total genomic dna Search Results


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  • 99
    Zymo Research total genomic dna gdna
    Total Genomic Dna Gdna, supplied by Zymo Research, used in various techniques. Bioz Stars score: 99/100, based on 104 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Thermo Fisher total genomic dna gdna
    Gel electrophoresis of chromosomal and plasmid <t>DNA</t> from L. <t>plantarum</t> LL441 (A) and Southern blot results (B) of the gel in A after transferring of the DNA to a membrane and hybridizing with a digoxigenin-labeled probe (Roche) based on an internal 1-kbp fragment of the lanM gene ( Figure 1 ) amplified by PCR. Order of the samples: 1, undigested chromosomal DNA from LL441; 2, 3, and 4, chromosomal DNA digested with PstI, EcoRI, and HindIII, respectively; 5, undigested plasmid DNA from LL441; 6, 7, and 8, plasmid DNA digested with PstI, EcoRI, and HindIII, respectively. A and B, pre-hybridized molecular weight markers: lambda DNA digested with PstI and lambda DNA digested with HindIII, respectively.
    Total Genomic Dna Gdna, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 99/100, based on 81 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Qiagen genomic dna gdna
    Sex differences in human immunodeficiency virus <t>(HIV)-1</t> infection occur during single-round infection and result in differences in viral deoxyribonucleic acid <t>(DNA)</t> accumulation. (A) Monocyte-derived macrophages (MDMs) were infected on day 7 postdifferentiation with HIV-1-ΔEnv-GFP/VSVG and analyzed 48 hours later for reporter gene expression in n = 20 male donors and n = 20 female donors in 42 separate experiments. Values are represented as percentage of GFP + cells as analyzed by flow cytometry. (B) Monocyte-derived macrophages from 6 healthy donors (3 males and 3 females) were infected with HIV-1-ΔEnv-GFP/VSVG and analyzed 48 hours postinfection for GFP expression. (C) Gag-polymerase chain reaction conducted on genomic DNA isolated from MDM infected in (B). Values indicate copies of gag per 100 ng of genomic DNA input. P values determined using the Wilcoxon matched-pairs signed-rank test.
    Genomic Dna Gdna, supplied by Qiagen, used in various techniques. Bioz Stars score: 99/100, based on 3360 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Millipore total genomic dna
    PCR detection of the <t>LINE1-c-</t> myc gene rearrangement of CTVT origin from cell-derived FNA samples. PCR products (550 bp) were resolved on a 1.5% (w/v) agarose gel. (Lane 1=100 bp <t>DNA</t> marker, Lane 2=positive control, Lane 3=negative control, Lanes 4–9 are samples from the vaginal mass (case 1), skin mass (case 2), nasal mass (case 7), nasal mass (case 8), nasal mass (case 11 in Table 2 ) and chronic inflammation tissue (case 9), respectively.)
    Total Genomic Dna, supplied by Millipore, used in various techniques. Bioz Stars score: 99/100, based on 580 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Millipore genomic dna
    Genome painting-like sequence specific for F . pratensis chromosomes in a F . pratensis × L . perenne hybrid. A) Distribution of clone L16 Fp04 (green), 5S rDNA (red) and 35S rDNA (green); chromosomes were counterstained with DAPI (blue); B) <t>GISH</t> with the total genomic <t>DNA</t> of L . perenne (green); chromosomes were counterstained with propidium iodide (orange).
    Genomic Dna, supplied by Millipore, used in various techniques. Bioz Stars score: 99/100, based on 10774 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Pacific Biosciences system total genomic dna gdna
    Genome painting-like sequence specific for F . pratensis chromosomes in a F . pratensis × L . perenne hybrid. A) Distribution of clone L16 Fp04 (green), 5S rDNA (red) and 35S rDNA (green); chromosomes were counterstained with DAPI (blue); B) <t>GISH</t> with the total genomic <t>DNA</t> of L . perenne (green); chromosomes were counterstained with propidium iodide (orange).
    System Total Genomic Dna Gdna, supplied by Pacific Biosciences, used in various techniques. Bioz Stars score: 93/100, based on 7 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Millipore genomic dna gdna extraction
    Analysis of the right border (RB) junctions. Color codes are shown in the legend and a pPZP RB model, in scale, is provided in the upper left corner. From left to right, each junction is described by: (1) an alphanumeric code identifying the transgenic event, if multiple junctions are isolated from the same event, these are identified by a lowercase letter; (2) a graphical representation, in scale, of the rearrangement occurred during integration at the RB, along with the number of the deleted (Δ) bp, in comparison with the expected intact <t>T-DNA</t> sequence; (3) the sequence showing the 30 bp 5′ and 3′ of the junction; letters in lowercase indicate putative <t>gDNA</t> sequences (not verifiable by BLAST analysis, Table S1 ) Letters in red identify bases belonging to the RB.
    Genomic Dna Gdna Extraction, supplied by Millipore, used in various techniques. Bioz Stars score: 99/100, based on 32 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Millipore human gdna
    Analysis of the right border (RB) junctions. Color codes are shown in the legend and a pPZP RB model, in scale, is provided in the upper left corner. From left to right, each junction is described by: (1) an alphanumeric code identifying the transgenic event, if multiple junctions are isolated from the same event, these are identified by a lowercase letter; (2) a graphical representation, in scale, of the rearrangement occurred during integration at the RB, along with the number of the deleted (Δ) bp, in comparison with the expected intact <t>T-DNA</t> sequence; (3) the sequence showing the 30 bp 5′ and 3′ of the junction; letters in lowercase indicate putative <t>gDNA</t> sequences (not verifiable by BLAST analysis, Table S1 ) Letters in red identify bases belonging to the RB.
    Human Gdna, supplied by Millipore, used in various techniques. Bioz Stars score: 95/100, based on 19 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Agilent technologies genomic dna
    Analysis of the right border (RB) junctions. Color codes are shown in the legend and a pPZP RB model, in scale, is provided in the upper left corner. From left to right, each junction is described by: (1) an alphanumeric code identifying the transgenic event, if multiple junctions are isolated from the same event, these are identified by a lowercase letter; (2) a graphical representation, in scale, of the rearrangement occurred during integration at the RB, along with the number of the deleted (Δ) bp, in comparison with the expected intact <t>T-DNA</t> sequence; (3) the sequence showing the 30 bp 5′ and 3′ of the junction; letters in lowercase indicate putative <t>gDNA</t> sequences (not verifiable by BLAST analysis, Table S1 ) Letters in red identify bases belonging to the RB.
    Genomic Dna, supplied by Agilent technologies, used in various techniques. Bioz Stars score: 94/100, based on 3133 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Promega genomic dna
    Analysis of the right border (RB) junctions. Color codes are shown in the legend and a pPZP RB model, in scale, is provided in the upper left corner. From left to right, each junction is described by: (1) an alphanumeric code identifying the transgenic event, if multiple junctions are isolated from the same event, these are identified by a lowercase letter; (2) a graphical representation, in scale, of the rearrangement occurred during integration at the RB, along with the number of the deleted (Δ) bp, in comparison with the expected intact <t>T-DNA</t> sequence; (3) the sequence showing the 30 bp 5′ and 3′ of the junction; letters in lowercase indicate putative <t>gDNA</t> sequences (not verifiable by BLAST analysis, Table S1 ) Letters in red identify bases belonging to the RB.
    Genomic Dna, supplied by Promega, used in various techniques. Bioz Stars score: 95/100, based on 27358 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Red Sea total genomic dna
    Analysis of the right border (RB) junctions. Color codes are shown in the legend and a pPZP RB model, in scale, is provided in the upper left corner. From left to right, each junction is described by: (1) an alphanumeric code identifying the transgenic event, if multiple junctions are isolated from the same event, these are identified by a lowercase letter; (2) a graphical representation, in scale, of the rearrangement occurred during integration at the RB, along with the number of the deleted (Δ) bp, in comparison with the expected intact <t>T-DNA</t> sequence; (3) the sequence showing the 30 bp 5′ and 3′ of the junction; letters in lowercase indicate putative <t>gDNA</t> sequences (not verifiable by BLAST analysis, Table S1 ) Letters in red identify bases belonging to the RB.
    Total Genomic Dna, supplied by Red Sea, used in various techniques. Bioz Stars score: 93/100, based on 21 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    ATUM total genomic dna
    Analysis of the right border (RB) junctions. Color codes are shown in the legend and a pPZP RB model, in scale, is provided in the upper left corner. From left to right, each junction is described by: (1) an alphanumeric code identifying the transgenic event, if multiple junctions are isolated from the same event, these are identified by a lowercase letter; (2) a graphical representation, in scale, of the rearrangement occurred during integration at the RB, along with the number of the deleted (Δ) bp, in comparison with the expected intact <t>T-DNA</t> sequence; (3) the sequence showing the 30 bp 5′ and 3′ of the junction; letters in lowercase indicate putative <t>gDNA</t> sequences (not verifiable by BLAST analysis, Table S1 ) Letters in red identify bases belonging to the RB.
    Total Genomic Dna, supplied by ATUM, used in various techniques. Bioz Stars score: 93/100, based on 112 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Zymo Research quick gdna kit
    Analysis of the right border (RB) junctions. Color codes are shown in the legend and a pPZP RB model, in scale, is provided in the upper left corner. From left to right, each junction is described by: (1) an alphanumeric code identifying the transgenic event, if multiple junctions are isolated from the same event, these are identified by a lowercase letter; (2) a graphical representation, in scale, of the rearrangement occurred during integration at the RB, along with the number of the deleted (Δ) bp, in comparison with the expected intact <t>T-DNA</t> sequence; (3) the sequence showing the 30 bp 5′ and 3′ of the junction; letters in lowercase indicate putative <t>gDNA</t> sequences (not verifiable by BLAST analysis, Table S1 ) Letters in red identify bases belonging to the RB.
    Quick Gdna Kit, supplied by Zymo Research, used in various techniques. Bioz Stars score: 99/100, based on 62 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    92
    Thermo Fisher chargeswitch
    Analysis of the right border (RB) junctions. Color codes are shown in the legend and a pPZP RB model, in scale, is provided in the upper left corner. From left to right, each junction is described by: (1) an alphanumeric code identifying the transgenic event, if multiple junctions are isolated from the same event, these are identified by a lowercase letter; (2) a graphical representation, in scale, of the rearrangement occurred during integration at the RB, along with the number of the deleted (Δ) bp, in comparison with the expected intact <t>T-DNA</t> sequence; (3) the sequence showing the 30 bp 5′ and 3′ of the junction; letters in lowercase indicate putative <t>gDNA</t> sequences (not verifiable by BLAST analysis, Table S1 ) Letters in red identify bases belonging to the RB.
    Chargeswitch, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 92/100, based on 9 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Image Search Results


    Gel electrophoresis of chromosomal and plasmid DNA from L. plantarum LL441 (A) and Southern blot results (B) of the gel in A after transferring of the DNA to a membrane and hybridizing with a digoxigenin-labeled probe (Roche) based on an internal 1-kbp fragment of the lanM gene ( Figure 1 ) amplified by PCR. Order of the samples: 1, undigested chromosomal DNA from LL441; 2, 3, and 4, chromosomal DNA digested with PstI, EcoRI, and HindIII, respectively; 5, undigested plasmid DNA from LL441; 6, 7, and 8, plasmid DNA digested with PstI, EcoRI, and HindIII, respectively. A and B, pre-hybridized molecular weight markers: lambda DNA digested with PstI and lambda DNA digested with HindIII, respectively.

    Journal: Frontiers in Microbiology

    Article Title: Genome Analysis of Lactobacillus plantarum LL441 and Genetic Characterisation of the Locus for the Lantibiotic Plantaricin C

    doi: 10.3389/fmicb.2018.01916

    Figure Lengend Snippet: Gel electrophoresis of chromosomal and plasmid DNA from L. plantarum LL441 (A) and Southern blot results (B) of the gel in A after transferring of the DNA to a membrane and hybridizing with a digoxigenin-labeled probe (Roche) based on an internal 1-kbp fragment of the lanM gene ( Figure 1 ) amplified by PCR. Order of the samples: 1, undigested chromosomal DNA from LL441; 2, 3, and 4, chromosomal DNA digested with PstI, EcoRI, and HindIII, respectively; 5, undigested plasmid DNA from LL441; 6, 7, and 8, plasmid DNA digested with PstI, EcoRI, and HindIII, respectively. A and B, pre-hybridized molecular weight markers: lambda DNA digested with PstI and lambda DNA digested with HindIII, respectively.

    Article Snippet: Briefly, total genomic DNA was extracted and purified from L. plantarum LL441, and then digested with PstI, EcoRI, or HindIII (Fermentas GmbH, Sankt Leon-Rot, Germany).

    Techniques: Nucleic Acid Electrophoresis, Plasmid Preparation, Southern Blot, Transferring, Labeling, Amplification, Polymerase Chain Reaction, Molecular Weight, Lambda DNA Preparation

    Schematic representation of the plantaricin C locus in Lactobacillus plantarum LL441, in which the orientation and size of the different open reading frames (ORFs) and the proteins they encode are indicated. Faced arrows above the ORFs indicate the presence of inverted repeat sequences resembling ρ-independent terminators. The position of relevant restriction sites in the contig and the segments of DNA homologous to those found in plasmids pPECL-6 from Pediococcus claussenii ATCC BAA-344 and pL11995-4 from Lactobacillus paracollinoides TMW 1.1995 and a plasmid from L. plantarum Nizo 3893 are also indicated.

    Journal: Frontiers in Microbiology

    Article Title: Genome Analysis of Lactobacillus plantarum LL441 and Genetic Characterisation of the Locus for the Lantibiotic Plantaricin C

    doi: 10.3389/fmicb.2018.01916

    Figure Lengend Snippet: Schematic representation of the plantaricin C locus in Lactobacillus plantarum LL441, in which the orientation and size of the different open reading frames (ORFs) and the proteins they encode are indicated. Faced arrows above the ORFs indicate the presence of inverted repeat sequences resembling ρ-independent terminators. The position of relevant restriction sites in the contig and the segments of DNA homologous to those found in plasmids pPECL-6 from Pediococcus claussenii ATCC BAA-344 and pL11995-4 from Lactobacillus paracollinoides TMW 1.1995 and a plasmid from L. plantarum Nizo 3893 are also indicated.

    Article Snippet: Briefly, total genomic DNA was extracted and purified from L. plantarum LL441, and then digested with PstI, EcoRI, or HindIII (Fermentas GmbH, Sankt Leon-Rot, Germany).

    Techniques: Plasmid Preparation

    RNase III is required for HvAV-3e pathology and DNA replication. (A) Phase-contrast images of HzFB cells at 48 hpi after mock transfection (subpanel 1) or transfection with RNase III (subpanel 2) and GFP dsRNA (subpanel 3). Subpanel 4 shows mock-transfected cells that were mock infected. (B) Northern hybridization showing downregulation of RNase III transcript levels in RNase III-specific dsRNA transfected cells after 48 h of virus infection. (C) qPCR analysis of total genomic DNA from cells treated as in panel A that shows the relative viral DNA levels in the treatments. Error bars represent the standard deviations of averages from three replicates.

    Journal: Journal of Virology

    Article Title: An Ascovirus-Encoded RNase III Autoregulates Its Expression and Suppresses RNA Interference-Mediated Gene Silencing ▿

    doi: 10.1128/JVI.02362-09

    Figure Lengend Snippet: RNase III is required for HvAV-3e pathology and DNA replication. (A) Phase-contrast images of HzFB cells at 48 hpi after mock transfection (subpanel 1) or transfection with RNase III (subpanel 2) and GFP dsRNA (subpanel 3). Subpanel 4 shows mock-transfected cells that were mock infected. (B) Northern hybridization showing downregulation of RNase III transcript levels in RNase III-specific dsRNA transfected cells after 48 h of virus infection. (C) qPCR analysis of total genomic DNA from cells treated as in panel A that shows the relative viral DNA levels in the treatments. Error bars represent the standard deviations of averages from three replicates.

    Article Snippet: DNA concentrations were measured with a Nanodrop, and 50 ng of total genomic DNA was used for each qPCR using SYBR green (Invitrogen) with a Rotor-Gene 6000.

    Techniques: Transfection, Infection, Northern Blot, Hybridization, Real-time Polymerase Chain Reaction

    Sex differences in human immunodeficiency virus (HIV)-1 infection occur during single-round infection and result in differences in viral deoxyribonucleic acid (DNA) accumulation. (A) Monocyte-derived macrophages (MDMs) were infected on day 7 postdifferentiation with HIV-1-ΔEnv-GFP/VSVG and analyzed 48 hours later for reporter gene expression in n = 20 male donors and n = 20 female donors in 42 separate experiments. Values are represented as percentage of GFP + cells as analyzed by flow cytometry. (B) Monocyte-derived macrophages from 6 healthy donors (3 males and 3 females) were infected with HIV-1-ΔEnv-GFP/VSVG and analyzed 48 hours postinfection for GFP expression. (C) Gag-polymerase chain reaction conducted on genomic DNA isolated from MDM infected in (B). Values indicate copies of gag per 100 ng of genomic DNA input. P values determined using the Wilcoxon matched-pairs signed-rank test.

    Journal: The Journal of Infectious Diseases

    Article Title: Sex Influences SAMHD1 Activity and Susceptibility to Human Immunodeficiency Virus-1 in Primary Human Macrophages

    doi: 10.1093/infdis/jiy583

    Figure Lengend Snippet: Sex differences in human immunodeficiency virus (HIV)-1 infection occur during single-round infection and result in differences in viral deoxyribonucleic acid (DNA) accumulation. (A) Monocyte-derived macrophages (MDMs) were infected on day 7 postdifferentiation with HIV-1-ΔEnv-GFP/VSVG and analyzed 48 hours later for reporter gene expression in n = 20 male donors and n = 20 female donors in 42 separate experiments. Values are represented as percentage of GFP + cells as analyzed by flow cytometry. (B) Monocyte-derived macrophages from 6 healthy donors (3 males and 3 females) were infected with HIV-1-ΔEnv-GFP/VSVG and analyzed 48 hours postinfection for GFP expression. (C) Gag-polymerase chain reaction conducted on genomic DNA isolated from MDM infected in (B). Values indicate copies of gag per 100 ng of genomic DNA input. P values determined using the Wilcoxon matched-pairs signed-rank test.

    Article Snippet: Total genomic DNA was isolated (QIAGEN) from mock-infected or HIV-1-ΔEnv-GFP/VSVG-infected macrophages 24 hours postinfection.

    Techniques: Infection, Derivative Assay, Expressing, Flow Cytometry, Polymerase Chain Reaction, Isolation

    PCR detection of the LINE1-c- myc gene rearrangement of CTVT origin from cell-derived FNA samples. PCR products (550 bp) were resolved on a 1.5% (w/v) agarose gel. (Lane 1=100 bp DNA marker, Lane 2=positive control, Lane 3=negative control, Lanes 4–9 are samples from the vaginal mass (case 1), skin mass (case 2), nasal mass (case 7), nasal mass (case 8), nasal mass (case 11 in Table 2 ) and chronic inflammation tissue (case 9), respectively.)

    Journal: The Journal of Veterinary Medical Science

    Article Title: Cell-based polymerase chain reaction for canine transmissible venereal tumor (CTVT) diagnosis

    doi: 10.1292/jvms.15-0710

    Figure Lengend Snippet: PCR detection of the LINE1-c- myc gene rearrangement of CTVT origin from cell-derived FNA samples. PCR products (550 bp) were resolved on a 1.5% (w/v) agarose gel. (Lane 1=100 bp DNA marker, Lane 2=positive control, Lane 3=negative control, Lanes 4–9 are samples from the vaginal mass (case 1), skin mass (case 2), nasal mass (case 7), nasal mass (case 8), nasal mass (case 11 in Table 2 ) and chronic inflammation tissue (case 9), respectively.)

    Article Snippet: The LINE1-c-myc PCR assay : Total genomic DNA was extracted from FNA-derived cells and fresh tissue using Mammalian genomic DNA miniprep kit (Sigma-Aldrich, St. Louis, MO, U.S.A.) following the manufacturer’s instruction.

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

    Phylogenetic tree of the LINE-c- myc CTVT sequence of this study and the related sequences from the Genbank database. CTVT from Thailand sequences: FNA sample (triangle) sequences of KU680469 (case 1), KU680470 (case 2), KU680471 (case 7), KU680472 (case 11 in Table 2 ) and KU680473 (case 8); and fresh tissue samples (circle) from KU680474 (case 4), KU680475 (case 5, skin mass), KU680476 (case 5, penile mass), KU680477 (case 6) and KU680478 (case 10). CTVT samples in Genbank: Canis lupus familiaris LINE-1 elememt DNA partial sequence (AB012217), LINE/c- myc junction sequence (S55298), Canis familiaris c- myc gene partial sequence (AY032723), Dog c- myc oncogene DNA with a retroposon insertion target sequence (M37386) and Dog c- myc oncogene with an inserted retroposon (M37385).

    Journal: The Journal of Veterinary Medical Science

    Article Title: Cell-based polymerase chain reaction for canine transmissible venereal tumor (CTVT) diagnosis

    doi: 10.1292/jvms.15-0710

    Figure Lengend Snippet: Phylogenetic tree of the LINE-c- myc CTVT sequence of this study and the related sequences from the Genbank database. CTVT from Thailand sequences: FNA sample (triangle) sequences of KU680469 (case 1), KU680470 (case 2), KU680471 (case 7), KU680472 (case 11 in Table 2 ) and KU680473 (case 8); and fresh tissue samples (circle) from KU680474 (case 4), KU680475 (case 5, skin mass), KU680476 (case 5, penile mass), KU680477 (case 6) and KU680478 (case 10). CTVT samples in Genbank: Canis lupus familiaris LINE-1 elememt DNA partial sequence (AB012217), LINE/c- myc junction sequence (S55298), Canis familiaris c- myc gene partial sequence (AY032723), Dog c- myc oncogene DNA with a retroposon insertion target sequence (M37386) and Dog c- myc oncogene with an inserted retroposon (M37385).

    Article Snippet: The LINE1-c-myc PCR assay : Total genomic DNA was extracted from FNA-derived cells and fresh tissue using Mammalian genomic DNA miniprep kit (Sigma-Aldrich, St. Louis, MO, U.S.A.) following the manufacturer’s instruction.

    Techniques: Sequencing

    PCR detection of the LINE1-c- myc gene from cell-derived FNA samples (cases 12 and 24, Table 2 ). PCR products (550 bp) were resolved on a 1.5% (w/v) agarose gel. (Lane1=100-bp DNA marker, Lane 2 =positive control, Lane 3 =case 12, Lane 4 =case 24 and Lane 5 =negative control)

    Journal: The Journal of Veterinary Medical Science

    Article Title: Cell-based polymerase chain reaction for canine transmissible venereal tumor (CTVT) diagnosis

    doi: 10.1292/jvms.15-0710

    Figure Lengend Snippet: PCR detection of the LINE1-c- myc gene from cell-derived FNA samples (cases 12 and 24, Table 2 ). PCR products (550 bp) were resolved on a 1.5% (w/v) agarose gel. (Lane1=100-bp DNA marker, Lane 2 =positive control, Lane 3 =case 12, Lane 4 =case 24 and Lane 5 =negative control)

    Article Snippet: The LINE1-c-myc PCR assay : Total genomic DNA was extracted from FNA-derived cells and fresh tissue using Mammalian genomic DNA miniprep kit (Sigma-Aldrich, St. Louis, MO, U.S.A.) following the manufacturer’s instruction.

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

    Genome painting-like sequence specific for F . pratensis chromosomes in a F . pratensis × L . perenne hybrid. A) Distribution of clone L16 Fp04 (green), 5S rDNA (red) and 35S rDNA (green); chromosomes were counterstained with DAPI (blue); B) GISH with the total genomic DNA of L . perenne (green); chromosomes were counterstained with propidium iodide (orange).

    Journal: PLoS ONE

    Article Title: Exploiting repetitive sequences and BAC clones in Festuca pratensis karyotyping

    doi: 10.1371/journal.pone.0179043

    Figure Lengend Snippet: Genome painting-like sequence specific for F . pratensis chromosomes in a F . pratensis × L . perenne hybrid. A) Distribution of clone L16 Fp04 (green), 5S rDNA (red) and 35S rDNA (green); chromosomes were counterstained with DAPI (blue); B) GISH with the total genomic DNA of L . perenne (green); chromosomes were counterstained with propidium iodide (orange).

    Article Snippet: In GISH, the total genomic DNA of L . perenne was used as a probe and labelled with digoxigenin using a DIG-Nick Translation Kit according to the manufacturer’s procedure (Sigma-Aldrich).

    Techniques: Sequencing

    Analysis of the right border (RB) junctions. Color codes are shown in the legend and a pPZP RB model, in scale, is provided in the upper left corner. From left to right, each junction is described by: (1) an alphanumeric code identifying the transgenic event, if multiple junctions are isolated from the same event, these are identified by a lowercase letter; (2) a graphical representation, in scale, of the rearrangement occurred during integration at the RB, along with the number of the deleted (Δ) bp, in comparison with the expected intact T-DNA sequence; (3) the sequence showing the 30 bp 5′ and 3′ of the junction; letters in lowercase indicate putative gDNA sequences (not verifiable by BLAST analysis, Table S1 ) Letters in red identify bases belonging to the RB.

    Journal: International Journal of Molecular Sciences

    Article Title: An Insight into T-DNA Integration Events in Medicago sativa

    doi: 10.3390/ijms18091951

    Figure Lengend Snippet: Analysis of the right border (RB) junctions. Color codes are shown in the legend and a pPZP RB model, in scale, is provided in the upper left corner. From left to right, each junction is described by: (1) an alphanumeric code identifying the transgenic event, if multiple junctions are isolated from the same event, these are identified by a lowercase letter; (2) a graphical representation, in scale, of the rearrangement occurred during integration at the RB, along with the number of the deleted (Δ) bp, in comparison with the expected intact T-DNA sequence; (3) the sequence showing the 30 bp 5′ and 3′ of the junction; letters in lowercase indicate putative gDNA sequences (not verifiable by BLAST analysis, Table S1 ) Letters in red identify bases belonging to the RB.

    Article Snippet: Isolation of Sequences Flanking T-DNA Insertions Total gDNA was extracted from young, fully expanded leaves collected from the 46 transgenic lines (events), using the GeneElute Plant Genomic DNA Miniprep Kit (SIGMA, St. Louis, MO, USA).

    Techniques: Transgenic Assay, Isolation, Sequencing

    ( a ) Southern hybridization of genomic DNA extracted from T1 A plants with probe RBINTpr (blue segment) or VBpr (purple segment). The bands that hybridized to both probes are marked with a white triangle. Nt: non transgenic; P: binary vector pPZP- hemL - nptII (not linearized); L: 1 Kb ladder; ( b – d ) schemes (not in scale) of the restriction fragments produced by Nco I digestion (black vertical dotted lines are Nco I sites); ( b ) canonical T-DNA processing; ( c ) wrong initiation at the LB and transfer of whole VB along with a single copy of T-DNA; ( d ) correct initiation at the RB and incorrect termination at the LB, resulting in the transfer of the whole VB sequence along with two T-DNA copies. The position of the probes and the length of the restriction fragments are indicated.

    Journal: International Journal of Molecular Sciences

    Article Title: An Insight into T-DNA Integration Events in Medicago sativa

    doi: 10.3390/ijms18091951

    Figure Lengend Snippet: ( a ) Southern hybridization of genomic DNA extracted from T1 A plants with probe RBINTpr (blue segment) or VBpr (purple segment). The bands that hybridized to both probes are marked with a white triangle. Nt: non transgenic; P: binary vector pPZP- hemL - nptII (not linearized); L: 1 Kb ladder; ( b – d ) schemes (not in scale) of the restriction fragments produced by Nco I digestion (black vertical dotted lines are Nco I sites); ( b ) canonical T-DNA processing; ( c ) wrong initiation at the LB and transfer of whole VB along with a single copy of T-DNA; ( d ) correct initiation at the RB and incorrect termination at the LB, resulting in the transfer of the whole VB sequence along with two T-DNA copies. The position of the probes and the length of the restriction fragments are indicated.

    Article Snippet: Isolation of Sequences Flanking T-DNA Insertions Total gDNA was extracted from young, fully expanded leaves collected from the 46 transgenic lines (events), using the GeneElute Plant Genomic DNA Miniprep Kit (SIGMA, St. Louis, MO, USA).

    Techniques: Hybridization, Transgenic Assay, Plasmid Preparation, Produced, Sequencing

    Analysis of left border (LB) junctions. Color codes are shown in the legend and the pPZP LB structure and sequence, in scale, is provided in the upper left corner. From left to right, each junction is described by: (1) an alphanumeric code identifying the transgenic event, if multiple junctions are isolated from the same event, these are identified by a lowercase letter; (2) a graphical representation, in scale, of the rearrangement occurred at the LB, along with the number of the deleted (Δ) or inserted (+) bp, in comparison with the expected intact transferred DNA (T-DNA) sequence (in one case T-DNA sequences with different orientations were detected, black arrows); (3) the sequence showing the 30 bp 5′ and 3′ of the junction; letters in lowercase indicate putative gDNA sequences (not verifiable by BLAST analysis, Table S1 ). Letters in red identify bases belonging to the LB.

    Journal: International Journal of Molecular Sciences

    Article Title: An Insight into T-DNA Integration Events in Medicago sativa

    doi: 10.3390/ijms18091951

    Figure Lengend Snippet: Analysis of left border (LB) junctions. Color codes are shown in the legend and the pPZP LB structure and sequence, in scale, is provided in the upper left corner. From left to right, each junction is described by: (1) an alphanumeric code identifying the transgenic event, if multiple junctions are isolated from the same event, these are identified by a lowercase letter; (2) a graphical representation, in scale, of the rearrangement occurred at the LB, along with the number of the deleted (Δ) or inserted (+) bp, in comparison with the expected intact transferred DNA (T-DNA) sequence (in one case T-DNA sequences with different orientations were detected, black arrows); (3) the sequence showing the 30 bp 5′ and 3′ of the junction; letters in lowercase indicate putative gDNA sequences (not verifiable by BLAST analysis, Table S1 ). Letters in red identify bases belonging to the LB.

    Article Snippet: Isolation of Sequences Flanking T-DNA Insertions Total gDNA was extracted from young, fully expanded leaves collected from the 46 transgenic lines (events), using the GeneElute Plant Genomic DNA Miniprep Kit (SIGMA, St. Louis, MO, USA).

    Techniques: Sequencing, Transgenic Assay, Isolation

    ( a ) Southern blot of genomic DNA extracted from T 1 B and C plants with probe NTPIIpr (blue segment) and VBpr (purple segment). The bands that hybridized to both probes are marked with a white triangle. Nt: non transgenic; P1: binary vector pPZP- hemL (linearized); P2: binary vector pPZP- nptII (linearized); L: 1 Kb ladder; ( b – d ) schemes (not in scale) of the restriction fragments produced by Nco I (black vertical dotted line) digestion ; ( b ) a canonical T-DNA processing; ( c ) wrong initiation at the LB and transfer of the whole VB along with a single copy of the T-DNA; ( d ) correct initiation at the RB and an incorrect termination at the LB, resulting in the transfer of the whole VB sequence along with two T-DNA copies. The position of the probes and of the restriction sites, and the length of the restriction fragments are indicated.

    Journal: International Journal of Molecular Sciences

    Article Title: An Insight into T-DNA Integration Events in Medicago sativa

    doi: 10.3390/ijms18091951

    Figure Lengend Snippet: ( a ) Southern blot of genomic DNA extracted from T 1 B and C plants with probe NTPIIpr (blue segment) and VBpr (purple segment). The bands that hybridized to both probes are marked with a white triangle. Nt: non transgenic; P1: binary vector pPZP- hemL (linearized); P2: binary vector pPZP- nptII (linearized); L: 1 Kb ladder; ( b – d ) schemes (not in scale) of the restriction fragments produced by Nco I (black vertical dotted line) digestion ; ( b ) a canonical T-DNA processing; ( c ) wrong initiation at the LB and transfer of the whole VB along with a single copy of the T-DNA; ( d ) correct initiation at the RB and an incorrect termination at the LB, resulting in the transfer of the whole VB sequence along with two T-DNA copies. The position of the probes and of the restriction sites, and the length of the restriction fragments are indicated.

    Article Snippet: Isolation of Sequences Flanking T-DNA Insertions Total gDNA was extracted from young, fully expanded leaves collected from the 46 transgenic lines (events), using the GeneElute Plant Genomic DNA Miniprep Kit (SIGMA, St. Louis, MO, USA).

    Techniques: Southern Blot, Transgenic Assay, Plasmid Preparation, Produced, Sequencing