whole genome amplified dna  (Qiagen)

 
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    Name:
    HotStarTaq DNA Polymerase
    Description:
    For highly specific amplification with minimal optimization Kit contents Qiagen HotStarTaq DNA Polymerase 250U 5U L 10 min at 97C 60 min at 94C Half life 2 to 4 kb min at 72C Extension Rate Genomic DNA and cDNA Sample Recombinant Enzyme Extra A Addition PCR Amplification Reaction Type High PCR Specificity For Highly Specific Amplification with Minimal Optimization Includes HotStarTaq DNA Polymerase 10x PCR Buffer 5x Q Solution 25mM MgCl2 Benefits Minimal optimization requirements High PCR specificity Easy handling and room temperature setup
    Catalog Number:
    203203
    Price:
    159
    Category:
    HotStarTaq DNA Polymerase
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    Structured Review

    Qiagen whole genome amplified dna
    HotStarTaq DNA Polymerase
    For highly specific amplification with minimal optimization Kit contents Qiagen HotStarTaq DNA Polymerase 250U 5U L 10 min at 97C 60 min at 94C Half life 2 to 4 kb min at 72C Extension Rate Genomic DNA and cDNA Sample Recombinant Enzyme Extra A Addition PCR Amplification Reaction Type High PCR Specificity For Highly Specific Amplification with Minimal Optimization Includes HotStarTaq DNA Polymerase 10x PCR Buffer 5x Q Solution 25mM MgCl2 Benefits Minimal optimization requirements High PCR specificity Easy handling and room temperature setup
    https://www.bioz.com/result/whole genome amplified dna/product/Qiagen
    Average 90 stars, based on 15406 article reviews
    Price from $9.99 to $1999.99
    whole genome amplified dna - by Bioz Stars, 2020-08
    90/100 stars

    Images

    1) Product Images from "The next generation of target capture technologies - large DNA fragment enrichment and sequencing determines regional genomic variation of high complexity"

    Article Title: The next generation of target capture technologies - large DNA fragment enrichment and sequencing determines regional genomic variation of high complexity

    Journal: BMC Genomics

    doi: 10.1186/s12864-016-2836-6

    Effects of RSE capture primer spacing on target enrichment. a Schematic representation of the distribution of captured genomic DNA copy number obtained around the primer hybridization site, indicated with a red triangle, as measured by qPCRs, placed at increasing distances from the primer hybridization site and shown with black inverted triangles. Gray bars indicate captured random DNA fragments. b qPCR results for RSE extracted material at seven non-contiguous genomic regions, plotted as the copy number ratio of targeted sites (indicated as diamonds) to a common non-targeted region (beta actin). The amount of targeted vs. off-target material decreases within about 10 kbp of the RSE extraction site
    Figure Legend Snippet: Effects of RSE capture primer spacing on target enrichment. a Schematic representation of the distribution of captured genomic DNA copy number obtained around the primer hybridization site, indicated with a red triangle, as measured by qPCRs, placed at increasing distances from the primer hybridization site and shown with black inverted triangles. Gray bars indicate captured random DNA fragments. b qPCR results for RSE extracted material at seven non-contiguous genomic regions, plotted as the copy number ratio of targeted sites (indicated as diamonds) to a common non-targeted region (beta actin). The amount of targeted vs. off-target material decreases within about 10 kbp of the RSE extraction site

    Techniques Used: Hybridization, Real-time Polymerase Chain Reaction

    Effects of RSE capture primer spacing on capture effectiveness. a 46 RSE primers were designed to capture ≈ 700 kbp of genomic sequence for four gene regions. b To examine the effect of RSE primer spacing on capture efficiency, we assumed that the midpoint between the RSE primers would produce the least amount of signal on the array. Each midpoint in the bins shown above was averaged across 20 array primers to account for array probe capture variability. The distance between RSE primers and the averaged array value is presented. c The distances between RSE primers were segregated into bins to show the collective effect of similar RSE primer spacing. As seen in the graph, capture of the material as used here at the midpoint between primers drops rapidly beyond ≈ 15 kbp with little to no capture evident at 25 kbp or greater for the type of genomic DNA used in this study (average length ≈ 20 kbp)
    Figure Legend Snippet: Effects of RSE capture primer spacing on capture effectiveness. a 46 RSE primers were designed to capture ≈ 700 kbp of genomic sequence for four gene regions. b To examine the effect of RSE primer spacing on capture efficiency, we assumed that the midpoint between the RSE primers would produce the least amount of signal on the array. Each midpoint in the bins shown above was averaged across 20 array primers to account for array probe capture variability. The distance between RSE primers and the averaged array value is presented. c The distances between RSE primers were segregated into bins to show the collective effect of similar RSE primer spacing. As seen in the graph, capture of the material as used here at the midpoint between primers drops rapidly beyond ≈ 15 kbp with little to no capture evident at 25 kbp or greater for the type of genomic DNA used in this study (average length ≈ 20 kbp)

    Techniques Used: Sequencing

    2) Product Images from "Abcg2 expression marks tissue-specific stem cells in multiple organs in a mouse progeny tracking model"

    Article Title: Abcg2 expression marks tissue-specific stem cells in multiple organs in a mouse progeny tracking model

    Journal: Stem cells (Dayton, Ohio)

    doi: 10.1002/stem.1002

    Abcg2 expression marks germline stem cells in seminiferous tubules from the testis
    Figure Legend Snippet: Abcg2 expression marks germline stem cells in seminiferous tubules from the testis

    Techniques Used: Expressing

    Reporter gene expression in liver and kidney confirms the expected expression pattern of the Abcg2 CreERT2 allele
    Figure Legend Snippet: Reporter gene expression in liver and kidney confirms the expected expression pattern of the Abcg2 CreERT2 allele

    Techniques Used: Expressing

    Expression of the YFP reporter gene in hematopoietic lineages after Tam treatment confirms activity in Abcg2 + hematopoietic stem cells
    Figure Legend Snippet: Expression of the YFP reporter gene in hematopoietic lineages after Tam treatment confirms activity in Abcg2 + hematopoietic stem cells

    Techniques Used: Expressing, Activity Assay

    Abcg2 expression marks long term stem cell activity in the small intestine
    Figure Legend Snippet: Abcg2 expression marks long term stem cell activity in the small intestine

    Techniques Used: Expressing, Activity Assay

    Targeted insertion of the ires-CreERT2 expression cassette into the Abcg2 locus
    Figure Legend Snippet: Targeted insertion of the ires-CreERT2 expression cassette into the Abcg2 locus

    Techniques Used: Expressing

    3) Product Images from "A novel perspective on MOL-PCR optimization and MAGPIX analysis of in-house multiplex foodborne pathogens detection assay"

    Article Title: A novel perspective on MOL-PCR optimization and MAGPIX analysis of in-house multiplex foodborne pathogens detection assay

    Journal: Scientific Reports

    doi: 10.1038/s41598-019-40035-5

    Impact evaluation of Master Mix used in singleplex PCR. In graph: Elizyme = 2X EliZyme HS Robust MIX (Elisabeth Pharmacon, Czech Republic); Accustart II = AccuStart II PCR ToughMix (QuantaBio, Massachusetts, USA); Amplitaq = AmpliTaq Gold 360 Master Mix (Thermo Fisher Scientific, Massachusetts, USA); OneTaq = OneTaq Hot Start 2X Master Mix with GC Buffer (New England BioLabs, Massachusetts, USA); Platinum = Platinum Hot Start PCR 2X Master Mix (Invitrogen, California, USA); HotStarTaq = HotStarTaq DNA Polymerase (Qiagen, Germany). YE = Y . enterocolitica; TG = T . gondii ; plus sign in legend = positive sample; minus sign = NTC.
    Figure Legend Snippet: Impact evaluation of Master Mix used in singleplex PCR. In graph: Elizyme = 2X EliZyme HS Robust MIX (Elisabeth Pharmacon, Czech Republic); Accustart II = AccuStart II PCR ToughMix (QuantaBio, Massachusetts, USA); Amplitaq = AmpliTaq Gold 360 Master Mix (Thermo Fisher Scientific, Massachusetts, USA); OneTaq = OneTaq Hot Start 2X Master Mix with GC Buffer (New England BioLabs, Massachusetts, USA); Platinum = Platinum Hot Start PCR 2X Master Mix (Invitrogen, California, USA); HotStarTaq = HotStarTaq DNA Polymerase (Qiagen, Germany). YE = Y . enterocolitica; TG = T . gondii ; plus sign in legend = positive sample; minus sign = NTC.

    Techniques Used: Polymerase Chain Reaction, Hot Start PCR

    4) Product Images from "CXCL8 histone H3 acetylation is dysfunctional in airway smooth muscle in asthma: regulation by BET"

    Article Title: CXCL8 histone H3 acetylation is dysfunctional in airway smooth muscle in asthma: regulation by BET

    Journal: American Journal of Physiology - Lung Cellular and Molecular Physiology

    doi: 10.1152/ajplung.00021.2015

    CXCL8 hypersecretion is not associated with differences in DNA methylation. Genomic DNA was isolated from ASM cells from 3 asthmatic and 3 nonasthmatic individuals and bisulfite converted. Regions of DNA containing CpG sites were PCR amplified and pyrosequenced. A : schematic showing the position of the 8 CXCL8 CpG sites, the PCR primers (gray arrows), and sequencing primers (black arrows). B : percent methylation of the individual CpG sites in ASM cells from both asthmatic and nonasthmatic individuals.
    Figure Legend Snippet: CXCL8 hypersecretion is not associated with differences in DNA methylation. Genomic DNA was isolated from ASM cells from 3 asthmatic and 3 nonasthmatic individuals and bisulfite converted. Regions of DNA containing CpG sites were PCR amplified and pyrosequenced. A : schematic showing the position of the 8 CXCL8 CpG sites, the PCR primers (gray arrows), and sequencing primers (black arrows). B : percent methylation of the individual CpG sites in ASM cells from both asthmatic and nonasthmatic individuals.

    Techniques Used: DNA Methylation Assay, Isolation, Polymerase Chain Reaction, Amplification, Sequencing, Methylation

    5) Product Images from "TRPV1 activity and substance P release are required for corneal cold nociception"

    Article Title: TRPV1 activity and substance P release are required for corneal cold nociception

    Journal: Nature Communications

    doi: 10.1038/s41467-019-13536-0

    Substance P release is required for corneal cold nociception. a The expression of neuropeptides in mouse TRPM8 + trigeminal ganglionic (TG) neurons based on single-cell RNA-seq data. Each dot represents a single TRPM8 + neuron. Full dataset and methods are available in Nguyen et al. 25 . b Single-cell RT-PCR using intron-spanning primers was performed on individual TRPM8-EGFPf sensory neurons that project to the cornea. All TRPM8 + /TRPV1 + neurons express substance P ( Tac1 ), while fewer TRPM8 + / TRPV1 - neurons express Tac1 . Negative control (−): No reverse transcription reaction on RNA sample from whole TG. Positive control (TG): cDNA from whole TG. c Cold treatments (bath temperature drops from 32 to15 °C) promote the release of substance P from dissociated trigeminal neurons, as revealed by ELISA assays. TRPV1 antagonist AMG9810 (AMG, 300 nM, 3 min pre-treatment before cold stimulations) suppressed the release of substance P, compared with the vehicle control (0.0006% DMSO). Cold-associated release of substance P was also suppressed by pre-desensitization of TRPM8 + neurons using TRPM8 agonist cryosim-3 (10 µM). d Both the reflex blinking and eye closing responses to air flow at 13 °C were significantly reduced in Tac1 −/− mice, compared with WT controls ( n = 5 mice/group). e – f NK1 antagonist alleviates cold nociception. The reflex blinking and eye closing responses to cold (air flow at 13 °C) and cryosim-3 (0.1 nmol in 1 μL) were significantly reduced 30 min after intracisternal injection of NK1 antagonist L733,060 hydrochloride (10 µg in 5 µL, n = 5 mice), compared with the vehicle-treated group (0.9% NaCl, n = 5 mice). g Model for neural pathways encoding corneal cold nociception and allodynia. SP: substance P. Data are expressed as mean ± s.e.m. Statistical analysis by two tailed Student’s t -test. * P
    Figure Legend Snippet: Substance P release is required for corneal cold nociception. a The expression of neuropeptides in mouse TRPM8 + trigeminal ganglionic (TG) neurons based on single-cell RNA-seq data. Each dot represents a single TRPM8 + neuron. Full dataset and methods are available in Nguyen et al. 25 . b Single-cell RT-PCR using intron-spanning primers was performed on individual TRPM8-EGFPf sensory neurons that project to the cornea. All TRPM8 + /TRPV1 + neurons express substance P ( Tac1 ), while fewer TRPM8 + / TRPV1 - neurons express Tac1 . Negative control (−): No reverse transcription reaction on RNA sample from whole TG. Positive control (TG): cDNA from whole TG. c Cold treatments (bath temperature drops from 32 to15 °C) promote the release of substance P from dissociated trigeminal neurons, as revealed by ELISA assays. TRPV1 antagonist AMG9810 (AMG, 300 nM, 3 min pre-treatment before cold stimulations) suppressed the release of substance P, compared with the vehicle control (0.0006% DMSO). Cold-associated release of substance P was also suppressed by pre-desensitization of TRPM8 + neurons using TRPM8 agonist cryosim-3 (10 µM). d Both the reflex blinking and eye closing responses to air flow at 13 °C were significantly reduced in Tac1 −/− mice, compared with WT controls ( n = 5 mice/group). e – f NK1 antagonist alleviates cold nociception. The reflex blinking and eye closing responses to cold (air flow at 13 °C) and cryosim-3 (0.1 nmol in 1 μL) were significantly reduced 30 min after intracisternal injection of NK1 antagonist L733,060 hydrochloride (10 µg in 5 µL, n = 5 mice), compared with the vehicle-treated group (0.9% NaCl, n = 5 mice). g Model for neural pathways encoding corneal cold nociception and allodynia. SP: substance P. Data are expressed as mean ± s.e.m. Statistical analysis by two tailed Student’s t -test. * P

    Techniques Used: Expressing, RNA Sequencing Assay, Reverse Transcription Polymerase Chain Reaction, Negative Control, Positive Control, Enzyme-linked Immunosorbent Assay, Flow Cytometry, Mouse Assay, Injection, Two Tailed Test

    6) Product Images from "Touchdown Enzyme Time Release-PCR for Detection and Identification of Chlamydia trachomatis, C. pneumoniae, and C. psittaci Using the 16S and 16S-23S Spacer rRNA Genes"

    Article Title: Touchdown Enzyme Time Release-PCR for Detection and Identification of Chlamydia trachomatis, C. pneumoniae, and C. psittaci Using the 16S and 16S-23S Spacer rRNA Genes

    Journal: Journal of Clinical Microbiology

    doi:

    Multiplex TETR-PCR products obtained for Chlamydia species with species-specific primer sets CTR 70/71, CPN 90/91, and CPS 100/101 targeting the 16S and 16S-23S spacer rRNA genes. One IFU per PCR was tested i ndividually and in combinations. Base-pair sizes of weight markers (wm) and PCR products are indicated in the margins. DNA from C. trachomatis VR 348 serovar E, C. pneumoniae BAL 37, and C. psittaci SM006 was amplified.
    Figure Legend Snippet: Multiplex TETR-PCR products obtained for Chlamydia species with species-specific primer sets CTR 70/71, CPN 90/91, and CPS 100/101 targeting the 16S and 16S-23S spacer rRNA genes. One IFU per PCR was tested i ndividually and in combinations. Base-pair sizes of weight markers (wm) and PCR products are indicated in the margins. DNA from C. trachomatis VR 348 serovar E, C. pneumoniae BAL 37, and C. psittaci SM006 was amplified.

    Techniques Used: Multiplex Assay, Polymerase Chain Reaction, Amplification

    7) Product Images from "Development of a genus-specific next generation sequencing approach for sensitive and quantitative determination of the Legionella microbiome in freshwater systems"

    Article Title: Development of a genus-specific next generation sequencing approach for sensitive and quantitative determination of the Legionella microbiome in freshwater systems

    Journal: BMC Microbiology

    doi: 10.1186/s12866-017-0987-5

    Sequencing error rate distribution. a) Error rate distribution along the full-length fragment (421 bp) after analysis of 15,000 reads of L. pneumophila amplified with HotStarTaq ( open blue circles ) and KAPA HiFi DNA polymerases ( red open circles ). LOESS curves illustrate the reduced error rate with KAPA HiFi polymerase and the higher error rate in fragment covered by reverse reads. b) Comparison of error rate per base position with HotStarTaq and KAPA HiFi enzymes. A linear regression model explains the relationship between the two variables. Coefficient of determination (R 2 ) of 0.73
    Figure Legend Snippet: Sequencing error rate distribution. a) Error rate distribution along the full-length fragment (421 bp) after analysis of 15,000 reads of L. pneumophila amplified with HotStarTaq ( open blue circles ) and KAPA HiFi DNA polymerases ( red open circles ). LOESS curves illustrate the reduced error rate with KAPA HiFi polymerase and the higher error rate in fragment covered by reverse reads. b) Comparison of error rate per base position with HotStarTaq and KAPA HiFi enzymes. A linear regression model explains the relationship between the two variables. Coefficient of determination (R 2 ) of 0.73

    Techniques Used: Sequencing, Amplification

    8) Product Images from "A novel perspective on MOL-PCR optimization and MAGPIX analysis of in-house multiplex foodborne pathogens detection assay"

    Article Title: A novel perspective on MOL-PCR optimization and MAGPIX analysis of in-house multiplex foodborne pathogens detection assay

    Journal: Scientific Reports

    doi: 10.1038/s41598-019-40035-5

    Impact evaluation of Master Mix used in singleplex PCR. In graph: Elizyme = 2X EliZyme HS Robust MIX (Elisabeth Pharmacon, Czech Republic); Accustart II = AccuStart II PCR ToughMix (QuantaBio, Massachusetts, USA); Amplitaq = AmpliTaq Gold 360 Master Mix (Thermo Fisher Scientific, Massachusetts, USA); OneTaq = OneTaq Hot Start 2X Master Mix with GC Buffer (New England BioLabs, Massachusetts, USA); Platinum = Platinum Hot Start PCR 2X Master Mix (Invitrogen, California, USA); HotStarTaq = HotStarTaq DNA Polymerase (Qiagen, Germany). YE = Y . enterocolitica; TG = T . gondii ; plus sign in legend = positive sample; minus sign = NTC.
    Figure Legend Snippet: Impact evaluation of Master Mix used in singleplex PCR. In graph: Elizyme = 2X EliZyme HS Robust MIX (Elisabeth Pharmacon, Czech Republic); Accustart II = AccuStart II PCR ToughMix (QuantaBio, Massachusetts, USA); Amplitaq = AmpliTaq Gold 360 Master Mix (Thermo Fisher Scientific, Massachusetts, USA); OneTaq = OneTaq Hot Start 2X Master Mix with GC Buffer (New England BioLabs, Massachusetts, USA); Platinum = Platinum Hot Start PCR 2X Master Mix (Invitrogen, California, USA); HotStarTaq = HotStarTaq DNA Polymerase (Qiagen, Germany). YE = Y . enterocolitica; TG = T . gondii ; plus sign in legend = positive sample; minus sign = NTC.

    Techniques Used: Polymerase Chain Reaction, Hot Start PCR

    9) Product Images from "Small-Molecule Inhibition of HIV pre-mRNA Splicing as a Novel Antiretroviral Therapy to Overcome Drug Resistance"

    Article Title: Small-Molecule Inhibition of HIV pre-mRNA Splicing as a Novel Antiretroviral Therapy to Overcome Drug Resistance

    Journal: PLoS Pathogens

    doi: 10.1371/journal.ppat.0030159

    Comparison of HIV-1 Inhibition in MT2 Cells Treated with AZT or IDC16 and Analysis of Splicing Profiles of Apoptotic Genes in PBMC-Treated Cells (A and B) MT2 cells cultured in a 96-well plate were infected with pNL4.3 at 100 TCID 50 in the absence or presence of IDC16 (A) or AZT (B) for 18 h. Cells were then washed and changed to fresh medium with/without IDC16 or AZT. Half of the culture medium was refreshed each 2 or 4 d in the presence of drugs. The formation of syncytia was scored at the indicated time points. (C) Four ug of total RNA from triplicate of PBMCs untreated (lane Ctl) or treated with IDC16 (lane IDC16) or AZT (lane AZT), was reverse transcribed with Omniscript reverse transcriptase (QIAGEN) using random hexamers and oligo dT and. The mixture was aliquoted in a 96-well plate and subjected to PCR amplification using 0.375U/15 μl of hotStarTaq DNA Polymerase with specific primers (0.3–0.6 μM) using the buffer provided by the manufacturer (QIAGEN). The PCR reaction was carried out in a GeneAmp 9700 PCR system. Following an incubation of 15 min at 95 °C, and 35 cycles of 30 s at 94 °C, 30 s at 55 °C, and 1 min at 72 °C, the reaction was ended with an extension step of 10 min at 72 °C. PCR products were fractionated on a LabChip HT DNA assay station (Caliper) for quantitation and sizing. The full data can be accessed through http://www.lgfus.ca/Tazi/ , username = Tazi, password = sc35. Three examples of genes altered by AZT treatment (HDM2), (BRCA1), and (DATF1) are shown.
    Figure Legend Snippet: Comparison of HIV-1 Inhibition in MT2 Cells Treated with AZT or IDC16 and Analysis of Splicing Profiles of Apoptotic Genes in PBMC-Treated Cells (A and B) MT2 cells cultured in a 96-well plate were infected with pNL4.3 at 100 TCID 50 in the absence or presence of IDC16 (A) or AZT (B) for 18 h. Cells were then washed and changed to fresh medium with/without IDC16 or AZT. Half of the culture medium was refreshed each 2 or 4 d in the presence of drugs. The formation of syncytia was scored at the indicated time points. (C) Four ug of total RNA from triplicate of PBMCs untreated (lane Ctl) or treated with IDC16 (lane IDC16) or AZT (lane AZT), was reverse transcribed with Omniscript reverse transcriptase (QIAGEN) using random hexamers and oligo dT and. The mixture was aliquoted in a 96-well plate and subjected to PCR amplification using 0.375U/15 μl of hotStarTaq DNA Polymerase with specific primers (0.3–0.6 μM) using the buffer provided by the manufacturer (QIAGEN). The PCR reaction was carried out in a GeneAmp 9700 PCR system. Following an incubation of 15 min at 95 °C, and 35 cycles of 30 s at 94 °C, 30 s at 55 °C, and 1 min at 72 °C, the reaction was ended with an extension step of 10 min at 72 °C. PCR products were fractionated on a LabChip HT DNA assay station (Caliper) for quantitation and sizing. The full data can be accessed through http://www.lgfus.ca/Tazi/ , username = Tazi, password = sc35. Three examples of genes altered by AZT treatment (HDM2), (BRCA1), and (DATF1) are shown.

    Techniques Used: Inhibition, Cell Culture, Infection, CTL Assay, Polymerase Chain Reaction, Amplification, Incubation, Quantitation Assay

    10) Product Images from "Epigenetic regulation of the X-chromosomal macrosatellite repeat encoding for the cancer/testis gene CT47"

    Article Title: Epigenetic regulation of the X-chromosomal macrosatellite repeat encoding for the cancer/testis gene CT47

    Journal: European Journal of Human Genetics

    doi: 10.1038/ejhg.2011.150

    Relative abundance of different histone modifications at CT47 in human male (WA14) and female (WA9) pluripotent hESCs and in differentiated hEBs. The relative abundance of H3K4me2, associated with transcriptionally permissive chromatin, is increasing during differentiation in male and female samples. The repressive chromatin mark H3K9me3 is detected at high levels at pluripotent state and slightly decreases after differentiation. H3K27me3, associated with transcriptional repression, is detected in pluripotent state and increasing during differentiation.
    Figure Legend Snippet: Relative abundance of different histone modifications at CT47 in human male (WA14) and female (WA9) pluripotent hESCs and in differentiated hEBs. The relative abundance of H3K4me2, associated with transcriptionally permissive chromatin, is increasing during differentiation in male and female samples. The repressive chromatin mark H3K9me3 is detected at high levels at pluripotent state and slightly decreases after differentiation. H3K27me3, associated with transcriptional repression, is detected in pluripotent state and increasing during differentiation.

    Techniques Used:

    ( a ) Expression levels of CT47 mRNA in different SCLC cell lines relative to the expression in human testis. Commercially available human total testis RNA and RNA isolated from SCLC lines were used for cDNA synthesis under identical conditions. CT47 expression levels are normalized to the expression levels measured in the testis. Different SCLC lines have different, but low levels of CT47 expression compared to the testis. Relative abundance of histone modifications and EZH2 at the CT47 promoter ( b ), exon 3 ( c ) and the distal region in SCLC cell lines ( d ). SCLC cell lines show individual variation in the abundance of different histone modifications. Generally, a loss of the repressive chromatin mark H3K9me3 can be observed in SCLCs. H3K27me3 levels are higher in SCLCs at the promoter and exon 3 region than in LCLs, but lower at the distal region. The relative abundance of the PRC2 component EZH2 responsible for generating H2K27me3 is dramatically reduced in SCLCs compared to LCLs at all region studied. ( e ) DNA methylation levels at CpGs located in the CT47 promoter region in LCL and SCLC samples. The methylation level of seven different CpGs, next to the transcriptional start site of CT47 , was determined by bisulfite sequencing and quantified by ESME program. There is a significant difference between the methylation level of LCLs and SCLCs at every CpG tested ( P
    Figure Legend Snippet: ( a ) Expression levels of CT47 mRNA in different SCLC cell lines relative to the expression in human testis. Commercially available human total testis RNA and RNA isolated from SCLC lines were used for cDNA synthesis under identical conditions. CT47 expression levels are normalized to the expression levels measured in the testis. Different SCLC lines have different, but low levels of CT47 expression compared to the testis. Relative abundance of histone modifications and EZH2 at the CT47 promoter ( b ), exon 3 ( c ) and the distal region in SCLC cell lines ( d ). SCLC cell lines show individual variation in the abundance of different histone modifications. Generally, a loss of the repressive chromatin mark H3K9me3 can be observed in SCLCs. H3K27me3 levels are higher in SCLCs at the promoter and exon 3 region than in LCLs, but lower at the distal region. The relative abundance of the PRC2 component EZH2 responsible for generating H2K27me3 is dramatically reduced in SCLCs compared to LCLs at all region studied. ( e ) DNA methylation levels at CpGs located in the CT47 promoter region in LCL and SCLC samples. The methylation level of seven different CpGs, next to the transcriptional start site of CT47 , was determined by bisulfite sequencing and quantified by ESME program. There is a significant difference between the methylation level of LCLs and SCLCs at every CpG tested ( P

    Techniques Used: Expressing, Isolation, DNA Methylation Assay, Methylation, Methylation Sequencing

    Schematic representation of CT47 macrosatellite array. The CT47 repeat array is localized on Xq24 at coordinates chrX: 119 893 246–119 948 579 according to hg18 assembly. The size of the array varies between 4 and 17 units, each unit being 4.8 kb in size. Chromatin markers were studied in the promoter region of the CT47 gene encoded by each unit (exons are indicated in gray boxes). Genomic locations where relative abundance of different histone modifications were quantified are represented by the black line; A represents ChIP primer set for CT47 promoter, B represents distal primer set located 3.7 kb from the array, C represents ChIP primer set for CT47 exon 3, and D represents the bisulfate primer set.
    Figure Legend Snippet: Schematic representation of CT47 macrosatellite array. The CT47 repeat array is localized on Xq24 at coordinates chrX: 119 893 246–119 948 579 according to hg18 assembly. The size of the array varies between 4 and 17 units, each unit being 4.8 kb in size. Chromatin markers were studied in the promoter region of the CT47 gene encoded by each unit (exons are indicated in gray boxes). Genomic locations where relative abundance of different histone modifications were quantified are represented by the black line; A represents ChIP primer set for CT47 promoter, B represents distal primer set located 3.7 kb from the array, C represents ChIP primer set for CT47 exon 3, and D represents the bisulfate primer set.

    Techniques Used: Chromatin Immunoprecipitation

    11) Product Images from "A novel perspective on MOL-PCR optimization and MAGPIX analysis of in-house multiplex foodborne pathogens detection assay"

    Article Title: A novel perspective on MOL-PCR optimization and MAGPIX analysis of in-house multiplex foodborne pathogens detection assay

    Journal: Scientific Reports

    doi: 10.1038/s41598-019-40035-5

    Impact evaluation of Master Mix used in singleplex PCR. In graph: Elizyme = 2X EliZyme HS Robust MIX (Elisabeth Pharmacon, Czech Republic); Accustart II = AccuStart II PCR ToughMix (QuantaBio, Massachusetts, USA); Amplitaq = AmpliTaq Gold 360 Master Mix (Thermo Fisher Scientific, Massachusetts, USA); OneTaq = OneTaq Hot Start 2X Master Mix with GC Buffer (New England BioLabs, Massachusetts, USA); Platinum = Platinum Hot Start PCR 2X Master Mix (Invitrogen, California, USA); HotStarTaq = HotStarTaq DNA Polymerase (Qiagen, Germany). YE = Y . enterocolitica; TG = T . gondii ; plus sign in legend = positive sample; minus sign = NTC.
    Figure Legend Snippet: Impact evaluation of Master Mix used in singleplex PCR. In graph: Elizyme = 2X EliZyme HS Robust MIX (Elisabeth Pharmacon, Czech Republic); Accustart II = AccuStart II PCR ToughMix (QuantaBio, Massachusetts, USA); Amplitaq = AmpliTaq Gold 360 Master Mix (Thermo Fisher Scientific, Massachusetts, USA); OneTaq = OneTaq Hot Start 2X Master Mix with GC Buffer (New England BioLabs, Massachusetts, USA); Platinum = Platinum Hot Start PCR 2X Master Mix (Invitrogen, California, USA); HotStarTaq = HotStarTaq DNA Polymerase (Qiagen, Germany). YE = Y . enterocolitica; TG = T . gondii ; plus sign in legend = positive sample; minus sign = NTC.

    Techniques Used: Polymerase Chain Reaction, Hot Start PCR

    12) Product Images from "Development of a genus-specific next generation sequencing approach for sensitive and quantitative determination of the Legionella microbiome in freshwater systems"

    Article Title: Development of a genus-specific next generation sequencing approach for sensitive and quantitative determination of the Legionella microbiome in freshwater systems

    Journal: BMC Microbiology

    doi: 10.1186/s12866-017-0987-5

    Sequencing error rate distribution. a) Error rate distribution along the full-length fragment (421 bp) after analysis of 15,000 reads of L. pneumophila amplified with HotStarTaq ( open blue circles ) and KAPA HiFi DNA polymerases ( red open circles ). LOESS curves illustrate the reduced error rate with KAPA HiFi polymerase and the higher error rate in fragment covered by reverse reads. b) Comparison of error rate per base position with HotStarTaq and KAPA HiFi enzymes. A linear regression model explains the relationship between the two variables. Coefficient of determination (R 2 ) of 0.73
    Figure Legend Snippet: Sequencing error rate distribution. a) Error rate distribution along the full-length fragment (421 bp) after analysis of 15,000 reads of L. pneumophila amplified with HotStarTaq ( open blue circles ) and KAPA HiFi DNA polymerases ( red open circles ). LOESS curves illustrate the reduced error rate with KAPA HiFi polymerase and the higher error rate in fragment covered by reverse reads. b) Comparison of error rate per base position with HotStarTaq and KAPA HiFi enzymes. A linear regression model explains the relationship between the two variables. Coefficient of determination (R 2 ) of 0.73

    Techniques Used: Sequencing, Amplification

    13) Product Images from "Development of a genus-specific next generation sequencing approach for sensitive and quantitative determination of the Legionella microbiome in freshwater systems"

    Article Title: Development of a genus-specific next generation sequencing approach for sensitive and quantitative determination of the Legionella microbiome in freshwater systems

    Journal: BMC Microbiology

    doi: 10.1186/s12866-017-0987-5

    Sequencing error rate distribution. a) Error rate distribution along the full-length fragment (421 bp) after analysis of 15,000 reads of L. pneumophila amplified with HotStarTaq ( open blue circles ) and KAPA HiFi DNA polymerases ( red open circles ). LOESS curves illustrate the reduced error rate with KAPA HiFi polymerase and the higher error rate in fragment covered by reverse reads. b) Comparison of error rate per base position with HotStarTaq and KAPA HiFi enzymes. A linear regression model explains the relationship between the two variables. Coefficient of determination (R 2 ) of 0.73
    Figure Legend Snippet: Sequencing error rate distribution. a) Error rate distribution along the full-length fragment (421 bp) after analysis of 15,000 reads of L. pneumophila amplified with HotStarTaq ( open blue circles ) and KAPA HiFi DNA polymerases ( red open circles ). LOESS curves illustrate the reduced error rate with KAPA HiFi polymerase and the higher error rate in fragment covered by reverse reads. b) Comparison of error rate per base position with HotStarTaq and KAPA HiFi enzymes. A linear regression model explains the relationship between the two variables. Coefficient of determination (R 2 ) of 0.73

    Techniques Used: Sequencing, Amplification

    14) Product Images from "Enhancers compete with a long non-coding RNA for regulation of the Kcnq1 domain"

    Article Title: Enhancers compete with a long non-coding RNA for regulation of the Kcnq1 domain

    Journal: Nucleic Acids Research

    doi: 10.1093/nar/gku1324

    The Kcnq1ot1 ncRNA is spliced. ( A ) Long RNA-sequencing data showing strand-specific expression from ENCODE, visualized in the UCSC genome browser. Minus strand codes for the Kcnq1ot1 lncRNA; the plus strand codes for Kcnq1 . Higher Kcnq1 expression correlates with lower and more discontinuous Kcnq1ot1 expression. ( B ) Confirmation of predicted splicing events for the Kcnq1ot1 lncRNA. Top, schematic of the Kcnq1ot coding region and the splicing variants (not to scale). cDNA from neonatal heart was used as substrates for qPCR. Shown is a 2% agarose gel with PCR products from neonatal heart. Primer sets 1F-2R and 2F-3R are designed to detect the junctions between exon 1 and 2 (190 bp), and 2 and 3 (369 bp), respectively. Primers 1F-i1R detect the unspliced version (297 bp). Exons 1 and 2 are 247 and 1043 bp, respectively.
    Figure Legend Snippet: The Kcnq1ot1 ncRNA is spliced. ( A ) Long RNA-sequencing data showing strand-specific expression from ENCODE, visualized in the UCSC genome browser. Minus strand codes for the Kcnq1ot1 lncRNA; the plus strand codes for Kcnq1 . Higher Kcnq1 expression correlates with lower and more discontinuous Kcnq1ot1 expression. ( B ) Confirmation of predicted splicing events for the Kcnq1ot1 lncRNA. Top, schematic of the Kcnq1ot coding region and the splicing variants (not to scale). cDNA from neonatal heart was used as substrates for qPCR. Shown is a 2% agarose gel with PCR products from neonatal heart. Primer sets 1F-2R and 2F-3R are designed to detect the junctions between exon 1 and 2 (190 bp), and 2 and 3 (369 bp), respectively. Primers 1F-i1R detect the unspliced version (297 bp). Exons 1 and 2 are 247 and 1043 bp, respectively.

    Techniques Used: RNA Sequencing Assay, Expressing, Real-time Polymerase Chain Reaction, Agarose Gel Electrophoresis, Polymerase Chain Reaction

    15) Product Images from "The next generation of target capture technologies - large DNA fragment enrichment and sequencing determines regional genomic variation of high complexity"

    Article Title: The next generation of target capture technologies - large DNA fragment enrichment and sequencing determines regional genomic variation of high complexity

    Journal: BMC Genomics

    doi: 10.1186/s12864-016-2836-6

    Effects of RSE capture primer spacing on target enrichment. a Schematic representation of the distribution of captured genomic DNA copy number obtained around the primer hybridization site, indicated with a red triangle, as measured by qPCRs, placed at increasing distances from the primer hybridization site and shown with black inverted triangles. Gray bars indicate captured random DNA fragments. b qPCR results for RSE extracted material at seven non-contiguous genomic regions, plotted as the copy number ratio of targeted sites (indicated as diamonds) to a common non-targeted region (beta actin). The amount of targeted vs. off-target material decreases within about 10 kbp of the RSE extraction site
    Figure Legend Snippet: Effects of RSE capture primer spacing on target enrichment. a Schematic representation of the distribution of captured genomic DNA copy number obtained around the primer hybridization site, indicated with a red triangle, as measured by qPCRs, placed at increasing distances from the primer hybridization site and shown with black inverted triangles. Gray bars indicate captured random DNA fragments. b qPCR results for RSE extracted material at seven non-contiguous genomic regions, plotted as the copy number ratio of targeted sites (indicated as diamonds) to a common non-targeted region (beta actin). The amount of targeted vs. off-target material decreases within about 10 kbp of the RSE extraction site

    Techniques Used: Hybridization, Real-time Polymerase Chain Reaction

    Effects of RSE capture primer spacing on capture effectiveness. a 46 RSE primers were designed to capture ≈ 700 kbp of genomic sequence for four gene regions. b To examine the effect of RSE primer spacing on capture efficiency, we assumed that the midpoint between the RSE primers would produce the least amount of signal on the array. Each midpoint in the bins shown above was averaged across 20 array primers to account for array probe capture variability. The distance between RSE primers and the averaged array value is presented. c The distances between RSE primers were segregated into bins to show the collective effect of similar RSE primer spacing. As seen in the graph, capture of the material as used here at the midpoint between primers drops rapidly beyond ≈ 15 kbp with little to no capture evident at 25 kbp or greater for the type of genomic DNA used in this study (average length ≈ 20 kbp)
    Figure Legend Snippet: Effects of RSE capture primer spacing on capture effectiveness. a 46 RSE primers were designed to capture ≈ 700 kbp of genomic sequence for four gene regions. b To examine the effect of RSE primer spacing on capture efficiency, we assumed that the midpoint between the RSE primers would produce the least amount of signal on the array. Each midpoint in the bins shown above was averaged across 20 array primers to account for array probe capture variability. The distance between RSE primers and the averaged array value is presented. c The distances between RSE primers were segregated into bins to show the collective effect of similar RSE primer spacing. As seen in the graph, capture of the material as used here at the midpoint between primers drops rapidly beyond ≈ 15 kbp with little to no capture evident at 25 kbp or greater for the type of genomic DNA used in this study (average length ≈ 20 kbp)

    Techniques Used: Sequencing

    16) Product Images from "Specific serum and CSF microRNA profiles distinguish sporadic behavioural variant of frontotemporal dementia compared with Alzheimer patients and cognitively healthy controls"

    Article Title: Specific serum and CSF microRNA profiles distinguish sporadic behavioural variant of frontotemporal dementia compared with Alzheimer patients and cognitively healthy controls

    Journal: PLoS ONE

    doi: 10.1371/journal.pone.0197329

    Differentially expressed miRNAs in bvFTD, AD and cognitively healthy control cases detected in CSF and serum. Expression levels of n = 96 circulating miRNAs were measured in CSF (n = 140) and serum (n = 131) samples from bvFTD (n = 48/48) and AD patients (n = 48/47) as well as healthy controls (n = 44/38) and compared using MANOVA and ROC curves. Displayed are signals with significantly different expression levels after multiple comparisons detected in (A) CSF: group comparisons of AD, bvFTD and healthy controls with (B-C) corresponding ROC curves and (D) serum: group comparisons of AD, bvFTD and healthy controls (up- and downregulated miRNAs) with (E-F) corresponding ROC curves, (G) serum: group comparisons of AD, bvFTD and healthy controls (only upregulated miRNAs) with (H-I) corresponding ROC curves and (J) serum: group comparisons of AD, bvFTD and healthy controls (only downregulated miRNAs) with (K-L) corresponding ROC curves. Expression ratio: ddCt = mean dCt AD or bvFTD − mean dCt HC . Dotted lines indicate ddCt cut-off of |0.58|. Error bars indicate mean ± SEM. BH = Benjamini-Hochberg.
    Figure Legend Snippet: Differentially expressed miRNAs in bvFTD, AD and cognitively healthy control cases detected in CSF and serum. Expression levels of n = 96 circulating miRNAs were measured in CSF (n = 140) and serum (n = 131) samples from bvFTD (n = 48/48) and AD patients (n = 48/47) as well as healthy controls (n = 44/38) and compared using MANOVA and ROC curves. Displayed are signals with significantly different expression levels after multiple comparisons detected in (A) CSF: group comparisons of AD, bvFTD and healthy controls with (B-C) corresponding ROC curves and (D) serum: group comparisons of AD, bvFTD and healthy controls (up- and downregulated miRNAs) with (E-F) corresponding ROC curves, (G) serum: group comparisons of AD, bvFTD and healthy controls (only upregulated miRNAs) with (H-I) corresponding ROC curves and (J) serum: group comparisons of AD, bvFTD and healthy controls (only downregulated miRNAs) with (K-L) corresponding ROC curves. Expression ratio: ddCt = mean dCt AD or bvFTD − mean dCt HC . Dotted lines indicate ddCt cut-off of |0.58|. Error bars indicate mean ± SEM. BH = Benjamini-Hochberg.

    Techniques Used: Expressing

    Correlations of miRNA expression levels in serum with CSF protein biomarkers. Depicted are normalized expression levels dCt = Ct ( Ct mean RefmiR − Ct miR ) of (A) miRNAs from the original 3-factor model that correlated with Factor 1 vs CSF levels of amylod-beta 1-42 in the control group and (B) miRNAs from the original 3-factor model that correlated with Factor 2 vs CSF levels of pNfH in the bvFTD group. pNfH = phosphorylated neurofilament heavy chain.
    Figure Legend Snippet: Correlations of miRNA expression levels in serum with CSF protein biomarkers. Depicted are normalized expression levels dCt = Ct ( Ct mean RefmiR − Ct miR ) of (A) miRNAs from the original 3-factor model that correlated with Factor 1 vs CSF levels of amylod-beta 1-42 in the control group and (B) miRNAs from the original 3-factor model that correlated with Factor 2 vs CSF levels of pNfH in the bvFTD group. pNfH = phosphorylated neurofilament heavy chain.

    Techniques Used: Expressing

    17) Product Images from "Development of a genus-specific next generation sequencing approach for sensitive and quantitative determination of the Legionella microbiome in freshwater systems"

    Article Title: Development of a genus-specific next generation sequencing approach for sensitive and quantitative determination of the Legionella microbiome in freshwater systems

    Journal: BMC Microbiology

    doi: 10.1186/s12866-017-0987-5

    Sequencing error rate distribution. a) Error rate distribution along the full-length fragment (421 bp) after analysis of 15,000 reads of L. pneumophila amplified with HotStarTaq ( open blue circles ) and KAPA HiFi DNA polymerases ( red open circles ). LOESS curves illustrate the reduced error rate with KAPA HiFi polymerase and the higher error rate in fragment covered by reverse reads. b) Comparison of error rate per base position with HotStarTaq and KAPA HiFi enzymes. A linear regression model explains the relationship between the two variables. Coefficient of determination (R 2 ) of 0.73
    Figure Legend Snippet: Sequencing error rate distribution. a) Error rate distribution along the full-length fragment (421 bp) after analysis of 15,000 reads of L. pneumophila amplified with HotStarTaq ( open blue circles ) and KAPA HiFi DNA polymerases ( red open circles ). LOESS curves illustrate the reduced error rate with KAPA HiFi polymerase and the higher error rate in fragment covered by reverse reads. b) Comparison of error rate per base position with HotStarTaq and KAPA HiFi enzymes. A linear regression model explains the relationship between the two variables. Coefficient of determination (R 2 ) of 0.73

    Techniques Used: Sequencing, Amplification

    Related Articles

    Amplification:

    Article Title: Small-Molecule Inhibition of HIV pre-mRNA Splicing as a Novel Antiretroviral Therapy to Overcome Drug Resistance
    Article Snippet: .. The mixture was aliquoted in a 96-well plate and subjected to PCR amplification using 0.375 U/15 μl of hotStarTaq DNA Polymerase with specific primers (0.3–0.6 μM) using the buffer provided by the manufacturer (QIAGEN). .. The PCR reaction was carried out in a GeneAmp 9700 PCR system.

    Article Title: Development of a genus-specific next generation sequencing approach for sensitive and quantitative determination of the Legionella microbiome in freshwater systems
    Article Snippet: .. The 16S rRNA sequences had an average substitution rate per base of 0.322% ± 0.277%, which represents a significant accuracy improvement to libraries amplified by HotStarTaq DNA polymerase (0.383% ± 0.275%) (T -test, P < 0.05). ..

    Hot Start PCR:

    Article Title: A novel perspective on MOL-PCR optimization and MAGPIX analysis of in-house multiplex foodborne pathogens detection assay
    Article Snippet: .. Several master mixes were tested in the optimization experiments, namely AccuStart II PCR ToughMix (QuantaBio, Massachusetts, USA), AmpliTaq Gold 360 Master Mix (Thermo Fisher Scientific, Massachusetts, USA), OneTaq Hot Start 2X Master Mix with GC Buffer (New England BioLabs, Massachusetts, USA), Platinum Hot Start PCR Master Mix (Invitrogen, California, USA), and HotStarTaq DNA Polymerase (Qiagen, Germany). .. Each singleplex PCR reaction and thermal cycling protocol was run according to the relevant instructions from the manufacturer.

    Concentration Assay:

    Article Title: Development of a genus-specific next generation sequencing approach for sensitive and quantitative determination of the Legionella microbiome in freshwater systems
    Article Snippet: .. Additionally, the mix contained 0.1 mM concentration of each dNTP (Bioline, Luckenwalde, Germany), 0.75 mM MgCl2 , 1X PCR reaction buffer, 0.03 U of HotStarTaq DNA polymerase (Qiagen, Hilden, Germany), 0.4 μM of each primer. ..

    other:

    Article Title: A novel perspective on MOL-PCR optimization and MAGPIX analysis of in-house multiplex foodborne pathogens detection assay
    Article Snippet: HotStarTaq DNA Polymerase, on the other hand, reached the highest MFI values.

    Article Title: A novel perspective on MOL-PCR optimization and MAGPIX analysis of in-house multiplex foodborne pathogens detection assay
    Article Snippet: In order to find a balance, the performance of six different master mixes was tested (Fig. ), including the previously utilized HotStarTaq DNA Polymerase – and the upgraded AmpliTaq Gold 360 Master Mix , .

    Polymerase Chain Reaction:

    Article Title: Development of a genus-specific next generation sequencing approach for sensitive and quantitative determination of the Legionella microbiome in freshwater systems
    Article Snippet: .. Additionally, the mix contained 0.1 mM concentration of each dNTP (Bioline, Luckenwalde, Germany), 0.75 mM MgCl2 , 1X PCR reaction buffer, 0.03 U of HotStarTaq DNA polymerase (Qiagen, Hilden, Germany), 0.4 μM of each primer. ..

    Article Title: CXCL8 histone H3 acetylation is dysfunctional in airway smooth muscle in asthma: regulation by BET
    Article Snippet: .. PCRs were performed with the HotStarTaq DNA polymerase PCR kit (Qiagen) under the following conditions: 95°C 5 min; 45 cycles of 94°C 30 s; 56°C 30 s; 72°C 30 s; finally 72°C 10 min, except the PCR primers for CpGs 7 and 8, which required an annealing temperature of 52.6°C. .. Amplification success was assessed by agarose gel electrophoresis and the resulting products were pyrosequenced with the Pyromark Q24 System (Qiagen).

    Article Title: Small-Molecule Inhibition of HIV pre-mRNA Splicing as a Novel Antiretroviral Therapy to Overcome Drug Resistance
    Article Snippet: .. The mixture was aliquoted in a 96-well plate and subjected to PCR amplification using 0.375 U/15 μl of hotStarTaq DNA Polymerase with specific primers (0.3–0.6 μM) using the buffer provided by the manufacturer (QIAGEN). .. The PCR reaction was carried out in a GeneAmp 9700 PCR system.

    Article Title: A novel perspective on MOL-PCR optimization and MAGPIX analysis of in-house multiplex foodborne pathogens detection assay
    Article Snippet: .. Several master mixes were tested in the optimization experiments, namely AccuStart II PCR ToughMix (QuantaBio, Massachusetts, USA), AmpliTaq Gold 360 Master Mix (Thermo Fisher Scientific, Massachusetts, USA), OneTaq Hot Start 2X Master Mix with GC Buffer (New England BioLabs, Massachusetts, USA), Platinum Hot Start PCR Master Mix (Invitrogen, California, USA), and HotStarTaq DNA Polymerase (Qiagen, Germany). .. Each singleplex PCR reaction and thermal cycling protocol was run according to the relevant instructions from the manufacturer.

    T-Test:

    Article Title: Development of a genus-specific next generation sequencing approach for sensitive and quantitative determination of the Legionella microbiome in freshwater systems
    Article Snippet: .. The 16S rRNA sequences had an average substitution rate per base of 0.322% ± 0.277%, which represents a significant accuracy improvement to libraries amplified by HotStarTaq DNA polymerase (0.383% ± 0.275%) (T -test, P < 0.05). ..

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    Qiagen hotstartaq dna polymerase
    Impact evaluation of Master Mix used in singleplex PCR. In graph: Elizyme = 2X EliZyme HS Robust MIX (Elisabeth Pharmacon, Czech Republic); Accustart II = AccuStart II PCR ToughMix (QuantaBio, Massachusetts, USA); Amplitaq = AmpliTaq Gold 360 Master Mix (Thermo Fisher Scientific, Massachusetts, USA); OneTaq = OneTaq Hot Start 2X Master Mix with GC Buffer (New England BioLabs, Massachusetts, USA); Platinum = Platinum Hot Start PCR 2X Master Mix (Invitrogen, California, USA); <t>HotStarTaq</t> = HotStarTaq <t>DNA</t> Polymerase (Qiagen, Germany). YE = Y . enterocolitica; TG = T . gondii ; plus sign in legend = positive sample; minus sign = NTC.
    Hotstartaq Dna Polymerase, supplied by Qiagen, used in various techniques. Bioz Stars score: 99/100, based on 753 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Impact evaluation of Master Mix used in singleplex PCR. In graph: Elizyme = 2X EliZyme HS Robust MIX (Elisabeth Pharmacon, Czech Republic); Accustart II = AccuStart II PCR ToughMix (QuantaBio, Massachusetts, USA); Amplitaq = AmpliTaq Gold 360 Master Mix (Thermo Fisher Scientific, Massachusetts, USA); OneTaq = OneTaq Hot Start 2X Master Mix with GC Buffer (New England BioLabs, Massachusetts, USA); Platinum = Platinum Hot Start PCR 2X Master Mix (Invitrogen, California, USA); HotStarTaq = HotStarTaq DNA Polymerase (Qiagen, Germany). YE = Y . enterocolitica; TG = T . gondii ; plus sign in legend = positive sample; minus sign = NTC.

    Journal: Scientific Reports

    Article Title: A novel perspective on MOL-PCR optimization and MAGPIX analysis of in-house multiplex foodborne pathogens detection assay

    doi: 10.1038/s41598-019-40035-5

    Figure Lengend Snippet: Impact evaluation of Master Mix used in singleplex PCR. In graph: Elizyme = 2X EliZyme HS Robust MIX (Elisabeth Pharmacon, Czech Republic); Accustart II = AccuStart II PCR ToughMix (QuantaBio, Massachusetts, USA); Amplitaq = AmpliTaq Gold 360 Master Mix (Thermo Fisher Scientific, Massachusetts, USA); OneTaq = OneTaq Hot Start 2X Master Mix with GC Buffer (New England BioLabs, Massachusetts, USA); Platinum = Platinum Hot Start PCR 2X Master Mix (Invitrogen, California, USA); HotStarTaq = HotStarTaq DNA Polymerase (Qiagen, Germany). YE = Y . enterocolitica; TG = T . gondii ; plus sign in legend = positive sample; minus sign = NTC.

    Article Snippet: In order to find a balance, the performance of six different master mixes was tested (Fig. ), including the previously utilized HotStarTaq DNA Polymerase – and the upgraded AmpliTaq Gold 360 Master Mix , .

    Techniques: Polymerase Chain Reaction, Hot Start PCR

    CXCL8 hypersecretion is not associated with differences in DNA methylation. Genomic DNA was isolated from ASM cells from 3 asthmatic and 3 nonasthmatic individuals and bisulfite converted. Regions of DNA containing CpG sites were PCR amplified and pyrosequenced. A : schematic showing the position of the 8 CXCL8 CpG sites, the PCR primers (gray arrows), and sequencing primers (black arrows). B : percent methylation of the individual CpG sites in ASM cells from both asthmatic and nonasthmatic individuals.

    Journal: American Journal of Physiology - Lung Cellular and Molecular Physiology

    Article Title: CXCL8 histone H3 acetylation is dysfunctional in airway smooth muscle in asthma: regulation by BET

    doi: 10.1152/ajplung.00021.2015

    Figure Lengend Snippet: CXCL8 hypersecretion is not associated with differences in DNA methylation. Genomic DNA was isolated from ASM cells from 3 asthmatic and 3 nonasthmatic individuals and bisulfite converted. Regions of DNA containing CpG sites were PCR amplified and pyrosequenced. A : schematic showing the position of the 8 CXCL8 CpG sites, the PCR primers (gray arrows), and sequencing primers (black arrows). B : percent methylation of the individual CpG sites in ASM cells from both asthmatic and nonasthmatic individuals.

    Article Snippet: PCRs were performed with the HotStarTaq DNA polymerase PCR kit (Qiagen) under the following conditions: 95°C 5 min; 45 cycles of 94°C 30 s; 56°C 30 s; 72°C 30 s; finally 72°C 10 min, except the PCR primers for CpGs 7 and 8, which required an annealing temperature of 52.6°C.

    Techniques: DNA Methylation Assay, Isolation, Polymerase Chain Reaction, Amplification, Sequencing, Methylation

    Multiplex TETR-PCR products obtained for Chlamydia species with species-specific primer sets CTR 70/71, CPN 90/91, and CPS 100/101 targeting the 16S and 16S-23S spacer rRNA genes. One IFU per PCR was tested i ndividually and in combinations. Base-pair sizes of weight markers (wm) and PCR products are indicated in the margins. DNA from C. trachomatis VR 348 serovar E, C. pneumoniae BAL 37, and C. psittaci SM006 was amplified.

    Journal: Journal of Clinical Microbiology

    Article Title: Touchdown Enzyme Time Release-PCR for Detection and Identification of Chlamydia trachomatis, C. pneumoniae, and C. psittaci Using the 16S and 16S-23S Spacer rRNA Genes

    doi:

    Figure Lengend Snippet: Multiplex TETR-PCR products obtained for Chlamydia species with species-specific primer sets CTR 70/71, CPN 90/91, and CPS 100/101 targeting the 16S and 16S-23S spacer rRNA genes. One IFU per PCR was tested i ndividually and in combinations. Base-pair sizes of weight markers (wm) and PCR products are indicated in the margins. DNA from C. trachomatis VR 348 serovar E, C. pneumoniae BAL 37, and C. psittaci SM006 was amplified.

    Article Snippet: In addition, analytical sensitivity with spiked clinical specimens were tested by use of the TETR-PCR protocol described above but with an alternative DNA polymerase (2 U of HotStarTaq DNA polymerase; Qiagen, Valencia, Calif.) and 1.5 mM MgCl2 .

    Techniques: Multiplex Assay, Polymerase Chain Reaction, Amplification

    Sequencing error rate distribution. a) Error rate distribution along the full-length fragment (421 bp) after analysis of 15,000 reads of L. pneumophila amplified with HotStarTaq ( open blue circles ) and KAPA HiFi DNA polymerases ( red open circles ). LOESS curves illustrate the reduced error rate with KAPA HiFi polymerase and the higher error rate in fragment covered by reverse reads. b) Comparison of error rate per base position with HotStarTaq and KAPA HiFi enzymes. A linear regression model explains the relationship between the two variables. Coefficient of determination (R 2 ) of 0.73

    Journal: BMC Microbiology

    Article Title: Development of a genus-specific next generation sequencing approach for sensitive and quantitative determination of the Legionella microbiome in freshwater systems

    doi: 10.1186/s12866-017-0987-5

    Figure Lengend Snippet: Sequencing error rate distribution. a) Error rate distribution along the full-length fragment (421 bp) after analysis of 15,000 reads of L. pneumophila amplified with HotStarTaq ( open blue circles ) and KAPA HiFi DNA polymerases ( red open circles ). LOESS curves illustrate the reduced error rate with KAPA HiFi polymerase and the higher error rate in fragment covered by reverse reads. b) Comparison of error rate per base position with HotStarTaq and KAPA HiFi enzymes. A linear regression model explains the relationship between the two variables. Coefficient of determination (R 2 ) of 0.73

    Article Snippet: The 16S rRNA sequences had an average substitution rate per base of 0.322% ± 0.277%, which represents a significant accuracy improvement to libraries amplified by HotStarTaq DNA polymerase (0.383% ± 0.275%) (T -test, P < 0.05).

    Techniques: Sequencing, Amplification