genomic dna gdna  (Qiagen)


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    Structured Review

    Qiagen genomic dna gdna
    —Prediction and horizontally transferred genes and genomic characterization of the two functioning units of C. zofingiensis genomic <t>DNA</t> (operons). ( A ) The negative cumulative GC-profile (violet line) for the Cz1030-34550 region of C. zofingiensis Un55705 chromosome (corresponding to the NLR-like gene cluster reported in panel C ), marked with the segmentation points (green square) revealed. ( B ) Gel shows the genetic transcription of Cz NLRs and the molecular validation of two erroneously split Cz NLR genes (g00129/g00130/g00131 and g00133/g00134/g00135). The primer pairs (green triangles) designed in the Cz1030-34640 region are shown at the top. Control RT-PCRs amplifying a section of the Cz05g19160 locus (ACT) or a portion of the actinA mRNA sequence are also shown ( Lee et al. 2015 ). ( C ) A cluster of NLR genes (red arrows) containing the two operons located on the Cz1030-34550 region of chromosome Un55705.
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    Images

    1) Product Images from "Alien Domains Shaped the Modular Structure of Plant NLR Proteins"

    Article Title: Alien Domains Shaped the Modular Structure of Plant NLR Proteins

    Journal: Genome Biology and Evolution

    doi: 10.1093/gbe/evz248

    —Prediction and horizontally transferred genes and genomic characterization of the two functioning units of C. zofingiensis genomic DNA (operons). ( A ) The negative cumulative GC-profile (violet line) for the Cz1030-34550 region of C. zofingiensis Un55705 chromosome (corresponding to the NLR-like gene cluster reported in panel C ), marked with the segmentation points (green square) revealed. ( B ) Gel shows the genetic transcription of Cz NLRs and the molecular validation of two erroneously split Cz NLR genes (g00129/g00130/g00131 and g00133/g00134/g00135). The primer pairs (green triangles) designed in the Cz1030-34640 region are shown at the top. Control RT-PCRs amplifying a section of the Cz05g19160 locus (ACT) or a portion of the actinA mRNA sequence are also shown ( Lee et al. 2015 ). ( C ) A cluster of NLR genes (red arrows) containing the two operons located on the Cz1030-34550 region of chromosome Un55705.
    Figure Legend Snippet: —Prediction and horizontally transferred genes and genomic characterization of the two functioning units of C. zofingiensis genomic DNA (operons). ( A ) The negative cumulative GC-profile (violet line) for the Cz1030-34550 region of C. zofingiensis Un55705 chromosome (corresponding to the NLR-like gene cluster reported in panel C ), marked with the segmentation points (green square) revealed. ( B ) Gel shows the genetic transcription of Cz NLRs and the molecular validation of two erroneously split Cz NLR genes (g00129/g00130/g00131 and g00133/g00134/g00135). The primer pairs (green triangles) designed in the Cz1030-34640 region are shown at the top. Control RT-PCRs amplifying a section of the Cz05g19160 locus (ACT) or a portion of the actinA mRNA sequence are also shown ( Lee et al. 2015 ). ( C ) A cluster of NLR genes (red arrows) containing the two operons located on the Cz1030-34550 region of chromosome Un55705.

    Techniques Used: Sequencing

    2) Product Images from "Identification of a novel gene fusion in ALT positive osteosarcoma"

    Article Title: Identification of a novel gene fusion in ALT positive osteosarcoma

    Journal: Oncotarget

    doi: 10.18632/oncotarget.26029

    Structural characterization of the DAXX gene locus ( A ) PCR amplification of the wild type DAXX gene locus or the DAXX-KIFC3 fusion using genomic DNA isolated from SJSA1 or G292 cells. GAPDH was amplified as a control. ( B ) Representative chromatogram from Sanger sequencing of the DAXX-KIFC3 gene fusion PCR product amplified from G292 cells. Sequence shown highlights the region where the fusion event occurs at the genomic DNA level now defined as t(6:16). ( C ) Schematic of the t(6;16) fusion in genomic DNA in G292. The 3’UTR of DAXX is fused to intron 9 of KIFC3. Wild type DAXX primers are shown in green, t(6;16) primers are shown in orange. ( D ) Representative metaphase from spectral karyotyping (SKY) analysis of G292 cells.
    Figure Legend Snippet: Structural characterization of the DAXX gene locus ( A ) PCR amplification of the wild type DAXX gene locus or the DAXX-KIFC3 fusion using genomic DNA isolated from SJSA1 or G292 cells. GAPDH was amplified as a control. ( B ) Representative chromatogram from Sanger sequencing of the DAXX-KIFC3 gene fusion PCR product amplified from G292 cells. Sequence shown highlights the region where the fusion event occurs at the genomic DNA level now defined as t(6:16). ( C ) Schematic of the t(6;16) fusion in genomic DNA in G292. The 3’UTR of DAXX is fused to intron 9 of KIFC3. Wild type DAXX primers are shown in green, t(6;16) primers are shown in orange. ( D ) Representative metaphase from spectral karyotyping (SKY) analysis of G292 cells.

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

    3) Product Images from "Transposase-assisted tagmentation of RNA/DNA hybrid duplexes"

    Article Title: Transposase-assisted tagmentation of RNA/DNA hybrid duplexes

    Journal: eLife

    doi: 10.7554/eLife.54919

    Tagmentation activity of Tn5 transposome on RNA/DNA hybrids. ( a ) Denaturing (8 M urea) polyacrylamide gel analysis of reverse transcription products of an in vitro transcribed mRNA (IRF9). Lane 1: ssRNA marker. Lane 2: in vitro transcribed mRNA (IRF9). Lane 3 and 4: reverse transcription products of an in vitro transcribed mRNA (IRF9). Lane 5: reverse transcription product treated with DNase I. Lane 6: reverse transcription product treated with RNase H. ssRNA and ssDNA is marked with a red asterisk and a blue pound sign, respectively. ( b ) Gel picture showing size distribution of RNA/DNA hybrids products of 50 μl reaction systems without Tn5 transposome, and with 5 μl, 10 μl, and 15 μl Tn5 transposome, respectively. The blue and orange patches denote small and large fragments, respectively. ( c ) qPCR amplification curve of tagmentation products without Tn5 treatment or with Tn5 treatment in three different buffers (see Methods). Average Ct values of two technical replicates are 26.41, 18.39, 18.33 and 18.34, respectively. ( d ) Sanger sequencing chromatograms of PCR products following RNA/DNA hybrid tagmentation and strand extension. Adaptor A and B sequences are highlighted with blue background color and insert sequences are highlighted with yellow background. ( e ) Assessment of gDNA contamination by qPCR of represented genes. ( f ) Dot blot analysis of a series of diluted samples using the anti-hybrid S9.6 antibody. S9.6 antibody showed no cross-reactivity with dsDNA and the successful hybrids productions were confirmed in CLuc annealed products and mRNA RT products. ( g ) Native PAGE analysis of 150 bp CLuc annealed products under different annealing conditions. (Annealed hybrids 1: RNA:DNA = 2:1; Annealed hybrids 2: RNA:DNA = 1.2:1; Annealed dsDNA 1: ssDNA:ssDNA-rev = 2:1; Annealed dsDNA 2: ssDNA:ssDNA-rev = 1.2:1; See Methods). ( h ) qPCR amplification curve of tagmentation products of CLuc annealed RNA/DNA hybrid and dsDNA products with Tn5 treatment or without Tn5 treatment. Average Ct values of three technical replicates of annealed hybrid products are 22.68 and 30.4, respectively. Average Ct values of three technical replicates of annealed dsDNA products are 18.08 and 30.83, respectively.
    Figure Legend Snippet: Tagmentation activity of Tn5 transposome on RNA/DNA hybrids. ( a ) Denaturing (8 M urea) polyacrylamide gel analysis of reverse transcription products of an in vitro transcribed mRNA (IRF9). Lane 1: ssRNA marker. Lane 2: in vitro transcribed mRNA (IRF9). Lane 3 and 4: reverse transcription products of an in vitro transcribed mRNA (IRF9). Lane 5: reverse transcription product treated with DNase I. Lane 6: reverse transcription product treated with RNase H. ssRNA and ssDNA is marked with a red asterisk and a blue pound sign, respectively. ( b ) Gel picture showing size distribution of RNA/DNA hybrids products of 50 μl reaction systems without Tn5 transposome, and with 5 μl, 10 μl, and 15 μl Tn5 transposome, respectively. The blue and orange patches denote small and large fragments, respectively. ( c ) qPCR amplification curve of tagmentation products without Tn5 treatment or with Tn5 treatment in three different buffers (see Methods). Average Ct values of two technical replicates are 26.41, 18.39, 18.33 and 18.34, respectively. ( d ) Sanger sequencing chromatograms of PCR products following RNA/DNA hybrid tagmentation and strand extension. Adaptor A and B sequences are highlighted with blue background color and insert sequences are highlighted with yellow background. ( e ) Assessment of gDNA contamination by qPCR of represented genes. ( f ) Dot blot analysis of a series of diluted samples using the anti-hybrid S9.6 antibody. S9.6 antibody showed no cross-reactivity with dsDNA and the successful hybrids productions were confirmed in CLuc annealed products and mRNA RT products. ( g ) Native PAGE analysis of 150 bp CLuc annealed products under different annealing conditions. (Annealed hybrids 1: RNA:DNA = 2:1; Annealed hybrids 2: RNA:DNA = 1.2:1; Annealed dsDNA 1: ssDNA:ssDNA-rev = 2:1; Annealed dsDNA 2: ssDNA:ssDNA-rev = 1.2:1; See Methods). ( h ) qPCR amplification curve of tagmentation products of CLuc annealed RNA/DNA hybrid and dsDNA products with Tn5 treatment or without Tn5 treatment. Average Ct values of three technical replicates of annealed hybrid products are 22.68 and 30.4, respectively. Average Ct values of three technical replicates of annealed dsDNA products are 18.08 and 30.83, respectively.

    Techniques Used: Activity Assay, In Vitro, Marker, Real-time Polymerase Chain Reaction, Amplification, Sequencing, Polymerase Chain Reaction, Dot Blot, Clear Native PAGE

    Related Articles

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    Article Title: Concordance of Genomic Alterations between Circulating Tumor DNA and Matched Tumor Tissue in Chinese Patients with Breast Cancer
    Article Snippet: Circulating cell-free DNA (cfDNA) was extracted from 3-4 mL plasma by the MagMAX™ Cell-Free DNA Isolation kit (Life technologies, A29319, USA). .. Genomic DNAs (gDNAs) were extracted from tumor tissue and buffy coat using a Qiamp FFPE tissue kit (Qiagen, 56404, Germany) and TiANamp Blood DNA Maxi kit (TianGen Biotech, DP332, China), respectively. .. Qubit dsDNA high-sensitivity (HS) assay kit (Invitrogen, Q32854, USA) was used to quantify the DNA concentration.

    Article Title: Microsatellite instability test using peptide nucleic acid probe-mediated melting point analysis: a comparison study
    Article Snippet: .. PNA probe-mediated real-time PCR sensing for detection of MSI status We tested the performance of the PNA method in detecting MSI status in colon cancer samples using genomic DNA samples (gDNAs) extracted from FFPE CRCs and matched normal tissues. gDNA was isolated according to the manufacturer’s instructions (QIAamp DNA FFPE Tissue Kit, Qiagen, Venlo, Netherlands; Maxwell® 16 FFPE Purification Kit for DNA, Promega). ..

    DNA Extraction:

    Article Title: A chromosome-level genome assembly of the oriental river prawn, Macrobrachium nipponense
    Article Snippet: .. DNA extraction and whole-genome sequencing Muscle tissues from the 5 individuals in each group were pooled, and then genomic DNAs (gDNAs) from the pooled samples were extracted using a Nucleic Acid Kit (Qiagen, Germantown, MD, USA) in accordance with the manufacturer's instructions. gDNAs were also extracted from the muscle of a single individual for the k -mer analysis. .. The extracted gDNA was then used to construct libraries for Illumina (Illumina Inc., San Diego, CA, USA) and PacBio (Menlo Park, CA, USA) sequencing.

    Sequencing:

    Article Title: A chromosome-level genome assembly of the oriental river prawn, Macrobrachium nipponense
    Article Snippet: .. DNA extraction and whole-genome sequencing Muscle tissues from the 5 individuals in each group were pooled, and then genomic DNAs (gDNAs) from the pooled samples were extracted using a Nucleic Acid Kit (Qiagen, Germantown, MD, USA) in accordance with the manufacturer's instructions. gDNAs were also extracted from the muscle of a single individual for the k -mer analysis. .. The extracted gDNA was then used to construct libraries for Illumina (Illumina Inc., San Diego, CA, USA) and PacBio (Menlo Park, CA, USA) sequencing.

    Mutagenesis:

    Article Title: Glycoside-specific glycosyltransferases catalyze regio-selective sequential glucosylations for a sesame lignan, sesaminol triglucoside.
    Article Snippet: Sesame (Sesamum indicum) seeds contain a large number of lignans, phenylpropanoid-related plant specialized metabolites. (+)-Sesamin and (+)-sesamolin are major hydrophobic lignans, whereas (+)-sesaminol primarily accumulates as a water-soluble sesaminol triglucoside (STG) with a sugar chain branched via β1→2 and β1→6-O-glucosidic linkages [i.e. (+)-sesaminol 2-O-β-d-glucosyl-(1→2)-O-β-d-glucoside-(1→6)-O-β-d-glucoside]. .. Sesame (Sesamum indicum) seeds contain a large number of lignans, phenylpropanoid-related plant specialized metabolites. (+)-Sesamin and (+)-sesamolin are major hydrophobic lignans, whereas (+)-sesaminol primarily accumulates as a water-soluble sesaminol triglucoside (STG) with a sugar chain branched via β1→2 and β1→6-O-glucosidic linkages [i.e. (+)-sesaminol 2-O-β-d-glucosyl-(1→2)-O-β-d-glucoside-(1→6)-O-β-d-glucoside]. .. Sesame (Sesamum indicum) seeds contain a large number of lignans, phenylpropanoid-related plant specialized metabolites. (+)-Sesamin and (+)-sesamolin are major hydrophobic lignans, whereas (+)-sesaminol primarily accumulates as a water-soluble sesaminol triglucoside (STG) with a sugar chain branched via β1→2 and β1→6-O-glucosidic linkages [i.e. (+)-sesaminol 2-O-β-d-glucosyl-(1→2)-O-β-d-glucoside-(1→6)-O-β-d-glucoside].

    Isolation:

    Article Title: Highly efficient homology-directed repair using transient CRISPR/Cpf1-geminiviral replicon in tomato
    Article Snippet: Southern analysis for ANT1 HDR GE1 plants The Southern blot technique was implemented using MSU Potato Lab’s protocol ( https:/msu.edu/course/css/451/LabProtocols/09SOUTHERNprocedit.pdf) with minor modification. .. Essentially, genomic DNAs (gDNAs) are isolated from tomato leaves using DNeasy Plant Maxi Kit (cat. no. 68163, Qiagen, Gemany). ..

    Article Title: Microsatellite instability test using peptide nucleic acid probe-mediated melting point analysis: a comparison study
    Article Snippet: .. PNA probe-mediated real-time PCR sensing for detection of MSI status We tested the performance of the PNA method in detecting MSI status in colon cancer samples using genomic DNA samples (gDNAs) extracted from FFPE CRCs and matched normal tissues. gDNA was isolated according to the manufacturer’s instructions (QIAamp DNA FFPE Tissue Kit, Qiagen, Venlo, Netherlands; Maxwell® 16 FFPE Purification Kit for DNA, Promega). ..

    Purification:

    Article Title: Differential DNA methylation in high-grade serous ovarian cancer (HGSOC) is associated with tumor behavior
    Article Snippet: .. Genomic DNAs (gDNAs) were purified from frozen tumor tissues using the DNeasy Blood and Tissue Kit according to manufacturer’s (QIAGEN) recommendations. .. Yield and purity were assessed on a NanoDrop Model 2000 spectrophotometer and used a 260 nm/280 nm absorbance ratio of ~1.8 with minimal to no degradation as shown through horizontal agarose gel electrophoresis.

    Article Title: Microsatellite instability test using peptide nucleic acid probe-mediated melting point analysis: a comparison study
    Article Snippet: .. PNA probe-mediated real-time PCR sensing for detection of MSI status We tested the performance of the PNA method in detecting MSI status in colon cancer samples using genomic DNA samples (gDNAs) extracted from FFPE CRCs and matched normal tissues. gDNA was isolated according to the manufacturer’s instructions (QIAamp DNA FFPE Tissue Kit, Qiagen, Venlo, Netherlands; Maxwell® 16 FFPE Purification Kit for DNA, Promega). ..

    Real-time Polymerase Chain Reaction:

    Article Title: Microsatellite instability test using peptide nucleic acid probe-mediated melting point analysis: a comparison study
    Article Snippet: .. PNA probe-mediated real-time PCR sensing for detection of MSI status We tested the performance of the PNA method in detecting MSI status in colon cancer samples using genomic DNA samples (gDNAs) extracted from FFPE CRCs and matched normal tissues. gDNA was isolated according to the manufacturer’s instructions (QIAamp DNA FFPE Tissue Kit, Qiagen, Venlo, Netherlands; Maxwell® 16 FFPE Purification Kit for DNA, Promega). ..

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    Qiagen genomic dna
    Determination of ankG variant transcripts. ( a ) Schematic overview of possible transcripts of the three different AnkG groups is shown. The first group is represented by NMI, the second group by 19/34, and the third group by Z3574-1/92. The numbers of the first base pair of potential internal start codons are given, which are in frame with the stop codon at base pair position 1,015–1,017 (group 1), 1,013–1,015 (group 2) or 1,004–1,006 (group 3). ( b ) DNase treated RNA was analyzed for <t>DNA</t> contamination using dotA specific primers. As positive control C. <t>burnetii</t> NMII gDNA was used in different amounts. Gel electrophoretic analysis was performed using a 2% agarose gel. ( c , d ) Gel electrophoresis image of the different ankG mRNA sections probed in the distinct C. burnetii strains. gDNA served as positive control, while the non-template control (NTC) contains only water. RNA was isolated from all axenically grown strains (2—grown in ACCM-2; D—grown in ACCM-D), reverse-transcribed in cDNA, and amplified by PCR. Gel electrophoretic analysis was performed using a 2% agarose gel. The cDNA was analyzed for the presence of (c) the mRNA region encoding the N-terminal part of the protein (base pairs 3–150) and (d) the full-length transcript (base pairs 3–1,014).
    Genomic Dna, supplied by Qiagen, used in various techniques. Bioz Stars score: 86/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Qiagen genomic dna gdna
    Amplification curves of RPA reactions carried out with RPA primer set 1 and untreated (blue) or treated (purple) reagents. Untreated reactions spiked with 100 copies of E. coli <t>gDNA</t> (green) exhibited a threshold time of 7.25 min, whereas <t>anti-DNA</t> antibody treated reactions spiked with 100 copies of E. coli gDNA (maroon) exhibited a threshold time of 9.5 min.
    Genomic Dna Gdna, supplied by Qiagen, used in various techniques. Bioz Stars score: 86/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Price from $9.99 to $1999.99
    genomic dna gdna - by Bioz Stars, 2021-05
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    86
    Qiagen hydroxymethylated loci genomic dna
    MspI and HpaII isoschizomer can distinguish between 5-hmC and 5-ghmC at the internal cytosine residue. Cleavage specificity is shown for MspI and HpaII on FAM-end-labeled oligonucleotide duplex with internal CG being symmetrically <t>hydroxymethylated</t> or hemihydroxymethylated in the presence or absence of β-GT. Complete cleavage products are labeled as 24 and 19 nt, respectively, on a non-denaturing acrylamide gel for double-hydroxymethylated ( upper panel ) and denaturing acrylamide gel for hemi-hydroxymethylated <t>DNA</t> ( lower panel ). The arrow at the right indicates small amounts of 24-nt-long product.
    Hydroxymethylated Loci Genomic Dna, supplied by Qiagen, used in various techniques. Bioz Stars score: 86/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Image Search Results


    Determination of ankG variant transcripts. ( a ) Schematic overview of possible transcripts of the three different AnkG groups is shown. The first group is represented by NMI, the second group by 19/34, and the third group by Z3574-1/92. The numbers of the first base pair of potential internal start codons are given, which are in frame with the stop codon at base pair position 1,015–1,017 (group 1), 1,013–1,015 (group 2) or 1,004–1,006 (group 3). ( b ) DNase treated RNA was analyzed for DNA contamination using dotA specific primers. As positive control C. burnetii NMII gDNA was used in different amounts. Gel electrophoretic analysis was performed using a 2% agarose gel. ( c , d ) Gel electrophoresis image of the different ankG mRNA sections probed in the distinct C. burnetii strains. gDNA served as positive control, while the non-template control (NTC) contains only water. RNA was isolated from all axenically grown strains (2—grown in ACCM-2; D—grown in ACCM-D), reverse-transcribed in cDNA, and amplified by PCR. Gel electrophoretic analysis was performed using a 2% agarose gel. The cDNA was analyzed for the presence of (c) the mRNA region encoding the N-terminal part of the protein (base pairs 3–150) and (d) the full-length transcript (base pairs 3–1,014).

    Journal: Scientific Reports

    Article Title: The anti-apoptotic Coxiella burnetii effector protein AnkG is a strain specific virulence factor

    doi: 10.1038/s41598-020-72340-9

    Figure Lengend Snippet: Determination of ankG variant transcripts. ( a ) Schematic overview of possible transcripts of the three different AnkG groups is shown. The first group is represented by NMI, the second group by 19/34, and the third group by Z3574-1/92. The numbers of the first base pair of potential internal start codons are given, which are in frame with the stop codon at base pair position 1,015–1,017 (group 1), 1,013–1,015 (group 2) or 1,004–1,006 (group 3). ( b ) DNase treated RNA was analyzed for DNA contamination using dotA specific primers. As positive control C. burnetii NMII gDNA was used in different amounts. Gel electrophoretic analysis was performed using a 2% agarose gel. ( c , d ) Gel electrophoresis image of the different ankG mRNA sections probed in the distinct C. burnetii strains. gDNA served as positive control, while the non-template control (NTC) contains only water. RNA was isolated from all axenically grown strains (2—grown in ACCM-2; D—grown in ACCM-D), reverse-transcribed in cDNA, and amplified by PCR. Gel electrophoretic analysis was performed using a 2% agarose gel. The cDNA was analyzed for the presence of (c) the mRNA region encoding the N-terminal part of the protein (base pairs 3–150) and (d) the full-length transcript (base pairs 3–1,014).

    Article Snippet: The next day genomic DNA of C. burnetii was isolated with the Qiagen DNeasy Blood and Tissue Kit and an RT-PCR was performed to determine the bacterial load.

    Techniques: Variant Assay, Positive Control, Agarose Gel Electrophoresis, Nucleic Acid Electrophoresis, Isolation, Amplification, Polymerase Chain Reaction

    Only AnkG NM is a bona fide T4BSS effector protein. ( a ) Representative confocal micrographs of mouse embryonic fibroblasts (MEFs) infected with C. burnetii expressing Flag-AnkG NM , Flag-AnkG Soyta or Flag-AnkG F3 . MEFs were fixed 48 h post-infection and were stained with an antibody specific for Flag (green) and Coxiella (red). DNA was stained with DAPI (blue). Scale bars, 10 μm. ( b ) The amount of cAMP is given in fmol/well for CHO cells either uninfected or infected for 72 h with C. burnetii producing Cya, Cya-AnkG NM , Cya-AnkG Soyta or Cya-AnkG F3 . The threshold for secretion was set to 2.5-fold the cAMP-level of the controls and is depicted as a dotted line. Shown is the mean of at least three experiments ± SD. ***p

    Journal: Scientific Reports

    Article Title: The anti-apoptotic Coxiella burnetii effector protein AnkG is a strain specific virulence factor

    doi: 10.1038/s41598-020-72340-9

    Figure Lengend Snippet: Only AnkG NM is a bona fide T4BSS effector protein. ( a ) Representative confocal micrographs of mouse embryonic fibroblasts (MEFs) infected with C. burnetii expressing Flag-AnkG NM , Flag-AnkG Soyta or Flag-AnkG F3 . MEFs were fixed 48 h post-infection and were stained with an antibody specific for Flag (green) and Coxiella (red). DNA was stained with DAPI (blue). Scale bars, 10 μm. ( b ) The amount of cAMP is given in fmol/well for CHO cells either uninfected or infected for 72 h with C. burnetii producing Cya, Cya-AnkG NM , Cya-AnkG Soyta or Cya-AnkG F3 . The threshold for secretion was set to 2.5-fold the cAMP-level of the controls and is depicted as a dotted line. Shown is the mean of at least three experiments ± SD. ***p

    Article Snippet: The next day genomic DNA of C. burnetii was isolated with the Qiagen DNeasy Blood and Tissue Kit and an RT-PCR was performed to determine the bacterial load.

    Techniques: Infection, Expressing, Staining

    Total genome-wide profiling of DNA methylation of A549 cells exposed to the seven aldehydes compared to vehicle control group (DMSO). The heatmap shows the DNA methylation profiles of aldehydes exposed A549 cells based on hierarchical clustering (Yellow: hypermethylation; Black: hypomethylation).

    Journal: Scientific Reports

    Article Title: DNA Methylome Analysis of Saturated Aliphatic Aldehydes in Pulmonary Toxicity

    doi: 10.1038/s41598-018-28813-z

    Figure Lengend Snippet: Total genome-wide profiling of DNA methylation of A549 cells exposed to the seven aldehydes compared to vehicle control group (DMSO). The heatmap shows the DNA methylation profiles of aldehydes exposed A549 cells based on hierarchical clustering (Yellow: hypermethylation; Black: hypomethylation).

    Article Snippet: Genomic DNA was extracted from A549 cells exposed to the seven aldehydes using the QIAamp DNA Mini Kit (Qiagen, Hilden, Germany) according to manufacturer’s instructions.

    Techniques: Genome Wide, DNA Methylation Assay

    Amplification curves of RPA reactions carried out with RPA primer set 1 and untreated (blue) or treated (purple) reagents. Untreated reactions spiked with 100 copies of E. coli gDNA (green) exhibited a threshold time of 7.25 min, whereas anti-DNA antibody treated reactions spiked with 100 copies of E. coli gDNA (maroon) exhibited a threshold time of 9.5 min.

    Journal: Frontiers in Cellular and Infection Microbiology

    Article Title: Akkermansia muciniphila as a Model Case for the Development of an Improved Quantitative RPA Microbiome Assay

    doi: 10.3389/fcimb.2018.00237

    Figure Lengend Snippet: Amplification curves of RPA reactions carried out with RPA primer set 1 and untreated (blue) or treated (purple) reagents. Untreated reactions spiked with 100 copies of E. coli gDNA (green) exhibited a threshold time of 7.25 min, whereas anti-DNA antibody treated reactions spiked with 100 copies of E. coli gDNA (maroon) exhibited a threshold time of 9.5 min.

    Article Snippet: Genomic DNA (gDNA) was isolated from E. coli cultures using an UltraClean Microbial DNA Isolation kit (Mo Bio Laboratories; Carlsbad, CA).

    Techniques: Amplification, Recombinase Polymerase Amplification

    (A) RPA amplification curves generated using the primer set 1, 0–10 6 copies of E. coli gDNA (2 μL per reaction; n = 2), and RPA reagents pre-treated with anti-dsDNA antibody-coupled magnetic particles. (B) RPA standard curve was generated using the average threshold times calculated from measurements in (A) ( n = 2). The fecal DNA exhibited an average threshold time of 7. 75 min (solid red line) and an estimated load of 6.3-log copies of bacterial gDNA per reaction (dotted red line) or a total bacterial load of 1.01 × 10 7 bacterial gDNA copies per 15 ng of isolated gDNA.

    Journal: Frontiers in Cellular and Infection Microbiology

    Article Title: Akkermansia muciniphila as a Model Case for the Development of an Improved Quantitative RPA Microbiome Assay

    doi: 10.3389/fcimb.2018.00237

    Figure Lengend Snippet: (A) RPA amplification curves generated using the primer set 1, 0–10 6 copies of E. coli gDNA (2 μL per reaction; n = 2), and RPA reagents pre-treated with anti-dsDNA antibody-coupled magnetic particles. (B) RPA standard curve was generated using the average threshold times calculated from measurements in (A) ( n = 2). The fecal DNA exhibited an average threshold time of 7. 75 min (solid red line) and an estimated load of 6.3-log copies of bacterial gDNA per reaction (dotted red line) or a total bacterial load of 1.01 × 10 7 bacterial gDNA copies per 15 ng of isolated gDNA.

    Article Snippet: Genomic DNA (gDNA) was isolated from E. coli cultures using an UltraClean Microbial DNA Isolation kit (Mo Bio Laboratories; Carlsbad, CA).

    Techniques: Recombinase Polymerase Amplification, Amplification, Generated, Isolation

    RPA standard curve of A. muciniphila gDNA (0-1,000,000 copies; ATCC BAA-835) amplified using real-time SYBR green-RPA and primer set 1 ( n = 3). The average threshold time of a 10-fold dilution of the fecal sample gDNA was 6.05 ± 0.1 min (solid red line, n = 3). The estimated load was 1.48 × 10 5 copies of A. muciniphila gDNA per reaction (dotted red line) or 2.99 × 10 5 copies of A. muciniphila gDNA per 15 ng of DNA isolated from the fecal sample.

    Journal: Frontiers in Cellular and Infection Microbiology

    Article Title: Akkermansia muciniphila as a Model Case for the Development of an Improved Quantitative RPA Microbiome Assay

    doi: 10.3389/fcimb.2018.00237

    Figure Lengend Snippet: RPA standard curve of A. muciniphila gDNA (0-1,000,000 copies; ATCC BAA-835) amplified using real-time SYBR green-RPA and primer set 1 ( n = 3). The average threshold time of a 10-fold dilution of the fecal sample gDNA was 6.05 ± 0.1 min (solid red line, n = 3). The estimated load was 1.48 × 10 5 copies of A. muciniphila gDNA per reaction (dotted red line) or 2.99 × 10 5 copies of A. muciniphila gDNA per 15 ng of DNA isolated from the fecal sample.

    Article Snippet: Genomic DNA (gDNA) was isolated from E. coli cultures using an UltraClean Microbial DNA Isolation kit (Mo Bio Laboratories; Carlsbad, CA).

    Techniques: Recombinase Polymerase Amplification, Amplification, SYBR Green Assay, Isolation

    MspI and HpaII isoschizomer can distinguish between 5-hmC and 5-ghmC at the internal cytosine residue. Cleavage specificity is shown for MspI and HpaII on FAM-end-labeled oligonucleotide duplex with internal CG being symmetrically hydroxymethylated or hemihydroxymethylated in the presence or absence of β-GT. Complete cleavage products are labeled as 24 and 19 nt, respectively, on a non-denaturing acrylamide gel for double-hydroxymethylated ( upper panel ) and denaturing acrylamide gel for hemi-hydroxymethylated DNA ( lower panel ). The arrow at the right indicates small amounts of 24-nt-long product.

    Journal: The Journal of Biological Chemistry

    Article Title: Tissue-specific Distribution and Dynamic Changes of 5-Hydroxymethylcytosine in Mammalian Genomes *

    doi: 10.1074/jbc.M110.217083

    Figure Lengend Snippet: MspI and HpaII isoschizomer can distinguish between 5-hmC and 5-ghmC at the internal cytosine residue. Cleavage specificity is shown for MspI and HpaII on FAM-end-labeled oligonucleotide duplex with internal CG being symmetrically hydroxymethylated or hemihydroxymethylated in the presence or absence of β-GT. Complete cleavage products are labeled as 24 and 19 nt, respectively, on a non-denaturing acrylamide gel for double-hydroxymethylated ( upper panel ) and denaturing acrylamide gel for hemi-hydroxymethylated DNA ( lower panel ). The arrow at the right indicates small amounts of 24-nt-long product.

    Article Snippet: Screen for Genomic DNA for Hydroxymethylated Loci Genomic DNA was extracted from E14 ES cells and embryoid bodies using the Qiagen DNeasy Blood and Tissue kit.

    Techniques: Labeling, Acrylamide Gel Assay