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    Qiagen dna genomic dna
    Biased degradation of unmethylated C-rich <t>DNA</t> after bisulfite treatment. a Post-bisulfite recovery of C-rich and C-poor DNA fragments treated with different BS conversion protocols. Fragment sequences originate from the <t>M13</t> phage sequence (Additional file 2 : Table S1). Statistical analysis was performed with a two-way ANOVA, p = 0.0034 for cytosine content (‘Heat’ and ‘Alkaline’ only) and p
    Dna 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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    Images

    1) Product Images from "Comparison of whole-genome bisulfite sequencing library preparation strategies identifies sources of biases affecting DNA methylation data"

    Article Title: Comparison of whole-genome bisulfite sequencing library preparation strategies identifies sources of biases affecting DNA methylation data

    Journal: Genome Biology

    doi: 10.1186/s13059-018-1408-2

    Biased degradation of unmethylated C-rich DNA after bisulfite treatment. a Post-bisulfite recovery of C-rich and C-poor DNA fragments treated with different BS conversion protocols. Fragment sequences originate from the M13 phage sequence (Additional file 2 : Table S1). Statistical analysis was performed with a two-way ANOVA, p = 0.0034 for cytosine content (‘Heat’ and ‘Alkaline’ only) and p
    Figure Legend Snippet: Biased degradation of unmethylated C-rich DNA after bisulfite treatment. a Post-bisulfite recovery of C-rich and C-poor DNA fragments treated with different BS conversion protocols. Fragment sequences originate from the M13 phage sequence (Additional file 2 : Table S1). Statistical analysis was performed with a two-way ANOVA, p = 0.0034 for cytosine content (‘Heat’ and ‘Alkaline’ only) and p

    Techniques Used: Sequencing

    2) Product Images from "piRNA-mediated regulation of transposon alternative splicing in soma and germline"

    Article Title: piRNA-mediated regulation of transposon alternative splicing in soma and germline

    Journal: Nature

    doi: 10.1038/nature25018

    P -element DNA transposon splicing is regulated in germ cells during hybrid dysgenesis a , P - M hybrid dysgenesis crossing scheme. P -cytotype designates animals containing P -elements, and M -cytotype those lacking them. Harwich strain contains P -element while w 1118 strain does not. b , Diagram of P -element DNA transposon. Arrowheads represent terminal inverted repeats; boxes, exons (ORF0-3); inverted triangles, introns (IVS1-3); ATG, start codon; TGA and TAA, stop codons. c , Fertility of non-dysgenic (N.D.) and dysgenic (D.) flies as measured by the number of [F2] adult progeny originated from single [F1] female crosses. (n=20 independent crosses). ***p
    Figure Legend Snippet: P -element DNA transposon splicing is regulated in germ cells during hybrid dysgenesis a , P - M hybrid dysgenesis crossing scheme. P -cytotype designates animals containing P -elements, and M -cytotype those lacking them. Harwich strain contains P -element while w 1118 strain does not. b , Diagram of P -element DNA transposon. Arrowheads represent terminal inverted repeats; boxes, exons (ORF0-3); inverted triangles, introns (IVS1-3); ATG, start codon; TGA and TAA, stop codons. c , Fertility of non-dysgenic (N.D.) and dysgenic (D.) flies as measured by the number of [F2] adult progeny originated from single [F1] female crosses. (n=20 independent crosses). ***p

    Techniques Used:

    Characterization of euchromatic P -element insertion in Harwich strain a, Ethidium bromide-stained gels displaying genomic PCR reactions with 25 primer sets flanking P -element insertions uncovered by DNA-seq analysis. PCR reactions were performed with genomic DNA extract from w 1118 and Harwich pools containing 20 adult females each. Size scale in base pairs (bp) is presented on the right side of each gel. Amplicon sizes representing absence (no insertion) or presence (truncated or full-length elements) of P-element insertion are indicated on the left of each gel. Targeted insertion and chromosome localization is displayed in the bottom of each gel. Experiments were repeated two times with similar results. For gel source data, see Supplementary Figure 1 . b, Schematic representation of five structurally different elements regrouping 24 P -element insertions characterized by DNA sequencing in the Harwich strain. Elements size, as well as a list of respective insertions is indicated on the right of each diagram. Arrowheads represent terminal inverted repeats; boxes, exons; inverted triangles, introns; ATG, start codon; TGA and TAA, stop codons. Dashed lines represent internal deletions.
    Figure Legend Snippet: Characterization of euchromatic P -element insertion in Harwich strain a, Ethidium bromide-stained gels displaying genomic PCR reactions with 25 primer sets flanking P -element insertions uncovered by DNA-seq analysis. PCR reactions were performed with genomic DNA extract from w 1118 and Harwich pools containing 20 adult females each. Size scale in base pairs (bp) is presented on the right side of each gel. Amplicon sizes representing absence (no insertion) or presence (truncated or full-length elements) of P-element insertion are indicated on the left of each gel. Targeted insertion and chromosome localization is displayed in the bottom of each gel. Experiments were repeated two times with similar results. For gel source data, see Supplementary Figure 1 . b, Schematic representation of five structurally different elements regrouping 24 P -element insertions characterized by DNA sequencing in the Harwich strain. Elements size, as well as a list of respective insertions is indicated on the right of each diagram. Arrowheads represent terminal inverted repeats; boxes, exons; inverted triangles, introns; ATG, start codon; TGA and TAA, stop codons. Dashed lines represent internal deletions.

    Techniques Used: Staining, Polymerase Chain Reaction, DNA Sequencing, Amplification

    3) Product Images from "Extensive duplication of the Wolbachia DNA in chromosome four of Drosophila ananassae"

    Article Title: Extensive duplication of the Wolbachia DNA in chromosome four of Drosophila ananassae

    Journal: BMC Genomics

    doi: 10.1186/1471-2164-15-1097

    Fluorescence in situ hybridization of polytene chromosomes. Polytene chromosomes were hybridized with a Wolbachia -specific WRi_004290 probe amplified directly from genomic DNA from the Wb- Hawaii line and visualized at 40X magnification. A single band is observed and not the 8–10 bands expected (Panel A) . Polytene chromosomes were again hybridized with the WRi_004290 probe amplified directly from genomic DNA from the Wb- Hawaii line and visualized at 20X (Panel B) and 40X (Panel C) . A single band is observed and not the 8–10 bands expected. Polytene chromosomes were simultaneously hybridized with differentially-labelled probes for the Wolbachia- specific WRi_004290 (Panel D , pink) and a D. ananassae actin gene (Panels E F , green) that were generated from sequence-verified plasmids and visualized at 40X. While hybridization by the plasmid-derived WRi_004290 probe is not detected, hybridization by the plasmid-derived actin probe is detected. This suggests that the previous detection with Wolbachia probes amplified directly from genomic DNA may be detecting hybridization of spurious amplification products and that the lateral gene transfer is heterochromatic.
    Figure Legend Snippet: Fluorescence in situ hybridization of polytene chromosomes. Polytene chromosomes were hybridized with a Wolbachia -specific WRi_004290 probe amplified directly from genomic DNA from the Wb- Hawaii line and visualized at 40X magnification. A single band is observed and not the 8–10 bands expected (Panel A) . Polytene chromosomes were again hybridized with the WRi_004290 probe amplified directly from genomic DNA from the Wb- Hawaii line and visualized at 20X (Panel B) and 40X (Panel C) . A single band is observed and not the 8–10 bands expected. Polytene chromosomes were simultaneously hybridized with differentially-labelled probes for the Wolbachia- specific WRi_004290 (Panel D , pink) and a D. ananassae actin gene (Panels E F , green) that were generated from sequence-verified plasmids and visualized at 40X. While hybridization by the plasmid-derived WRi_004290 probe is not detected, hybridization by the plasmid-derived actin probe is detected. This suggests that the previous detection with Wolbachia probes amplified directly from genomic DNA may be detecting hybridization of spurious amplification products and that the lateral gene transfer is heterochromatic.

    Techniques Used: Fluorescence, In Situ Hybridization, Amplification, Western Blot, Generated, Sequencing, Hybridization, Plasmid Preparation, Derivative Assay

    Coverage of India sequencing data. The copy number for the 3 kbp mate pair library from the India (Panels A and B) , and India x Florida (Panels C and D) genomic DNA was calculated over a 1 kbp window every 500 bp and plotted against the reference w Ri genome (left) and the first 1.5 Mbp of the largest scaffold (gi|109914400|gb|CH902617.1|) of the Drosophila ananassae caf1 assembly. The India genome shows the same relative pattern of duplication but is less abundant than single copy nuclear genes, as is the genome from offspring of a backcross of India with Florida. The spikes in the coverage for the India × Florida line reflect the mapping of transposase sequences.
    Figure Legend Snippet: Coverage of India sequencing data. The copy number for the 3 kbp mate pair library from the India (Panels A and B) , and India x Florida (Panels C and D) genomic DNA was calculated over a 1 kbp window every 500 bp and plotted against the reference w Ri genome (left) and the first 1.5 Mbp of the largest scaffold (gi|109914400|gb|CH902617.1|) of the Drosophila ananassae caf1 assembly. The India genome shows the same relative pattern of duplication but is less abundant than single copy nuclear genes, as is the genome from offspring of a backcross of India with Florida. The spikes in the coverage for the India × Florida line reflect the mapping of transposase sequences.

    Techniques Used: Sequencing

    Coverage of Indonesia sequencing data. The copy number for the 3 kbp mate pair library from the Indonesia genomic DNA was calculated over a 1 kbp window every 500 bp and plotted against the reference w Ri genome (left) and the first 1.5 Mbp of the largest scaffold (gi|109914400|gb|CH902617.1|) of the Drosophila ananassae caf1 assembly. The Indonesia line has a nuwt with even coverage similar to the rest of the Drosophila genome. The spikes in the coverage for the Indonesia line reflect the mapping of conserved DNA sequences (e.g. those from rRNA or tRNA) from bacterial contaminants like those in the guts of adult flies.
    Figure Legend Snippet: Coverage of Indonesia sequencing data. The copy number for the 3 kbp mate pair library from the Indonesia genomic DNA was calculated over a 1 kbp window every 500 bp and plotted against the reference w Ri genome (left) and the first 1.5 Mbp of the largest scaffold (gi|109914400|gb|CH902617.1|) of the Drosophila ananassae caf1 assembly. The Indonesia line has a nuwt with even coverage similar to the rest of the Drosophila genome. The spikes in the coverage for the Indonesia line reflect the mapping of conserved DNA sequences (e.g. those from rRNA or tRNA) from bacterial contaminants like those in the guts of adult flies.

    Techniques Used: Sequencing

    Coverage of Hawaii sequencing data. The copy number for the 3 kbp mate pair library from the Hawaii genomic DNA was calculated over a 1 kbp window every 500 bp and plotted against the reference w Ri genome (left) and the first 1.5 Mbp of the largest scaffold (gi|109914400|gb|CH902617.1|) of the Drosophila ananassae caf1 assembly. Approximately 5× coverage was expected to represent single copy Drosophila genes and single copy regions are apparent. However, most of the nuwt is present with at least two copies.
    Figure Legend Snippet: Coverage of Hawaii sequencing data. The copy number for the 3 kbp mate pair library from the Hawaii genomic DNA was calculated over a 1 kbp window every 500 bp and plotted against the reference w Ri genome (left) and the first 1.5 Mbp of the largest scaffold (gi|109914400|gb|CH902617.1|) of the Drosophila ananassae caf1 assembly. Approximately 5× coverage was expected to represent single copy Drosophila genes and single copy regions are apparent. However, most of the nuwt is present with at least two copies.

    Techniques Used: Sequencing

    4) Product Images from "Modeling neurological diseases with induced pluripotent cells reprogrammed from immortalized lymphoblastoid cell lines"

    Article Title: Modeling neurological diseases with induced pluripotent cells reprogrammed from immortalized lymphoblastoid cell lines

    Journal: Molecular Brain

    doi: 10.1186/s13041-016-0267-6

    Establishment and characterization of LCL-derived iPSCs. a Representative image of an LCL culture. Scale bar = 100 μm. b iPSCs derived from healthy control LCLs (LKA10, LKA29 and LKA36), isogenic dermal fibroblasts (DFs) (eKA3, KA11, and KA23) and LCLs from a PARK2 patient (LPB1, LPB3 and LPB7) were immunopositive for the pluripotent markers OCT4 (green) and TRA-1-60 (red). Scale bar = 200 μm. c – e The expression levels of pluripotent markers NANOG and OCT4 in LiPSCs (LKA10, LKA29 LKA36, LPB1, LPB3 and LPB7), DF-iPSCs (eKA3, KA11 and KA23) and LCLs (LCL(KA) and LCL(PB)) were assessed by quantitative reverse-transcription PCR (qPCR). The values from the previously established DF-iPSCs (201B7, a previously established human iPSC clone [ 5 ]) were set to 1.0 ( n = 3 independent experiments; means ± SEM; n.s., not significant; Student’s t -test). f The expression levels of EBV-related genes ( EBNA-1 , EBNA-2 , BZLF-1 , LMP-1 and OriP ) were analyzed by a PCR analysis of the genomic DNA obtained from parental LCLs and LCL-derived iPSCs. GAPDH was used a loading control. g Comparison of the global gene expression profiles of DF-iPSCs (eKA3 and KA11), LiPSCs (LKA29, LKA36, LPB1 and LPB7), TiPSCs (TKA4 and TKA9) [ 6 ], and the original cells (DF(KA), LCL(KA), LCL(PB) and T-cell(KA)). Principal component analysis of the gene expression data. Black: DF, Brown: LCLs, Yellow: T-cell, Green: DF-iPSCs, Red: LiPSCs, Blue: TiPSCs. h Hierarchical clustering analysis of the global gene expression profiles. The data discussed in this publication have been deposited in the NCBI Gene Expression Omnibus (GEO, http://www.ncbi.nlm.nih.gov/geo/ ) database and are accessible through GEO Series accession numbers GSE76832 [ 6 ] and GSE82159
    Figure Legend Snippet: Establishment and characterization of LCL-derived iPSCs. a Representative image of an LCL culture. Scale bar = 100 μm. b iPSCs derived from healthy control LCLs (LKA10, LKA29 and LKA36), isogenic dermal fibroblasts (DFs) (eKA3, KA11, and KA23) and LCLs from a PARK2 patient (LPB1, LPB3 and LPB7) were immunopositive for the pluripotent markers OCT4 (green) and TRA-1-60 (red). Scale bar = 200 μm. c – e The expression levels of pluripotent markers NANOG and OCT4 in LiPSCs (LKA10, LKA29 LKA36, LPB1, LPB3 and LPB7), DF-iPSCs (eKA3, KA11 and KA23) and LCLs (LCL(KA) and LCL(PB)) were assessed by quantitative reverse-transcription PCR (qPCR). The values from the previously established DF-iPSCs (201B7, a previously established human iPSC clone [ 5 ]) were set to 1.0 ( n = 3 independent experiments; means ± SEM; n.s., not significant; Student’s t -test). f The expression levels of EBV-related genes ( EBNA-1 , EBNA-2 , BZLF-1 , LMP-1 and OriP ) were analyzed by a PCR analysis of the genomic DNA obtained from parental LCLs and LCL-derived iPSCs. GAPDH was used a loading control. g Comparison of the global gene expression profiles of DF-iPSCs (eKA3 and KA11), LiPSCs (LKA29, LKA36, LPB1 and LPB7), TiPSCs (TKA4 and TKA9) [ 6 ], and the original cells (DF(KA), LCL(KA), LCL(PB) and T-cell(KA)). Principal component analysis of the gene expression data. Black: DF, Brown: LCLs, Yellow: T-cell, Green: DF-iPSCs, Red: LiPSCs, Blue: TiPSCs. h Hierarchical clustering analysis of the global gene expression profiles. The data discussed in this publication have been deposited in the NCBI Gene Expression Omnibus (GEO, http://www.ncbi.nlm.nih.gov/geo/ ) database and are accessible through GEO Series accession numbers GSE76832 [ 6 ] and GSE82159

    Techniques Used: Derivative Assay, Expressing, Polymerase Chain Reaction, Real-time Polymerase Chain Reaction

    5) Product Images from "Epigenetic silencing of serine protease HTRA1 drives polyploidy"

    Article Title: Epigenetic silencing of serine protease HTRA1 drives polyploidy

    Journal: BMC Cancer

    doi: 10.1186/s12885-016-2425-8

    Epigenetic regulation of HTRA1 expression in HCT116 cells. a Methylation of the human HTRA1 promoter (−388 bp to −115 bp) was determined by sequencing 4 independent clones of bisulfite treated DNA of HCT116 and SW480 cells. b Mean normalized expression (MNE) of HTRA1 in SW480 and HCT116 cells determined by qRT-PCR (n = 3 independent cell lines, each done in triplicates, two-tailed Mann–Whitney U test, p-value
    Figure Legend Snippet: Epigenetic regulation of HTRA1 expression in HCT116 cells. a Methylation of the human HTRA1 promoter (−388 bp to −115 bp) was determined by sequencing 4 independent clones of bisulfite treated DNA of HCT116 and SW480 cells. b Mean normalized expression (MNE) of HTRA1 in SW480 and HCT116 cells determined by qRT-PCR (n = 3 independent cell lines, each done in triplicates, two-tailed Mann–Whitney U test, p-value

    Techniques Used: Expressing, Methylation, Sequencing, Clone Assay, Quantitative RT-PCR, Two Tailed Test, MANN-WHITNEY

    Htra1 expression and methylation of the Htra1 promoter in polyps. Mean normalized expression (MNE) of Htra1 in polyps isolated from Apc Min+ mice was determined by qRT-PCR. Methylation of the murine Htra1 promoter (−252 bp to −12 bp) was determined by sequencing 3 independent clones of bisulfite treated DNA isolated from the same polyps that were used for measuring mRNA levels by qRT-PCR. Controls are four independent samples taken from large intestine
    Figure Legend Snippet: Htra1 expression and methylation of the Htra1 promoter in polyps. Mean normalized expression (MNE) of Htra1 in polyps isolated from Apc Min+ mice was determined by qRT-PCR. Methylation of the murine Htra1 promoter (−252 bp to −12 bp) was determined by sequencing 3 independent clones of bisulfite treated DNA isolated from the same polyps that were used for measuring mRNA levels by qRT-PCR. Controls are four independent samples taken from large intestine

    Techniques Used: Expressing, Methylation, Isolation, Mouse Assay, Quantitative RT-PCR, Sequencing, Clone Assay

    6) Product Images from "Enhancing the throughput and multiplexing capabilities of next generation sequencing for efficient implementation of pooled shRNA and CRISPR screens"

    Article Title: Enhancing the throughput and multiplexing capabilities of next generation sequencing for efficient implementation of pooled shRNA and CRISPR screens

    Journal: Scientific Reports

    doi: 10.1038/s41598-017-01170-z

    Steps involved in shRNA library sequencing. Workflow showing steps involved in sequencing shRNA library from the genomic DNA. Step1: PCR amplification of shRNA library from gDNA. Step 2: PCR purification of the amplified library. Step 3: Gel extraction of the 205 bp library amplicon. Step 4: Quality assessment of the library using a Bioanalyzer. Step 5: shRNA library sequencing using Ion Torrent platform. Representative agarose gel, electropherogram from the Bioanalyzer and read-length histogram from Ion Torrent are shown. The sequence length is plotted in the X-axis and the frequency is plotted in the Y-axis. The shRNA library is 152 bp, excluding the A and P1 sequence.
    Figure Legend Snippet: Steps involved in shRNA library sequencing. Workflow showing steps involved in sequencing shRNA library from the genomic DNA. Step1: PCR amplification of shRNA library from gDNA. Step 2: PCR purification of the amplified library. Step 3: Gel extraction of the 205 bp library amplicon. Step 4: Quality assessment of the library using a Bioanalyzer. Step 5: shRNA library sequencing using Ion Torrent platform. Representative agarose gel, electropherogram from the Bioanalyzer and read-length histogram from Ion Torrent are shown. The sequence length is plotted in the X-axis and the frequency is plotted in the Y-axis. The shRNA library is 152 bp, excluding the A and P1 sequence.

    Techniques Used: shRNA, Sequencing, Polymerase Chain Reaction, Amplification, Purification, Gel Extraction, Agarose Gel Electrophoresis

    Related Articles

    Sample Prep:

    Article Title: Microbiomes Associated With Foods From Plant and Animal Sources
    Article Snippet: .. Preparation of Genomic DNA Genomic DNA was prepared from the bacterial pellets of the microbiomes of masala spice mixes, cilantro, cucumber, mung bean sprouts, and smoked salmon using the DNAeasy Blood and Tissue (Qiagen, Germantown, MD, United States) protocol on the QIAcube (Qiagen, Germantown, MD, United States) automated sample preparation instrumentation. .. 16S rRNA Gene Amplicon Library Preparation and Sequencing 16S rRNA gene library preparation, sequencing, data processing and analyses were performed as described by .

    Isolation:

    Article Title: DNA Methylation Is Involved in the Expression of miR-142-3p in Fibroblasts and Induced Pluripotent Stem Cells
    Article Snippet: Expression levels of mRNA were compared to known standard samples and normalized to GAPDH. .. Isolation and Bisulfite Treatment of Genomic DNA Genomic DNA was isolated from ~5 × 106 cells using the QIAamp DNA Mini and Blood Mini kit (Qiagen). .. Genomic DNA (1 μ g) was subjected for bisulfite conversion using EpiTect Bisulfite (Qiagen).

    Article Title: Ultra-Rapid Virological Response, Young Age, Low ?-GT/ALT-Ratio, and Absence of Steatosis Identify a Subgroup of HCV Genotype 3 Patients Who Achieve SVR with IFN-?2a Monotherapy
    Article Snippet: Determination of HCV Genotypes In HCV RNA-positive sera, virus genotyping was performed using the Innolipa HCV II line probe assay (Innogenetics, Ghent, Belgium). .. Isolation of Genomic DNA Genomic DNA was purified from peripheral blood mononuclear cells (PBMCs) through the use of the QIAamp DNA Mini Kit following the manufacturer’s blood and body fluid spin protocol (Qiagen). .. The concentration and the purity of the DNA isolated from PBMCs were determined photometrically by reading the absorbance levels at 260 and 280 nm.

    Article Title: DNA Methylation of Alternative Promoters Directs Tissue Specific Expression of Epac2 Isoforms
    Article Snippet: .. Isolation of Genomic DNA Genomic DNA from mouse tissues, paraffin sections or primary cells was isolated employing the QIAGEN DNeasy kit (Gaithersburg, USA) following the manufacturer’s instructions. .. RNA Isolation and Reverse Transcriptase PCR (RT-PCR) RNA was isolated from materials pre-stored at RNA-later buffer, using the RNeasy Protect Mini Kit (QIAGEN, Gaithersburg, USA).

    DNA Purification:

    Article Title: Simultaneous Detection of Different MicroRNA Types Using the ZIP-Code Array System
    Article Snippet: The reverse transcription reaction was performed for 1.5 hours at 37°C and subsequently heat inactivated at 70°C for 10 min. After adding 2 U Ribonuclease H (Invitrogen, Darmstadt, Germany) to each sample to degrade RNA and incubation for 20 min at 37°C, samples were unified, followed by column purification of cDNA by QIAquick Nucleotide Removal Kit (Qiagen, Hilden, Germany). cDNA was eluted with 31.5 μ L elution buffer. .. Preparation of Genomic DNA Genomic DNA was extracted from HaCaT cell pellets containing 107 cells, using AllPrep DNA/RNA Mini Kit (Qiagen, Hilden, Germany) according to the protocol “Genomic DNA Purification Protocol from Animal Cells .” DNA concentration and quality were determined photometrically. ..

    Concentration Assay:

    Article Title: Simultaneous Detection of Different MicroRNA Types Using the ZIP-Code Array System
    Article Snippet: The reverse transcription reaction was performed for 1.5 hours at 37°C and subsequently heat inactivated at 70°C for 10 min. After adding 2 U Ribonuclease H (Invitrogen, Darmstadt, Germany) to each sample to degrade RNA and incubation for 20 min at 37°C, samples were unified, followed by column purification of cDNA by QIAquick Nucleotide Removal Kit (Qiagen, Hilden, Germany). cDNA was eluted with 31.5 μ L elution buffer. .. Preparation of Genomic DNA Genomic DNA was extracted from HaCaT cell pellets containing 107 cells, using AllPrep DNA/RNA Mini Kit (Qiagen, Hilden, Germany) according to the protocol “Genomic DNA Purification Protocol from Animal Cells .” DNA concentration and quality were determined photometrically. ..

    Purification:

    Article Title: Ultra-Rapid Virological Response, Young Age, Low ?-GT/ALT-Ratio, and Absence of Steatosis Identify a Subgroup of HCV Genotype 3 Patients Who Achieve SVR with IFN-?2a Monotherapy
    Article Snippet: Determination of HCV Genotypes In HCV RNA-positive sera, virus genotyping was performed using the Innolipa HCV II line probe assay (Innogenetics, Ghent, Belgium). .. Isolation of Genomic DNA Genomic DNA was purified from peripheral blood mononuclear cells (PBMCs) through the use of the QIAamp DNA Mini Kit following the manufacturer’s blood and body fluid spin protocol (Qiagen). .. The concentration and the purity of the DNA isolated from PBMCs were determined photometrically by reading the absorbance levels at 260 and 280 nm.

    Southern Blot:

    Article Title: A WDR Gene Is a Conserved Member of a Chitin Synthase Gene Cluster and Influences the Cell Wall in Aspergillus nidulans
    Article Snippet: .. Southern Blotting and PCR of Genomic DNA Genomic DNA was extracted using the Qiagen DNeasy Mini Kit (Qiagen, Leusden, The Netherlands), analyzed for integrity by agarose gel electrophoresis and quantified using a NanoDrop ND-1000 spectrophotometer (Thermo scientific, Villebon-sur-Yvette, France). .. Ten µg of genomic DNA from the control (SAA.111) and transformed strains were digested with 20 units of BamHI and PstI at 37 °C, then resolved by electrophoresis and transferred to Hybond N+ membranes (GE Healthcare, Piscataway, NJ, USA), as described in [ ].

    Polymerase Chain Reaction:

    Article Title: A WDR Gene Is a Conserved Member of a Chitin Synthase Gene Cluster and Influences the Cell Wall in Aspergillus nidulans
    Article Snippet: .. Southern Blotting and PCR of Genomic DNA Genomic DNA was extracted using the Qiagen DNeasy Mini Kit (Qiagen, Leusden, The Netherlands), analyzed for integrity by agarose gel electrophoresis and quantified using a NanoDrop ND-1000 spectrophotometer (Thermo scientific, Villebon-sur-Yvette, France). .. Ten µg of genomic DNA from the control (SAA.111) and transformed strains were digested with 20 units of BamHI and PstI at 37 °C, then resolved by electrophoresis and transferred to Hybond N+ membranes (GE Healthcare, Piscataway, NJ, USA), as described in [ ].

    Agarose Gel Electrophoresis:

    Article Title: A WDR Gene Is a Conserved Member of a Chitin Synthase Gene Cluster and Influences the Cell Wall in Aspergillus nidulans
    Article Snippet: .. Southern Blotting and PCR of Genomic DNA Genomic DNA was extracted using the Qiagen DNeasy Mini Kit (Qiagen, Leusden, The Netherlands), analyzed for integrity by agarose gel electrophoresis and quantified using a NanoDrop ND-1000 spectrophotometer (Thermo scientific, Villebon-sur-Yvette, France). .. Ten µg of genomic DNA from the control (SAA.111) and transformed strains were digested with 20 units of BamHI and PstI at 37 °C, then resolved by electrophoresis and transferred to Hybond N+ membranes (GE Healthcare, Piscataway, NJ, USA), as described in [ ].

    Spectrophotometry:

    Article Title: A WDR Gene Is a Conserved Member of a Chitin Synthase Gene Cluster and Influences the Cell Wall in Aspergillus nidulans
    Article Snippet: .. Southern Blotting and PCR of Genomic DNA Genomic DNA was extracted using the Qiagen DNeasy Mini Kit (Qiagen, Leusden, The Netherlands), analyzed for integrity by agarose gel electrophoresis and quantified using a NanoDrop ND-1000 spectrophotometer (Thermo scientific, Villebon-sur-Yvette, France). .. Ten µg of genomic DNA from the control (SAA.111) and transformed strains were digested with 20 units of BamHI and PstI at 37 °C, then resolved by electrophoresis and transferred to Hybond N+ membranes (GE Healthcare, Piscataway, NJ, USA), as described in [ ].

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    qiagen genomic dna cfdna 10 ng
    Overview of copy number variations via plasma cell-free <t>DNA</t> analysis in the included patients. (A) copy number variation genome of gallbladder cancer. (B) copy number variation genome of cholangiocarcinoma. (C) Copy number changes of benign biliary lesions. (D) heatmap of copy number variation quantified by chromosome Z-scores for all patients. GC, gallbladder cancer; CC, cholangiocarcinoma; BE, benign lesions.
    Genomic Dna Cfdna 10 Ng, 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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    Qiagen genomic dna
    qAS-PCR of AITL and PTCL-NOS samples. A, Shown are [mut]/([wt]+[mut]) values for each sample. N, mutation negative determined by MiSeq; P, mutation positive determined by MiSeq; Amp, amplified; PLP, periodate/lysine/paraformaldehyde-fixed; <t>FFPE,</t> formalin-fixed/paraffin-embedded. B, Comparison of [mut]/([wt]+[mut]) values by qAS-PCR and mutant allele frequencies as determined by MiSeq for 95 original or whole genome-amplified <t>DNA</t> samples, including 43 AITL and 52 PTCL-NOS. Cut-off values were determined as 1.5×10 −2 for [mut]/([wt]+[mut]) by qAS-PCR and as 0.02 for mutant allele frequencies as determined by MiSeq. C, Comparison of [mut]/([wt]+[mut]) values by qAS-PCR and mutant allele frequencies as determined by MiSeq for 95 DNA samples in a log scales. D, Comparison of [mut]/([wt]+[mut]) values by qAS-PCR and mutant allele frequencies as determined by MiSeq for 13 FFPE PCR-amplicon samples.
    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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    ( A ) Venn diagram shows the differentially methylated genes exposed under each aldehyde exposure. The intersection regions are the number of common differentially methylated genes following exposure to the seven aldehydes. ( B ) Hierarchical clustering of methylated genes that commonly altered <t>DNA</t> methylation in <t>A549</t> cells exposed to the seven aldehydes with a fold-change ≥3.0-fold and p -value
    Dna 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
    https://www.bioz.com/result/dna genomic dna/product/Qiagen
    Average 86 stars, based on 1 article reviews
    Price from $9.99 to $1999.99
    dna genomic dna - by Bioz Stars, 2021-05
    86/100 stars
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    Overview of copy number variations via plasma cell-free DNA analysis in the included patients. (A) copy number variation genome of gallbladder cancer. (B) copy number variation genome of cholangiocarcinoma. (C) Copy number changes of benign biliary lesions. (D) heatmap of copy number variation quantified by chromosome Z-scores for all patients. GC, gallbladder cancer; CC, cholangiocarcinoma; BE, benign lesions.

    Journal: Translational Oncology

    Article Title: Non-invasive detection of biliary tract cancer by low-coverage whole genome sequencing from plasma cell-free DNA: A prospective cohort study

    doi: 10.1016/j.tranon.2020.100908

    Figure Lengend Snippet: Overview of copy number variations via plasma cell-free DNA analysis in the included patients. (A) copy number variation genome of gallbladder cancer. (B) copy number variation genome of cholangiocarcinoma. (C) Copy number changes of benign biliary lesions. (D) heatmap of copy number variation quantified by chromosome Z-scores for all patients. GC, gallbladder cancer; CC, cholangiocarcinoma; BE, benign lesions.

    Article Snippet: DNA was fragmented into an average size of 300 bp (cfDNA without fragmentation), and then 100 ng of fragmented genomic DNA (cfDNA 10 ng) was used for the preparation of sequencing libraries (NEBnext Ultra II).

    Techniques:

    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

    qAS-PCR of AITL and PTCL-NOS samples. A, Shown are [mut]/([wt]+[mut]) values for each sample. N, mutation negative determined by MiSeq; P, mutation positive determined by MiSeq; Amp, amplified; PLP, periodate/lysine/paraformaldehyde-fixed; FFPE, formalin-fixed/paraffin-embedded. B, Comparison of [mut]/([wt]+[mut]) values by qAS-PCR and mutant allele frequencies as determined by MiSeq for 95 original or whole genome-amplified DNA samples, including 43 AITL and 52 PTCL-NOS. Cut-off values were determined as 1.5×10 −2 for [mut]/([wt]+[mut]) by qAS-PCR and as 0.02 for mutant allele frequencies as determined by MiSeq. C, Comparison of [mut]/([wt]+[mut]) values by qAS-PCR and mutant allele frequencies as determined by MiSeq for 95 DNA samples in a log scales. D, Comparison of [mut]/([wt]+[mut]) values by qAS-PCR and mutant allele frequencies as determined by MiSeq for 13 FFPE PCR-amplicon samples.

    Journal: PLoS ONE

    Article Title: Detection of the G17V RHOA Mutation in Angioimmunoblastic T-Cell Lymphoma and Related Lymphomas Using Quantitative Allele-Specific PCR

    doi: 10.1371/journal.pone.0109714

    Figure Lengend Snippet: qAS-PCR of AITL and PTCL-NOS samples. A, Shown are [mut]/([wt]+[mut]) values for each sample. N, mutation negative determined by MiSeq; P, mutation positive determined by MiSeq; Amp, amplified; PLP, periodate/lysine/paraformaldehyde-fixed; FFPE, formalin-fixed/paraffin-embedded. B, Comparison of [mut]/([wt]+[mut]) values by qAS-PCR and mutant allele frequencies as determined by MiSeq for 95 original or whole genome-amplified DNA samples, including 43 AITL and 52 PTCL-NOS. Cut-off values were determined as 1.5×10 −2 for [mut]/([wt]+[mut]) by qAS-PCR and as 0.02 for mutant allele frequencies as determined by MiSeq. C, Comparison of [mut]/([wt]+[mut]) values by qAS-PCR and mutant allele frequencies as determined by MiSeq for 95 DNA samples in a log scales. D, Comparison of [mut]/([wt]+[mut]) values by qAS-PCR and mutant allele frequencies as determined by MiSeq for 13 FFPE PCR-amplicon samples.

    Article Snippet: Genomic DNA was extracted from 13 formalin-fixed/paraffin-embedded (FFPE), 47 periodate/lysine/paraformaldehyde (PLP)-fixed, and 228 fresh frozen specimens, using an FFPE tissue kit (QIAGEN, Hilden, Germany) for FFPE and PLP samples and a Puregene DNA blood kit (QIAGEN) for fresh frozen specimens, according to manufacturer’s instructions.

    Techniques: Polymerase Chain Reaction, Mutagenesis, Amplification, Plasmid Purification, Formalin-fixed Paraffin-Embedded

    ( A ) Venn diagram shows the differentially methylated genes exposed under each aldehyde exposure. The intersection regions are the number of common differentially methylated genes following exposure to the seven aldehydes. ( B ) Hierarchical clustering of methylated genes that commonly altered DNA methylation in A549 cells exposed to the seven aldehydes with a fold-change ≥3.0-fold and p -value

    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: ( A ) Venn diagram shows the differentially methylated genes exposed under each aldehyde exposure. The intersection regions are the number of common differentially methylated genes following exposure to the seven aldehydes. ( B ) Hierarchical clustering of methylated genes that commonly altered DNA methylation in A549 cells exposed to the seven aldehydes with a fold-change ≥3.0-fold and p -value

    Article Snippet: Preparation of genomic DNA 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: Methylation, DNA Methylation Assay

    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: Preparation of genomic DNA 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