taq i  (New England Biolabs)


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    Name:
    Taq I Methyltransferase
    Description:
    Taq I Methyltransferase 1 000 units
    Catalog Number:
    m0219s
    Price:
    74
    Size:
    1 000 units
    Category:
    DNA Methylases
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    Structured Review

    New England Biolabs taq i
    Taq I Methyltransferase
    Taq I Methyltransferase 1 000 units
    https://www.bioz.com/result/taq i/product/New England Biolabs
    Average 93 stars, based on 2 article reviews
    Price from $9.99 to $1999.99
    taq i - by Bioz Stars, 2020-01
    93/100 stars

    Images

    1) Product Images from "A Recurrent Stop-Codon Mutation in Succinate Dehydrogenase Subunit B Gene in Normal Peripheral Blood and Childhood T-Cell Acute Leukemia"

    Article Title: A Recurrent Stop-Codon Mutation in Succinate Dehydrogenase Subunit B Gene in Normal Peripheral Blood and Childhood T-Cell Acute Leukemia

    Journal: PLoS ONE

    doi: 10.1371/journal.pone.0000436

    The steady-state fraction of mutant SDHB cDNAs resistant to Taq I RE digestion. Each circle represents a sample from a different subject (total indicated by n) except for those in the PHA stimulated PBMCs which were obtained from two normal donors, stimulated by 2.5 µg/ml and 5.0 µg/ml concentrations of PHA and tested at days 2, 5 and 8 for a total of 12 samples. The value corresponding to each circle was derived from three RT-PCR reactions. Two outlier PBMC values were shown at the top with their mutant transcript fractions in parentheses. Boxes and the vertical lines denote the means and their 95% confidence intervals of samples sets. “PBMC mutation carrier” group contains 5 SDHC and 24 SDHD mutation carriers. The leukemic cell lines were derived from B cells (n = 3), T cells (n = 9), NK cells (n = 1) and monocytes (n = 2).
    Figure Legend Snippet: The steady-state fraction of mutant SDHB cDNAs resistant to Taq I RE digestion. Each circle represents a sample from a different subject (total indicated by n) except for those in the PHA stimulated PBMCs which were obtained from two normal donors, stimulated by 2.5 µg/ml and 5.0 µg/ml concentrations of PHA and tested at days 2, 5 and 8 for a total of 12 samples. The value corresponding to each circle was derived from three RT-PCR reactions. Two outlier PBMC values were shown at the top with their mutant transcript fractions in parentheses. Boxes and the vertical lines denote the means and their 95% confidence intervals of samples sets. “PBMC mutation carrier” group contains 5 SDHC and 24 SDHD mutation carriers. The leukemic cell lines were derived from B cells (n = 3), T cells (n = 9), NK cells (n = 1) and monocytes (n = 2).

    Techniques Used: Mutagenesis, Derivative Assay, Reverse Transcription Polymerase Chain Reaction

    SDHB mutations in genomic DNAs (gDNAs). A. Taq I RE digestion of PCR-amplified exon 2 shows no evidence of undigested mutant DNAs at 260 bp size (pointed by an arrow head). Taq I RE digestion products of the wild-type DNA co-migrate at sizes of 128 and 132 bps (denoted by a star). B. Gel electrophoresis of Taq I RE-digested (mutation) enrichment PCR ( e PCR) products shows variable amounts of mutant gDNAs at 233 bp size (pointed by an arrow head), which are confirmed to be primarily composed of c.136C > T by sequencing ( Table 1 ). Taq I digestion of wild-type e PCR products gives two bands at sizes, 101 and 132 bp (shown by a star). C. e PCR analyses of leukemic cell lines demonstrate the presence of mutant gDNA in the MOLT-4 cell line (pointed by an arrow head) but not in other leukemic cell lines in this experiment. D. Direct sequence analysis of a gDNA e PCR product shows selective enrichment of the R46X mutation. E, F. Sequence chromatograms of the heterozygous DNA mutations detected in two T-ALL cell lines are shown.
    Figure Legend Snippet: SDHB mutations in genomic DNAs (gDNAs). A. Taq I RE digestion of PCR-amplified exon 2 shows no evidence of undigested mutant DNAs at 260 bp size (pointed by an arrow head). Taq I RE digestion products of the wild-type DNA co-migrate at sizes of 128 and 132 bps (denoted by a star). B. Gel electrophoresis of Taq I RE-digested (mutation) enrichment PCR ( e PCR) products shows variable amounts of mutant gDNAs at 233 bp size (pointed by an arrow head), which are confirmed to be primarily composed of c.136C > T by sequencing ( Table 1 ). Taq I digestion of wild-type e PCR products gives two bands at sizes, 101 and 132 bp (shown by a star). C. e PCR analyses of leukemic cell lines demonstrate the presence of mutant gDNA in the MOLT-4 cell line (pointed by an arrow head) but not in other leukemic cell lines in this experiment. D. Direct sequence analysis of a gDNA e PCR product shows selective enrichment of the R46X mutation. E, F. Sequence chromatograms of the heterozygous DNA mutations detected in two T-ALL cell lines are shown.

    Techniques Used: Polymerase Chain Reaction, Amplification, Mutagenesis, Nucleic Acid Electrophoresis, Sequencing

    Analysis of SDHB R46X mRNA mutation. A. The SDHB gene has 843 bp coding nucleotides spread to 8 exons within ∼35 kb at chromosome band 1p36.13. The 5′- portion of the gene shows the position of the R46X mutation and the mitochondrial signal peptide cleavage site (filled circle). B. Sequence chromatograms of RT-PCR products show samples that have high (top), low (middle), or undetectable (bottom) amounts of mutant R46X sequences. C. Quantification of the mutant fraction involved Taq I RE digestion of fluorescently-labeled RT-PCR products and capillary gel electrophoresis. The red peaks denote the molecular weight marker. D. The agarose gel electrophoresis shows variable fractions of mutant RT-PCR products from normal PBMCs detected by Taq I RE digestion, which releases two bands 159 and 126 bp in size from the wild-type sequence (also see Fig. S1A ). E. Fractions of Taq I RE resistant transcripts in the purified PBMC cell types are shown in an agarose gel. The negative image is presented to enhance the visibility of mutant transcripts.
    Figure Legend Snippet: Analysis of SDHB R46X mRNA mutation. A. The SDHB gene has 843 bp coding nucleotides spread to 8 exons within ∼35 kb at chromosome band 1p36.13. The 5′- portion of the gene shows the position of the R46X mutation and the mitochondrial signal peptide cleavage site (filled circle). B. Sequence chromatograms of RT-PCR products show samples that have high (top), low (middle), or undetectable (bottom) amounts of mutant R46X sequences. C. Quantification of the mutant fraction involved Taq I RE digestion of fluorescently-labeled RT-PCR products and capillary gel electrophoresis. The red peaks denote the molecular weight marker. D. The agarose gel electrophoresis shows variable fractions of mutant RT-PCR products from normal PBMCs detected by Taq I RE digestion, which releases two bands 159 and 126 bp in size from the wild-type sequence (also see Fig. S1A ). E. Fractions of Taq I RE resistant transcripts in the purified PBMC cell types are shown in an agarose gel. The negative image is presented to enhance the visibility of mutant transcripts.

    Techniques Used: Mutagenesis, Sequencing, Reverse Transcription Polymerase Chain Reaction, Labeling, Nucleic Acid Electrophoresis, Molecular Weight, Marker, Agarose Gel Electrophoresis, Purification

    2) Product Images from "A Recurrent Stop-Codon Mutation in Succinate Dehydrogenase Subunit B Gene in Normal Peripheral Blood and Childhood T-Cell Acute Leukemia"

    Article Title: A Recurrent Stop-Codon Mutation in Succinate Dehydrogenase Subunit B Gene in Normal Peripheral Blood and Childhood T-Cell Acute Leukemia

    Journal: PLoS ONE

    doi: 10.1371/journal.pone.0000436

    The steady-state fraction of mutant SDHB cDNAs resistant to Taq I RE digestion. Each circle represents a sample from a different subject (total indicated by n) except for those in the PHA stimulated PBMCs which were obtained from two normal donors, stimulated by 2.5 µg/ml and 5.0 µg/ml concentrations of PHA and tested at days 2, 5 and 8 for a total of 12 samples. The value corresponding to each circle was derived from three RT-PCR reactions. Two outlier PBMC values were shown at the top with their mutant transcript fractions in parentheses. Boxes and the vertical lines denote the means and their 95% confidence intervals of samples sets. “PBMC mutation carrier” group contains 5 SDHC and 24 SDHD mutation carriers. The leukemic cell lines were derived from B cells (n = 3), T cells (n = 9), NK cells (n = 1) and monocytes (n = 2).
    Figure Legend Snippet: The steady-state fraction of mutant SDHB cDNAs resistant to Taq I RE digestion. Each circle represents a sample from a different subject (total indicated by n) except for those in the PHA stimulated PBMCs which were obtained from two normal donors, stimulated by 2.5 µg/ml and 5.0 µg/ml concentrations of PHA and tested at days 2, 5 and 8 for a total of 12 samples. The value corresponding to each circle was derived from three RT-PCR reactions. Two outlier PBMC values were shown at the top with their mutant transcript fractions in parentheses. Boxes and the vertical lines denote the means and their 95% confidence intervals of samples sets. “PBMC mutation carrier” group contains 5 SDHC and 24 SDHD mutation carriers. The leukemic cell lines were derived from B cells (n = 3), T cells (n = 9), NK cells (n = 1) and monocytes (n = 2).

    Techniques Used: Mutagenesis, Derivative Assay, Reverse Transcription Polymerase Chain Reaction

    SDHB mutations in genomic DNAs (gDNAs). A. Taq I RE digestion of PCR-amplified exon 2 shows no evidence of undigested mutant DNAs at 260 bp size (pointed by an arrow head). Taq I RE digestion products of the wild-type DNA co-migrate at sizes of 128 and 132 bps (denoted by a star). B. Gel electrophoresis of Taq I RE-digested (mutation) enrichment PCR ( e PCR) products shows variable amounts of mutant gDNAs at 233 bp size (pointed by an arrow head), which are confirmed to be primarily composed of c.136C > T by sequencing ( Table 1 ). Taq I digestion of wild-type e PCR products gives two bands at sizes, 101 and 132 bp (shown by a star). C. e PCR analyses of leukemic cell lines demonstrate the presence of mutant gDNA in the MOLT-4 cell line (pointed by an arrow head) but not in other leukemic cell lines in this experiment. D. Direct sequence analysis of a gDNA e PCR product shows selective enrichment of the R46X mutation. E, F. Sequence chromatograms of the heterozygous DNA mutations detected in two T-ALL cell lines are shown.
    Figure Legend Snippet: SDHB mutations in genomic DNAs (gDNAs). A. Taq I RE digestion of PCR-amplified exon 2 shows no evidence of undigested mutant DNAs at 260 bp size (pointed by an arrow head). Taq I RE digestion products of the wild-type DNA co-migrate at sizes of 128 and 132 bps (denoted by a star). B. Gel electrophoresis of Taq I RE-digested (mutation) enrichment PCR ( e PCR) products shows variable amounts of mutant gDNAs at 233 bp size (pointed by an arrow head), which are confirmed to be primarily composed of c.136C > T by sequencing ( Table 1 ). Taq I digestion of wild-type e PCR products gives two bands at sizes, 101 and 132 bp (shown by a star). C. e PCR analyses of leukemic cell lines demonstrate the presence of mutant gDNA in the MOLT-4 cell line (pointed by an arrow head) but not in other leukemic cell lines in this experiment. D. Direct sequence analysis of a gDNA e PCR product shows selective enrichment of the R46X mutation. E, F. Sequence chromatograms of the heterozygous DNA mutations detected in two T-ALL cell lines are shown.

    Techniques Used: Polymerase Chain Reaction, Amplification, Mutagenesis, Nucleic Acid Electrophoresis, Sequencing

    Analysis of SDHB R46X mRNA mutation. A. The SDHB gene has 843 bp coding nucleotides spread to 8 exons within ∼35 kb at chromosome band 1p36.13. The 5′- portion of the gene shows the position of the R46X mutation and the mitochondrial signal peptide cleavage site (filled circle). B. Sequence chromatograms of RT-PCR products show samples that have high (top), low (middle), or undetectable (bottom) amounts of mutant R46X sequences. C. Quantification of the mutant fraction involved Taq I RE digestion of fluorescently-labeled RT-PCR products and capillary gel electrophoresis. The red peaks denote the molecular weight marker. D. The agarose gel electrophoresis shows variable fractions of mutant RT-PCR products from normal PBMCs detected by Taq I RE digestion, which releases two bands 159 and 126 bp in size from the wild-type sequence (also see Fig. S1A ). E. Fractions of Taq I RE resistant transcripts in the purified PBMC cell types are shown in an agarose gel. The negative image is presented to enhance the visibility of mutant transcripts.
    Figure Legend Snippet: Analysis of SDHB R46X mRNA mutation. A. The SDHB gene has 843 bp coding nucleotides spread to 8 exons within ∼35 kb at chromosome band 1p36.13. The 5′- portion of the gene shows the position of the R46X mutation and the mitochondrial signal peptide cleavage site (filled circle). B. Sequence chromatograms of RT-PCR products show samples that have high (top), low (middle), or undetectable (bottom) amounts of mutant R46X sequences. C. Quantification of the mutant fraction involved Taq I RE digestion of fluorescently-labeled RT-PCR products and capillary gel electrophoresis. The red peaks denote the molecular weight marker. D. The agarose gel electrophoresis shows variable fractions of mutant RT-PCR products from normal PBMCs detected by Taq I RE digestion, which releases two bands 159 and 126 bp in size from the wild-type sequence (also see Fig. S1A ). E. Fractions of Taq I RE resistant transcripts in the purified PBMC cell types are shown in an agarose gel. The negative image is presented to enhance the visibility of mutant transcripts.

    Techniques Used: Mutagenesis, Sequencing, Reverse Transcription Polymerase Chain Reaction, Labeling, Nucleic Acid Electrophoresis, Molecular Weight, Marker, Agarose Gel Electrophoresis, Purification

    3) Product Images from "DNA Methylation of the ABO Promoter Underlies Loss of ABO Allelic Expression in a Significant Proportion of Leukemic Patients"

    Article Title: DNA Methylation of the ABO Promoter Underlies Loss of ABO Allelic Expression in a Significant Proportion of Leukemic Patients

    Journal: PLoS ONE

    doi: 10.1371/journal.pone.0004788

    Loss of A expression by RT-PCR and restriction enzyme digestion. (A) Schematic representation of ABO allelic expression analysis. Kpn I digestion results in a 130 bp band if the O allele is present and no digestion of the A or B allele. BstE II digestion results in a 130 bp band if the A or B allele is present and no digestion of the O allele. (B) Lane M is the pUC19/ Hpa II marker while lane 1 is the uncut ABO RT-PCR product. Lanes 2, 4, 6 and 8 are digested with Kpn I while lanes 3, 5, 7 and 9 are digested with BstE II. Lanes 2 and 3 are from cDNA of patient F7, lanes 4 and 5 from F11, lanes 6 and 7 from F15 and lanes 8 and 9 from F17. F7 and F11 are AO patients with loss of the A allele, F17 is an AO patient with no loss of ABO allelic expression. Patient F15 has an A 1 A 2 genotype, hence no cutting with Kpn I was expected. (C) Lanes 1, 3 and 5 are ABO RT-PCR product digested with Kpn I while lanes 2, 4 and 6 are digests with BstE II. Lanes 1 and 2 are from cDNA of patient F23, an A 2 B genotype, hence no cutting with Kpn I was expected. Lanes 3 and 4 are F53, an A 1 O 1 patient with loss of A at the mRNA level. Lanes 5 and 6 are S8, which is a patient with an A 1 O 1 genotype with loss of A allelic expression. (D) The ABO CpG island promoter region assessed for methylation. The methylated and bisulfite modified sequence is shown and the primer sequences are double underlined. The capital Ts identify thymines that are a result of bisulfite modification of cytosines and the CpGs are shown in bold. The start of transcription is marked with +1. The different restriction enzymes used for assessing methylation by digestion are as follows: eight BstU I sites ( cg/cg ), two Taq I ( T/cga ) sites (however one is found in the primer and hence will cut regardless of methylation status), one Hinf I ( g/aTTc ) site. Regions 161–173 and 198–210 harbor Sp1 sites [55] .
    Figure Legend Snippet: Loss of A expression by RT-PCR and restriction enzyme digestion. (A) Schematic representation of ABO allelic expression analysis. Kpn I digestion results in a 130 bp band if the O allele is present and no digestion of the A or B allele. BstE II digestion results in a 130 bp band if the A or B allele is present and no digestion of the O allele. (B) Lane M is the pUC19/ Hpa II marker while lane 1 is the uncut ABO RT-PCR product. Lanes 2, 4, 6 and 8 are digested with Kpn I while lanes 3, 5, 7 and 9 are digested with BstE II. Lanes 2 and 3 are from cDNA of patient F7, lanes 4 and 5 from F11, lanes 6 and 7 from F15 and lanes 8 and 9 from F17. F7 and F11 are AO patients with loss of the A allele, F17 is an AO patient with no loss of ABO allelic expression. Patient F15 has an A 1 A 2 genotype, hence no cutting with Kpn I was expected. (C) Lanes 1, 3 and 5 are ABO RT-PCR product digested with Kpn I while lanes 2, 4 and 6 are digests with BstE II. Lanes 1 and 2 are from cDNA of patient F23, an A 2 B genotype, hence no cutting with Kpn I was expected. Lanes 3 and 4 are F53, an A 1 O 1 patient with loss of A at the mRNA level. Lanes 5 and 6 are S8, which is a patient with an A 1 O 1 genotype with loss of A allelic expression. (D) The ABO CpG island promoter region assessed for methylation. The methylated and bisulfite modified sequence is shown and the primer sequences are double underlined. The capital Ts identify thymines that are a result of bisulfite modification of cytosines and the CpGs are shown in bold. The start of transcription is marked with +1. The different restriction enzymes used for assessing methylation by digestion are as follows: eight BstU I sites ( cg/cg ), two Taq I ( T/cga ) sites (however one is found in the primer and hence will cut regardless of methylation status), one Hinf I ( g/aTTc ) site. Regions 161–173 and 198–210 harbor Sp1 sites [55] .

    Techniques Used: Expressing, Reverse Transcription Polymerase Chain Reaction, Marker, Methylation, Modification, Sequencing

    ABO promoter methylation in leukemic cell lines. (A) MS-SSCA analysis of the ABO BIS PCR products. PBMNC refers to peripheral blood mononuclear cells and PBSC to peripheral blood stem cells. These were used as unmethylated controls. It is clear from the SSCA gel that only the K-562 leukemic cell line is unmethylated as it has the same banding pattern as the PBMNC and PBSC. The other cell lines all have varying amounts of methylation as seen by the various banding patterns. The JURKAT and RAJI cell lines were hypermethylated, as seen by the dramatic shift of the bottom doublet of bands. (B) Restriction enzyme digests of the ABO BIS PCR products. Digestion with any of the restriction enzymes is indicative of methylation at that CpG site within the restriction enzyme recognition sequence. All the products will cut with Taq I since there is a Taq I site in the reverse primer. (C) ABO re-expression in the JURKAT cell line after 24 h treatment with 5-aza-2′-deoxycytidine treatment. On the gel, the NEGATIVE was an RT control (RNA only), the VEHICLE lane was JURKAT cells treated with ultra pure water, the following lanes are JURKAT cells treated with 1 µM or 2 µM of 5-aza-2′-deoxycytidine respectively showing ABO re-expression. PBGD is the reference gene. (D) The ABO promoter is demethylated in JURKAT cells after 5-aza-2′-deoxycytidine treatment. In the VEHICLE treated JURKAT cells there is no evidence of unmethylated ABO promoter which would be a band at the same size as the UNCUT sample. However, after treatment with 1 or 2 µM of 5-aza-2′-deoxycytidine the ABO promoter is unmethylated as evidenced by a band at the same size as the UNCUT sample.
    Figure Legend Snippet: ABO promoter methylation in leukemic cell lines. (A) MS-SSCA analysis of the ABO BIS PCR products. PBMNC refers to peripheral blood mononuclear cells and PBSC to peripheral blood stem cells. These were used as unmethylated controls. It is clear from the SSCA gel that only the K-562 leukemic cell line is unmethylated as it has the same banding pattern as the PBMNC and PBSC. The other cell lines all have varying amounts of methylation as seen by the various banding patterns. The JURKAT and RAJI cell lines were hypermethylated, as seen by the dramatic shift of the bottom doublet of bands. (B) Restriction enzyme digests of the ABO BIS PCR products. Digestion with any of the restriction enzymes is indicative of methylation at that CpG site within the restriction enzyme recognition sequence. All the products will cut with Taq I since there is a Taq I site in the reverse primer. (C) ABO re-expression in the JURKAT cell line after 24 h treatment with 5-aza-2′-deoxycytidine treatment. On the gel, the NEGATIVE was an RT control (RNA only), the VEHICLE lane was JURKAT cells treated with ultra pure water, the following lanes are JURKAT cells treated with 1 µM or 2 µM of 5-aza-2′-deoxycytidine respectively showing ABO re-expression. PBGD is the reference gene. (D) The ABO promoter is demethylated in JURKAT cells after 5-aza-2′-deoxycytidine treatment. In the VEHICLE treated JURKAT cells there is no evidence of unmethylated ABO promoter which would be a band at the same size as the UNCUT sample. However, after treatment with 1 or 2 µM of 5-aza-2′-deoxycytidine the ABO promoter is unmethylated as evidenced by a band at the same size as the UNCUT sample.

    Techniques Used: Methylation, Mass Spectrometry, Polymerase Chain Reaction, Sequencing, Expressing

    4) Product Images from "Phenotypic and Molecular Characterization of Tetracycline- and Erythromycin-Resistant Strains of Streptococcus pneumoniae"

    Article Title: Phenotypic and Molecular Characterization of Tetracycline- and Erythromycin-Resistant Strains of Streptococcus pneumoniae

    Journal: Antimicrobial Agents and Chemotherapy

    doi: 10.1128/AAC.47.7.2236-2241.2003

    Different fingerprinting profiles obtained by digesting the tet (M) amplicons from 64 tet (M)-positive pneumococci with four endonucleases. Lane M, molecular size marker (100-bp ladder). Lane A, undigested tet (M) amplicon. Lanes 1a to 1e, different Aci I profiles ( Aci I 1 to Aci I 5 ). Lanes 2a and 2b, different Rsa I profiles ( Rsa I 1 and Rsa I 2 ). Lane 3, Mse I profile. Lane 4, Taq I profile.
    Figure Legend Snippet: Different fingerprinting profiles obtained by digesting the tet (M) amplicons from 64 tet (M)-positive pneumococci with four endonucleases. Lane M, molecular size marker (100-bp ladder). Lane A, undigested tet (M) amplicon. Lanes 1a to 1e, different Aci I profiles ( Aci I 1 to Aci I 5 ). Lanes 2a and 2b, different Rsa I profiles ( Rsa I 1 and Rsa I 2 ). Lane 3, Mse I profile. Lane 4, Taq I profile.

    Techniques Used: Marker, Amplification

    HRRA patterns of two tet (M)-positive pneumococci with restriction types A and B. Lane M, molecular size marker (100-bp ladder). Lane A, undigested tet (M) amplicon of the strain exhibiting restriction type A; lanes A1 to A4, restriction profiles yielded by endonucleases Aci I, Rsa I, Mse I, and Taq I, respectively. Lane B, undigested tet (M) amplicon of the strain exhibiting restriction type B; lanes B1 to B4, restriction profiles yielded by endonucleases Aci I, Rsa I, Mse I, and Taq I, respectively.
    Figure Legend Snippet: HRRA patterns of two tet (M)-positive pneumococci with restriction types A and B. Lane M, molecular size marker (100-bp ladder). Lane A, undigested tet (M) amplicon of the strain exhibiting restriction type A; lanes A1 to A4, restriction profiles yielded by endonucleases Aci I, Rsa I, Mse I, and Taq I, respectively. Lane B, undigested tet (M) amplicon of the strain exhibiting restriction type B; lanes B1 to B4, restriction profiles yielded by endonucleases Aci I, Rsa I, Mse I, and Taq I, respectively.

    Techniques Used: Marker, Amplification

    5) Product Images from "Coyotes (Canis latrans) as the Reservoir for a Human Pathogenic Bartonella sp.: Molecular Epidemiology of Bartonella vinsonii subsp. berkhoffii Infection in Coyotes from Central Coastal California"

    Article Title: Coyotes (Canis latrans) as the Reservoir for a Human Pathogenic Bartonella sp.: Molecular Epidemiology of Bartonella vinsonii subsp. berkhoffii Infection in Coyotes from Central Coastal California

    Journal: Journal of Clinical Microbiology

    doi:

    PCR (lanes 2 to 5) and PCR-RFLP (lanes 6 to 9, Taq I digestion; lanes 10 to 13, Hha I digestion) analyses of the gltA ). Lanes 1 and 14, standard 100-bp molecular ladder; lanes 2, 6, and 10, coyote isolates; lanes 3, 7, and 11, B. vinsonii subsp. berkhoffii ATCC 51672; lanes 4, 8, and 12, B. vinsonii ATCC VR152; lanes 5, 9 and 13, B. henselae (strain U-4, University of California, Davis).
    Figure Legend Snippet: PCR (lanes 2 to 5) and PCR-RFLP (lanes 6 to 9, Taq I digestion; lanes 10 to 13, Hha I digestion) analyses of the gltA ). Lanes 1 and 14, standard 100-bp molecular ladder; lanes 2, 6, and 10, coyote isolates; lanes 3, 7, and 11, B. vinsonii subsp. berkhoffii ATCC 51672; lanes 4, 8, and 12, B. vinsonii ATCC VR152; lanes 5, 9 and 13, B. henselae (strain U-4, University of California, Davis).

    Techniques Used: Polymerase Chain Reaction

    PCR-RFLP analysis (lanes 2 to 11, Taq I digestion; lanes 12 to 21, Mse I digestion) of the gltA ). Lanes 1 and 22, standard 100-bp molecular ladder; lanes 2 to 9 and 12 to 19, coyote isolates; lanes 10 and 20, B. vinsonii subsp. berkhoffii ATCC 51672; lanes 11 and 21, B. henselae (strain U-4; University of California, Davis).
    Figure Legend Snippet: PCR-RFLP analysis (lanes 2 to 11, Taq I digestion; lanes 12 to 21, Mse I digestion) of the gltA ). Lanes 1 and 22, standard 100-bp molecular ladder; lanes 2 to 9 and 12 to 19, coyote isolates; lanes 10 and 20, B. vinsonii subsp. berkhoffii ATCC 51672; lanes 11 and 21, B. henselae (strain U-4; University of California, Davis).

    Techniques Used: Polymerase Chain Reaction

    6) Product Images from "Epigenetic control of the ubiquitin carboxyl terminal hydrolase 1 in renal cell carcinoma"

    Article Title: Epigenetic control of the ubiquitin carboxyl terminal hydrolase 1 in renal cell carcinoma

    Journal: Journal of Translational Medicine

    doi: 10.1186/1479-5876-7-90

    UCHL1 promoter DNA methylation in RCC lesions, tumor adjacent kidney epithelium and RCC cell lines . A) Representative COBRA analysis of three RCC tumor lesions and one RCC cell line. Genomic DNA extracted from tumor lesions (2874TU, 2876TU and 2878) and the cell line MZ1940RC was treated with bisulfite and amplified by nested PCR as described in the Methods section. The resulting 265 bp amplicons were either digested with Taq I (+) or left untreated (-) and subsequently separated in 2% agarose gels in TAE buffer. A 100 base pair DNA ruler loaded in the first lane served as length standard. B) Distribution pattern for UCHL1 promoter DNA methylation in tumor adjacent kidney epithelium, autologous primary RCC lesions and RCC cell lines. Grey bars represent samples with unmethylated (U), striped bars with partially methylated (P) and black bars with fully methylated (M) CpG islets within the UCHL1 promoter core region as indicated.
    Figure Legend Snippet: UCHL1 promoter DNA methylation in RCC lesions, tumor adjacent kidney epithelium and RCC cell lines . A) Representative COBRA analysis of three RCC tumor lesions and one RCC cell line. Genomic DNA extracted from tumor lesions (2874TU, 2876TU and 2878) and the cell line MZ1940RC was treated with bisulfite and amplified by nested PCR as described in the Methods section. The resulting 265 bp amplicons were either digested with Taq I (+) or left untreated (-) and subsequently separated in 2% agarose gels in TAE buffer. A 100 base pair DNA ruler loaded in the first lane served as length standard. B) Distribution pattern for UCHL1 promoter DNA methylation in tumor adjacent kidney epithelium, autologous primary RCC lesions and RCC cell lines. Grey bars represent samples with unmethylated (U), striped bars with partially methylated (P) and black bars with fully methylated (M) CpG islets within the UCHL1 promoter core region as indicated.

    Techniques Used: DNA Methylation Assay, Combined Bisulfite Restriction Analysis Assay, Amplification, Nested PCR, Methylation

    7) Product Images from "Dynamic Evolution of Telomeric Sequences in the Green Algal Order Chlamydomonadales"

    Article Title: Dynamic Evolution of Telomeric Sequences in the Green Algal Order Chlamydomonadales

    Journal: Genome Biology and Evolution

    doi: 10.1093/gbe/evs007

    Results of terminal restriction fragment (TRF) analysis. Genomic DNA samples from the Chloromonadinia (TEL159), the Stephanosphaeria (TEL106), and the Dunaliellinia (TEL173) were digested by Taq I (T), Mbo I (M), Alu I (A), or Rsa I (R) restriction endonuclease (−, non-digested) and separated on an 0.9% agarose gel (marker lengths in kilo bases). Control algal DNA samples for the Arabidopsis type (TTTAGGG) and the Chlamydomonas type (TTTTAGGG) were included. The hybridization pattern of the probes specific for the telomeric types—the Arabidopsis type (ATSB), the Chlamydomonas type (CHSB), the human type (HUSB), and the chlorarachniophyte nucleomorph type (CASB) is shown ( table 1 ). Only the part of minisatellite probes is shown here, full version of the TRF analysis is available as supplementary fig. S2 ( Supplementary Material online)
    Figure Legend Snippet: Results of terminal restriction fragment (TRF) analysis. Genomic DNA samples from the Chloromonadinia (TEL159), the Stephanosphaeria (TEL106), and the Dunaliellinia (TEL173) were digested by Taq I (T), Mbo I (M), Alu I (A), or Rsa I (R) restriction endonuclease (−, non-digested) and separated on an 0.9% agarose gel (marker lengths in kilo bases). Control algal DNA samples for the Arabidopsis type (TTTAGGG) and the Chlamydomonas type (TTTTAGGG) were included. The hybridization pattern of the probes specific for the telomeric types—the Arabidopsis type (ATSB), the Chlamydomonas type (CHSB), the human type (HUSB), and the chlorarachniophyte nucleomorph type (CASB) is shown ( table 1 ). Only the part of minisatellite probes is shown here, full version of the TRF analysis is available as supplementary fig. S2 ( Supplementary Material online)

    Techniques Used: Agarose Gel Electrophoresis, Marker, Hybridization

    8) Product Images from "A novel method for the efficient and selective identification of 5-hydroxymethylcytosine in genomic DNA"

    Article Title: A novel method for the efficient and selective identification of 5-hydroxymethylcytosine in genomic DNA

    Journal: Nucleic Acids Research

    doi: 10.1093/nar/gkr051

    The β-gt can specifically modify 5hmC residues at a high efficiency. ( a ) Oligonucleotides that were either incubated in the presence or absence of the β-gt were digested with Taq I, treated with alkaline phosphatase, 5′-end labeled using T4 polynucleotide kinase and digested to 5′-mononucleotides using DNase I and Snake Venom Phosphodiesterase. Radiolabeled mononucleotides were analyzed by two-dimensional TLC. C, 3′-deoxyribocytosine-5′-monophosphate; T, 3′-deoxyribothymidine-5′-monophosphate; 5meC, 3′-deoxyribo-N5-methylcytosine-5′-monophosphate; 5hmC, 3′-deoxyribo-N5-hydroxymethylcytosine-5′-monophosphate. ( b ) HPLC coupled to tandem mass spectrometry was used to measure the efficiency of the β-gt reaction. Substrates analyzed were 2.7 kb linear PCR products of pUC18: the dC substrate contained only cytosine residues; the 5meC substrate was created by methylating the CpG dinucleotide of the cytosine substrate; the 5hmC substrate was created by using d5hmC in place of dCTP in the PCR reactions; the β-glu-5hmC substrate was created by incubating the 5hmC substrate with the β-gt in the presence of UDP-glucose. Control DNA was prepared from salmon sperm. LC/MS/MS chromatograms of the cytosine residues from each of the substrates are presented. Abbreviations: dC, 3′-deoxyribocytosine; 5me(dC), 3′-deoxyribo-N5-methylcytosine; 5hm(dC), 3′-deoxyribo-N5-hydroxymethylcytosine; 5-glu-hm(dC), 3′-deoxyribo-N5-(β- d -glucosyl(hydroxymethyl))cytosine. Asterisks indictes that cytosines are only 5meC modified at CpG sequences.
    Figure Legend Snippet: The β-gt can specifically modify 5hmC residues at a high efficiency. ( a ) Oligonucleotides that were either incubated in the presence or absence of the β-gt were digested with Taq I, treated with alkaline phosphatase, 5′-end labeled using T4 polynucleotide kinase and digested to 5′-mononucleotides using DNase I and Snake Venom Phosphodiesterase. Radiolabeled mononucleotides were analyzed by two-dimensional TLC. C, 3′-deoxyribocytosine-5′-monophosphate; T, 3′-deoxyribothymidine-5′-monophosphate; 5meC, 3′-deoxyribo-N5-methylcytosine-5′-monophosphate; 5hmC, 3′-deoxyribo-N5-hydroxymethylcytosine-5′-monophosphate. ( b ) HPLC coupled to tandem mass spectrometry was used to measure the efficiency of the β-gt reaction. Substrates analyzed were 2.7 kb linear PCR products of pUC18: the dC substrate contained only cytosine residues; the 5meC substrate was created by methylating the CpG dinucleotide of the cytosine substrate; the 5hmC substrate was created by using d5hmC in place of dCTP in the PCR reactions; the β-glu-5hmC substrate was created by incubating the 5hmC substrate with the β-gt in the presence of UDP-glucose. Control DNA was prepared from salmon sperm. LC/MS/MS chromatograms of the cytosine residues from each of the substrates are presented. Abbreviations: dC, 3′-deoxyribocytosine; 5me(dC), 3′-deoxyribo-N5-methylcytosine; 5hm(dC), 3′-deoxyribo-N5-hydroxymethylcytosine; 5-glu-hm(dC), 3′-deoxyribo-N5-(β- d -glucosyl(hydroxymethyl))cytosine. Asterisks indictes that cytosines are only 5meC modified at CpG sequences.

    Techniques Used: Incubation, Labeling, Thin Layer Chromatography, High Performance Liquid Chromatography, Mass Spectrometry, Polymerase Chain Reaction, Liquid Chromatography with Mass Spectroscopy, Modification

    9) Product Images from "Toll-like receptor triggering in cord blood mesenchymal stem cells"

    Article Title: Toll-like receptor triggering in cord blood mesenchymal stem cells

    Journal: Journal of Cellular and Molecular Medicine

    doi: 10.1111/j.1582-4934.2009.00653.x

    The TNFα promoter is methylated in USSCs. (A) TNFα mRNA was detected by means of non-quantitative RT-PCR in monocytes (Mono), immature DC (imDC), DC stimulated with LPS for 6 hrs (DC, 6-hr LPS), tolerogenic DC (tolDC), tolerogenic DC stimulated with LPS for 6 hrs (tolDC, 6-hr LPS) and USSCs from donor 5016 (USSC-5016). The promoter of TNFα in imDC appeared to be unmethylated, as demonstrated by the resistance of methylation-specific genomic PCR products to Taq I digestion. (B) The TNF-α promoter in USSCs from two different donors (USSC-5016 and -DD) is methylated, as methylation-specific genomic PCR products derived from these cells are sensitive to Taq I digestion, irrespective of LPS or flagellin stimulation for 2 hrs. Arrows indicate full-length (183 bp; upper arrow), 141 bp and 42 bp products.
    Figure Legend Snippet: The TNFα promoter is methylated in USSCs. (A) TNFα mRNA was detected by means of non-quantitative RT-PCR in monocytes (Mono), immature DC (imDC), DC stimulated with LPS for 6 hrs (DC, 6-hr LPS), tolerogenic DC (tolDC), tolerogenic DC stimulated with LPS for 6 hrs (tolDC, 6-hr LPS) and USSCs from donor 5016 (USSC-5016). The promoter of TNFα in imDC appeared to be unmethylated, as demonstrated by the resistance of methylation-specific genomic PCR products to Taq I digestion. (B) The TNF-α promoter in USSCs from two different donors (USSC-5016 and -DD) is methylated, as methylation-specific genomic PCR products derived from these cells are sensitive to Taq I digestion, irrespective of LPS or flagellin stimulation for 2 hrs. Arrows indicate full-length (183 bp; upper arrow), 141 bp and 42 bp products.

    Techniques Used: Methylation, Quantitative RT-PCR, Polymerase Chain Reaction, Derivative Assay

    10) Product Images from "HLJ1 (DNAJB4) Gene Is a Novel Biomarker Candidate in Breast Cancer"

    Article Title: HLJ1 (DNAJB4) Gene Is a Novel Biomarker Candidate in Breast Cancer

    Journal: OMICS : a Journal of Integrative Biology

    doi: 10.1089/omi.2017.0016

    COBRA. Taq I (A) and Hpy 188I (B) restriction enzymes were used for region-1 and region-2, respectively. (−), No restriction digestion; M, marker. An amplicon having an Hpy 188I cutting site was used with (+) and without (Uncut) a restriction enzyme.
    Figure Legend Snippet: COBRA. Taq I (A) and Hpy 188I (B) restriction enzymes were used for region-1 and region-2, respectively. (−), No restriction digestion; M, marker. An amplicon having an Hpy 188I cutting site was used with (+) and without (Uncut) a restriction enzyme.

    Techniques Used: Combined Bisulfite Restriction Analysis Assay, Marker, Amplification

    11) Product Images from "Genotyping of Epidemic Methicillin-Resistant Staphylococcus aureus Phage Type 15 Isolates by Fluorescent Amplified-Fragment Length Polymorphism Analysis"

    Article Title: Genotyping of Epidemic Methicillin-Resistant Staphylococcus aureus Phage Type 15 Isolates by Fluorescent Amplified-Fragment Length Polymorphism Analysis

    Journal: Journal of Clinical Microbiology

    doi:

    GeneScan version 2.1 software-derived electropherograms of the predominant EMRSA-15 FAFLP profile for Apa I+0 and Taq I+G (a) and for Eco RI+0 and Mse I+C (b). The solid arrowheads and peaks indicate fragments that are present in the predominant profile but absent in other EMRSA-15 isolates (sizes are indicated in base pairs). The open arrowheads indicate the absence from the predominant profile of a polymorphic fragment that is present in another EMRSA-15 isolate.
    Figure Legend Snippet: GeneScan version 2.1 software-derived electropherograms of the predominant EMRSA-15 FAFLP profile for Apa I+0 and Taq I+G (a) and for Eco RI+0 and Mse I+C (b). The solid arrowheads and peaks indicate fragments that are present in the predominant profile but absent in other EMRSA-15 isolates (sizes are indicated in base pairs). The open arrowheads indicate the absence from the predominant profile of a polymorphic fragment that is present in another EMRSA-15 isolate.

    Techniques Used: Software, Derivative Assay

    UPGMA dendrograms derived from FAFLP data. (a) Apa I+0 and Taq I+G; (b) Eco RI+0 and Mse I+C; (c) combined data from both primer pairs. The d ). The horizontal scale bars represent 5% divergence.
    Figure Legend Snippet: UPGMA dendrograms derived from FAFLP data. (a) Apa I+0 and Taq I+G; (b) Eco RI+0 and Mse I+C; (c) combined data from both primer pairs. The d ). The horizontal scale bars represent 5% divergence.

    Techniques Used: Derivative Assay

    12) Product Images from "Protein genes in repetitive sequence--antifreeze glycoproteins in Atlantic cod genome"

    Article Title: Protein genes in repetitive sequence--antifreeze glycoproteins in Atlantic cod genome

    Journal: BMC Genomics

    doi: 10.1186/1471-2164-13-293

    Southern blot analysis of Atlantic cod genomic DNA showing presence of AFGP coding sequences. Taq I digested genomic DNA (~10–15 μg) from Atlantic cod (lanes 1–14) and polar cod (lanes 15–17) hybridized strongly to a polar cod B. saida AFGP coding sequence probe. Atlantic cod individuals include Norwegian coastal cod (NCC) and North East Arctic cod (NEAC) from the Finnmark coast and marginal Barents Sea sites: (lanes 1–3) N69° 26.91′ E19° 37.56′; (lanes 4–5) N69° 58.34′ E30° 2.37′; (lanes 6–8) N70° 7.24′ E30° 48.47′; (lanes 9–13) N71° 11.93′ E27° 59.29′, and one individual (lane 14) from Øresund, Denmark. NEAC and NCC are distinguished by their Pan I genotype, BB and AA respectively as indicated, while AB can either be NEAC or NCC. For comparison, the related freshwater cod Lota lota (lane 18) that does not have AFGP shows no hybridization.
    Figure Legend Snippet: Southern blot analysis of Atlantic cod genomic DNA showing presence of AFGP coding sequences. Taq I digested genomic DNA (~10–15 μg) from Atlantic cod (lanes 1–14) and polar cod (lanes 15–17) hybridized strongly to a polar cod B. saida AFGP coding sequence probe. Atlantic cod individuals include Norwegian coastal cod (NCC) and North East Arctic cod (NEAC) from the Finnmark coast and marginal Barents Sea sites: (lanes 1–3) N69° 26.91′ E19° 37.56′; (lanes 4–5) N69° 58.34′ E30° 2.37′; (lanes 6–8) N70° 7.24′ E30° 48.47′; (lanes 9–13) N71° 11.93′ E27° 59.29′, and one individual (lane 14) from Øresund, Denmark. NEAC and NCC are distinguished by their Pan I genotype, BB and AA respectively as indicated, while AB can either be NEAC or NCC. For comparison, the related freshwater cod Lota lota (lane 18) that does not have AFGP shows no hybridization.

    Techniques Used: Southern Blot, Sequencing, Hybridization

    13) Product Images from "The association of NR1H3 gene with lipid deposition in the pig"

    Article Title: The association of NR1H3 gene with lipid deposition in the pig

    Journal: Lipids in Health and Disease

    doi: 10.1186/s12944-016-0269-5

    The electrophoresis of PCR- Taq I-RFLP for NR1H3 exon 5-A201C in pigs. Note: The individual with 348 and 113 bp fragments had genotype AA (lanes 1, 2, 3, 6, 7, 9, 10, 13, 14), the individual with 348, 290, 113, and 58 bp fragments had genotype AC (lanes 4, 5, 8, 11, 12), and the individual with 290, 113, and 58 bp fragments had genotype CC (lanes 15, 16)
    Figure Legend Snippet: The electrophoresis of PCR- Taq I-RFLP for NR1H3 exon 5-A201C in pigs. Note: The individual with 348 and 113 bp fragments had genotype AA (lanes 1, 2, 3, 6, 7, 9, 10, 13, 14), the individual with 348, 290, 113, and 58 bp fragments had genotype AC (lanes 4, 5, 8, 11, 12), and the individual with 290, 113, and 58 bp fragments had genotype CC (lanes 15, 16)

    Techniques Used: Electrophoresis, Polymerase Chain Reaction

    14) Product Images from "SIP1 is downregulated in hepatocellular carcinoma by promoter hypermethylation"

    Article Title: SIP1 is downregulated in hepatocellular carcinoma by promoter hypermethylation

    Journal: BMC Cancer

    doi: 10.1186/1471-2407-11-223

    Methylation analysis of promoter regions by COBRA . Photographs are representative of tumor-specific methylation in three promoter regions. Amplicons of P1 and P2 are cut with Bst UI (left and middle), and Taq I digestion is applied to the PCR products of the P3 region (right). N: normal; T: tumor; M: marker.
    Figure Legend Snippet: Methylation analysis of promoter regions by COBRA . Photographs are representative of tumor-specific methylation in three promoter regions. Amplicons of P1 and P2 are cut with Bst UI (left and middle), and Taq I digestion is applied to the PCR products of the P3 region (right). N: normal; T: tumor; M: marker.

    Techniques Used: Methylation, Combined Bisulfite Restriction Analysis Assay, Polymerase Chain Reaction, Marker

    15) Product Images from "Bin mapping of tomato diversity array (DArT) markers to genomic regions of Solanum lycopersicum x Solanum pennellii introgression lines"

    Article Title: Bin mapping of tomato diversity array (DArT) markers to genomic regions of Solanum lycopersicum x Solanum pennellii introgression lines

    Journal: TAG. Theoretical and Applied Genetics. Theoretische Und Angewandte Genetik

    doi: 10.1007/s00122-011-1759-5

    Digested-PCR products of DArT marker sequences reveal predicted polymorphisms and chromosomal locations. CAPs analysis of DArT marker sequences from parental and introgression lines. SYBR Safe-stained 2% TAE agarose gels highlighting the polymorphisms observed between Heinz, M82, S. pennellii and different IL lines DNAs. a Taq I digestion of PCR-amplified DNA corresponding to S. lycopersicum DArT marker 441173 using primers DArT39 and DArT40. b Mnl I digestion of PCR-amplified DNA corresponding to S. pennellii DArT marker 436990 using primers DArT41 and DArT42. Template DNA; S. lycopersicum cv. Heinz (H), S. lycopersicum cv. M82 (M82), S. pennellii ( Sp ), Introgression lines (IL), molecular weight Hyperladder IV (BIOLINE) (M)
    Figure Legend Snippet: Digested-PCR products of DArT marker sequences reveal predicted polymorphisms and chromosomal locations. CAPs analysis of DArT marker sequences from parental and introgression lines. SYBR Safe-stained 2% TAE agarose gels highlighting the polymorphisms observed between Heinz, M82, S. pennellii and different IL lines DNAs. a Taq I digestion of PCR-amplified DNA corresponding to S. lycopersicum DArT marker 441173 using primers DArT39 and DArT40. b Mnl I digestion of PCR-amplified DNA corresponding to S. pennellii DArT marker 436990 using primers DArT41 and DArT42. Template DNA; S. lycopersicum cv. Heinz (H), S. lycopersicum cv. M82 (M82), S. pennellii ( Sp ), Introgression lines (IL), molecular weight Hyperladder IV (BIOLINE) (M)

    Techniques Used: Polymerase Chain Reaction, Marker, Staining, Amplification, Molecular Weight

    16) Product Images from "Reliable molecular identification of nine tropical whitefly species"

    Article Title: Reliable molecular identification of nine tropical whitefly species

    Journal: Ecology and Evolution

    doi: 10.1002/ece3.1204

    Displays two 2% agarose gels showing the restriction fragment length polymorphism profiles obtained by digesting the COI with Alu I (A) and Ase I + Taq I (B) enzyme from Lecanoideus floccissimus (lane 1) , Aleurotrachelus socialis (lane 2) , Bemisia tabaci (Sample 1, lane 3) , B. tabaci (Sample 2, lane 4) , Trialeurodes vaporiariorum (lane 5) , Aleurodicus dispersus (lane 6) , Aleurothrixus floccosus (lane 7) , Aleurotrachelus trachoides (lane 8) , Trialeurodes variabilis (lane 9) , Aleuronudus melzeri (lane 10). Molecular size markers are shown on the right and left side of the figure. Number filled in black corresponds to fragments size expected based on available sequence information and those in red to fragments expected by sequence variation due to intraspecies variation detected by RFLP-PCR of the COI amplicon.
    Figure Legend Snippet: Displays two 2% agarose gels showing the restriction fragment length polymorphism profiles obtained by digesting the COI with Alu I (A) and Ase I + Taq I (B) enzyme from Lecanoideus floccissimus (lane 1) , Aleurotrachelus socialis (lane 2) , Bemisia tabaci (Sample 1, lane 3) , B. tabaci (Sample 2, lane 4) , Trialeurodes vaporiariorum (lane 5) , Aleurodicus dispersus (lane 6) , Aleurothrixus floccosus (lane 7) , Aleurotrachelus trachoides (lane 8) , Trialeurodes variabilis (lane 9) , Aleuronudus melzeri (lane 10). Molecular size markers are shown on the right and left side of the figure. Number filled in black corresponds to fragments size expected based on available sequence information and those in red to fragments expected by sequence variation due to intraspecies variation detected by RFLP-PCR of the COI amplicon.

    Techniques Used: Sequencing, Polymerase Chain Reaction, Amplification

    17) Product Images from "Changes in Populations of Rhizosphere Bacteria Associated with Take-All Disease of Wheat"

    Article Title: Changes in Populations of Rhizosphere Bacteria Associated with Take-All Disease of Wheat

    Journal: Applied and Environmental Microbiology

    doi: 10.1128/AEM.67.10.4414-4425.2001

    Genotyping of phlD -containing bacteria present in the soils of Mount Vernon, Wash. Representative results for the growth chamber assays are shown. The phlD sequences were amplified using gene-specific primers B2BF and BPR4 and subsequently digested with either Hae III or Taq I. Set 1 includes samples of several terminal phlD + dilutions and isolates obtained from rhizospheres of wheat grown in soils A and B. Set 2 includes three isolates of a different genotype obtained from a Lind, Wash., soil for contrast. A known 2,4-DAPG-producing, BOX D genotype strain of Pseudomonas fluorescens (Q8r1–96) was used as a positive control for comparison (lane C). The sizes of individual fragments were determined based on the 100-bp ladder shown in lanes M.
    Figure Legend Snippet: Genotyping of phlD -containing bacteria present in the soils of Mount Vernon, Wash. Representative results for the growth chamber assays are shown. The phlD sequences were amplified using gene-specific primers B2BF and BPR4 and subsequently digested with either Hae III or Taq I. Set 1 includes samples of several terminal phlD + dilutions and isolates obtained from rhizospheres of wheat grown in soils A and B. Set 2 includes three isolates of a different genotype obtained from a Lind, Wash., soil for contrast. A known 2,4-DAPG-producing, BOX D genotype strain of Pseudomonas fluorescens (Q8r1–96) was used as a positive control for comparison (lane C). The sizes of individual fragments were determined based on the 100-bp ladder shown in lanes M.

    Techniques Used: Amplification, Positive Control

    18) Product Images from "Serum 25-hydroxyvitamin D, serum calcium and vitamin D receptor (VDR) polymorphisms in a selected population with lumbar disc herniation—A case control study"

    Article Title: Serum 25-hydroxyvitamin D, serum calcium and vitamin D receptor (VDR) polymorphisms in a selected population with lumbar disc herniation—A case control study

    Journal: PLoS ONE

    doi: 10.1371/journal.pone.0205841

    Agarose gel electrophoresis for restriction fragment length polymorphism of VDR Taq I .
    Figure Legend Snippet: Agarose gel electrophoresis for restriction fragment length polymorphism of VDR Taq I .

    Techniques Used: Agarose Gel Electrophoresis

    19) Product Images from "Serum 25-hydroxyvitamin D, serum calcium and vitamin D receptor (VDR) polymorphisms in a selected population with lumbar disc herniation—A case control study"

    Article Title: Serum 25-hydroxyvitamin D, serum calcium and vitamin D receptor (VDR) polymorphisms in a selected population with lumbar disc herniation—A case control study

    Journal: PLoS ONE

    doi: 10.1371/journal.pone.0205841

    Agarose gel electrophoresis for restriction fragment length polymorphism of VDR Taq I .
    Figure Legend Snippet: Agarose gel electrophoresis for restriction fragment length polymorphism of VDR Taq I .

    Techniques Used: Agarose Gel Electrophoresis

    20) Product Images from "Patterns and Possible Roles of LINE-1 Methylation Changes in Smoke-Exposed Epithelia"

    Article Title: Patterns and Possible Roles of LINE-1 Methylation Changes in Smoke-Exposed Epithelia

    Journal: PLoS ONE

    doi: 10.1371/journal.pone.0045292

    Methylation patterns of COBRALINE-1. (A) The LINE-1 amplicons were 160 bp and had 2 CpG dinucleotides. Four patterns of methylated CpGs were detected, including hypermethylation ( m C m C), hypomethylation ( u C u C), and two forms of partial methylation ( m C u C and u C m C). The Tas I enzyme targets unmethylated cytosine site 1, and Taq I targets methylated cytosine site 2. (B) After restriction digestion with Tas I and Taq I, four sizes of products (160, 98, 80, and 62 bp) were identified, depending on the methylation status of both CpG loci. (C) Examples of bisulfite sequencing. Left side represents sequences of the two CpG dinucleotides at Tas I and Taq I cut site whereas the right side represents the CpG dinucleotides in the amplified PCR products. Each circle exemplifies the methylation status of each selected clone. Black and white circles are methylated and unmethylated CpG dinucleotides, respectively. x is mutated sequence and – is deleted sequence.
    Figure Legend Snippet: Methylation patterns of COBRALINE-1. (A) The LINE-1 amplicons were 160 bp and had 2 CpG dinucleotides. Four patterns of methylated CpGs were detected, including hypermethylation ( m C m C), hypomethylation ( u C u C), and two forms of partial methylation ( m C u C and u C m C). The Tas I enzyme targets unmethylated cytosine site 1, and Taq I targets methylated cytosine site 2. (B) After restriction digestion with Tas I and Taq I, four sizes of products (160, 98, 80, and 62 bp) were identified, depending on the methylation status of both CpG loci. (C) Examples of bisulfite sequencing. Left side represents sequences of the two CpG dinucleotides at Tas I and Taq I cut site whereas the right side represents the CpG dinucleotides in the amplified PCR products. Each circle exemplifies the methylation status of each selected clone. Black and white circles are methylated and unmethylated CpG dinucleotides, respectively. x is mutated sequence and – is deleted sequence.

    Techniques Used: Methylation, Methylation Sequencing, Amplification, Polymerase Chain Reaction, Sequencing

    21) Product Images from "Differentiation of Clinical Mycobacterium tuberculosis Complex Isolates by gyrB DNA Sequence Polymorphism Analysis"

    Article Title: Differentiation of Clinical Mycobacterium tuberculosis Complex Isolates by gyrB DNA Sequence Polymorphism Analysis

    Journal: Journal of Clinical Microbiology

    doi:

    RFLP patterns of PCR products obtained by Rsa I digestion (a), Sac II digestion (b), and Taq I (c) digestion of the 1,020-bp gyrB PCR fragment. Lanes: 1 and 9, 100-bp ladder; 2, M. tuberculosis ; 3, M. bovis resistant to PZA; 4 and 5, M. bovis susceptible to PZA; 6, M. africanum subtype I; 7, M. africanum subtype II; 8, M. microti .
    Figure Legend Snippet: RFLP patterns of PCR products obtained by Rsa I digestion (a), Sac II digestion (b), and Taq I (c) digestion of the 1,020-bp gyrB PCR fragment. Lanes: 1 and 9, 100-bp ladder; 2, M. tuberculosis ; 3, M. bovis resistant to PZA; 4 and 5, M. bovis susceptible to PZA; 6, M. africanum subtype I; 7, M. africanum subtype II; 8, M. microti .

    Techniques Used: Polymerase Chain Reaction

    22) Product Images from "Further examination of the Xist promoter-switch hypothesis in X inactivation: Evidence against the existence and function of a P0 promoter"

    Article Title: Further examination of the Xist promoter-switch hypothesis in X inactivation: Evidence against the existence and function of a P0 promoter

    Journal: Proceedings of the National Academy of Sciences of the United States of America

    doi:

    The RNA detected by CJ11–CJ12 is found in the cytoplasm and is exclusively derived from autosomal Rps12 expression. ( A ) Nuclear and cytoplasmic distribution of the “P 0 RNA” isolated from male (M) and female (F) fibroblasts (Fib) and ES cells, RNA was reverse transcribed and amplified with CJ11 and CJ12. Xist ), which spans exons 3 to 6 of Xist. ( B ) Taq I and Hin fI restriction maps for pS12X and Rps12 fragments bounded by CJ11 and CJ12. Sizes are shown for polymorphic fragments. Asterisks indicate RFLP positions. ( C ) RFLP analysis of CJ11–CJ12 RT-PCR products. PCR products were diluted and extended one cycle to minimize heteroduplex formation and then digested with Taq I or Hin fI. Polymorphic restriction fragments were detected by hybridization to radiolabeled nested oligonucleotide CJ10. + and − indicate the presence or absence, respectively, of restriction enzyme during incubation. ( D ) Sensitivity of the RFLP assay of CJ11–CJ12 amplification. A constant amount of Rps12 RT-PCR product was mixed with 10-fold dilutions of pS12X PCR product, digested with Taq I, and visualized by hybridization to CJ10 oligonucleotide. pS12X fragments were visible at 10 −3 dilution (shown) and at 10 −4 dilution on the original autoradiogram (data not shown).
    Figure Legend Snippet: The RNA detected by CJ11–CJ12 is found in the cytoplasm and is exclusively derived from autosomal Rps12 expression. ( A ) Nuclear and cytoplasmic distribution of the “P 0 RNA” isolated from male (M) and female (F) fibroblasts (Fib) and ES cells, RNA was reverse transcribed and amplified with CJ11 and CJ12. Xist ), which spans exons 3 to 6 of Xist. ( B ) Taq I and Hin fI restriction maps for pS12X and Rps12 fragments bounded by CJ11 and CJ12. Sizes are shown for polymorphic fragments. Asterisks indicate RFLP positions. ( C ) RFLP analysis of CJ11–CJ12 RT-PCR products. PCR products were diluted and extended one cycle to minimize heteroduplex formation and then digested with Taq I or Hin fI. Polymorphic restriction fragments were detected by hybridization to radiolabeled nested oligonucleotide CJ10. + and − indicate the presence or absence, respectively, of restriction enzyme during incubation. ( D ) Sensitivity of the RFLP assay of CJ11–CJ12 amplification. A constant amount of Rps12 RT-PCR product was mixed with 10-fold dilutions of pS12X PCR product, digested with Taq I, and visualized by hybridization to CJ10 oligonucleotide. pS12X fragments were visible at 10 −3 dilution (shown) and at 10 −4 dilution on the original autoradiogram (data not shown).

    Techniques Used: Derivative Assay, Expressing, Isolation, Amplification, Reverse Transcription Polymerase Chain Reaction, Polymerase Chain Reaction, Hybridization, Incubation, RFLP Assay

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    Article Snippet: .. To genotype mice, genomic DNA was isolated from mouse tails, the target SCN5A PCR amplicon (c.3688 to c.4082) was incubated with Taq I (New England Biolabs, Ipswich, MA), and then was electrophoresed in agarose gels. ..

    Article Title:
    Article Snippet: The resulting amplicon (536 bp) was subjected to a nested PCR amplification with a set of internal primers (sense: 5'-GGT TTT GTT TTT GTT TTT TTT GTA TAG GTT-3' and antisense: 5'-AAA AAC AAA TAC AAA AAA AAA AAC AAA ACC-3') using 1/5th of the first PCR product using the same PCR conditions, but extended to 30 cycles. .. Subsequently, 20-50 ng of the resulting PCR products (265 bp) were digested with 10 U BstU I and Taq I (New England Biolabs, Beverly, MA, USA) prior to separation on 2% Tris-acetate EDTA agarose gels.

    Article Title:
    Article Snippet: .. Half of the amplified product was digested with Taq I (NEB) or BstU I (NEB) and the other half was mock digested as a control, prior to visualization on 1.5-2% agarose gels. .. DNA methylation was also quantitated by a qPCR approach where genomic DNA was aliquoted into three equal portions where one was mock digested to quantitate the total amount of DNA, one was digested with the methyl-sensitive restriction enzyme Hpa II to quantitate unmethylated DNA, and the final aliquot was digested with the methyl-insensitive isoschizomer Msp I as a negative control.

    Article Title:
    Article Snippet: .. To determine the genotype of phlD + populations, amplification products were digested with Hae III or Taq I (New England Biolabs, Beverly, Mass.). .. DNA fragments were separated on agarose gels in 0.5× Tris-borate-EDTA and visualized by ethidium bromide staining.

    Article Title:
    Article Snippet: The screening for the silent polymorphism g.1679 C > G (c.816 C > G, L272L) of NPC1L1 gene [GenBank: NG_013088.1] was performed by amplification of the central portion of exon 2 using the following primers: 5’-CCA GCT AGG GTC TGG ACA ACT CC -3’ (forward) and 5’-GGA TGA CAG ATA GCA CCA AGA TGG -3’ (reverse). .. Since the presence of G allele eliminates a Taq I restriction site (T/CGA), the PCR product was incubated with 10 U of Taq I (New England Biolabs, Beverly, MA, USA) at 65°C for 1 h and the digestion products (387 and 269 bp for the C allele and 656 bp for the G allele) were separated on 2% agarose gel.

    Article Title:
    Article Snippet: .. The digestion products were then diluted 1 to 10 in TE buffer and PCR amplified in the second round. e PCR started with overnight-digestion of 0.5–1.0 µg of genomic DNA (gDNA) by 10 U of Taq I (New England Biolabs) in a 20 µL reaction volume. .. Four µL of the RE digestion product were then directly used for nested PCR amplifications in two rounds.

    Article Title:
    Article Snippet: .. Restriction enzyme digestion mixture for Taq I which consisted of 2 μL of 10X buffer (50 mM Potassium acetate, 20 mM Tris acetate, 10 mM Magnesium acetate, 100 μg/mL BSA, pH 7.9), 0.5 μL of Taq I enzyme (New England Bio Labs, UK), 5 μL of amplified PCR product (740 bp). ..

    Article Title:
    Article Snippet: The primers for NR1H3 exon 5 were forward-AAG AAA CTG AAG CGG CAA GAG and reverse-ATC GCA GAG GTC TTT AGG AGG, and the restriction enzyme was Taq I (New England Biolabs, USA). .. The amplicon size was 426 bp, and individuals with 348 and 113 bp fragments had genotype AA; individuals with 348, 290, 113, and 58 bp fragments had genotype AC; and individuals with 290, 113, and 58 bp fragments had genotype CC.

    Article Title:
    Article Snippet: PCR was performed in a 20-μl volume containing 1.5 μl of ligated DNA, 15 μl of Amplification Core mix (Perkin-Elmer Applied Biosystems, Warrington, Cheshire, United Kingdom), 5 pmol of Mse I adaptor-specific primer (Perkin-Elmer Applied Biosystems), and 1 pmol of 5-carboxyfluoroscein-labelled Eco RI adaptor-specific primer ( Eco RI+0) (Perkin-Elmer Applied Biosystems). .. The enzymes Apa I and Taq I were used to digest DNA as follows: approximately 500 ng of DNA was incubated with 4 U of Apa I (NEB), 1× buffer 4 (NEB), 1× bovine serum albumin (NEB), and 0.5 mg of DNase-free RNase A ml−1 in a final volume of 20 μl at 25°C for 1 h. Five units of Taq I (NEB) was subsequently added to each reaction mixture, and the mixtures were incubated for a further 1 h at 65°C.

    Expressing:

    Article Title:
    Article Snippet: For the present study, we used the same technique to generate DN mice, in which the exchanged construct was identical to that previously used for the H/H mice with the exception of (1) a c.3823G→A mutation resulting in p.D1275N and (2) insertion of a FLAG epitope between residues 153 and 154 of the extracellular linker S1-S2 in domain I; the FLAG insertion into S1-S2 linker has previously been found to have no effect on channel gating or cell surface expression., We also generated FG mice bearing the wild-type SCN5A allele with the FLAG tag. .. To genotype mice, genomic DNA was isolated from mouse tails, the target SCN5A PCR amplicon (c.3688 to c.4082) was incubated with Taq I (New England Biolabs, Ipswich, MA), and then was electrophoresed in agarose gels.

    Synthesized:

    Article Title:
    Article Snippet: .. The second strand was synthesized immediately afterwards by the Gubler and Hofman procedure using E. coli DNA Polymerase I, RNAse H and DNA ligase at 16°C for 2 h. Double-stranded cDNA was blunted by T4 DNA polymerase for 30 min at 16°C and digested with 15 U Rsa I (Pro-mega) or Taq I (New England Biolabs) at 37°C for 1.5 h to obtain short cDNA fragments. .. After heat in-activation, phenol/chloroform extraction, and ethanol precipitation, approximately 7% of both cDNAs were ligated with 10 pmol of adaptor 1 and the ligation efficiency was tested by a PCR-based assay according to the manual (PCR Select, Clontech).

    Article Title:
    Article Snippet: Annealed RNA was split in two for +RT and −RT reactions, and first-strand cDNA was synthesized in a volume of 20 μl with 200 units Moloney murine leukemia virus-RT for 1 h at 37°C followed by incubation at 80°C for 10 min. cDNA (1 μl) was used as a template for PCR under the cycling protocol reported ( ) with 100 ng each of CJ11 and CJ12 primer in a 25-μl reaction. .. Pellets were digested with 4 units of Hin fI or Taq I (New England Biolabs) at 37°C or 65°C, respectively, and electrophoresed on a 2.5% agarose gel.

    TA Cloning:

    Article Title:
    Article Snippet: Subsequently, 20-50 ng of the resulting PCR products (265 bp) were digested with 10 U BstU I and Taq I (New England Biolabs, Beverly, MA, USA) prior to separation on 2% Tris-acetate EDTA agarose gels. .. To analyse single sequences the purified PCR products were cloned into the pCR II vector using the TOPO TA Cloning Kit (Invitrogen) and subsequently the inserts of individual colonies subjected to sequence analysis.

    Construct:

    Article Title:
    Article Snippet: Diversity array construction Genomic representations were produced by digesting 100 ng of tomato DNA with 2U Pst I and 2U Taq I (NEB, Beverly, MA). .. Libraries of genomic representations were constructed from amplified fragments as described by (Jaccoud et al. ).

    Article Title:
    Article Snippet: For the present study, we used the same technique to generate DN mice, in which the exchanged construct was identical to that previously used for the H/H mice with the exception of (1) a c.3823G→A mutation resulting in p.D1275N and (2) insertion of a FLAG epitope between residues 153 and 154 of the extracellular linker S1-S2 in domain I; the FLAG insertion into S1-S2 linker has previously been found to have no effect on channel gating or cell surface expression., We also generated FG mice bearing the wild-type SCN5A allele with the FLAG tag. .. To genotype mice, genomic DNA was isolated from mouse tails, the target SCN5A PCR amplicon (c.3688 to c.4082) was incubated with Taq I (New England Biolabs, Ipswich, MA), and then was electrophoresed in agarose gels.

    SYBR Green Assay:

    Article Title:
    Article Snippet: For COBRA, the ABO BIS products were digested with the following restriction enzymes: BstU I, Hinf I and Taq I (all New England Biolabs, Beverly, MA). .. Each reaction consisted of 10 µl of 2× Quantitect Sybr Green real time PCR mix (Qiagen), 2 µl of each primer (5 µM stock), and 6 µl of bisulfite modified DNA.

    Article Title:
    Article Snippet: The LINE-1 amplicons (160 bp) were digested with 2 U of Taq I and 2 U of Tas I in NEB3 buffer (New England Biolabs, Ontario, Canada) at 65°C overnight. .. The products were identified by polyacrylamide gel electrophoresis (8% non-denaturing) and stained with SYBR green nucleic acid stain (Sigma-Aldrich, St. Louis, Missouri).

    Incubation:

    Article Title:
    Article Snippet: .. COI -RFLP assay Restriction endonuclease digestion of amplified COI fragments was performed with one unit of restriction endonucleases Alu I, Mbo I, and Taq I (NEB, Beverly, MA), 1× supplied restriction buffer and sterile Milli-Q H2 O in a final volume of 20 μ L. Reactions were incubated at 37°C for 2 h. Restriction digestion products were resolved in 2% agarose gels in boric acid (BA) buffer at 80 V for 3 h, stained with GelRed™ (Biotium, Hayward, CA). .. Gel images were capture with a GelDoc™ BioRad documentation system and analyzed with the Image LAB™ software (BioRad, Hercules, CA).

    Article Title:
    Article Snippet: .. Pellets were suspended in 50 µl NEB buffer 4 and 10 U Taq I (NEB) and were allowed to incubate at 65°C for 16 h. Taq I was inactivated by heating to 80°C for 20 min followed by an incubation with 2.5 U of shrimp alkaline phosphatase (NEB) for 30 min. ..

    Article Title:
    Article Snippet: Restriction enzyme digestion mixture for Taq I which consisted of 2 μL of 10X buffer (50 mM Potassium acetate, 20 mM Tris acetate, 10 mM Magnesium acetate, 100 μg/mL BSA, pH 7.9), 0.5 μL of Taq I enzyme (New England Bio Labs, UK), 5 μL of amplified PCR product (740 bp). .. The mixture was incubated at 65 °C for 15–20 minutes and resolved initially at 50 V for 5 minutes followed by 100 V on 2% agarose gel for 2 hours and was stained with ethidium bromide.

    Article Title:
    Article Snippet: .. To genotype mice, genomic DNA was isolated from mouse tails, the target SCN5A PCR amplicon (c.3688 to c.4082) was incubated with Taq I (New England Biolabs, Ipswich, MA), and then was electrophoresed in agarose gels. ..

    Article Title:
    Article Snippet: .. Since the presence of G allele eliminates a Taq I restriction site (T/CGA), the PCR product was incubated with 10 U of Taq I (New England Biolabs, Beverly, MA, USA) at 65°C for 1 h and the digestion products (387 and 269 bp for the C allele and 656 bp for the G allele) were separated on 2% agarose gel. .. Statistical analyses The statistical analyses were performed using PASW 18.0 statistical software package (SPSS Inc., Chicago, IL).

    Article Title:
    Article Snippet: The extracted DNA was digested with Taq I (New England Biolabs) for 2 h at 65 °C. .. To circularize DNA fragments, samples were incubated with 10 µl Quick T4 DNA Ligase (New England Biolabs) in a total reaction volume of 200 μl and kept at room temperature overnight.

    Article Title:
    Article Snippet: Restriction enzyme digestion mixture for Taq I which consisted of 2 μL of 10X buffer (50 mM Potassium acetate, 20 mM Tris acetate, 10 mM Magnesium acetate, 100 μg/mL BSA, pH 7.9), 0.5 μL of Taq I enzyme (New England Bio Labs, UK), 5 μL of amplified PCR product (740 bp). .. The mixture was incubated at 65 °C for 15–20 minutes and resolved initially at 50 V for 5 minutes followed by 100 V on 2% agarose gel for 2 hours and was stained with ethidium bromide.

    Article Title:
    Article Snippet: .. The enzymes Apa I and Taq I were used to digest DNA as follows: approximately 500 ng of DNA was incubated with 4 U of Apa I (NEB), 1× buffer 4 (NEB), 1× bovine serum albumin (NEB), and 0.5 mg of DNase-free RNase A ml−1 in a final volume of 20 μl at 25°C for 1 h. Five units of Taq I (NEB) was subsequently added to each reaction mixture, and the mixtures were incubated for a further 1 h at 65°C. .. A 20-μl solution containing 4 pmol of Apa I adaptors (MWG-Biotech UK Ltd., Milton Keynes, United Kingdom), 40 pmol of Taq I adaptors (MWG-Biotech), 1× T4 ligase buffer (NEB), and 40 U of T4 DNA ligase (NEB) was added to 20 μl of double-digested DNA.

    Article Title:
    Article Snippet: Annealed RNA was split in two for +RT and −RT reactions, and first-strand cDNA was synthesized in a volume of 20 μl with 200 units Moloney murine leukemia virus-RT for 1 h at 37°C followed by incubation at 80°C for 10 min. cDNA (1 μl) was used as a template for PCR under the cycling protocol reported ( ) with 100 ng each of CJ11 and CJ12 primer in a 25-μl reaction. .. Pellets were digested with 4 units of Hin fI or Taq I (New England Biolabs) at 37°C or 65°C, respectively, and electrophoresed on a 2.5% agarose gel.

    Activity Assay:

    Article Title:
    Article Snippet: Paragraph title: β-gt specificity and activity assay ... Pellets were suspended in 50 µl NEB buffer 4 and 10 U Taq I (NEB) and were allowed to incubate at 65°C for 16 h. Taq I was inactivated by heating to 80°C for 20 min followed by an incubation with 2.5 U of shrimp alkaline phosphatase (NEB) for 30 min.

    Mass Spectrometry:

    Article Title:
    Article Snippet: For MS-SSCA, the ABO BIS products were analyzed on 0.5× and/or 0.75× MDE gels (FMC, Rockland, ME) . .. For COBRA, the ABO BIS products were digested with the following restriction enzymes: BstU I, Hinf I and Taq I (all New England Biolabs, Beverly, MA).

    Modification:

    Article Title:
    Article Snippet: The 269 bp PCR product (‘ABO BIS’) was amplified from bisulfite modified DNA with the following PCR conditions: 10 cycles (60 s at 94°C, 45 s at 65°C - 1°C per cycle, 45 s at 72°C) followed by 35 cycles of (60 s at 94°C, 60 s at 55°C, 60 s at 72°C). .. For COBRA, the ABO BIS products were digested with the following restriction enzymes: BstU I, Hinf I and Taq I (all New England Biolabs, Beverly, MA).

    Article Title:
    Article Snippet: Genomic DNAs were treated with bisulfite by using Methylamp™ DNA Modification Kit (EpiGentek, NY, USA) according to the manufacturer's instructions. .. To analyze the methylation status, amplicons were restriction digested with Taq I and Hpy 188I (New England BioLabs, Ipswich, MA), as previously described (Xiong and Laird, ).

    Article Title:
    Article Snippet: Sodium bisulfite treatment and combined bisulfite restriction analysis (COBRA) Genomic DNA was extracted from the cell lines using the Qiagen DNeasy Tissue kit (Hilden, Germany) and bisulfite treated with the Epigentek Methylamp™ DNA Modification kit (Brooklyn, NY) according to the manufacturers' instructions. .. Nested primer pairs targeted to SIP1 CpG islands were used to amplify bisulfite-treated DNAs (the list of primers is given in Additional file ) and PCR products were restriction digested by Bst UI or Taq I (New England BioLabs, Ipswich, MA) to detect methylation status, as previously described [ ].

    Article Title:
    Article Snippet: Upon isolation of genomic DNA from established RCC cell lines and/or biopsy specimens with the QIAamp DNA Mini Kit (Qiagen), 1 μg of DNA sample was subjected to bisulfite modification as previously described [ ]. .. Subsequently, 20-50 ng of the resulting PCR products (265 bp) were digested with 10 U BstU I and Taq I (New England Biolabs, Beverly, MA, USA) prior to separation on 2% Tris-acetate EDTA agarose gels.

    Western Blot:

    Article Title:
    Article Snippet: Genotyping Genomic DNA was extracted and purified from peripheral blood with DNA Extractor WB Kit (Wako Pure Chemical Industries, Ltd. Japan) according to the product description. rs2431697 polymorphism was determined based on polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) assay. .. The reaction conditions were as follows: denaturation at 94 °C for 5 min, followed by 35ccycles of denaturation at 94 °C for 30 s, annealing for 1 min at 57 °C and extension at 72 °C for 45 s, and a final extension at 72 °C for 5 min. PCR products were subsequently digested by Taq I (New England Biolabs, UK) at 65 °C for 2 h and separated on a 3 % agarose gel.

    Real-time Polymerase Chain Reaction:

    Article Title:
    Article Snippet: For COBRA, the ABO BIS products were digested with the following restriction enzymes: BstU I, Hinf I and Taq I (all New England Biolabs, Beverly, MA). .. For methylation analysis by MCA, the ABO BIS PCR reactions were performed in 20 µl reactions using a Rotorgene 3000 real time PCR machine (Corbett Research, Sydney, Australia).

    Article Title:
    Article Snippet: Half of the amplified product was digested with Taq I (NEB) or BstU I (NEB) and the other half was mock digested as a control, prior to visualization on 1.5-2% agarose gels. .. DNA methylation was also quantitated by a qPCR approach where genomic DNA was aliquoted into three equal portions where one was mock digested to quantitate the total amount of DNA, one was digested with the methyl-sensitive restriction enzyme Hpa II to quantitate unmethylated DNA, and the final aliquot was digested with the methyl-insensitive isoschizomer Msp I as a negative control.

    Hybridization:

    Article Title:
    Article Snippet: .. Dot-Blot Hybridization, Restriction Digestion, and Southern Hybridization Genomic DNA samples (1–5 μg) were digested by restriction endonucleases Rsa I, Alu I, Mbo I, or Taq I (NEB) and run on a 0.9% agarose gel in TAE buffer. .. DNA fragments were alkali blotted onto Hybond-XL nylon membrane (Amersham) using a standard protocol ( ) and hybridized with radioactively end-labeled oligonucleotide probes (ATSB, CHSB, HUSB, CASB, TTCAGGG-SB, CHTRTRev2, TTTAGGC-SB, T3AG2-SB, T3G3-SB, supplementary table S2 , Supplementary Material online) as described in with minor modifications according to .

    Article Title:
    Article Snippet: Paragraph title: Specimens, DNA isolation and Southern blot hybridization ... About 10–15 μg of Taq I (NEB) digested DNA was vacuum blotted onto Hybond-N membrane (GE Health Science).

    Southern Blot:

    Article Title:
    Article Snippet: Paragraph title: Specimens, DNA isolation and Southern blot hybridization ... About 10–15 μg of Taq I (NEB) digested DNA was vacuum blotted onto Hybond-N membrane (GE Health Science).

    Ligation:

    Article Title:
    Article Snippet: Diversity array construction Genomic representations were produced by digesting 100 ng of tomato DNA with 2U Pst I and 2U Taq I (NEB, Beverly, MA). .. A 1 μl aliquot of the ligation mixture was the template in a subsequent 50 μl amplification reaction using primer DArT-Pst I (5′-GAT GGA TCC AGT GCA G-3′) according to the following specifications: 94°C for 1 min, followed by 30 cycles of 94°C for 20 s, 58°C for 40 s, 72°C for 1 min and finally 72°C for 7 min.

    Article Title:
    Article Snippet: Paragraph title: cDNA Synthesis and Adaptor Ligation ... The second strand was synthesized immediately afterwards by the Gubler and Hofman procedure using E. coli DNA Polymerase I, RNAse H and DNA ligase at 16°C for 2 h. Double-stranded cDNA was blunted by T4 DNA polymerase for 30 min at 16°C and digested with 15 U Rsa I (Pro-mega) or Taq I (New England Biolabs) at 37°C for 1.5 h to obtain short cDNA fragments.

    Chromatin Immunoprecipitation:

    Article Title:
    Article Snippet: Size was estimated using a high sensitivity DNA chip (Agilent Technologies). .. Half of the amplified product was digested with Taq I (NEB) or BstU I (NEB) and the other half was mock digested as a control, prior to visualization on 1.5-2% agarose gels.

    Genomic Sequencing:

    Article Title:
    Article Snippet: Subsequently, 20-50 ng of the resulting PCR products (265 bp) were digested with 10 U BstU I and Taq I (New England Biolabs, Beverly, MA, USA) prior to separation on 2% Tris-acetate EDTA agarose gels. .. For bisulfite genomic sequencing, the PCR products were gel-purified employing the PCR Purification Kit (Qiagen) according to the manufacturer's instructions and thereafter directly subjected to sequence analysis by a commercially available service provider (MWG Biotech, Martinsried, Germany).

    Cell Culture:

    Article Title:
    Article Snippet: Paragraph title: Enumeration of cultured bacterial populations. ... To determine the genotype of phlD + populations, amplification products were digested with Hae III or Taq I (New England Biolabs, Beverly, Mass.).

    RFLP Assay:

    Article Title:
    Article Snippet: .. COI -RFLP assay Restriction endonuclease digestion of amplified COI fragments was performed with one unit of restriction endonucleases Alu I, Mbo I, and Taq I (NEB, Beverly, MA), 1× supplied restriction buffer and sterile Milli-Q H2 O in a final volume of 20 μ L. Reactions were incubated at 37°C for 2 h. Restriction digestion products were resolved in 2% agarose gels in boric acid (BA) buffer at 80 V for 3 h, stained with GelRed™ (Biotium, Hayward, CA). .. Gel images were capture with a GelDoc™ BioRad documentation system and analyzed with the Image LAB™ software (BioRad, Hercules, CA).

    Reverse Transcription Polymerase Chain Reaction:

    Article Title:
    Article Snippet: .. RT- e PCR involved overnight-digestion of 10 µL of the first-round PfuUltra-amplified RT-PCR products by 10 U of Taq I (New England Biolabs) in a 20 µL reaction volume. .. The digestion products were then diluted 1 to 10 in TE buffer and PCR amplified in the second round. e PCR started with overnight-digestion of 0.5–1.0 µg of genomic DNA (gDNA) by 10 U of Taq I (New England Biolabs) in a 20 µL reaction volume.

    Article Title:
    Article Snippet: Paragraph title: Allele-specific RT-PCR ... Following PCR, restriction digest was performed with a Taq I (New England Biolabs) and products were run on 7% PAGE [ ].

    Article Title:
    Article Snippet: RT- e PCR involved overnight-digestion of 10 µL of the first-round PfuUltra-amplified RT-PCR products by 10 U of Taq I (New England Biolabs) in a 20 µL reaction volume. .. The digestion products were then diluted 1 to 10 in TE buffer and PCR amplified in the second round. e PCR started with overnight-digestion of 0.5–1.0 µg of genomic DNA (gDNA) by 10 U of Taq I (New England Biolabs) in a 20 µL reaction volume.

    Article Title:
    Article Snippet: Paragraph title: Restriction Fragment Length Polymorphism (RFLP) Analysis of CJ11–CJ12 RT-PCR Products. ... Pellets were digested with 4 units of Hin fI or Taq I (New England Biolabs) at 37°C or 65°C, respectively, and electrophoresed on a 2.5% agarose gel.

    Generated:

    Article Title:
    Article Snippet: The primers of IL-12B rs3212227 were 5′-GATATCTTTGCTGTATTTGTATAGTT-3′ (forward) and 5′-AATATTTAAATAGCATGAAGGC-3′ (reverse), which generated a 118-bp fragment. .. Fragments were then digested by Taq I (New England BioLabs, Ipswich, MA, USA).

    Article Title:
    Article Snippet: H/H, DN/H, and DN/DN mice were generated from DN/H × DN/H matings and H/H littermates were used as controls for all experiments. .. To genotype mice, genomic DNA was isolated from mouse tails, the target SCN5A PCR amplicon (c.3688 to c.4082) was incubated with Taq I (New England Biolabs, Ipswich, MA), and then was electrophoresed in agarose gels.

    Imaging:

    Article Title:
    Article Snippet: To determine the genotype of phlD + populations, amplification products were digested with Hae III or Taq I (New England Biolabs, Beverly, Mass.). .. Gel images were processed using a Kodak (Rochester, N.Y.) EDAS120 or EDAS290 digital imaging system.

    Polymerase Chain Reaction:

    Article Title:
    Article Snippet: .. RT- e PCR involved overnight-digestion of 10 µL of the first-round PfuUltra-amplified RT-PCR products by 10 U of Taq I (New England Biolabs) in a 20 µL reaction volume. .. The digestion products were then diluted 1 to 10 in TE buffer and PCR amplified in the second round. e PCR started with overnight-digestion of 0.5–1.0 µg of genomic DNA (gDNA) by 10 U of Taq I (New England Biolabs) in a 20 µL reaction volume.

    Article Title:
    Article Snippet: Paragraph title: PCR-RFLP analysis of the oxyR DNA polymorphism at position 285 and of the gyrB DNA polymorphisms. ... DNA polymorphisms in the 1,020-bp gyrB fragment amplified with the primer pair MTUB-f and MTUB-r were analyzed by restriction with Rsa I, Sac II, and Taq I in a volume of 10 μl, respectively, as instructed by the manufacturer (New England BioLabs, Schwalbach, Germany).

    Article Title:
    Article Snippet: Paragraph title: (i) PCR-RFLP procedures. ... Taq I and Mse I (New England BioLabs) restriction endonucleases were utilized when using the set of primers suggested by Norman et al. ( ).

    Article Title:
    Article Snippet: .. PCRs consisted of one cycle of 95°C for 5 min., 35 cycles of 30 sec. at 55°C, 30 sec. at 72°C, 30 sec. at 95°C and one cycle at 72°C for 5 min. Purified PCR products were subjected to digestion with Taq I (New England Biolabs, Ipswich, MA, USA), which is methylation insensitive and recognizes the sequence 5′ TCGA 3′. ..

    Article Title:
    Article Snippet: .. Following PCR, restriction digest was performed with a Taq I (New England Biolabs) and products were run on 7% PAGE [ ]. ..

    Article Title:
    Article Snippet: .. Briefly, a 10-μl aliquot of the PCR product obtained by using the primer pair described by Corso et al. ( ) from each tet (M)-positive isolate was digested with the following restriction endonucleases: Aci I, Mse I, Rsa I, and Taq I (New England Biolabs). .. Restriction fragments were separated by agarose (4%) gel electrophoresis and visualized by staining with ethidium bromide.

    Article Title:
    Article Snippet: .. PCR products were digested with restriction enzymes Bst UI and Taq I (NEB). .. Digested products were then loaded on an 8% PAGE gel, separated by electrophoresis, and stained by SYBR Gold (Invitrogen).

    Article Title:
    Article Snippet: The ABO BIS PCR products were analyzed by methylation sensitive - single strand conformation analysis (MS-SSCA) and/or COBRA (combined bisulfite restriction analysis) and/or melt curve analysis (MCA) , . .. For COBRA, the ABO BIS products were digested with the following restriction enzymes: BstU I, Hinf I and Taq I (all New England Biolabs, Beverly, MA).

    Article Title:
    Article Snippet: Fragments were then digested by Taq I (New England BioLabs, Ipswich, MA, USA). .. Polymerase chain reaction (PCR) cycling conditions were performed as follows: one cycle at 94 °C for 5 min; 35 cycles of 94 °C for 30 s, 55 °C for 30 s, and 72 °C for 30 s; and a final extension at 72 °C for 10 min. Products were separated on a 3% agarose gel at 100 volts for 20 min. Genotype analysis was performed blinded by three independent researchers.

    Article Title:
    Article Snippet: .. Restriction enzyme digestion mixture for Taq I which consisted of 2 μL of 10X buffer (50 mM Potassium acetate, 20 mM Tris acetate, 10 mM Magnesium acetate, 100 μg/mL BSA, pH 7.9), 0.5 μL of Taq I enzyme (New England Bio Labs, UK), 5 μL of amplified PCR product (740 bp). ..

    Article Title:
    Article Snippet: .. Nested primer pairs targeted to SIP1 CpG islands were used to amplify bisulfite-treated DNAs (the list of primers is given in Additional file ) and PCR products were restriction digested by Bst UI or Taq I (New England BioLabs, Ipswich, MA) to detect methylation status, as previously described [ ]. .. Differential SIP1 expression in HCC cell lines We first identified the mRNA expression of SIP1 in 14 HCC cell lines by multiplex semi-quantitative RT-PCR (Figure ).

    Article Title:
    Article Snippet: .. To genotype mice, genomic DNA was isolated from mouse tails, the target SCN5A PCR amplicon (c.3688 to c.4082) was incubated with Taq I (New England Biolabs, Ipswich, MA), and then was electrophoresed in agarose gels. ..

    Article Title:
    Article Snippet: .. Subsequently, 20-50 ng of the resulting PCR products (265 bp) were digested with 10 U BstU I and Taq I (New England Biolabs, Beverly, MA, USA) prior to separation on 2% Tris-acetate EDTA agarose gels. .. For bisulfite genomic sequencing, the PCR products were gel-purified employing the PCR Purification Kit (Qiagen) according to the manufacturer's instructions and thereafter directly subjected to sequence analysis by a commercially available service provider (MWG Biotech, Martinsried, Germany).

    Article Title:
    Article Snippet: The abundance and diversity of 2,4-DAPG-producing Pseudomonas spp. in the dilution cultures were determined using a previously described PCR-based assay ( ). .. To determine the genotype of phlD + populations, amplification products were digested with Hae III or Taq I (New England Biolabs, Beverly, Mass.).

    Article Title:
    Article Snippet: One microlitre of bisulphite DNA was then subjected to 35 cycles of PCR, at a 50°C annealing temperature using the following primer sets: LINE-1-F (5′-CCGTAAGGGGTTAGGGAGTTTTT-3′) and LINE-1-R (5′-RTAAAACCCTCCRAACCAAATATAAA-3′). .. The LINE-1 amplicons (160 bp) were digested with 2 U of Taq I and 2 U of Tas I in NEB3 buffer (New England Biolabs, Ontario, Canada) at 65°C overnight.

    Article Title:
    Article Snippet: .. Since the presence of G allele eliminates a Taq I restriction site (T/CGA), the PCR product was incubated with 10 U of Taq I (New England Biolabs, Beverly, MA, USA) at 65°C for 1 h and the digestion products (387 and 269 bp for the C allele and 656 bp for the G allele) were separated on 2% agarose gel. .. Statistical analyses The statistical analyses were performed using PASW 18.0 statistical software package (SPSS Inc., Chicago, IL).

    Article Title:
    Article Snippet: .. The digestion products were then diluted 1 to 10 in TE buffer and PCR amplified in the second round. e PCR started with overnight-digestion of 0.5–1.0 µg of genomic DNA (gDNA) by 10 U of Taq I (New England Biolabs) in a 20 µL reaction volume. .. Four µL of the RE digestion product were then directly used for nested PCR amplifications in two rounds.

    Article Title:
    Article Snippet: Since the unknown lentiviral flanking region was entrapped between two known sequences, it was possible to amplify the viral integration site by PCR. .. The extracted DNA was digested with Taq I (New England Biolabs) for 2 h at 65 °C.

    Article Title:
    Article Snippet: .. Restriction enzyme digestion mixture for Taq I which consisted of 2 μL of 10X buffer (50 mM Potassium acetate, 20 mM Tris acetate, 10 mM Magnesium acetate, 100 μg/mL BSA, pH 7.9), 0.5 μL of Taq I enzyme (New England Bio Labs, UK), 5 μL of amplified PCR product (740 bp). ..

    Article Title:
    Article Snippet: SNP genotyping After screening, the SNP genotypes of exon 5-A201C of the NR1H3 gene were determined using PCR-restriction fragment length polymorphism (RFLP). .. The primers for NR1H3 exon 5 were forward-AAG AAA CTG AAG CGG CAA GAG and reverse-ATC GCA GAG GTC TTT AGG AGG, and the restriction enzyme was Taq I (New England Biolabs, USA).

    Article Title:
    Article Snippet: .. The reaction conditions were as follows: denaturation at 94 °C for 5 min, followed by 35ccycles of denaturation at 94 °C for 30 s, annealing for 1 min at 57 °C and extension at 72 °C for 45 s, and a final extension at 72 °C for 5 min. PCR products were subsequently digested by Taq I (New England Biolabs, UK) at 65 °C for 2 h and separated on a 3 % agarose gel. ..

    Article Title:
    Article Snippet: The second strand was synthesized immediately afterwards by the Gubler and Hofman procedure using E. coli DNA Polymerase I, RNAse H and DNA ligase at 16°C for 2 h. Double-stranded cDNA was blunted by T4 DNA polymerase for 30 min at 16°C and digested with 15 U Rsa I (Pro-mega) or Taq I (New England Biolabs) at 37°C for 1.5 h to obtain short cDNA fragments. .. After heat in-activation, phenol/chloroform extraction, and ethanol precipitation, approximately 7% of both cDNAs were ligated with 10 pmol of adaptor 1 and the ligation efficiency was tested by a PCR-based assay according to the manual (PCR Select, Clontech).

    Article Title:
    Article Snippet: PCR was performed in a 20-μl volume containing 1.5 μl of ligated DNA, 15 μl of Amplification Core mix (Perkin-Elmer Applied Biosystems, Warrington, Cheshire, United Kingdom), 5 pmol of Mse I adaptor-specific primer (Perkin-Elmer Applied Biosystems), and 1 pmol of 5-carboxyfluoroscein-labelled Eco RI adaptor-specific primer ( Eco RI+0) (Perkin-Elmer Applied Biosystems). .. The enzymes Apa I and Taq I were used to digest DNA as follows: approximately 500 ng of DNA was incubated with 4 U of Apa I (NEB), 1× buffer 4 (NEB), 1× bovine serum albumin (NEB), and 0.5 mg of DNase-free RNase A ml−1 in a final volume of 20 μl at 25°C for 1 h. Five units of Taq I (NEB) was subsequently added to each reaction mixture, and the mixtures were incubated for a further 1 h at 65°C.

    Article Title:
    Article Snippet: After 30 cycles, 1 μl was diluted 25-fold into a mixture of fresh buffer, dNTPs, primers, and Taq polymerase and extended for one additional cycle (94°C for 1 min, 55°C for 45 s, and 72°C for 2 min) to minimize possible heteroduplex products arising from annealing of Rps12 / pS12X PCR products. .. Pellets were digested with 4 units of Hin fI or Taq I (New England Biolabs) at 37°C or 65°C, respectively, and electrophoresed on a 2.5% agarose gel.

    Binding Assay:

    Article Title:
    Article Snippet: Methylation-specific restriction polymerase chain reaction Methylation-specific primers that flank the critical nuclear factor and activator of T cells (NFAT) binding κ3 binding site within the TNF promoter were designed ( http://www.urogene.org/methprimer/ ) [ ]. .. PCRs consisted of one cycle of 95°C for 5 min., 35 cycles of 30 sec. at 55°C, 30 sec. at 72°C, 30 sec. at 95°C and one cycle at 72°C for 5 min. Purified PCR products were subjected to digestion with Taq I (New England Biolabs, Ipswich, MA, USA), which is methylation insensitive and recognizes the sequence 5′ TCGA 3′.

    Cellular Antioxidant Activity Assay:

    Article Title:
    Article Snippet: .. The primers for NR1H3 exon 5 were forward-AAG AAA CTG AAG CGG CAA GAG and reverse-ATC GCA GAG GTC TTT AGG AGG, and the restriction enzyme was Taq I (New England Biolabs, USA). .. The amplicon size was 426 bp, and individuals with 348 and 113 bp fragments had genotype AA; individuals with 348, 290, 113, and 58 bp fragments had genotype AC; and individuals with 290, 113, and 58 bp fragments had genotype CC.

    Molecular Weight:

    Article Title:
    Article Snippet: Briefly, high molecular weight DNA was bisulfite treated (see above) and 1 ng of bisulfite converted DNA was amplified 35-40 times using JumpStart Taq polymerase (Sigma) and bisulfite primers ( ). .. Half of the amplified product was digested with Taq I (NEB) or BstU I (NEB) and the other half was mock digested as a control, prior to visualization on 1.5-2% agarose gels.

    DNA Extraction:

    Article Title:
    Article Snippet: Paragraph title: DNA extraction and analysis of the methylation status of the UCHL1 promoter ... Subsequently, 20-50 ng of the resulting PCR products (265 bp) were digested with 10 U BstU I and Taq I (New England Biolabs, Beverly, MA, USA) prior to separation on 2% Tris-acetate EDTA agarose gels.

    Article Title:
    Article Snippet: Paragraph title: Specimens, DNA isolation and Southern blot hybridization ... About 10–15 μg of Taq I (NEB) digested DNA was vacuum blotted onto Hybond-N membrane (GE Health Science).

    Nucleic Acid Electrophoresis:

    Article Title:
    Article Snippet: An approximately 400-bp fragment of the gltA gene, 1,500-bp fragment of the 16S rRNA gene, and 2,900-bp fragment of the 16S-23S ITS gene were amplified and then verified by gel electrophoresis. .. Taq I and Mse I (New England BioLabs) restriction endonucleases were utilized when using the set of primers suggested by Norman et al. ( ).

    Article Title:
    Article Snippet: Briefly, a 10-μl aliquot of the PCR product obtained by using the primer pair described by Corso et al. ( ) from each tet (M)-positive isolate was digested with the following restriction endonucleases: Aci I, Mse I, Rsa I, and Taq I (New England Biolabs). .. Restriction fragments were separated by agarose (4%) gel electrophoresis and visualized by staining with ethidium bromide.

    Combined Bisulfite Restriction Analysis Assay:

    Article Title:
    Article Snippet: Combined bisulfite restriction analysis Combined bisulfite restriction analysis (COBRA) was carried out as described previously . .. PCR products were digested with restriction enzymes Bst UI and Taq I (NEB).

    Article Title:
    Article Snippet: .. For COBRA, the ABO BIS products were digested with the following restriction enzymes: BstU I, Hinf I and Taq I (all New England Biolabs, Beverly, MA). .. The restriction enzymes only digested the PCR product if the cytosine within the restriction enzyme recognition sequence was methylated.

    Article Title:
    Article Snippet: Paragraph title: Sodium bisulfite treatment and combined bisulfite restriction analysis (COBRA) ... Nested primer pairs targeted to SIP1 CpG islands were used to amplify bisulfite-treated DNAs (the list of primers is given in Additional file ) and PCR products were restriction digested by Bst UI or Taq I (New England BioLabs, Ipswich, MA) to detect methylation status, as previously described [ ].

    Article Title:
    Article Snippet: The methylation status of the UCHL1 promoter was determined using combined bisulfite restriction analysis (COBRA) as well as sequencing [ ]. .. Subsequently, 20-50 ng of the resulting PCR products (265 bp) were digested with 10 U BstU I and Taq I (New England Biolabs, Beverly, MA, USA) prior to separation on 2% Tris-acetate EDTA agarose gels.

    Article Title:
    Article Snippet: Combined Bisulfite Restriction Analysis (COBRA) was performed similar to that previously described . .. Half of the amplified product was digested with Taq I (NEB) or BstU I (NEB) and the other half was mock digested as a control, prior to visualization on 1.5-2% agarose gels.

    Article Title:
    Article Snippet: COBRALINE-1 COBRA for LINE-1 was performed as previously described, the 5′UTR of LINE-1.2 (L1Hs) sequence from NCBI Accession Number M80343 was used . .. The LINE-1 amplicons (160 bp) were digested with 2 U of Taq I and 2 U of Tas I in NEB3 buffer (New England Biolabs, Ontario, Canada) at 65°C overnight.

    Animal Model:

    Article Title:
    Article Snippet: Paragraph title: Animal model ... To genotype mice, genomic DNA was isolated from mouse tails, the target SCN5A PCR amplicon (c.3688 to c.4082) was incubated with Taq I (New England Biolabs, Ipswich, MA), and then was electrophoresed in agarose gels.

    Methylation:

    Article Title:
    Article Snippet: .. PCRs consisted of one cycle of 95°C for 5 min., 35 cycles of 30 sec. at 55°C, 30 sec. at 72°C, 30 sec. at 95°C and one cycle at 72°C for 5 min. Purified PCR products were subjected to digestion with Taq I (New England Biolabs, Ipswich, MA, USA), which is methylation insensitive and recognizes the sequence 5′ TCGA 3′. ..

    Article Title:
    Article Snippet: The ABO BIS PCR products were analyzed by methylation sensitive - single strand conformation analysis (MS-SSCA) and/or COBRA (combined bisulfite restriction analysis) and/or melt curve analysis (MCA) , . .. For COBRA, the ABO BIS products were digested with the following restriction enzymes: BstU I, Hinf I and Taq I (all New England Biolabs, Beverly, MA).

    Article Title:
    Article Snippet: .. To analyze the methylation status, amplicons were restriction digested with Taq I and Hpy 188I (New England BioLabs, Ipswich, MA), as previously described (Xiong and Laird, ). ..

    Article Title:
    Article Snippet: .. Nested primer pairs targeted to SIP1 CpG islands were used to amplify bisulfite-treated DNAs (the list of primers is given in Additional file ) and PCR products were restriction digested by Bst UI or Taq I (New England BioLabs, Ipswich, MA) to detect methylation status, as previously described [ ]. .. Differential SIP1 expression in HCC cell lines We first identified the mRNA expression of SIP1 in 14 HCC cell lines by multiplex semi-quantitative RT-PCR (Figure ).

    Article Title:
    Article Snippet: Paragraph title: DNA extraction and analysis of the methylation status of the UCHL1 promoter ... Subsequently, 20-50 ng of the resulting PCR products (265 bp) were digested with 10 U BstU I and Taq I (New England Biolabs, Beverly, MA, USA) prior to separation on 2% Tris-acetate EDTA agarose gels.

    Article Title:
    Article Snippet: In brief, the DNA samples were converted by a bisulphite reaction such that unmethylated cytosine (u C) would be converted to uracil (U), whereas methylated cytosine (m C) would remain as cytosine. .. The LINE-1 amplicons (160 bp) were digested with 2 U of Taq I and 2 U of Tas I in NEB3 buffer (New England Biolabs, Ontario, Canada) at 65°C overnight.

    Mutagenesis:

    Article Title:
    Article Snippet: Paragraph title: Enrichment PCR for the R46X mutation ... RT- e PCR involved overnight-digestion of 10 µL of the first-round PfuUltra-amplified RT-PCR products by 10 U of Taq I (New England Biolabs) in a 20 µL reaction volume.

    Article Title:
    Article Snippet: For the present study, we used the same technique to generate DN mice, in which the exchanged construct was identical to that previously used for the H/H mice with the exception of (1) a c.3823G→A mutation resulting in p.D1275N and (2) insertion of a FLAG epitope between residues 153 and 154 of the extracellular linker S1-S2 in domain I; the FLAG insertion into S1-S2 linker has previously been found to have no effect on channel gating or cell surface expression., We also generated FG mice bearing the wild-type SCN5A allele with the FLAG tag. .. To genotype mice, genomic DNA was isolated from mouse tails, the target SCN5A PCR amplicon (c.3688 to c.4082) was incubated with Taq I (New England Biolabs, Ipswich, MA), and then was electrophoresed in agarose gels.

    Article Title:
    Article Snippet: Approximately 2 μg poly(A)+ RNA was reverse transcribed with RNAse H− mutant Moloney murine leukemia virus reverse transcriptase (Promega) and oligo-(dT)15 primers. .. The second strand was synthesized immediately afterwards by the Gubler and Hofman procedure using E. coli DNA Polymerase I, RNAse H and DNA ligase at 16°C for 2 h. Double-stranded cDNA was blunted by T4 DNA polymerase for 30 min at 16°C and digested with 15 U Rsa I (Pro-mega) or Taq I (New England Biolabs) at 37°C for 1.5 h to obtain short cDNA fragments.

    Isolation:

    Article Title:
    Article Snippet: Taq I and Mse I (New England BioLabs) restriction endonucleases were utilized when using the set of primers suggested by Norman et al. ( ). .. Banding patterns were compared with those of a domestic dog isolate (American Type Culture Collection [ATCC] 51672) of B. vinsonii subsp. berkhoffii ), B. vinsonii subsp. vinsonii (ATCC VR152), B. henselae (strain U-4; University of California, Davis) and B. clarridgeiae (ATCC 51734); the last two Bartonella species are usually isolated from domestic cats.

    Article Title:
    Article Snippet: .. To genotype mice, genomic DNA was isolated from mouse tails, the target SCN5A PCR amplicon (c.3688 to c.4082) was incubated with Taq I (New England Biolabs, Ipswich, MA), and then was electrophoresed in agarose gels. ..

    Article Title:
    Article Snippet: Upon isolation of genomic DNA from established RCC cell lines and/or biopsy specimens with the QIAamp DNA Mini Kit (Qiagen), 1 μg of DNA sample was subjected to bisulfite modification as previously described [ ]. .. Subsequently, 20-50 ng of the resulting PCR products (265 bp) were digested with 10 U BstU I and Taq I (New England Biolabs, Beverly, MA, USA) prior to separation on 2% Tris-acetate EDTA agarose gels.

    Article Title:
    Article Snippet: DNA was isolated from liver or gill tissues using standard Tris.HCl/SDS lysis and phenol/chloroform extractions. .. About 10–15 μg of Taq I (NEB) digested DNA was vacuum blotted onto Hybond-N membrane (GE Health Science).

    Article Title:
    Article Snippet: Genomic DNA was extracted separately from populations of cardiomyocytes, ECs, fibroblasts and c-kit-BMCs with QIAamp DNA Mini Kit (QIAGEN) isolated from 8 cell-treated hearts. .. The extracted DNA was digested with Taq I (New England Biolabs) for 2 h at 65 °C.

    Article Title:
    Article Snippet: Total RNA (5 μg) isolated with Trizol (GIBCO/BRL) was DNase treated and heat inactivated as described above, precipitated, and annealed to 200 ng of random hexamer for 10 min at 70°C. .. Pellets were digested with 4 units of Hin fI or Taq I (New England Biolabs) at 37°C or 65°C, respectively, and electrophoresed on a 2.5% agarose gel.

    Negative Control:

    Article Title:
    Article Snippet: Half of the amplified product was digested with Taq I (NEB) or BstU I (NEB) and the other half was mock digested as a control, prior to visualization on 1.5-2% agarose gels. .. DNA methylation was also quantitated by a qPCR approach where genomic DNA was aliquoted into three equal portions where one was mock digested to quantitate the total amount of DNA, one was digested with the methyl-sensitive restriction enzyme Hpa II to quantitate unmethylated DNA, and the final aliquot was digested with the methyl-insensitive isoschizomer Msp I as a negative control.

    Article Title:
    Article Snippet: The LINE-1 amplicons (160 bp) were digested with 2 U of Taq I and 2 U of Tas I in NEB3 buffer (New England Biolabs, Ontario, Canada) at 65°C overnight. .. Distilled water was used as a negative control.

    Size-exclusion Chromatography:

    Article Title:
    Article Snippet: .. PCRs consisted of one cycle of 95°C for 5 min., 35 cycles of 30 sec. at 55°C, 30 sec. at 72°C, 30 sec. at 95°C and one cycle at 72°C for 5 min. Purified PCR products were subjected to digestion with Taq I (New England Biolabs, Ipswich, MA, USA), which is methylation insensitive and recognizes the sequence 5′ TCGA 3′. ..

    Article Title:
    Article Snippet: Briefly, 100 ng bisulfite treated DNA was amplified in 25 μl reaction buffer containing 0.2 mM dNTP mix, 1.5 mM MgCl2 , 2 U Taq polymerase and 10 pmol of the primers 5'-GAG TTT TAG AGT AAT TGG GAT GGT GAA-A-3' and 5'-CCA CTC ACT TTA TTC AAC ATC TAA AAA ACA-3' using the following conditions: denaturation at 95°C for 3 min and 20 sec, primer annealing at 56°C for 25 seconds (25×) and primer extension at 72°C for 40 seconds and 5 min. .. Subsequently, 20-50 ng of the resulting PCR products (265 bp) were digested with 10 U BstU I and Taq I (New England Biolabs, Beverly, MA, USA) prior to separation on 2% Tris-acetate EDTA agarose gels.

    Labeling:

    Article Title:
    Article Snippet: About 10–15 μg of Taq I (NEB) digested DNA was vacuum blotted onto Hybond-N membrane (GE Health Science). .. Hybridization to a P32 -labeled B. saida AFGP coding sequence probe (AFGP gene Bs3-1, [ ]) was carried out in PerfectHyb (Sigma) at 55°C.

    Purification:

    Article Title:
    Article Snippet: Reactions were terminated by the addition of 10 µl Stop Buffer [20 µg Protenase K, 50 mM Tris–HCl (pH 8.0), 100 mM EDTA (pH 8.0), 2% (w/v) SDS] followed by incubation at 42°C for 60 min. Oligonucleotides were purified by phenol:CHCl3 :IAA extraction followed by an ethanol precipitation. .. Pellets were suspended in 50 µl NEB buffer 4 and 10 U Taq I (NEB) and were allowed to incubate at 65°C for 16 h. Taq I was inactivated by heating to 80°C for 20 min followed by an incubation with 2.5 U of shrimp alkaline phosphatase (NEB) for 30 min.

    Article Title:
    Article Snippet: .. PCRs consisted of one cycle of 95°C for 5 min., 35 cycles of 30 sec. at 55°C, 30 sec. at 72°C, 30 sec. at 95°C and one cycle at 72°C for 5 min. Purified PCR products were subjected to digestion with Taq I (New England Biolabs, Ipswich, MA, USA), which is methylation insensitive and recognizes the sequence 5′ TCGA 3′. ..

    Article Title:
    Article Snippet: The PCR reaction mixture (50 μL) consisted of 100–200 ng of purified genomic DNA, 5 μL of PCR buffer (with 20 mM MgCl2 ), 2 μL of forward and reverse primers (10 pmol), 10 mM dNTPs (1 μL) and 1.5 units of Taq DNA polymerase (0.5 μL). .. Restriction enzyme digestion mixture for Taq I which consisted of 2 μL of 10X buffer (50 mM Potassium acetate, 20 mM Tris acetate, 10 mM Magnesium acetate, 100 μg/mL BSA, pH 7.9), 0.5 μL of Taq I enzyme (New England Bio Labs, UK), 5 μL of amplified PCR product (740 bp).

    Article Title:
    Article Snippet: Subsequently, 20-50 ng of the resulting PCR products (265 bp) were digested with 10 U BstU I and Taq I (New England Biolabs, Beverly, MA, USA) prior to separation on 2% Tris-acetate EDTA agarose gels. .. For bisulfite genomic sequencing, the PCR products were gel-purified employing the PCR Purification Kit (Qiagen) according to the manufacturer's instructions and thereafter directly subjected to sequence analysis by a commercially available service provider (MWG Biotech, Martinsried, Germany).

    Article Title:
    Article Snippet: The PCR reaction mixture (50 μL) consisted of 100–200 ng of purified genomic DNA, 5 μL of PCR buffer (with 20 mM MgCl2 ), 2 μL of forward and reverse primers (10 pmol), 10 mM dNTPs (1 μL) and 1.5 units of Taq DNA polymerase (0.5 μL). .. Restriction enzyme digestion mixture for Taq I which consisted of 2 μL of 10X buffer (50 mM Potassium acetate, 20 mM Tris acetate, 10 mM Magnesium acetate, 100 μg/mL BSA, pH 7.9), 0.5 μL of Taq I enzyme (New England Bio Labs, UK), 5 μL of amplified PCR product (740 bp).

    Article Title:
    Article Snippet: Genotyping Genomic DNA was extracted and purified from peripheral blood with DNA Extractor WB Kit (Wako Pure Chemical Industries, Ltd. Japan) according to the product description. rs2431697 polymorphism was determined based on polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) assay. .. The reaction conditions were as follows: denaturation at 94 °C for 5 min, followed by 35ccycles of denaturation at 94 °C for 30 s, annealing for 1 min at 57 °C and extension at 72 °C for 45 s, and a final extension at 72 °C for 5 min. PCR products were subsequently digested by Taq I (New England Biolabs, UK) at 65 °C for 2 h and separated on a 3 % agarose gel.

    Article Title:
    Article Snippet: Approximately 2 × 108 RA-induced and untreated cells were used for total RNA extraction using the TRIzol™ reagent (Life Technologies) and poly(A)+ RNA purified with two rounds of DynaBeads (Dynal). .. The second strand was synthesized immediately afterwards by the Gubler and Hofman procedure using E. coli DNA Polymerase I, RNAse H and DNA ligase at 16°C for 2 h. Double-stranded cDNA was blunted by T4 DNA polymerase for 30 min at 16°C and digested with 15 U Rsa I (Pro-mega) or Taq I (New England Biolabs) at 37°C for 1.5 h to obtain short cDNA fragments.

    Dot Blot:

    Article Title:
    Article Snippet: .. Dot-Blot Hybridization, Restriction Digestion, and Southern Hybridization Genomic DNA samples (1–5 μg) were digested by restriction endonucleases Rsa I, Alu I, Mbo I, or Taq I (NEB) and run on a 0.9% agarose gel in TAE buffer. .. DNA fragments were alkali blotted onto Hybond-XL nylon membrane (Amersham) using a standard protocol ( ) and hybridized with radioactively end-labeled oligonucleotide probes (ATSB, CHSB, HUSB, CASB, TTCAGGG-SB, CHTRTRev2, TTTAGGC-SB, T3AG2-SB, T3G3-SB, supplementary table S2 , Supplementary Material online) as described in with minor modifications according to .

    Sequencing:

    Article Title:
    Article Snippet: .. PCRs consisted of one cycle of 95°C for 5 min., 35 cycles of 30 sec. at 55°C, 30 sec. at 72°C, 30 sec. at 95°C and one cycle at 72°C for 5 min. Purified PCR products were subjected to digestion with Taq I (New England Biolabs, Ipswich, MA, USA), which is methylation insensitive and recognizes the sequence 5′ TCGA 3′. ..

    Article Title:
    Article Snippet: For COBRA, the ABO BIS products were digested with the following restriction enzymes: BstU I, Hinf I and Taq I (all New England Biolabs, Beverly, MA). .. The restriction enzymes only digested the PCR product if the cytosine within the restriction enzyme recognition sequence was methylated.

    Article Title:
    Article Snippet: Fragments were then digested by Taq I (New England BioLabs, Ipswich, MA, USA). .. Approximately 5% of the samples for each SNP were randomly selected for direct sequencing and the results from PCR-RFLP and direct sequencing were 100% concordant.

    Article Title:
    Article Snippet: The methylation status of the UCHL1 promoter was determined using combined bisulfite restriction analysis (COBRA) as well as sequencing [ ]. .. Subsequently, 20-50 ng of the resulting PCR products (265 bp) were digested with 10 U BstU I and Taq I (New England Biolabs, Beverly, MA, USA) prior to separation on 2% Tris-acetate EDTA agarose gels.

    Article Title:
    Article Snippet: COBRALINE-1 COBRA for LINE-1 was performed as previously described, the 5′UTR of LINE-1.2 (L1Hs) sequence from NCBI Accession Number M80343 was used . .. The LINE-1 amplicons (160 bp) were digested with 2 U of Taq I and 2 U of Tas I in NEB3 buffer (New England Biolabs, Ontario, Canada) at 65°C overnight.

    Article Title:
    Article Snippet: About 10–15 μg of Taq I (NEB) digested DNA was vacuum blotted onto Hybond-N membrane (GE Health Science). .. Hybridization to a P32 -labeled B. saida AFGP coding sequence probe (AFGP gene Bs3-1, [ ]) was carried out in PerfectHyb (Sigma) at 55°C.

    Article Title:
    Article Snippet: This step created a genomic sequence of variable length due to the random location of the RE site within the lentiviral flanking region. .. The extracted DNA was digested with Taq I (New England Biolabs) for 2 h at 65 °C.

    Article Title:
    Article Snippet: The enzymes Apa I and Taq I were used to digest DNA as follows: approximately 500 ng of DNA was incubated with 4 U of Apa I (NEB), 1× buffer 4 (NEB), 1× bovine serum albumin (NEB), and 0.5 mg of DNase-free RNase A ml−1 in a final volume of 20 μl at 25°C for 1 h. Five units of Taq I (NEB) was subsequently added to each reaction mixture, and the mixtures were incubated for a further 1 h at 65°C. .. The sequence of the Apa I adaptor was 3′ CATCTGACGCATGT, 5′ TCGTAGACTGCGTACAGGCC.

    Marker:

    Article Title:
    Article Snippet: Briefly, a 10-μl aliquot of the PCR product obtained by using the primer pair described by Corso et al. ( ) from each tet (M)-positive isolate was digested with the following restriction endonucleases: Aci I, Mse I, Rsa I, and Taq I (New England Biolabs). .. The molecular size marker (100-bp DNA ladder) was from M-Medical Genenco, Florence, Italy.

    Polyacrylamide Gel Electrophoresis:

    Article Title:
    Article Snippet: .. Following PCR, restriction digest was performed with a Taq I (New England Biolabs) and products were run on 7% PAGE [ ]. ..

    Article Title:
    Article Snippet: PCR products were digested with restriction enzymes Bst UI and Taq I (NEB). .. Digested products were then loaded on an 8% PAGE gel, separated by electrophoresis, and stained by SYBR Gold (Invitrogen).

    Article Title:
    Article Snippet: The LINE-1 amplicons (160 bp) were digested with 2 U of Taq I and 2 U of Tas I in NEB3 buffer (New England Biolabs, Ontario, Canada) at 65°C overnight. .. The products were identified by polyacrylamide gel electrophoresis (8% non-denaturing) and stained with SYBR green nucleic acid stain (Sigma-Aldrich, St. Louis, Missouri).

    Staining:

    Article Title:
    Article Snippet: .. COI -RFLP assay Restriction endonuclease digestion of amplified COI fragments was performed with one unit of restriction endonucleases Alu I, Mbo I, and Taq I (NEB, Beverly, MA), 1× supplied restriction buffer and sterile Milli-Q H2 O in a final volume of 20 μ L. Reactions were incubated at 37°C for 2 h. Restriction digestion products were resolved in 2% agarose gels in boric acid (BA) buffer at 80 V for 3 h, stained with GelRed™ (Biotium, Hayward, CA). .. Gel images were capture with a GelDoc™ BioRad documentation system and analyzed with the Image LAB™ software (BioRad, Hercules, CA).

    Article Title:
    Article Snippet: Briefly, a 10-μl aliquot of the PCR product obtained by using the primer pair described by Corso et al. ( ) from each tet (M)-positive isolate was digested with the following restriction endonucleases: Aci I, Mse I, Rsa I, and Taq I (New England Biolabs). .. Restriction fragments were separated by agarose (4%) gel electrophoresis and visualized by staining with ethidium bromide.

    Article Title:
    Article Snippet: PCR products were digested with restriction enzymes Bst UI and Taq I (NEB). .. Digested products were then loaded on an 8% PAGE gel, separated by electrophoresis, and stained by SYBR Gold (Invitrogen).

    Article Title:
    Article Snippet: Restriction enzyme digestion mixture for Taq I which consisted of 2 μL of 10X buffer (50 mM Potassium acetate, 20 mM Tris acetate, 10 mM Magnesium acetate, 100 μg/mL BSA, pH 7.9), 0.5 μL of Taq I enzyme (New England Bio Labs, UK), 5 μL of amplified PCR product (740 bp). .. The mixture was incubated at 65 °C for 15–20 minutes and resolved initially at 50 V for 5 minutes followed by 100 V on 2% agarose gel for 2 hours and was stained with ethidium bromide.

    Article Title:
    Article Snippet: To determine the genotype of phlD + populations, amplification products were digested with Hae III or Taq I (New England Biolabs, Beverly, Mass.). .. DNA fragments were separated on agarose gels in 0.5× Tris-borate-EDTA and visualized by ethidium bromide staining.

    Article Title:
    Article Snippet: The LINE-1 amplicons (160 bp) were digested with 2 U of Taq I and 2 U of Tas I in NEB3 buffer (New England Biolabs, Ontario, Canada) at 65°C overnight. .. The products were identified by polyacrylamide gel electrophoresis (8% non-denaturing) and stained with SYBR green nucleic acid stain (Sigma-Aldrich, St. Louis, Missouri).

    Article Title:
    Article Snippet: Restriction enzyme digestion mixture for Taq I which consisted of 2 μL of 10X buffer (50 mM Potassium acetate, 20 mM Tris acetate, 10 mM Magnesium acetate, 100 μg/mL BSA, pH 7.9), 0.5 μL of Taq I enzyme (New England Bio Labs, UK), 5 μL of amplified PCR product (740 bp). .. The mixture was incubated at 65 °C for 15–20 minutes and resolved initially at 50 V for 5 minutes followed by 100 V on 2% agarose gel for 2 hours and was stained with ethidium bromide.

    Nested PCR:

    Article Title:
    Article Snippet: RT- e PCR involved overnight-digestion of 10 µL of the first-round PfuUltra-amplified RT-PCR products by 10 U of Taq I (New England Biolabs) in a 20 µL reaction volume. .. Four µL of the RE digestion product were then directly used for nested PCR amplifications in two rounds.

    Article Title:
    Article Snippet: The resulting amplicon (536 bp) was subjected to a nested PCR amplification with a set of internal primers (sense: 5'-GGT TTT GTT TTT GTT TTT TTT GTA TAG GTT-3' and antisense: 5'-AAA AAC AAA TAC AAA AAA AAA AAC AAA ACC-3') using 1/5th of the first PCR product using the same PCR conditions, but extended to 30 cycles. .. Subsequently, 20-50 ng of the resulting PCR products (265 bp) were digested with 10 U BstU I and Taq I (New England Biolabs, Beverly, MA, USA) prior to separation on 2% Tris-acetate EDTA agarose gels.

    Activated Clotting Time Assay:

    Article Title:
    Article Snippet: Briefly, 100 ng bisulfite treated DNA was amplified in 25 μl reaction buffer containing 0.2 mM dNTP mix, 1.5 mM MgCl2 , 2 U Taq polymerase and 10 pmol of the primers 5'-GAG TTT TAG AGT AAT TGG GAT GGT GAA-A-3' and 5'-CCA CTC ACT TTA TTC AAC ATC TAA AAA ACA-3' using the following conditions: denaturation at 95°C for 3 min and 20 sec, primer annealing at 56°C for 25 seconds (25×) and primer extension at 72°C for 40 seconds and 5 min. .. Subsequently, 20-50 ng of the resulting PCR products (265 bp) were digested with 10 U BstU I and Taq I (New England Biolabs, Beverly, MA, USA) prior to separation on 2% Tris-acetate EDTA agarose gels.

    Article Title:
    Article Snippet: The screening for the silent polymorphism g.1679 C > G (c.816 C > G, L272L) of NPC1L1 gene [GenBank: NG_013088.1] was performed by amplification of the central portion of exon 2 using the following primers: 5’-CCA GCT AGG GTC TGG ACA ACT CC -3’ (forward) and 5’-GGA TGA CAG ATA GCA CCA AGA TGG -3’ (reverse). .. Since the presence of G allele eliminates a Taq I restriction site (T/CGA), the PCR product was incubated with 10 U of Taq I (New England Biolabs, Beverly, MA, USA) at 65°C for 1 h and the digestion products (387 and 269 bp for the C allele and 656 bp for the G allele) were separated on 2% agarose gel.

    Mouse Assay:

    Article Title:
    Article Snippet: .. To genotype mice, genomic DNA was isolated from mouse tails, the target SCN5A PCR amplicon (c.3688 to c.4082) was incubated with Taq I (New England Biolabs, Ipswich, MA), and then was electrophoresed in agarose gels. ..

    Inter Assay:

    Article Title:
    Article Snippet: The LINE-1 amplicons (160 bp) were digested with 2 U of Taq I and 2 U of Tas I in NEB3 buffer (New England Biolabs, Ontario, Canada) at 65°C overnight. .. The same preparation of DNA from 3 cell lines, HeLa (cervical cancer), Daudi (Human Burkitt’s lymphoma), and Jurkat (acute T cell leukemia) (ATCC, Manassas, VA, USA) were used as positive controls in all experiments and for inter-assay variation adjustment .

    Plasmid Preparation:

    Article Title:
    Article Snippet: Subsequently, 20-50 ng of the resulting PCR products (265 bp) were digested with 10 U BstU I and Taq I (New England Biolabs, Beverly, MA, USA) prior to separation on 2% Tris-acetate EDTA agarose gels. .. To analyse single sequences the purified PCR products were cloned into the pCR II vector using the TOPO TA Cloning Kit (Invitrogen) and subsequently the inserts of individual colonies subjected to sequence analysis.

    Software:

    Article Title:
    Article Snippet: COI -RFLP assay Restriction endonuclease digestion of amplified COI fragments was performed with one unit of restriction endonucleases Alu I, Mbo I, and Taq I (NEB, Beverly, MA), 1× supplied restriction buffer and sterile Milli-Q H2 O in a final volume of 20 μ L. Reactions were incubated at 37°C for 2 h. Restriction digestion products were resolved in 2% agarose gels in boric acid (BA) buffer at 80 V for 3 h, stained with GelRed™ (Biotium, Hayward, CA). .. Gel images were capture with a GelDoc™ BioRad documentation system and analyzed with the Image LAB™ software (BioRad, Hercules, CA).

    Electrophoresis:

    Article Title:
    Article Snippet: PCR products were digested with restriction enzymes Bst UI and Taq I (NEB). .. Digested products were then loaded on an 8% PAGE gel, separated by electrophoresis, and stained by SYBR Gold (Invitrogen).

    RNA Extraction:

    Article Title:
    Article Snippet: Approximately 2 × 108 RA-induced and untreated cells were used for total RNA extraction using the TRIzol™ reagent (Life Technologies) and poly(A)+ RNA purified with two rounds of DynaBeads (Dynal). .. The second strand was synthesized immediately afterwards by the Gubler and Hofman procedure using E. coli DNA Polymerase I, RNAse H and DNA ligase at 16°C for 2 h. Double-stranded cDNA was blunted by T4 DNA polymerase for 30 min at 16°C and digested with 15 U Rsa I (Pro-mega) or Taq I (New England Biolabs) at 37°C for 1.5 h to obtain short cDNA fragments.

    Agarose Gel Electrophoresis:

    Article Title:
    Article Snippet: DNA polymorphisms in the 1,020-bp gyrB fragment amplified with the primer pair MTUB-f and MTUB-r were analyzed by restriction with Rsa I, Sac II, and Taq I in a volume of 10 μl, respectively, as instructed by the manufacturer (New England BioLabs, Schwalbach, Germany). .. The total reaction mixture was analyzed by 2% agarose gel electrophoresis in Tris-acetate buffer.

    Article Title:
    Article Snippet: .. Dot-Blot Hybridization, Restriction Digestion, and Southern Hybridization Genomic DNA samples (1–5 μg) were digested by restriction endonucleases Rsa I, Alu I, Mbo I, or Taq I (NEB) and run on a 0.9% agarose gel in TAE buffer. .. DNA fragments were alkali blotted onto Hybond-XL nylon membrane (Amersham) using a standard protocol ( ) and hybridized with radioactively end-labeled oligonucleotide probes (ATSB, CHSB, HUSB, CASB, TTCAGGG-SB, CHTRTRev2, TTTAGGC-SB, T3AG2-SB, T3G3-SB, supplementary table S2 , Supplementary Material online) as described in with minor modifications according to .

    Article Title:
    Article Snippet: Fragments were then digested by Taq I (New England BioLabs, Ipswich, MA, USA). .. Polymerase chain reaction (PCR) cycling conditions were performed as follows: one cycle at 94 °C for 5 min; 35 cycles of 94 °C for 30 s, 55 °C for 30 s, and 72 °C for 30 s; and a final extension at 72 °C for 10 min. Products were separated on a 3% agarose gel at 100 volts for 20 min. Genotype analysis was performed blinded by three independent researchers.

    Article Title:
    Article Snippet: Amplified DNA was electrophoresed on 2% agarose gel to verify the size of amplicons (740 bp). .. Restriction enzyme digestion mixture for Taq I which consisted of 2 μL of 10X buffer (50 mM Potassium acetate, 20 mM Tris acetate, 10 mM Magnesium acetate, 100 μg/mL BSA, pH 7.9), 0.5 μL of Taq I enzyme (New England Bio Labs, UK), 5 μL of amplified PCR product (740 bp).

    Article Title:
    Article Snippet: Amplified DNA was electrophoresed on 2% agarose gel to verify the size of amplicons (740 bp). .. Restriction enzyme digestion mixture for Taq I which consisted of 2 μL of 10X buffer (50 mM Potassium acetate, 20 mM Tris acetate, 10 mM Magnesium acetate, 100 μg/mL BSA, pH 7.9), 0.5 μL of Taq I enzyme (New England Bio Labs, UK), 5 μL of amplified PCR product (740 bp).

    Article Title:
    Article Snippet: .. The reaction conditions were as follows: denaturation at 94 °C for 5 min, followed by 35ccycles of denaturation at 94 °C for 30 s, annealing for 1 min at 57 °C and extension at 72 °C for 45 s, and a final extension at 72 °C for 5 min. PCR products were subsequently digested by Taq I (New England Biolabs, UK) at 65 °C for 2 h and separated on a 3 % agarose gel. ..

    Article Title:
    Article Snippet: .. Pellets were digested with 4 units of Hin fI or Taq I (New England Biolabs) at 37°C or 65°C, respectively, and electrophoresed on a 2.5% agarose gel. ..

    Ethanol Precipitation:

    Article Title:
    Article Snippet: Reactions were terminated by the addition of 10 µl Stop Buffer [20 µg Protenase K, 50 mM Tris–HCl (pH 8.0), 100 mM EDTA (pH 8.0), 2% (w/v) SDS] followed by incubation at 42°C for 60 min. Oligonucleotides were purified by phenol:CHCl3 :IAA extraction followed by an ethanol precipitation. .. Pellets were suspended in 50 µl NEB buffer 4 and 10 U Taq I (NEB) and were allowed to incubate at 65°C for 16 h. Taq I was inactivated by heating to 80°C for 20 min followed by an incubation with 2.5 U of shrimp alkaline phosphatase (NEB) for 30 min.

    Article Title:
    Article Snippet: The second strand was synthesized immediately afterwards by the Gubler and Hofman procedure using E. coli DNA Polymerase I, RNAse H and DNA ligase at 16°C for 2 h. Double-stranded cDNA was blunted by T4 DNA polymerase for 30 min at 16°C and digested with 15 U Rsa I (Pro-mega) or Taq I (New England Biolabs) at 37°C for 1.5 h to obtain short cDNA fragments. .. After heat in-activation, phenol/chloroform extraction, and ethanol precipitation, approximately 7% of both cDNAs were ligated with 10 pmol of adaptor 1 and the ligation efficiency was tested by a PCR-based assay according to the manual (PCR Select, Clontech).

    Random Hexamer Labeling:

    Article Title:
    Article Snippet: Total RNA (5 μg) isolated with Trizol (GIBCO/BRL) was DNase treated and heat inactivated as described above, precipitated, and annealed to 200 ng of random hexamer for 10 min at 70°C. .. Pellets were digested with 4 units of Hin fI or Taq I (New England Biolabs) at 37°C or 65°C, respectively, and electrophoresed on a 2.5% agarose gel.

    DNA Methylation Assay:

    Article Title:
    Article Snippet: Paragraph title: DNA methylation analysis ... For COBRA, the ABO BIS products were digested with the following restriction enzymes: BstU I, Hinf I and Taq I (all New England Biolabs, Beverly, MA).

    Article Title:
    Article Snippet: Paragraph title: DNA methylation assays ... Half of the amplified product was digested with Taq I (NEB) or BstU I (NEB) and the other half was mock digested as a control, prior to visualization on 1.5-2% agarose gels.

    Produced:

    Article Title:
    Article Snippet: .. Diversity array construction Genomic representations were produced by digesting 100 ng of tomato DNA with 2U Pst I and 2U Taq I (NEB, Beverly, MA). .. A Pst I adapter (5′-CAC GAT GGA TCC AGT GCA-3′ annealed to 5′-CTG GAT CCA TCG TGC CA-3′) was simultaneously ligated to the genomic fragments using 4U T4 ligase (NEB, Beverly, MA).

    Article Title:
    Article Snippet: As for IL-12A rs568408, the wild-type allele IL-12A rs568408G produced 2 fragments of 98 and 23 bp and the variant allele IL-12A rs568408A resulted in one fragment of 121 bp. .. Fragments were then digested by Taq I (New England BioLabs, Ipswich, MA, USA).

    Concentration Assay:

    Article Title:
    Article Snippet: Adaptor-ligated bisulfite treated libraries were amplified 10-15 times using HiFi Uracil+ Polymerase (KAPA Biosystems) and library concentration was estimated using the KAPA quantification kit (KAPA Biosystems). .. Half of the amplified product was digested with Taq I (NEB) or BstU I (NEB) and the other half was mock digested as a control, prior to visualization on 1.5-2% agarose gels.

    FLAG-tag:

    Article Title:
    Article Snippet: For the present study, we used the same technique to generate DN mice, in which the exchanged construct was identical to that previously used for the H/H mice with the exception of (1) a c.3823G→A mutation resulting in p.D1275N and (2) insertion of a FLAG epitope between residues 153 and 154 of the extracellular linker S1-S2 in domain I; the FLAG insertion into S1-S2 linker has previously been found to have no effect on channel gating or cell surface expression., We also generated FG mice bearing the wild-type SCN5A allele with the FLAG tag. .. To genotype mice, genomic DNA was isolated from mouse tails, the target SCN5A PCR amplicon (c.3688 to c.4082) was incubated with Taq I (New England Biolabs, Ipswich, MA), and then was electrophoresed in agarose gels.

    CTG Assay:

    Article Title:
    Article Snippet: .. The primers for NR1H3 exon 5 were forward-AAG AAA CTG AAG CGG CAA GAG and reverse-ATC GCA GAG GTC TTT AGG AGG, and the restriction enzyme was Taq I (New England Biolabs, USA). .. The amplicon size was 426 bp, and individuals with 348 and 113 bp fragments had genotype AA; individuals with 348, 290, 113, and 58 bp fragments had genotype AC; and individuals with 290, 113, and 58 bp fragments had genotype CC.

    Lysis:

    Article Title:
    Article Snippet: DNA was isolated from liver or gill tissues using standard Tris.HCl/SDS lysis and phenol/chloroform extractions. .. About 10–15 μg of Taq I (NEB) digested DNA was vacuum blotted onto Hybond-N membrane (GE Health Science).

    Variant Assay:

    Article Title:
    Article Snippet: As for IL-12A rs568408, the wild-type allele IL-12A rs568408G produced 2 fragments of 98 and 23 bp and the variant allele IL-12A rs568408A resulted in one fragment of 121 bp. .. Fragments were then digested by Taq I (New England BioLabs, Ipswich, MA, USA).

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    New England Biolabs r0149m
    R0149m, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 90/100, based on 12 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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