dna sequencing Search Results


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  • 89
    Gene Codes Inc sequencher dna sequence analysis software
    Sequencher Dna Sequence Analysis Software, supplied by Gene Codes Inc, used in various techniques. Bioz Stars score: 89/100, based on 102 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Average 89 stars, based on 102 article reviews
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    92
    4Gene sequencher dna sequence analysis software
    Sequencher Dna Sequence Analysis Software, supplied by 4Gene, used in various techniques. Bioz Stars score: 92/100, based on 15 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    85
    Gene Codes Inc sequencher dna sequencing analysis software
    Sequencher Dna Sequencing Analysis Software, supplied by Gene Codes Inc, used in various techniques. Bioz Stars score: 85/100, based on 24 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    91
    Eurofins dna sequencing analysis
    Denaturing electrophoresis of RNA extracted from particles and particle migration under non-denaturing conditions . (A) Denaturing agarose electrophoresis of nucleic acid extracted from TCV and particles formed by the infiltration of leaves with <t>pEAQ-</t> HT -P38. Yellow numbering denotes the size of the RNA (kb) ladder in lane M, catalog number 15623-200 (Invitrogen). (B) Migration of denatured viral proteins in 12% NuPAGE gel. (C) Separation of particles in a non-denaturing 1.2% agarose gel. Upper panel stained with Coomassie Brilliant Blue, the lower panel stained with ethidium bromide. 1, TCV; 2, pEAQ- HT -P38; 3, pEAQ- HT -P29; 4, CPMV eVLPs; 5, CPMV. Right lane lower panel, a commercially available <t>DNA</t> ladder (Bioline) confirming that the gel was stained with ethidium bromide.
    Dna Sequencing Analysis, supplied by Eurofins, used in various techniques. Bioz Stars score: 91/100, based on 48 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Eurofins Genomics dna sequencing analysis
    Denaturing electrophoresis of RNA extracted from particles and particle migration under non-denaturing conditions . (A) Denaturing agarose electrophoresis of nucleic acid extracted from TCV and particles formed by the infiltration of leaves with <t>pEAQ-</t> HT -P38. Yellow numbering denotes the size of the RNA (kb) ladder in lane M, catalog number 15623-200 (Invitrogen). (B) Migration of denatured viral proteins in 12% NuPAGE gel. (C) Separation of particles in a non-denaturing 1.2% agarose gel. Upper panel stained with Coomassie Brilliant Blue, the lower panel stained with ethidium bromide. 1, TCV; 2, pEAQ- HT -P38; 3, pEAQ- HT -P29; 4, CPMV eVLPs; 5, CPMV. Right lane lower panel, a commercially available <t>DNA</t> ladder (Bioline) confirming that the gel was stained with ethidium bromide.
    Dna Sequencing Analysis, supplied by Eurofins Genomics, used in various techniques. Bioz Stars score: 93/100, based on 48 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    91
    Thermo Fisher dna sequencing analysis
    Denaturing electrophoresis of RNA extracted from particles and particle migration under non-denaturing conditions . (A) Denaturing agarose electrophoresis of nucleic acid extracted from TCV and particles formed by the infiltration of leaves with <t>pEAQ-</t> HT -P38. Yellow numbering denotes the size of the RNA (kb) ladder in lane M, catalog number 15623-200 (Invitrogen). (B) Migration of denatured viral proteins in 12% NuPAGE gel. (C) Separation of particles in a non-denaturing 1.2% agarose gel. Upper panel stained with Coomassie Brilliant Blue, the lower panel stained with ethidium bromide. 1, TCV; 2, pEAQ- HT -P38; 3, pEAQ- HT -P29; 4, CPMV eVLPs; 5, CPMV. Right lane lower panel, a commercially available <t>DNA</t> ladder (Bioline) confirming that the gel was stained with ethidium bromide.
    Dna Sequencing Analysis, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 91/100, based on 662 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    92
    Elim Bio dna sequence analysis
    Determination of nucleotides at the 5′ and 3′ ends of <t>HCV</t> replicon RNAs recovered from G418-resistant Huh7 cells. (A) Schematic of the RNA ligase-mediated rapid amplification of cDNA ends (RLM-RACE) (Ambion). An adapter RNA (open bar) was ligated to the 5′ end of either the positive-strand (for determination of the 5′-end nucleotide) or the negative-strand (for determination of the 3′-end nucleotide) HCV replicon RNA isolated from different cell lines. The cDNAs of both positive and negative strands of HCV RNA were reverse transcribed by using HCV-specific primers and amplified by PCR with 5′RACE outer/inner primers (gray arrow) and HCV-specific primers (open arrow). The 5′-end nucleotides of both positive and negative strands of HCV RNA were determined by <t>DNA</t> sequence analysis. (B) 5′- and 3′-end nucleotides of HCV RNA determined by RLM-RACE. Letters indicate nucleotides at the 5′ and 3′ ends as shown on the top. The number indicates the number of cell clones from which HCV replicon RNAs were analyzed. Numbers in parentheses indicate the frequency of the nucleotides determined. The HCV replicon RNAs given on the left column were the ones transcribed in vitro by a T7 RNA polymerase.
    Dna Sequence Analysis, supplied by Elim Bio, used in various techniques. Bioz Stars score: 92/100, based on 63 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    92
    MWG-Biotech dna sequence analysis
    Determination of nucleotides at the 5′ and 3′ ends of <t>HCV</t> replicon RNAs recovered from G418-resistant Huh7 cells. (A) Schematic of the RNA ligase-mediated rapid amplification of cDNA ends (RLM-RACE) (Ambion). An adapter RNA (open bar) was ligated to the 5′ end of either the positive-strand (for determination of the 5′-end nucleotide) or the negative-strand (for determination of the 3′-end nucleotide) HCV replicon RNA isolated from different cell lines. The cDNAs of both positive and negative strands of HCV RNA were reverse transcribed by using HCV-specific primers and amplified by PCR with 5′RACE outer/inner primers (gray arrow) and HCV-specific primers (open arrow). The 5′-end nucleotides of both positive and negative strands of HCV RNA were determined by <t>DNA</t> sequence analysis. (B) 5′- and 3′-end nucleotides of HCV RNA determined by RLM-RACE. Letters indicate nucleotides at the 5′ and 3′ ends as shown on the top. The number indicates the number of cell clones from which HCV replicon RNAs were analyzed. Numbers in parentheses indicate the frequency of the nucleotides determined. The HCV replicon RNAs given on the left column were the ones transcribed in vitro by a T7 RNA polymerase.
    Dna Sequence Analysis, supplied by MWG-Biotech, used in various techniques. Bioz Stars score: 92/100, based on 75 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Average 92 stars, based on 75 article reviews
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    92
    ACGT Inc dna sequence analysis
    Determination of nucleotides at the 5′ and 3′ ends of <t>HCV</t> replicon RNAs recovered from G418-resistant Huh7 cells. (A) Schematic of the RNA ligase-mediated rapid amplification of cDNA ends (RLM-RACE) (Ambion). An adapter RNA (open bar) was ligated to the 5′ end of either the positive-strand (for determination of the 5′-end nucleotide) or the negative-strand (for determination of the 3′-end nucleotide) HCV replicon RNA isolated from different cell lines. The cDNAs of both positive and negative strands of HCV RNA were reverse transcribed by using HCV-specific primers and amplified by PCR with 5′RACE outer/inner primers (gray arrow) and HCV-specific primers (open arrow). The 5′-end nucleotides of both positive and negative strands of HCV RNA were determined by <t>DNA</t> sequence analysis. (B) 5′- and 3′-end nucleotides of HCV RNA determined by RLM-RACE. Letters indicate nucleotides at the 5′ and 3′ ends as shown on the top. The number indicates the number of cell clones from which HCV replicon RNAs were analyzed. Numbers in parentheses indicate the frequency of the nucleotides determined. The HCV replicon RNAs given on the left column were the ones transcribed in vitro by a T7 RNA polymerase.
    Dna Sequence Analysis, supplied by ACGT Inc, used in various techniques. Bioz Stars score: 92/100, based on 22 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    GATC Biotech dna sequence analysis
    Determination of nucleotides at the 5′ and 3′ ends of <t>HCV</t> replicon RNAs recovered from G418-resistant Huh7 cells. (A) Schematic of the RNA ligase-mediated rapid amplification of cDNA ends (RLM-RACE) (Ambion). An adapter RNA (open bar) was ligated to the 5′ end of either the positive-strand (for determination of the 5′-end nucleotide) or the negative-strand (for determination of the 3′-end nucleotide) HCV replicon RNA isolated from different cell lines. The cDNAs of both positive and negative strands of HCV RNA were reverse transcribed by using HCV-specific primers and amplified by PCR with 5′RACE outer/inner primers (gray arrow) and HCV-specific primers (open arrow). The 5′-end nucleotides of both positive and negative strands of HCV RNA were determined by <t>DNA</t> sequence analysis. (B) 5′- and 3′-end nucleotides of HCV RNA determined by RLM-RACE. Letters indicate nucleotides at the 5′ and 3′ ends as shown on the top. The number indicates the number of cell clones from which HCV replicon RNAs were analyzed. Numbers in parentheses indicate the frequency of the nucleotides determined. The HCV replicon RNAs given on the left column were the ones transcribed in vitro by a T7 RNA polymerase.
    Dna Sequence Analysis, supplied by GATC Biotech, used in various techniques. Bioz Stars score: 92/100, based on 116 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Cosmo Genetech Co dna sequencing analysis
    Determination of nucleotides at the 5′ and 3′ ends of <t>HCV</t> replicon RNAs recovered from G418-resistant Huh7 cells. (A) Schematic of the RNA ligase-mediated rapid amplification of cDNA ends (RLM-RACE) (Ambion). An adapter RNA (open bar) was ligated to the 5′ end of either the positive-strand (for determination of the 5′-end nucleotide) or the negative-strand (for determination of the 3′-end nucleotide) HCV replicon RNA isolated from different cell lines. The cDNAs of both positive and negative strands of HCV RNA were reverse transcribed by using HCV-specific primers and amplified by PCR with 5′RACE outer/inner primers (gray arrow) and HCV-specific primers (open arrow). The 5′-end nucleotides of both positive and negative strands of HCV RNA were determined by <t>DNA</t> sequence analysis. (B) 5′- and 3′-end nucleotides of HCV RNA determined by RLM-RACE. Letters indicate nucleotides at the 5′ and 3′ ends as shown on the top. The number indicates the number of cell clones from which HCV replicon RNAs were analyzed. Numbers in parentheses indicate the frequency of the nucleotides determined. The HCV replicon RNAs given on the left column were the ones transcribed in vitro by a T7 RNA polymerase.
    Dna Sequencing Analysis, supplied by Cosmo Genetech Co, used in various techniques. Bioz Stars score: 92/100, based on 47 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    90
    Geno Technology dna sequencing analysis
    Determination of nucleotides at the 5′ and 3′ ends of <t>HCV</t> replicon RNAs recovered from G418-resistant Huh7 cells. (A) Schematic of the RNA ligase-mediated rapid amplification of cDNA ends (RLM-RACE) (Ambion). An adapter RNA (open bar) was ligated to the 5′ end of either the positive-strand (for determination of the 5′-end nucleotide) or the negative-strand (for determination of the 3′-end nucleotide) HCV replicon RNA isolated from different cell lines. The cDNAs of both positive and negative strands of HCV RNA were reverse transcribed by using HCV-specific primers and amplified by PCR with 5′RACE outer/inner primers (gray arrow) and HCV-specific primers (open arrow). The 5′-end nucleotides of both positive and negative strands of HCV RNA were determined by <t>DNA</t> sequence analysis. (B) 5′- and 3′-end nucleotides of HCV RNA determined by RLM-RACE. Letters indicate nucleotides at the 5′ and 3′ ends as shown on the top. The number indicates the number of cell clones from which HCV replicon RNAs were analyzed. Numbers in parentheses indicate the frequency of the nucleotides determined. The HCV replicon RNAs given on the left column were the ones transcribed in vitro by a T7 RNA polymerase.
    Dna Sequencing Analysis, supplied by Geno Technology, used in various techniques. Bioz Stars score: 90/100, based on 29 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Average 90 stars, based on 29 article reviews
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    92
    Macrogen dna sequence analysis
    Site directed mutagenesis of the KRRIH region of Msm <t>UdgX</t> and its activity assay. ( A ( i ) and B ( i )) Line diagrams of Msm UdgX and its mutants highlighting the regions targeted by site directed mutagenesis. Motif A, motif B and the KRRIH loop region are shown in red, blue and yellow boxes, respectively. ( A ( ii )) Uracil excision/binding assays with Msm UdgX (WT) and its R107S, H109S and SSAS mutant derivatives. ∼200 ng of each protein was reacted with 5′ 32 P-labeled SSU9, the reaction mix was resolved on 8 M urea-PAGE (15%) and analyzed by phosphor imaging. The presence of uracil excision activity is seen by the fast migrating product band, ‘P’ whereas the <t>uracil-DNA</t> binding activity by the slow migrating complex, ‘C’. ( B ( ii )) Uracil excision/binding assays with Msm UdgX (WT) and its F4, F1, LD and F4 LD mutant derivatives (∼200 ng each) using SSU9. ( C ) Uracil release assay of Msm UdgX H109S (∼200 ng) using 3 H-uracil containing DNA (21 000 c.p.m) as substrate. Released uracil was separated by TLC (CEL 300 PEI/UV254) and seen as a fast migrating species upon phosphor imaging (the radioactive spot comigrated with the cold uracil spot detected by UV shadowing). ( D ) Uracil excision/binding assay with Msm UdgX and its H109S, H109G, H109Q, H109A and C27S derivatives. ∼200 ng of each protein was used in a standard UDG assay with SSU9 substrate.
    Dna Sequence Analysis, supplied by Macrogen, used in various techniques. Bioz Stars score: 92/100, based on 169 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    91
    Sangon Biotech dna sequence analysis
    Detection of the Sj28S gene component in the different parasite developmental stages of S. japonicum in O. hupensis by the <t>LAMP</t> method. 1. Negative control (nuclease-free water); 2. Positive control (Sj28 plasmid <t>DNA);</t> 3. Cercariae; 4. Specificity control ( Trichobilharzia cercariae); 5. Negative control (pooled snail DNA from a non-endemic area); 6. Mother sporocyst; 7. Daughter sporocyst.
    Dna Sequence Analysis, supplied by Sangon Biotech, used in various techniques. Bioz Stars score: 91/100, based on 67 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    92
    Sequetech dna sequence analysis
    Detection of the Sj28S gene component in the different parasite developmental stages of S. japonicum in O. hupensis by the <t>LAMP</t> method. 1. Negative control (nuclease-free water); 2. Positive control (Sj28 plasmid <t>DNA);</t> 3. Cercariae; 4. Specificity control ( Trichobilharzia cercariae); 5. Negative control (pooled snail DNA from a non-endemic area); 6. Mother sporocyst; 7. Daughter sporocyst.
    Dna Sequence Analysis, supplied by Sequetech, used in various techniques. Bioz Stars score: 92/100, based on 71 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Average 92 stars, based on 71 article reviews
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    92
    SolGent dna sequence analysis
    Detection of the Sj28S gene component in the different parasite developmental stages of S. japonicum in O. hupensis by the <t>LAMP</t> method. 1. Negative control (nuclease-free water); 2. Positive control (Sj28 plasmid <t>DNA);</t> 3. Cercariae; 4. Specificity control ( Trichobilharzia cercariae); 5. Negative control (pooled snail DNA from a non-endemic area); 6. Mother sporocyst; 7. Daughter sporocyst.
    Dna Sequence Analysis, supplied by SolGent, used in various techniques. Bioz Stars score: 92/100, based on 21 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Average 92 stars, based on 21 article reviews
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    91
    ACGT Inc dna sequencing analysis
    Detection of the Sj28S gene component in the different parasite developmental stages of S. japonicum in O. hupensis by the <t>LAMP</t> method. 1. Negative control (nuclease-free water); 2. Positive control (Sj28 plasmid <t>DNA);</t> 3. Cercariae; 4. Specificity control ( Trichobilharzia cercariae); 5. Negative control (pooled snail DNA from a non-endemic area); 6. Mother sporocyst; 7. Daughter sporocyst.
    Dna Sequencing Analysis, supplied by ACGT Inc, used in various techniques. Bioz Stars score: 91/100, based on 11 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Average 91 stars, based on 11 article reviews
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    90
    Bioneer Corporation dna sequencing analysis
    Agarose gel electrophoresis of <t>PCR</t> assay for the identification of Erysipelothrix rhusiopathiae. Lane 1: 100bp <t>DNA</t> marker; Lanes 2–8 and 11: positive samples; Lanes 10: negative control; Lane 12: Erysipelothrix rhusiopathiae ATCC 19414 as positive control.
    Dna Sequencing Analysis, supplied by Bioneer Corporation, used in various techniques. Bioz Stars score: 90/100, based on 16 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Average 90 stars, based on 16 article reviews
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    dna sequencing analysis - by Bioz Stars, 2020-05
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    91
    Elim Bio dna sequencing analysis
    Agarose gel electrophoresis of <t>PCR</t> assay for the identification of Erysipelothrix rhusiopathiae. Lane 1: 100bp <t>DNA</t> marker; Lanes 2–8 and 11: positive samples; Lanes 10: negative control; Lane 12: Erysipelothrix rhusiopathiae ATCC 19414 as positive control.
    Dna Sequencing Analysis, supplied by Elim Bio, used in various techniques. Bioz Stars score: 91/100, based on 14 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Average 91 stars, based on 14 article reviews
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    91
    Beckman Coulter dna sequencing analysis
    Mapping Transcription Start Sites (TSS) of E. chaffeensis genes by primer extension (PE) and 5’ <t>RACE.</t> A) The primer extended products resolved on sequencing gels with TSS identified for the genes dnaK, hup, DNAbp <t>(DNA</t> binding protein gene), clpA, clpB , operons of groE * ( groES and groEL genes), and hsIV* ( hslV and hslU genes). The location of the TSS for each gene was identified by comparing the Sanger’s DNA sequencing runs generated with the same primers used for the PE reactions, but using plasmid DNAs containing the respective gene segments. All genes had one TSS with the exception of hup, which contained two TSS. [The location of the TSS established from the PE results for all 7 genes (bold and underlined text) relative to the initiation codon of each gene were presented under gel data.] B) 5’RACE data identifying the TSS of the genes dksA and grpE , and the operon glyQ * ( glyQ, glyS and dnaJ genes). Sequences generated from the 5’RACE products are compared with the sequences generated with DNA templates and are shown for each gene relative to the initiation codon. TSS are identified with bold and underlined text. The underlined G rich tails are added upstream to TSS during the 5’RACE reaction.
    Dna Sequencing Analysis, supplied by Beckman Coulter, used in various techniques. Bioz Stars score: 91/100, based on 29 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    93
    Macrogen dna sequencing analysis
    DAPI staining of intestinal epithelial cells (T84) and Madin-Darby Canine Kidney (MDCK) cells. (a) Control of untreated T84 cells showing normal nuclei. (b) T84 cells treated with <t>VacA</t> (150 µg mL −1 ) cells showing chromatin condensation and <t>DNA</t> fragmentation. (c) Control of untreated MDCK cells. (d) MDCK cells treated with VacA (150 µg mL −1 ) showing chromatin condensation and DNA fragmentation. DAPI was used at 1000-fold dilution in buffer and the magnification of images is 1000×.
    Dna Sequencing Analysis, supplied by Macrogen, used in various techniques. Bioz Stars score: 93/100, based on 28 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    91
    MWG-Biotech dna sequencing analysis
    DAPI staining of intestinal epithelial cells (T84) and Madin-Darby Canine Kidney (MDCK) cells. (a) Control of untreated T84 cells showing normal nuclei. (b) T84 cells treated with <t>VacA</t> (150 µg mL −1 ) cells showing chromatin condensation and <t>DNA</t> fragmentation. (c) Control of untreated MDCK cells. (d) MDCK cells treated with VacA (150 µg mL −1 ) showing chromatin condensation and DNA fragmentation. DAPI was used at 1000-fold dilution in buffer and the magnification of images is 1000×.
    Dna Sequencing Analysis, supplied by MWG-Biotech, used in various techniques. Bioz Stars score: 91/100, based on 7 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    94
    Eton Bioscience dna sequencing
    DAPI staining of intestinal epithelial cells (T84) and Madin-Darby Canine Kidney (MDCK) cells. (a) Control of untreated T84 cells showing normal nuclei. (b) T84 cells treated with <t>VacA</t> (150 µg mL −1 ) cells showing chromatin condensation and <t>DNA</t> fragmentation. (c) Control of untreated MDCK cells. (d) MDCK cells treated with VacA (150 µg mL −1 ) showing chromatin condensation and DNA fragmentation. DAPI was used at 1000-fold dilution in buffer and the magnification of images is 1000×.
    Dna Sequencing, supplied by Eton Bioscience, used in various techniques. Bioz Stars score: 94/100, based on 335 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    97
    Eurofins dna sequencing
    DAPI staining of intestinal epithelial cells (T84) and Madin-Darby Canine Kidney (MDCK) cells. (a) Control of untreated T84 cells showing normal nuclei. (b) T84 cells treated with <t>VacA</t> (150 µg mL −1 ) cells showing chromatin condensation and <t>DNA</t> fragmentation. (c) Control of untreated MDCK cells. (d) MDCK cells treated with VacA (150 µg mL −1 ) showing chromatin condensation and DNA fragmentation. DAPI was used at 1000-fold dilution in buffer and the magnification of images is 1000×.
    Dna Sequencing, supplied by Eurofins, used in various techniques. Bioz Stars score: 97/100, based on 3317 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Average 97 stars, based on 3317 article reviews
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    92
    Genewiz dna sequence analysis
    The <t>bbb22</t> gene alone is not sufficient to maintain wild-type levels of spirochete loads in infected mouse tissues. <t>DNA</t> was isolated from ear, heart, and joint tissues of C3H/HeN mice inoculated with 1 × 10 4 bbb22-23 + or 22dist p -bbb22 + spirochetes.
    Dna Sequence Analysis, supplied by Genewiz, used in various techniques. Bioz Stars score: 92/100, based on 234 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Average 92 stars, based on 234 article reviews
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    Denaturing electrophoresis of RNA extracted from particles and particle migration under non-denaturing conditions . (A) Denaturing agarose electrophoresis of nucleic acid extracted from TCV and particles formed by the infiltration of leaves with pEAQ- HT -P38. Yellow numbering denotes the size of the RNA (kb) ladder in lane M, catalog number 15623-200 (Invitrogen). (B) Migration of denatured viral proteins in 12% NuPAGE gel. (C) Separation of particles in a non-denaturing 1.2% agarose gel. Upper panel stained with Coomassie Brilliant Blue, the lower panel stained with ethidium bromide. 1, TCV; 2, pEAQ- HT -P38; 3, pEAQ- HT -P29; 4, CPMV eVLPs; 5, CPMV. Right lane lower panel, a commercially available DNA ladder (Bioline) confirming that the gel was stained with ethidium bromide.

    Journal: Frontiers in Plant Science

    Article Title: The Generation of Turnip Crinkle Virus-Like Particles in Plants by the Transient Expression of Wild-Type and Modified Forms of Its Coat Protein

    doi: 10.3389/fpls.2015.01138

    Figure Lengend Snippet: Denaturing electrophoresis of RNA extracted from particles and particle migration under non-denaturing conditions . (A) Denaturing agarose electrophoresis of nucleic acid extracted from TCV and particles formed by the infiltration of leaves with pEAQ- HT -P38. Yellow numbering denotes the size of the RNA (kb) ladder in lane M, catalog number 15623-200 (Invitrogen). (B) Migration of denatured viral proteins in 12% NuPAGE gel. (C) Separation of particles in a non-denaturing 1.2% agarose gel. Upper panel stained with Coomassie Brilliant Blue, the lower panel stained with ethidium bromide. 1, TCV; 2, pEAQ- HT -P38; 3, pEAQ- HT -P29; 4, CPMV eVLPs; 5, CPMV. Right lane lower panel, a commercially available DNA ladder (Bioline) confirming that the gel was stained with ethidium bromide.

    Article Snippet: The sequence of all the resulting gene constructs, both in pDONR207 and in pEAQ-HT -DEST1 were subsequently confirmed by DNA sequencing analysis (Eurofins Genomics).

    Techniques: Electrophoresis, Migration, Agarose Gel Electrophoresis, Staining

    Determination of nucleotides at the 5′ and 3′ ends of HCV replicon RNAs recovered from G418-resistant Huh7 cells. (A) Schematic of the RNA ligase-mediated rapid amplification of cDNA ends (RLM-RACE) (Ambion). An adapter RNA (open bar) was ligated to the 5′ end of either the positive-strand (for determination of the 5′-end nucleotide) or the negative-strand (for determination of the 3′-end nucleotide) HCV replicon RNA isolated from different cell lines. The cDNAs of both positive and negative strands of HCV RNA were reverse transcribed by using HCV-specific primers and amplified by PCR with 5′RACE outer/inner primers (gray arrow) and HCV-specific primers (open arrow). The 5′-end nucleotides of both positive and negative strands of HCV RNA were determined by DNA sequence analysis. (B) 5′- and 3′-end nucleotides of HCV RNA determined by RLM-RACE. Letters indicate nucleotides at the 5′ and 3′ ends as shown on the top. The number indicates the number of cell clones from which HCV replicon RNAs were analyzed. Numbers in parentheses indicate the frequency of the nucleotides determined. The HCV replicon RNAs given on the left column were the ones transcribed in vitro by a T7 RNA polymerase.

    Journal: Journal of Virology

    Article Title: Effects of Mutations of the Initiation Nucleotides on Hepatitis C Virus RNA Replication in the Cell

    doi: 10.1128/JVI.78.7.3633-3643.2004

    Figure Lengend Snippet: Determination of nucleotides at the 5′ and 3′ ends of HCV replicon RNAs recovered from G418-resistant Huh7 cells. (A) Schematic of the RNA ligase-mediated rapid amplification of cDNA ends (RLM-RACE) (Ambion). An adapter RNA (open bar) was ligated to the 5′ end of either the positive-strand (for determination of the 5′-end nucleotide) or the negative-strand (for determination of the 3′-end nucleotide) HCV replicon RNA isolated from different cell lines. The cDNAs of both positive and negative strands of HCV RNA were reverse transcribed by using HCV-specific primers and amplified by PCR with 5′RACE outer/inner primers (gray arrow) and HCV-specific primers (open arrow). The 5′-end nucleotides of both positive and negative strands of HCV RNA were determined by DNA sequence analysis. (B) 5′- and 3′-end nucleotides of HCV RNA determined by RLM-RACE. Letters indicate nucleotides at the 5′ and 3′ ends as shown on the top. The number indicates the number of cell clones from which HCV replicon RNAs were analyzed. Numbers in parentheses indicate the frequency of the nucleotides determined. The HCV replicon RNAs given on the left column were the ones transcribed in vitro by a T7 RNA polymerase.

    Article Snippet: Further analyses of HCV RNA derived from this patient by cDNA cloning and DNA sequence analysis revealed that the mixture of HCV RNA consists of 60% of RNA with a 5′-end nucleotide G and 40% of RNA with a 5′-end nucleotide A.

    Techniques: Rapid Amplification of cDNA Ends, Isolation, Amplification, Polymerase Chain Reaction, Sequencing, Clone Assay, In Vitro

    Site directed mutagenesis of the KRRIH region of Msm UdgX and its activity assay. ( A ( i ) and B ( i )) Line diagrams of Msm UdgX and its mutants highlighting the regions targeted by site directed mutagenesis. Motif A, motif B and the KRRIH loop region are shown in red, blue and yellow boxes, respectively. ( A ( ii )) Uracil excision/binding assays with Msm UdgX (WT) and its R107S, H109S and SSAS mutant derivatives. ∼200 ng of each protein was reacted with 5′ 32 P-labeled SSU9, the reaction mix was resolved on 8 M urea-PAGE (15%) and analyzed by phosphor imaging. The presence of uracil excision activity is seen by the fast migrating product band, ‘P’ whereas the uracil-DNA binding activity by the slow migrating complex, ‘C’. ( B ( ii )) Uracil excision/binding assays with Msm UdgX (WT) and its F4, F1, LD and F4 LD mutant derivatives (∼200 ng each) using SSU9. ( C ) Uracil release assay of Msm UdgX H109S (∼200 ng) using 3 H-uracil containing DNA (21 000 c.p.m) as substrate. Released uracil was separated by TLC (CEL 300 PEI/UV254) and seen as a fast migrating species upon phosphor imaging (the radioactive spot comigrated with the cold uracil spot detected by UV shadowing). ( D ) Uracil excision/binding assay with Msm UdgX and its H109S, H109G, H109Q, H109A and C27S derivatives. ∼200 ng of each protein was used in a standard UDG assay with SSU9 substrate.

    Journal: Nucleic Acids Research

    Article Title: A unique uracil-DNA binding protein of the uracil DNA glycosylase superfamily

    doi: 10.1093/nar/gkv854

    Figure Lengend Snippet: Site directed mutagenesis of the KRRIH region of Msm UdgX and its activity assay. ( A ( i ) and B ( i )) Line diagrams of Msm UdgX and its mutants highlighting the regions targeted by site directed mutagenesis. Motif A, motif B and the KRRIH loop region are shown in red, blue and yellow boxes, respectively. ( A ( ii )) Uracil excision/binding assays with Msm UdgX (WT) and its R107S, H109S and SSAS mutant derivatives. ∼200 ng of each protein was reacted with 5′ 32 P-labeled SSU9, the reaction mix was resolved on 8 M urea-PAGE (15%) and analyzed by phosphor imaging. The presence of uracil excision activity is seen by the fast migrating product band, ‘P’ whereas the uracil-DNA binding activity by the slow migrating complex, ‘C’. ( B ( ii )) Uracil excision/binding assays with Msm UdgX (WT) and its F4, F1, LD and F4 LD mutant derivatives (∼200 ng each) using SSU9. ( C ) Uracil release assay of Msm UdgX H109S (∼200 ng) using 3 H-uracil containing DNA (21 000 c.p.m) as substrate. Released uracil was separated by TLC (CEL 300 PEI/UV254) and seen as a fast migrating species upon phosphor imaging (the radioactive spot comigrated with the cold uracil spot detected by UV shadowing). ( D ) Uracil excision/binding assay with Msm UdgX and its H109S, H109G, H109Q, H109A and C27S derivatives. ∼200 ng of each protein was used in a standard UDG assay with SSU9 substrate.

    Article Snippet: The PCR product (662 bp) was blunt end ligated into pJET1.2 (MBI) vector to generate pJETMsm UdgX and confirmed by restriction digestion and DNA sequence analysis (Macrogen, S. Korea).

    Techniques: Mutagenesis, Activity Assay, Binding Assay, Labeling, Polyacrylamide Gel Electrophoresis, Imaging, Release Assay, Thin Layer Chromatography

    Activity assay of Msm UdgX. ( A ) Assay of Msm UdgX (100 ng) on 5′ 32 P-end labeled SSU9:G and SSU9 substrate, ‘S’ (∼10,000 c.p.m). Family 1 UDG (Ung) was used as control, Ugi was added as indicated. Reactions were resolved on 8 M Urea PAGE (15%) and analyzed by phosphor imaging. The presence of uracil excision activity can be seen as a fast migrating species forming a product ‘P’ whereas uracil binding activity form a slow migrating complex ‘C’ [panel (i) on left shows a diagrammatic sketch whereas the panel on right (ii) shows the results of the experiment]. ( B ) Proteinase K (1.2 U) digestion of the complex, ‘C’ observed in A, and re-resolved on 8 M Urea PAGE (15%) and analyzed by phosphor imaging. ( C ) Uracil release assay using 3 H-uracil containing DNA substrate. Msm UdgX (∼1 μg) or Ung (100 ng) was allowed to react with 3 H-uracil DNA substrate (∼21 000 c.p.m.), the samples were mixed with unlabeled uracil and spotted on the CEL 300 PEI/UV254, resolved using a mobile phase of 0.2% formic acid (v/v) containing 0.55 M LiCl at 4°C and analyzed by phosphor imaging. Released uracil is seen as a fast migrating species. ( D ) Binding of Msm UdgX (∼1 μg) with unlabeled uracil containing DNA oligomers (50 pmol) of different sizes resolved on 15% SDS PAGE and visualized by Coomassie blue staining. ( E ) Activity assay of Msm UdgX (4 pmol) in the presence of Msm Ung (4 pmol) using 5′ 32 P-labeled SSU9:G. Reactions were resolved on 8 M urea-PAGE (15%) and analyzed by phosphor imaging. The 1 st and 2 nd represents the order of addition, and ‘+’ in both Msm Ung and Msm UdgX indicates that both the protein are added simultaneously.

    Journal: Nucleic Acids Research

    Article Title: A unique uracil-DNA binding protein of the uracil DNA glycosylase superfamily

    doi: 10.1093/nar/gkv854

    Figure Lengend Snippet: Activity assay of Msm UdgX. ( A ) Assay of Msm UdgX (100 ng) on 5′ 32 P-end labeled SSU9:G and SSU9 substrate, ‘S’ (∼10,000 c.p.m). Family 1 UDG (Ung) was used as control, Ugi was added as indicated. Reactions were resolved on 8 M Urea PAGE (15%) and analyzed by phosphor imaging. The presence of uracil excision activity can be seen as a fast migrating species forming a product ‘P’ whereas uracil binding activity form a slow migrating complex ‘C’ [panel (i) on left shows a diagrammatic sketch whereas the panel on right (ii) shows the results of the experiment]. ( B ) Proteinase K (1.2 U) digestion of the complex, ‘C’ observed in A, and re-resolved on 8 M Urea PAGE (15%) and analyzed by phosphor imaging. ( C ) Uracil release assay using 3 H-uracil containing DNA substrate. Msm UdgX (∼1 μg) or Ung (100 ng) was allowed to react with 3 H-uracil DNA substrate (∼21 000 c.p.m.), the samples were mixed with unlabeled uracil and spotted on the CEL 300 PEI/UV254, resolved using a mobile phase of 0.2% formic acid (v/v) containing 0.55 M LiCl at 4°C and analyzed by phosphor imaging. Released uracil is seen as a fast migrating species. ( D ) Binding of Msm UdgX (∼1 μg) with unlabeled uracil containing DNA oligomers (50 pmol) of different sizes resolved on 15% SDS PAGE and visualized by Coomassie blue staining. ( E ) Activity assay of Msm UdgX (4 pmol) in the presence of Msm Ung (4 pmol) using 5′ 32 P-labeled SSU9:G. Reactions were resolved on 8 M urea-PAGE (15%) and analyzed by phosphor imaging. The 1 st and 2 nd represents the order of addition, and ‘+’ in both Msm Ung and Msm UdgX indicates that both the protein are added simultaneously.

    Article Snippet: The PCR product (662 bp) was blunt end ligated into pJET1.2 (MBI) vector to generate pJETMsm UdgX and confirmed by restriction digestion and DNA sequence analysis (Macrogen, S. Korea).

    Techniques: Activity Assay, Labeling, Polyacrylamide Gel Electrophoresis, Imaging, Binding Assay, Release Assay, SDS Page, Staining

    Proposed pathway for repair of uracil- Msm UdgX complexes. Binding of Msm UdgX to uracil would stall replication which could in turn lead to generation of single stranded gaps or double stranded breaks. Activation of RecA protein upon binding to ss DNA would induce the SOS response through cleavage of LexA. RecBCD proteins would also repair the complex through homologous recombination repair pathway.

    Journal: Nucleic Acids Research

    Article Title: A unique uracil-DNA binding protein of the uracil DNA glycosylase superfamily

    doi: 10.1093/nar/gkv854

    Figure Lengend Snippet: Proposed pathway for repair of uracil- Msm UdgX complexes. Binding of Msm UdgX to uracil would stall replication which could in turn lead to generation of single stranded gaps or double stranded breaks. Activation of RecA protein upon binding to ss DNA would induce the SOS response through cleavage of LexA. RecBCD proteins would also repair the complex through homologous recombination repair pathway.

    Article Snippet: The PCR product (662 bp) was blunt end ligated into pJET1.2 (MBI) vector to generate pJETMsm UdgX and confirmed by restriction digestion and DNA sequence analysis (Macrogen, S. Korea).

    Techniques: Binding Assay, Activation Assay, Homologous Recombination

    Detection of the Sj28S gene component in the different parasite developmental stages of S. japonicum in O. hupensis by the LAMP method. 1. Negative control (nuclease-free water); 2. Positive control (Sj28 plasmid DNA); 3. Cercariae; 4. Specificity control ( Trichobilharzia cercariae); 5. Negative control (pooled snail DNA from a non-endemic area); 6. Mother sporocyst; 7. Daughter sporocyst.

    Journal: Tropical Medicine and Infectious Disease

    Article Title: Field Evaluation of a Loop-Mediated Isothermal Amplification (LAMP) Platform for the Detection of Schistosoma japonicum Infection in Oncomelania hupensis Snails

    doi: 10.3390/tropicalmed3040124

    Figure Lengend Snippet: Detection of the Sj28S gene component in the different parasite developmental stages of S. japonicum in O. hupensis by the LAMP method. 1. Negative control (nuclease-free water); 2. Positive control (Sj28 plasmid DNA); 3. Cercariae; 4. Specificity control ( Trichobilharzia cercariae); 5. Negative control (pooled snail DNA from a non-endemic area); 6. Mother sporocyst; 7. Daughter sporocyst.

    Article Snippet: Out of the 232 pooled snail samples tested, 217 were found to be negative and 14 positive by both assays , while the remaining single sample, found positive by LAMP but negative by PCR, was found to be positive by DNA sequence analysis, underlining LAMP’s superiority.

    Techniques: Negative Control, Positive Control, Plasmid Preparation

    Agarose gel electrophoresis of PCR assay for the identification of Erysipelothrix rhusiopathiae. Lane 1: 100bp DNA marker; Lanes 2–8 and 11: positive samples; Lanes 10: negative control; Lane 12: Erysipelothrix rhusiopathiae ATCC 19414 as positive control.

    Journal: Iranian Journal of Medical Sciences

    Article Title: Isolation and Detection of Erysipelothrix rhusiopathiae and Its Distribution in Humans and Animals by Phenotypical and Molecular Methods in Ahvaz-Iran in 2015

    doi:

    Figure Lengend Snippet: Agarose gel electrophoresis of PCR assay for the identification of Erysipelothrix rhusiopathiae. Lane 1: 100bp DNA marker; Lanes 2–8 and 11: positive samples; Lanes 10: negative control; Lane 12: Erysipelothrix rhusiopathiae ATCC 19414 as positive control.

    Article Snippet: DNA Sequencing Analysis All the PCR products (20 cases) were sequenced at Bioneer Company (Korea), and all the sequences were compared with GenBank.

    Techniques: Agarose Gel Electrophoresis, Polymerase Chain Reaction, Marker, Negative Control, Positive Control

    Mapping Transcription Start Sites (TSS) of E. chaffeensis genes by primer extension (PE) and 5’ RACE. A) The primer extended products resolved on sequencing gels with TSS identified for the genes dnaK, hup, DNAbp (DNA binding protein gene), clpA, clpB , operons of groE * ( groES and groEL genes), and hsIV* ( hslV and hslU genes). The location of the TSS for each gene was identified by comparing the Sanger’s DNA sequencing runs generated with the same primers used for the PE reactions, but using plasmid DNAs containing the respective gene segments. All genes had one TSS with the exception of hup, which contained two TSS. [The location of the TSS established from the PE results for all 7 genes (bold and underlined text) relative to the initiation codon of each gene were presented under gel data.] B) 5’RACE data identifying the TSS of the genes dksA and grpE , and the operon glyQ * ( glyQ, glyS and dnaJ genes). Sequences generated from the 5’RACE products are compared with the sequences generated with DNA templates and are shown for each gene relative to the initiation codon. TSS are identified with bold and underlined text. The underlined G rich tails are added upstream to TSS during the 5’RACE reaction.

    Journal: PLoS ONE

    Article Title: Transcription of Ehrlichia chaffeensis Genes Is Accomplished by RNA Polymerase Holoenzyme Containing either Sigma 32 or Sigma 70

    doi: 10.1371/journal.pone.0081780

    Figure Lengend Snippet: Mapping Transcription Start Sites (TSS) of E. chaffeensis genes by primer extension (PE) and 5’ RACE. A) The primer extended products resolved on sequencing gels with TSS identified for the genes dnaK, hup, DNAbp (DNA binding protein gene), clpA, clpB , operons of groE * ( groES and groEL genes), and hsIV* ( hslV and hslU genes). The location of the TSS for each gene was identified by comparing the Sanger’s DNA sequencing runs generated with the same primers used for the PE reactions, but using plasmid DNAs containing the respective gene segments. All genes had one TSS with the exception of hup, which contained two TSS. [The location of the TSS established from the PE results for all 7 genes (bold and underlined text) relative to the initiation codon of each gene were presented under gel data.] B) 5’RACE data identifying the TSS of the genes dksA and grpE , and the operon glyQ * ( glyQ, glyS and dnaJ genes). Sequences generated from the 5’RACE products are compared with the sequences generated with DNA templates and are shown for each gene relative to the initiation codon. TSS are identified with bold and underlined text. The underlined G rich tails are added upstream to TSS during the 5’RACE reaction.

    Article Snippet: The final products were resolved in a 1% agarose gel; the major amplicons were gel isolated and used to perform DNA sequencing analysis. (5’RACE primers are listed in .)

    Techniques: Sequencing, Binding Assay, DNA Sequencing, Generated, Plasmid Preparation

    DAPI staining of intestinal epithelial cells (T84) and Madin-Darby Canine Kidney (MDCK) cells. (a) Control of untreated T84 cells showing normal nuclei. (b) T84 cells treated with VacA (150 µg mL −1 ) cells showing chromatin condensation and DNA fragmentation. (c) Control of untreated MDCK cells. (d) MDCK cells treated with VacA (150 µg mL −1 ) showing chromatin condensation and DNA fragmentation. DAPI was used at 1000-fold dilution in buffer and the magnification of images is 1000×.

    Journal: BioMed Research International

    Article Title: Sequence and Apoptotic Activity of VacA Cytotoxin Cloned from a Helicobacter pylori Thai Clinical Isolate

    doi: 10.1155/2014/398350

    Figure Lengend Snippet: DAPI staining of intestinal epithelial cells (T84) and Madin-Darby Canine Kidney (MDCK) cells. (a) Control of untreated T84 cells showing normal nuclei. (b) T84 cells treated with VacA (150 µg mL −1 ) cells showing chromatin condensation and DNA fragmentation. (c) Control of untreated MDCK cells. (d) MDCK cells treated with VacA (150 µg mL −1 ) showing chromatin condensation and DNA fragmentation. DAPI was used at 1000-fold dilution in buffer and the magnification of images is 1000×.

    Article Snippet: The correct sequence of the recombinant pTrcHisA/VacA construct was verified by restriction digestion and DNA sequencing analysis (Macrogen Inc., South Korea).

    Techniques: Staining

    The bbb22 gene alone is not sufficient to maintain wild-type levels of spirochete loads in infected mouse tissues. DNA was isolated from ear, heart, and joint tissues of C3H/HeN mice inoculated with 1 × 10 4 bbb22-23 + or 22dist p -bbb22 + spirochetes.

    Journal: Infection and Immunity

    Article Title: Molecular Dissection of a Borrelia burgdorferiIn Vivo Essential Purine Transport System

    doi: 10.1128/IAI.02859-14

    Figure Lengend Snippet: The bbb22 gene alone is not sufficient to maintain wild-type levels of spirochete loads in infected mouse tissues. DNA was isolated from ear, heart, and joint tissues of C3H/HeN mice inoculated with 1 × 10 4 bbb22-23 + or 22dist p -bbb22 + spirochetes.

    Article Snippet: Plasmids pBSV2G 22dist p - bbb22 + and pBSV2G 22prox p - bbb22 + were confirmed by restriction digestion and DNA sequence analysis (Genewiz).

    Techniques: Infection, Isolation, Mouse Assay