi network through a predicted C-terminal leucine-rich helix in transfected cells
Article Snippet: Paragraph title: Plasmid construction and transfection ... The PCR was performed using KOD FX Neo DNA polymerase (TOYOBO, Japan) according to the manufacturer’s instructions at a final 50 μL reaction volume containing 2× buffer (25 μL), forward primer (2.5 μL; 10 μM), reverse primer (2.5 μL; 10 μM), KOD FX Neo (1.25 μL; 1 unit/μL), dNTP (7.5 μL; 2 mM each), genomic DNA (~ 200 ng) and ddH2 O.

Article Title: Masc‐induced dosage compensation in silkworm cultured cells
Article Snippet: Reverse transcription polymerase chain reaction (RT‐PCR) Total RNA was prepared from transfected cells using TRIzol reagent (Invitrogen) and used for reverse transcription using avian myeloblastosis virus reverse transcriptase with an oligo‐dT primer (TaKaRa, Kusatsu, Japan). .. PCR was performed using KOD FX‐neo DNA polymerase (TOYOBO, Osaka, Japan).

Inverse PCR:

Article Title: Redox environment is an intracellular factor to operate distinct pathways for aggregation of Cu,Zn-superoxide dismutase in amyotrophic lateral sclerosis
Article Snippet: .. Mutations were introduced by an inverse PCR method using KOD-FX-neo DNA polymerase (TOYOBO), and all constructs used in this study were confirmed by DNA sequencing. .. Competent cells of E. coli , BL21(DE3; New England Biolabs) and SHuffleTM T7 Express lysY (New England Biolabs), were transformed with a plasmid.

Nick Translation:

Article Title: Segmental and tandem chromosome duplications led to divergent evolution of the chalcone synthase gene family in Phalaenopsis orchids
Article Snippet: The CHS-containing DNA fragments were amplified by PCR, which was performed using 10 ng of genomic DNA, 1× PCR buffer, 0.4 mm of each dNTP, 0.3 μm each of forward and reverse primer, and 1.0 U of KOD FX Neo DNA polymerase (TOYOBO, Osaka, Japan) in a total reaction volume of 50 μL. .. Plasmid DNA was extracted using a Plasmid Miniprep Purification Kit (GMbiolab, Taichung, Taiwan), and 1.8 μg of plasmid DNA was labelled with either biotin-dUTP or digoxigenin-dUTP using standard nick translation following the manufacturer’s protocol (Roche, Basel, Switzerland).

Cell Culture:

Article Title: Redox environment is an intracellular factor to operate distinct pathways for aggregation of Cu,Zn-superoxide dismutase in amyotrophic lateral sclerosis
Article Snippet: Mutations were introduced by an inverse PCR method using KOD-FX-neo DNA polymerase (TOYOBO), and all constructs used in this study were confirmed by DNA sequencing. .. E. coli cells harboring a plasmid were cultured in Luria-Broth media containing 50 mg/L ampicillin (LB/Amp) by shaking at 200 rpm, and the expression of SOD1 proteins was induced with 1 mM isopropyl 1-thio-β-D-galactopyranoside at 37°C for 6 h. To test effects of Zn2 + ions on SOD1 aggregation, 1 mM ZnSO4 was further added at the induction of protein expression.

Polymerase Chain Reaction:

Article Title: Chitin-based barrier immunity and its loss predated mucus-colonization by indigenous gut microbiota
Article Snippet: .. Specimens were treated with 180 μL of 50 mM NaOH at 95 °C for 10 min, mixed with 20 μL of 1 M Tri-HCl (pH 8.0) and centrifuged at 12,500×g at RT for 10 min. Supernatants were collected for PCR amplification using KOD FX Neo DNA polymerase (Toyobo, Japan) and 16S universal primers: 27f (AGAGTTTGATCMTGGCTCAG) and 1492r (TACGGYTACCTTGTTACGACTT). .. Reaction products were assessed by agarose gel electrophoresis followed by SYBR safe staining (Thermo Fisher Scientific, USA).

Article Title: Impaired neuronal KCC2 function by biallelic SLC12A5 mutations in migrating focal seizures and severe developmental delay
Article Snippet: .. SLC12A5 coding exons were amplified by PCR using KOD FX Neo DNA polymerase (Toyobo), with amplified DNA as the template. .. DNA libraries were prepared by using the Nextera DNA Sample Preparation Kit (Illumina) and sequenced on the MiSeq (Illumina) with 150 bp paired-end reads.

Article Title: A GFP-tagged version of the pseudorabies virus protein UL56 localizes to the Golgi and trans-Golgi network through a predicted C-terminal leucine-rich helix in transfected cells
Article Snippet: .. The PCR was performed using KOD FX Neo DNA polymerase (TOYOBO, Japan) according to the manufacturer’s instructions at a final 50 μL reaction volume containing 2× buffer (25 μL), forward primer (2.5 μL; 10 μM), reverse primer (2.5 μL; 10 μM), KOD FX Neo (1.25 μL; 1 unit/μL), dNTP (7.5 μL; 2 mM each), genomic DNA (~ 200 ng) and ddH2 O. .. The designated plasmids pAcGFP-UL56, p3 × Flag-UL56 or pCMV-HA-UL56 were constructed by cloning the UL56 PCR product into pAcGFP1-C1, p3 × Flag, or pCMV-HA at indicated restriction sites (Additional file : Table S1).

Article Title: Engineering a synthetic pathway for maleate in Escherichia coli
Article Snippet: .. Polymerase chain reaction (PCR) was performed using the KOD FX Neo DNA polymerase (Toyobo, Osaka, Japan) and the appropriate primer pairs. .. Each gene was assembled with the respective plasmid using Gibson Assembly (New England Biolabs, Ipswich, MA, USA).

Article Title: Segmental and tandem chromosome duplications led to divergent evolution of the chalcone synthase gene family in Phalaenopsis orchids
Article Snippet: .. The CHS-containing DNA fragments were amplified by PCR, which was performed using 10 ng of genomic DNA, 1× PCR buffer, 0.4 mm of each dNTP, 0.3 μm each of forward and reverse primer, and 1.0 U of KOD FX Neo DNA polymerase (TOYOBO, Osaka, Japan) in a total reaction volume of 50 μL. .. The PCR step-down cycling conditions were as follows: 94 °C for 2 min; five cycles of 98 °C for 10 s and 70 °C for 3.5 min; five cycles of 98 °C for 10 s and 68 °C for 3.5 min; five cycles of 98 °C for 10 s and 65 °C for 3.5 min; 20 cycles of 98 °C for 10 s and 60 °C for 3.5 min; 68 °C for 7 min; and then 25° C for 10 s. The PCR products were then cloned into the pZeroback vector (TIANGEN Biotech, Beijing, China) and transformed into Escherichia coli DH5α.

Article Title: Overexpression of Tisochrysis lutea Akd1 identifies a key cold-induced alkenone desaturase enzyme
Article Snippet: Expression analysis of TOD-1 and -2 All primer sequences and PCR protocols are summarised in Supplementary Table . .. The complete ORF encoding TOD-1 and -2 was amplified with the following primer pairs; eORF2F1 and eORF2aR1 for TOD-1 , and eORF2F1 and eORF2bR1 for TOD-2 using KOD FX Neo DNA polymerase (Toyobo).

Article Title: Dynamics of Sulfate-Reducing Bacteria Community Structure in Surface Sediment of a Seasonally Hypoxic Enclosed Bay
Article Snippet: .. PCR was performed in a 30-μL reaction mixture using PCR buffer, 15 U of KOD FX Neo DNA polymerase (Toyobo, Osaka, Japan), 12 nmol of dNTP mix, 6 pmol of each primer, and 30 ng of extracted DNA. .. The reaction was performed in a thermal cycler (DNA engine PTC-200; Bio-Rad, Hercules, CA, USA) using the following program: 1 cycle at 94°C for 2 min, followed by 30 cycles of 98°C for 10 s, 54°C for 30 s and 68°C for 60 s. The correct sizes of PCR products were verified by agarose gel electrophoresis (approximately 930 bp), and PCR products were further purified (QIAquick PCR purification kit; Qiagen, Hilden, Germany).

Article Title: Masc‐induced dosage compensation in silkworm cultured cells
Article Snippet: .. PCR was performed using KOD FX‐neo DNA polymerase (TOYOBO, Osaka, Japan). .. Sex‐specific splicing of Bmdsx was examined with RT‐PCR as reported previously .

Article Title: Evaluation of ATM heterozygous mutations underlying individual differences in radiosensitivity using genome editing in human cultured cells
Article Snippet: .. PCR-based and Sanger sequencing genotyping of the neomycin-resistant clones PCR genotyping to screen for the ATM -edited hTERT-RPE1 cell clones was performed using extracted genomic DNA as a template and KOD-FX Neo DNA polymerase (TOYOBO) with three types of primer pair: the first primer pair consisted of ATM gene exon 11 forward Fp (5′-TCCTGCAGTATGCTGTTTGACTTTGGC-3′) and ATM gene exon 11 reverse Rp (5′-CTGTGAAGAATTGGAGGCACTTCTGTGC-3′) primers for detecting ATM gene exon 11; the second primer pair consisted of ATM gene exon 11 forward Fp and Neo r -reverse Np (5′-GCGGATCTGACGGTTCACTAAACCAGC-3′) primers for detecting the forward insertion of the drug-resistant gene cassette into ATM gene; and the third primer pair consisted of ATM gene exon 11 reverse Rp and Neo r -reverse Np primers for detecting the reversed insertion. ..

Article Title: Morphology, taxonomy and mating-type loci in natural populations of Volvox carteri in Taiwan
Article Snippet: .. PCR was carried out using KOD FX Neo DNA polymerase (TOYOBO, Osaka, Japan) according to the manufacturer’s instructions. ..

Article Title: Wild-type Cu/Zn-superoxide dismutase is misfolded in cerebrospinal fluid of sporadic amyotrophic lateral sclerosis
Article Snippet: .. Each of five exons in the SOD1 gene was amplified with PCR using KOD FX Neo DNA polymerase (TOYOBO). .. Primers used for amplification of the exons are summarized in Additional file : Table S1.

DNA Sequencing:

Article Title: Redox environment is an intracellular factor to operate distinct pathways for aggregation of Cu,Zn-superoxide dismutase in amyotrophic lateral sclerosis
Article Snippet: .. Mutations were introduced by an inverse PCR method using KOD-FX-neo DNA polymerase (TOYOBO), and all constructs used in this study were confirmed by DNA sequencing. .. Competent cells of E. coli , BL21(DE3; New England Biolabs) and SHuffleTM T7 Express lysY (New England Biolabs), were transformed with a plasmid.

Article Title: A low-frequency IL4R locus variant in Japanese patients with intravenous immunoglobulin therapy-unresponsive Kawasaki disease
Article Snippet: Paragraph title: Pooled genomic DNA sequencing ... Candidate genetic regions were individually amplified with specific primers (Additional file : Table S1, S2), KOD FX neo DNA polymerase (Toyobo, Osaka, Japan), and 200 ng of pooled genome as a template.

Article Title: Wild-type Cu/Zn-superoxide dismutase is misfolded in cerebrospinal fluid of sporadic amyotrophic lateral sclerosis
Article Snippet: Paragraph title: DNA sequencing ... Each of five exons in the SOD1 gene was amplified with PCR using KOD FX Neo DNA polymerase (TOYOBO).

Sequencing:

Article Title: Chitin-based barrier immunity and its loss predated mucus-colonization by indigenous gut microbiota
Article Snippet: Specimens were treated with 180 μL of 50 mM NaOH at 95 °C for 10 min, mixed with 20 μL of 1 M Tri-HCl (pH 8.0) and centrifuged at 12,500×g at RT for 10 min. Supernatants were collected for PCR amplification using KOD FX Neo DNA polymerase (Toyobo, Japan) and 16S universal primers: 27f (AGAGTTTGATCMTGGCTCAG) and 1492r (TACGGYTACCTTGTTACGACTT). .. Amplification of 16S rRNA genes was confirmed by subcloning and Sanger sequencing of PCR products.

Article Title: Impaired neuronal KCC2 function by biallelic SLC12A5 mutations in migrating focal seizures and severe developmental delay
Article Snippet: SLC12A5 coding exons were amplified by PCR using KOD FX Neo DNA polymerase (Toyobo), with amplified DNA as the template. .. SLC12A5 variants were annotated based on transcript variant 2 (encoding KCC2b, NM_020708.4), and were validated by Sanger sequencing using genomic DNA.

Article Title: A low-frequency IL4R locus variant in Japanese patients with intravenous immunoglobulin therapy-unresponsive Kawasaki disease
Article Snippet: Candidate genetic regions were individually amplified with specific primers (Additional file : Table S1, S2), KOD FX neo DNA polymerase (Toyobo, Osaka, Japan), and 200 ng of pooled genome as a template. .. Sequencing templates were prepared with the Ion PGM Template OT2 Reagents 200 Kit (Thermo Fisher, Waltham, MA, USA), and next-generation sequencing was performed by Ion PGM with a 318 chip (Thermo Fisher), according to the Ion torrent protocol.

Article Title: Evaluation of ATM heterozygous mutations underlying individual differences in radiosensitivity using genome editing in human cultured cells
Article Snippet: .. PCR-based and Sanger sequencing genotyping of the neomycin-resistant clones PCR genotyping to screen for the ATM -edited hTERT-RPE1 cell clones was performed using extracted genomic DNA as a template and KOD-FX Neo DNA polymerase (TOYOBO) with three types of primer pair: the first primer pair consisted of ATM gene exon 11 forward Fp (5′-TCCTGCAGTATGCTGTTTGACTTTGGC-3′) and ATM gene exon 11 reverse Rp (5′-CTGTGAAGAATTGGAGGCACTTCTGTGC-3′) primers for detecting ATM gene exon 11; the second primer pair consisted of ATM gene exon 11 forward Fp and Neo r -reverse Np (5′-GCGGATCTGACGGTTCACTAAACCAGC-3′) primers for detecting the forward insertion of the drug-resistant gene cassette into ATM gene; and the third primer pair consisted of ATM gene exon 11 reverse Rp and Neo r -reverse Np primers for detecting the reversed insertion. ..

Sonication:

Article Title: A low-frequency IL4R locus variant in Japanese patients with intravenous immunoglobulin therapy-unresponsive Kawasaki disease
Article Snippet: Candidate genetic regions were individually amplified with specific primers (Additional file : Table S1, S2), KOD FX neo DNA polymerase (Toyobo, Osaka, Japan), and 200 ng of pooled genome as a template. .. Amplified products were purified with Agencourt AMPure XP (Beckman Coulter, Brea, CA, USA) and shearing was performed by sonication.

Quantitative RT-PCR:

Article Title: Overexpression of Tisochrysis lutea Akd1 identifies a key cold-induced alkenone desaturase enzyme
Article Snippet: The complete ORF encoding TOD-1 and -2 was amplified with the following primer pairs; eORF2F1 and eORF2aR1 for TOD-1 , and eORF2F1 and eORF2bR1 for TOD-2 using KOD FX Neo DNA polymerase (Toyobo). .. Expression of TOD-1 and -2 was investigated by quantitative real-time PCR (qRT-PCR) as follows: (1) Total RNA was extracted from the cells using Trizol (Invitrogen) and the RNeasy Plant Mini Kit (Qiagen); the extracted RNA was treated with the TurboDNase Kit (Ambion). (2) Using 1 μg of total RNA as the template, cDNA was synthesised using the poly-T20 primer and SuperScriptIII reverse transcriptase (Invitrogen) in a 20 μL reaction mixture. (3) To examine the expression of TOD-1 and -2 , qRT-PCR was performed using 5 ng of cDNA as a template on the Applied Biosystems StepOnePlus Real-Time PCR System (ThermoFisher Scientific) using RT-qPCR SYBR GREEN Reagents (GoTaq qPCR Master Mix, Promega).

Article Title: Masc‐induced dosage compensation in silkworm cultured cells
Article Snippet: PCR was performed using KOD FX‐neo DNA polymerase (TOYOBO, Osaka, Japan). .. Quantitative RT‐PCR (RT‐qPCR) of BmIMPM and rp49 was performed using a KAPA™ SYBR FAST qPCR kit (Kapa Biosystems, Wilmington, MA, USA), as previously described .

DNA Extraction:

Article Title: Dynamics of Sulfate-Reducing Bacteria Community Structure in Surface Sediment of a Seasonally Hypoxic Enclosed Bay
Article Snippet: Approximately 1 g (wet weight) of thawed sediment was used for DNA extraction using an ISOIL DNA extraction kit (Nippon Gene, Tokyo, Japan), according to the protocols described by the manufacturer. .. PCR was performed in a 30-μL reaction mixture using PCR buffer, 15 U of KOD FX Neo DNA polymerase (Toyobo, Osaka, Japan), 12 nmol of dNTP mix, 6 pmol of each primer, and 30 ng of extracted DNA.

Fluorescence:

Article Title: Segmental and tandem chromosome duplications led to divergent evolution of the chalcone synthase gene family in Phalaenopsis orchids
Article Snippet: Paragraph title: Cloning and labelling of DNA probes for fluorescence in situ hybridization (FISH) mapping ... The CHS-containing DNA fragments were amplified by PCR, which was performed using 10 ng of genomic DNA, 1× PCR buffer, 0.4 mm of each dNTP, 0.3 μm each of forward and reverse primer, and 1.0 U of KOD FX Neo DNA polymerase (TOYOBO, Osaka, Japan) in a total reaction volume of 50 μL.

Isolation:

Article Title: Chitin-based barrier immunity and its loss predated mucus-colonization by indigenous gut microbiota
Article Snippet: Confirmation of axenic conditions using PCR Intestines were surgically isolated from anesthetized adult specimens of C. intestinalis Type A (n = 3), rinsed with PBS and transferred to a sterile petri dish. .. Specimens were treated with 180 μL of 50 mM NaOH at 95 °C for 10 min, mixed with 20 μL of 1 M Tri-HCl (pH 8.0) and centrifuged at 12,500×g at RT for 10 min. Supernatants were collected for PCR amplification using KOD FX Neo DNA polymerase (Toyobo, Japan) and 16S universal primers: 27f (AGAGTTTGATCMTGGCTCAG) and 1492r (TACGGYTACCTTGTTACGACTT).

Article Title: Wild-type Cu/Zn-superoxide dismutase is misfolded in cerebrospinal fluid of sporadic amyotrophic lateral sclerosis
Article Snippet: DNA sequencing Genomic DNA was isolated from the samples (spinal cord, sera, and skeletal muscle) using GenoPlus Genomic DNA Mini (Viogene) according to the manufacturer’s protocol. .. Each of five exons in the SOD1 gene was amplified with PCR using KOD FX Neo DNA polymerase (TOYOBO).

Subcloning:

Article Title: Chitin-based barrier immunity and its loss predated mucus-colonization by indigenous gut microbiota
Article Snippet: Specimens were treated with 180 μL of 50 mM NaOH at 95 °C for 10 min, mixed with 20 μL of 1 M Tri-HCl (pH 8.0) and centrifuged at 12,500×g at RT for 10 min. Supernatants were collected for PCR amplification using KOD FX Neo DNA polymerase (Toyobo, Japan) and 16S universal primers: 27f (AGAGTTTGATCMTGGCTCAG) and 1492r (TACGGYTACCTTGTTACGACTT). .. Amplification of 16S rRNA genes was confirmed by subcloning and Sanger sequencing of PCR products.

Purification:

Article Title: Segmental and tandem chromosome duplications led to divergent evolution of the chalcone synthase gene family in Phalaenopsis orchids
Article Snippet: The CHS-containing DNA fragments were amplified by PCR, which was performed using 10 ng of genomic DNA, 1× PCR buffer, 0.4 mm of each dNTP, 0.3 μm each of forward and reverse primer, and 1.0 U of KOD FX Neo DNA polymerase (TOYOBO, Osaka, Japan) in a total reaction volume of 50 μL. .. Plasmid DNA was extracted using a Plasmid Miniprep Purification Kit (GMbiolab, Taichung, Taiwan), and 1.8 μg of plasmid DNA was labelled with either biotin-dUTP or digoxigenin-dUTP using standard nick translation following the manufacturer’s protocol (Roche, Basel, Switzerland).

Article Title: A low-frequency IL4R locus variant in Japanese patients with intravenous immunoglobulin therapy-unresponsive Kawasaki disease
Article Snippet: Candidate genetic regions were individually amplified with specific primers (Additional file : Table S1, S2), KOD FX neo DNA polymerase (Toyobo, Osaka, Japan), and 200 ng of pooled genome as a template. .. Amplified products were purified with Agencourt AMPure XP (Beckman Coulter, Brea, CA, USA) and shearing was performed by sonication.

Article Title: Dynamics of Sulfate-Reducing Bacteria Community Structure in Surface Sediment of a Seasonally Hypoxic Enclosed Bay
Article Snippet: PCR was performed in a 30-μL reaction mixture using PCR buffer, 15 U of KOD FX Neo DNA polymerase (Toyobo, Osaka, Japan), 12 nmol of dNTP mix, 6 pmol of each primer, and 30 ng of extracted DNA. .. The reaction was performed in a thermal cycler (DNA engine PTC-200; Bio-Rad, Hercules, CA, USA) using the following program: 1 cycle at 94°C for 2 min, followed by 30 cycles of 98°C for 10 s, 54°C for 30 s and 68°C for 60 s. The correct sizes of PCR products were verified by agarose gel electrophoresis (approximately 930 bp), and PCR products were further purified (QIAquick PCR purification kit; Qiagen, Hilden, Germany).

Reverse Transcription Polymerase Chain Reaction:

Article Title: Masc‐induced dosage compensation in silkworm cultured cells
Article Snippet: Paragraph title: Reverse transcription polymerase chain reaction (RT‐PCR) ... PCR was performed using KOD FX‐neo DNA polymerase (TOYOBO, Osaka, Japan).

Terminal Restriction Fragment Length Polymorphism:

Article Title: Dynamics of Sulfate-Reducing Bacteria Community Structure in Surface Sediment of a Seasonally Hypoxic Enclosed Bay
Article Snippet: Paragraph title: T-RFLP analysis of dsrA genes ... PCR was performed in a 30-μL reaction mixture using PCR buffer, 15 U of KOD FX Neo DNA polymerase (Toyobo, Osaka, Japan), 12 nmol of dNTP mix, 6 pmol of each primer, and 30 ng of extracted DNA.

Agarose Gel Electrophoresis:

Article Title: Chitin-based barrier immunity and its loss predated mucus-colonization by indigenous gut microbiota
Article Snippet: Specimens were treated with 180 μL of 50 mM NaOH at 95 °C for 10 min, mixed with 20 μL of 1 M Tri-HCl (pH 8.0) and centrifuged at 12,500×g at RT for 10 min. Supernatants were collected for PCR amplification using KOD FX Neo DNA polymerase (Toyobo, Japan) and 16S universal primers: 27f (AGAGTTTGATCMTGGCTCAG) and 1492r (TACGGYTACCTTGTTACGACTT). .. Reaction products were assessed by agarose gel electrophoresis followed by SYBR safe staining (Thermo Fisher Scientific, USA).

Article Title: A low-frequency IL4R locus variant in Japanese patients with intravenous immunoglobulin therapy-unresponsive Kawasaki disease
Article Snippet: Candidate genetic regions were individually amplified with specific primers (Additional file : Table S1, S2), KOD FX neo DNA polymerase (Toyobo, Osaka, Japan), and 200 ng of pooled genome as a template. .. Fragmented amplicons were individually separated by agarose gel electrophoresis and 230–250 bp fragments were collected.

Article Title: Dynamics of Sulfate-Reducing Bacteria Community Structure in Surface Sediment of a Seasonally Hypoxic Enclosed Bay
Article Snippet: PCR was performed in a 30-μL reaction mixture using PCR buffer, 15 U of KOD FX Neo DNA polymerase (Toyobo, Osaka, Japan), 12 nmol of dNTP mix, 6 pmol of each primer, and 30 ng of extracted DNA. .. The reaction was performed in a thermal cycler (DNA engine PTC-200; Bio-Rad, Hercules, CA, USA) using the following program: 1 cycle at 94°C for 2 min, followed by 30 cycles of 98°C for 10 s, 54°C for 30 s and 68°C for 60 s. The correct sizes of PCR products were verified by agarose gel electrophoresis (approximately 930 bp), and PCR products were further purified (QIAquick PCR purification kit; Qiagen, Hilden, Germany).

Chromatin Immunoprecipitation:

Article Title: A low-frequency IL4R locus variant in Japanese patients with intravenous immunoglobulin therapy-unresponsive Kawasaki disease
Article Snippet: Candidate genetic regions were individually amplified with specific primers (Additional file : Table S1, S2), KOD FX neo DNA polymerase (Toyobo, Osaka, Japan), and 200 ng of pooled genome as a template. .. Sequencing templates were prepared with the Ion PGM Template OT2 Reagents 200 Kit (Thermo Fisher, Waltham, MA, USA), and next-generation sequencing was performed by Ion PGM with a 318 chip (Thermo Fisher), according to the Ion torrent protocol.

In Situ Hybridization:

Article Title: Segmental and tandem chromosome duplications led to divergent evolution of the chalcone synthase gene family in Phalaenopsis orchids
Article Snippet: Paragraph title: Cloning and labelling of DNA probes for fluorescence in situ hybridization (FISH) mapping ... The CHS-containing DNA fragments were amplified by PCR, which was performed using 10 ng of genomic DNA, 1× PCR buffer, 0.4 mm of each dNTP, 0.3 μm each of forward and reverse primer, and 1.0 U of KOD FX Neo DNA polymerase (TOYOBO, Osaka, Japan) in a total reaction volume of 50 μL.

Plasmid Preparation:

Article Title: A GFP-tagged version of the pseudorabies virus protein UL56 localizes to the Golgi and trans-Golgi network through a predicted C-terminal leucine-rich helix in transfected cells
Article Snippet: Paragraph title: Plasmid construction and transfection ... The PCR was performed using KOD FX Neo DNA polymerase (TOYOBO, Japan) according to the manufacturer’s instructions at a final 50 μL reaction volume containing 2× buffer (25 μL), forward primer (2.5 μL; 10 μM), reverse primer (2.5 μL; 10 μM), KOD FX Neo (1.25 μL; 1 unit/μL), dNTP (7.5 μL; 2 mM each), genomic DNA (~ 200 ng) and ddH2 O.

Article Title: Redox environment is an intracellular factor to operate distinct pathways for aggregation of Cu,Zn-superoxide dismutase in amyotrophic lateral sclerosis
Article Snippet: PLASMIDS, E. coli STRAINS AND PROTEIN EXPRESSION A vector, pET15b (Novagen), was used for the construction of plasmids expressing human SOD1 without any tags; a SalI site was first introduced between BamHI and Bpu1102I sites of pET15b, and cDNA of human SOD1 was then cloned between NcoI and SalI site. .. Mutations were introduced by an inverse PCR method using KOD-FX-neo DNA polymerase (TOYOBO), and all constructs used in this study were confirmed by DNA sequencing.

Article Title: Engineering a synthetic pathway for maleate in Escherichia coli
Article Snippet: Paragraph title: Strains and plasmid construction ... Polymerase chain reaction (PCR) was performed using the KOD FX Neo DNA polymerase (Toyobo, Osaka, Japan) and the appropriate primer pairs.

Article Title: Segmental and tandem chromosome duplications led to divergent evolution of the chalcone synthase gene family in Phalaenopsis orchids
Article Snippet: The CHS-containing DNA fragments were amplified by PCR, which was performed using 10 ng of genomic DNA, 1× PCR buffer, 0.4 mm of each dNTP, 0.3 μm each of forward and reverse primer, and 1.0 U of KOD FX Neo DNA polymerase (TOYOBO, Osaka, Japan) in a total reaction volume of 50 μL. .. The PCR step-down cycling conditions were as follows: 94 °C for 2 min; five cycles of 98 °C for 10 s and 70 °C for 3.5 min; five cycles of 98 °C for 10 s and 68 °C for 3.5 min; five cycles of 98 °C for 10 s and 65 °C for 3.5 min; 20 cycles of 98 °C for 10 s and 60 °C for 3.5 min; 68 °C for 7 min; and then 25° C for 10 s. The PCR products were then cloned into the pZeroback vector (TIANGEN Biotech, Beijing, China) and transformed into Escherichia coli DH5α.

Software:

Article Title: Overexpression of Tisochrysis lutea Akd1 identifies a key cold-induced alkenone desaturase enzyme
Article Snippet: The complete ORF encoding TOD-1 and -2 was amplified with the following primer pairs; eORF2F1 and eORF2aR1 for TOD-1 , and eORF2F1 and eORF2bR1 for TOD-2 using KOD FX Neo DNA polymerase (Toyobo). .. Applied Biosystems StepOne Software v2.1 was used to operate the qRT-PCR system and to determine the crossing point for each amplification reaction. (4) The data were analysed using the ∆∆Ct method and normalised to Hsp70 expression.

SYBR Green Assay:

Article Title: Overexpression of Tisochrysis lutea Akd1 identifies a key cold-induced alkenone desaturase enzyme
Article Snippet: The complete ORF encoding TOD-1 and -2 was amplified with the following primer pairs; eORF2F1 and eORF2aR1 for TOD-1 , and eORF2F1 and eORF2bR1 for TOD-2 using KOD FX Neo DNA polymerase (Toyobo). .. Expression of TOD-1 and -2 was investigated by quantitative real-time PCR (qRT-PCR) as follows: (1) Total RNA was extracted from the cells using Trizol (Invitrogen) and the RNeasy Plant Mini Kit (Qiagen); the extracted RNA was treated with the TurboDNase Kit (Ambion). (2) Using 1 μg of total RNA as the template, cDNA was synthesised using the poly-T20 primer and SuperScriptIII reverse transcriptase (Invitrogen) in a 20 μL reaction mixture. (3) To examine the expression of TOD-1 and -2 , qRT-PCR was performed using 5 ng of cDNA as a template on the Applied Biosystems StepOnePlus Real-Time PCR System (ThermoFisher Scientific) using RT-qPCR SYBR GREEN Reagents (GoTaq qPCR Master Mix, Promega).

Sample Prep:

Article Title: Impaired neuronal KCC2 function by biallelic SLC12A5 mutations in migrating focal seizures and severe developmental delay
Article Snippet: SLC12A5 coding exons were amplified by PCR using KOD FX Neo DNA polymerase (Toyobo), with amplified DNA as the template. .. DNA libraries were prepared by using the Nextera DNA Sample Preparation Kit (Illumina) and sequenced on the MiSeq (Illumina) with 150 bp paired-end reads.

Sulforhodamine B Assay:

Article Title: Dynamics of Sulfate-Reducing Bacteria Community Structure in Surface Sediment of a Seasonally Hypoxic Enclosed Bay
Article Snippet: We used a T-RFLP analysis based on dsrA genes to reveal the SRB community structure. .. PCR was performed in a 30-μL reaction mixture using PCR buffer, 15 U of KOD FX Neo DNA polymerase (Toyobo, Osaka, Japan), 12 nmol of dNTP mix, 6 pmol of each primer, and 30 ng of extracted DNA.

Next-Generation Sequencing:

Article Title: A low-frequency IL4R locus variant in Japanese patients with intravenous immunoglobulin therapy-unresponsive Kawasaki disease
Article Snippet: Each 500 ng of genomic DNA from 30 IVIG-unresponsive KD patients were pooled and used to prepare next-generation sequencing libraries. .. Candidate genetic regions were individually amplified with specific primers (Additional file : Table S1, S2), KOD FX neo DNA polymerase (Toyobo, Osaka, Japan), and 200 ng of pooled genome as a template.

Marker:

Article Title: Dynamics of Sulfate-Reducing Bacteria Community Structure in Surface Sediment of a Seasonally Hypoxic Enclosed Bay
Article Snippet: PCR was performed in a 30-μL reaction mixture using PCR buffer, 15 U of KOD FX Neo DNA polymerase (Toyobo, Osaka, Japan), 12 nmol of dNTP mix, 6 pmol of each primer, and 30 ng of extracted DNA. .. Digested PCR products were then run on a 3730 DNA analyzer with the 1200LIZ marker (Applied Biosystems, Foster City, CA, USA), operating as a fragment analyzer.

Staining:

Article Title: Chitin-based barrier immunity and its loss predated mucus-colonization by indigenous gut microbiota
Article Snippet: Specimens were treated with 180 μL of 50 mM NaOH at 95 °C for 10 min, mixed with 20 μL of 1 M Tri-HCl (pH 8.0) and centrifuged at 12,500×g at RT for 10 min. Supernatants were collected for PCR amplification using KOD FX Neo DNA polymerase (Toyobo, Japan) and 16S universal primers: 27f (AGAGTTTGATCMTGGCTCAG) and 1492r (TACGGYTACCTTGTTACGACTT). .. Reaction products were assessed by agarose gel electrophoresis followed by SYBR safe staining (Thermo Fisher Scientific, USA).

Variant Assay:

Article Title: Impaired neuronal KCC2 function by biallelic SLC12A5 mutations in migrating focal seizures and severe developmental delay
Article Snippet: SLC12A5 coding exons were amplified by PCR using KOD FX Neo DNA polymerase (Toyobo), with amplified DNA as the template. .. SLC12A5 variants were annotated based on transcript variant 2 (encoding KCC2b, NM_020708.4), and were validated by Sanger sequencing using genomic DNA.

Fluorescence In Situ Hybridization:

Article Title: Segmental and tandem chromosome duplications led to divergent evolution of the chalcone synthase gene family in Phalaenopsis orchids
Article Snippet: Paragraph title: Cloning and labelling of DNA probes for fluorescence in situ hybridization (FISH) mapping ... The CHS-containing DNA fragments were amplified by PCR, which was performed using 10 ng of genomic DNA, 1× PCR buffer, 0.4 mm of each dNTP, 0.3 μm each of forward and reverse primer, and 1.0 U of KOD FX Neo DNA polymerase (TOYOBO, Osaka, Japan) in a total reaction volume of 50 μL.

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  • 80
    Toyobo fidelity dna polymerases
    <t>PCR</t> product patterns amplified by the primer pair CS1-F/CS1-R targeting the partial S gene. Samples from left to right: (1) JAi-23, (2) JMi-69, (3) JMi-124, (4) JKa-230, (5) JA0-56, (6) JMi-231, (M) <t>DNA</t> marker. The dashed arrows indicate products of PEDV variants with large genomic deletions (approximately 0.2–0.3 kbp) and the solid arrow indicates the predicted product (872 bp).
    Fidelity Dna Polymerases, supplied by Toyobo, used in various techniques. Bioz Stars score: 80/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/fidelity dna polymerases/product/Toyobo
    Average 80 stars, based on 1 article reviews
    Price from $9.99 to $1999.99
    fidelity dna polymerases - by Bioz Stars, 2020-01
    80/100 stars
      Buy from Supplier

    85
    Toyobo high fidelity kod fx neo dna polymerase
    <t>PCR</t> product patterns amplified by the primer pair CS1-F/CS1-R targeting the partial S gene. Samples from left to right: (1) JAi-23, (2) JMi-69, (3) JMi-124, (4) JKa-230, (5) JA0-56, (6) JMi-231, (M) <t>DNA</t> marker. The dashed arrows indicate products of PEDV variants with large genomic deletions (approximately 0.2–0.3 kbp) and the solid arrow indicates the predicted product (872 bp).
    High Fidelity Kod Fx Neo Dna Polymerase, supplied by Toyobo, used in various techniques. Bioz Stars score: 85/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/high fidelity kod fx neo dna polymerase/product/Toyobo
    Average 85 stars, based on 1 article reviews
    Price from $9.99 to $1999.99
    high fidelity kod fx neo dna polymerase - by Bioz Stars, 2020-01
    85/100 stars
      Buy from Supplier

    99
    Toyobo kod fx neo dna polymerase
    <t>PCR</t> product patterns amplified by the primer pair CS1-F/CS1-R targeting the partial S gene. Samples from left to right: (1) JAi-23, (2) JMi-69, (3) JMi-124, (4) JKa-230, (5) JA0-56, (6) JMi-231, (M) <t>DNA</t> marker. The dashed arrows indicate products of PEDV variants with large genomic deletions (approximately 0.2–0.3 kbp) and the solid arrow indicates the predicted product (872 bp).
    Kod Fx Neo Dna Polymerase, supplied by Toyobo, used in various techniques. Bioz Stars score: 99/100, based on 114 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/kod fx neo dna polymerase/product/Toyobo
    Average 99 stars, based on 114 article reviews
    Price from $9.99 to $1999.99
    kod fx neo dna polymerase - by Bioz Stars, 2020-01
    99/100 stars
      Buy from Supplier

    Image Search Results


    PCR product patterns amplified by the primer pair CS1-F/CS1-R targeting the partial S gene. Samples from left to right: (1) JAi-23, (2) JMi-69, (3) JMi-124, (4) JKa-230, (5) JA0-56, (6) JMi-231, (M) DNA marker. The dashed arrows indicate products of PEDV variants with large genomic deletions (approximately 0.2–0.3 kbp) and the solid arrow indicates the predicted product (872 bp).

    Journal: PLoS ONE

    Article Title: Novel Porcine Epidemic Diarrhea Virus (PEDV) Variants with Large Deletions in the Spike (S) Gene Coexist with PEDV Strains Possessing an Intact S Gene in Domestic Pigs in Japan: A New Disease Situation

    doi: 10.1371/journal.pone.0170126

    Figure Lengend Snippet: PCR product patterns amplified by the primer pair CS1-F/CS1-R targeting the partial S gene. Samples from left to right: (1) JAi-23, (2) JMi-69, (3) JMi-124, (4) JKa-230, (5) JA0-56, (6) JMi-231, (M) DNA marker. The dashed arrows indicate products of PEDV variants with large genomic deletions (approximately 0.2–0.3 kbp) and the solid arrow indicates the predicted product (872 bp).

    Article Snippet: The same result was observed when one-step RT-PCR tests (AccessQuick RT-PCR System kit, Promega Corp, WI, USA) were performed from extracted RNA and PCR tests using other kits containing high fidelity DNA polymerases (KOD FX, KOD FX neo, and Blend–Tag Plus Kits, Toyobo Co., Japan) were performed from cDNA templates to amplify the CS1 fragment.

    Techniques: Polymerase Chain Reaction, Amplification, Marker