qiaquick gel extraction kit cat 28704  (Qiagen)


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    Qiaquick gel extraction kit
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    Catalog Number:
    28704
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    Score:
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    Qiagen qiaquick gel extraction kit cat 28704

    https://www.bioz.com/result/qiaquick gel extraction kit cat 28704/product/Qiagen
    Average 99 stars, based on 3 article reviews
    Price from $9.99 to $1999.99
    qiaquick gel extraction kit cat 28704 - by Bioz Stars, 2019-12
    99/100 stars

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    Related Articles

    Diagnostic Assay:

    Article Title: Blood parasites infecting the Hoatzin (Opisthocomus hoazin), a unique neotropical folivorous bird
    Article Snippet: Paragraph title: Molecular diagnostic of haemosporidian parasites ... Then, we excised two independent PCR products (50 ul) from the gel (bands of approximately 6 kbp) and purified using QIAquick® Gel extraction kit (Qiagen, GmbH, Hilden, Germany).

    Clone Assay:

    Article Title: Genome-wide identification of new reference genes for RT-qPCR normalization in CGMMV-infected Lagenaria siceraria
    Article Snippet: All primers were synthesized by a commercial supplier (Biosune, Hangzhou, China). .. To check the specificity of all primers, the cDNA of each sample was amplified by PCR, and the amplified products were separated by electrophoresis on 3% agarose gel and purified using a QIAquick Gel Extraction Kit (Qiagen, Hilden, Germany) according to the manufacturer’s instructions, and cloned into pEASY-Blunt zero (Transgen, Beijing, China) followed by sequencing. .. The quantification cycle (Cq) values obtained by qRT-PCR on a standard curve generated from a fourfold dilution series of one sample at six dilution points for three technical replicates were used to draw the standard curve to get R2 and slope values.

    Article Title: Blood parasites infecting the Hoatzin (Opisthocomus hoazin), a unique neotropical folivorous bird
    Article Snippet: Then, we excised two independent PCR products (50 ul) from the gel (bands of approximately 6 kbp) and purified using QIAquick® Gel extraction kit (Qiagen, GmbH, Hilden, Germany). .. We cloned at least two independent PCR products using pGEM® -T Easy Vector Systems (Promega, Madison, WI, USA), and we sequenced four clones from each individual.

    Article Title: Inhibitor of intramembrane protease RseP blocks the σE response causing lethal accumulation of unfolded outer membrane proteins
    Article Snippet: Paragraph title: RseP Cloning, Deletion, and Mutagenesis. ... The purified product obtained after isolation with the QIAquick Gel Extraction Kit (Qiagen) was used as template to amplify a variable allele library of rseP .

    Article Title: Mutations in Escherichia coli aceE and ribB Genes Allow Survival of Strains Defective in the First Step of the Isoprenoid Biosynthesis Pathway
    Article Snippet: Fragments of 2–4 kb were gel-purified using the Qiaquick (Qiagen) system and ligated into the Bam HI site of pUC19. .. Plasmid DNA isolated from these transformants was used to transform new EcAB4-2 cells to confirm that it conferred the ability to grow in the absence of MVA.

    Amplification:

    Article Title: Feeding and growth of the marine heterotrophic nanoflagellates, Procryptobia sorokini and Paraphysomonas imperforata on a bacterium, Pseudoalteromonas sp. with an inducible defence against grazing
    Article Snippet: The DNA regions encoding part of the 18S and 16S rDNA regions were amplified from 25–50 ng genomic DNA template using primer pairs F-566/R-1200, cryso240/ cryso651, and 27F/1492R, respectively (Table B in ). .. PCR products were subsequently purified with either the QIAquick PCR Purification Kit (Qiagen, Germany) or the QIAquick Gel Extraction Kit (Qiagen, Germany) and outsourced for sequencing at Eurofins Genomics (Eurofins, Germany).

    Article Title: Composition and richness of the serum microbiome differ by age and link to systemic inflammation
    Article Snippet: Paragraph title: Microbiome analyses—16S PCR amplification ... The band was excised and purified from the agarose using Qiagen QIAquick Gel Extraction Kit according to the manufacturer’s instructions.

    Article Title: Haplotyping of Cornus florida and C. kousa chloroplasts: Insights into species-level differences and patterns of plastic DNA variation in cultivars
    Article Snippet: Paragraph title: PCR amplification, plastid DNA restriction site analyses, and sequencing ... PCR products were purified for sequencing using the QIAquick Gel Extraction Kit (Qiagen) or ExoSap-It kit (Affymetrix, Cleveland, OH, USA).

    Article Title: Tackling critical parameters in metazoan meta-barcoding experiments: a preliminary study based on coxI DNA barcode
    Article Snippet: Paragraph title: DNA extraction and amplification of coxI barcode ... PCR products were subsequently gel purified using QIAquick Gel Extraction Kit (Qiagen, Hilden, Germany).

    Article Title: Genome-wide identification of new reference genes for RT-qPCR normalization in CGMMV-infected Lagenaria siceraria
    Article Snippet: All primers were synthesized by a commercial supplier (Biosune, Hangzhou, China). .. To check the specificity of all primers, the cDNA of each sample was amplified by PCR, and the amplified products were separated by electrophoresis on 3% agarose gel and purified using a QIAquick Gel Extraction Kit (Qiagen, Hilden, Germany) according to the manufacturer’s instructions, and cloned into pEASY-Blunt zero (Transgen, Beijing, China) followed by sequencing. .. The quantification cycle (Cq) values obtained by qRT-PCR on a standard curve generated from a fourfold dilution series of one sample at six dilution points for three technical replicates were used to draw the standard curve to get R2 and slope values.

    Article Title: Prognostic significance of CD117 expression and TP53 missense mutations in triple-negative breast cancer
    Article Snippet: PCR was performed using a Mastercycler gradient PCR machine (Eppendorf, Hamburg, Germany) under the following amplification conditions: 94°C for 10 min; 40 cycles of 94°C for 45 sec, 61°C for 45 sec, and 72°C for 45 sec; with a final extension at 72°C for 7 min. .. The PCR products were purified using a QIAquick Gel Extraction kit (Qiagen GmbH) and were prepared for sequencing via a 3500Dx genetic analyzer (Applied Biosystems; Thermo Fisher Scientific, Inc., Waltham, MA, USA) with a BigDye Terminator Cycle Sequencing Ready Reaction kit (Applied Biosystems; Thermo Fisher Scientific, Inc.).

    Article Title: Blood parasites infecting the Hoatzin (Opisthocomus hoazin), a unique neotropical folivorous bird
    Article Snippet: For those samples that were positive using the cytb PCR protocol, we amplified between 5,515 to 5,838 bp of the parasite mitochondrial genomes (mtDNA) using a nested PCR with Takara LA Taq™ Polymerase (TaKaRa Takara Mirus Bio) following manufacturers’ directions. .. Then, we excised two independent PCR products (50 ul) from the gel (bands of approximately 6 kbp) and purified using QIAquick® Gel extraction kit (Qiagen, GmbH, Hilden, Germany).

    Article Title: Epstein-Barr virus nuclear antigen EBNA-LP is essential for transforming naïve B cells, and facilitates recruitment of transcription factors to the viral genome
    Article Snippet: After proteinase K treatment for 2 hours at 50 degrees, DNA was then purified using the Qiagen QIAQuick gel extraction kit, and eluted in 120 μl water. .. Absolute quantity (relative to input) was calculated from standard curves generated from input DNA that was serially diluted 1:4, four times.

    Article Title: Inhibitor of intramembrane protease RseP blocks the σE response causing lethal accumulation of unfolded outer membrane proteins
    Article Snippet: The purified product obtained after isolation with the QIAquick Gel Extraction Kit (Qiagen) was used as template to amplify a variable allele library of rseP . .. To facilitate cloning by multiple methods and reduce background during library production, a new plasmid was constructed incorporating a low copy number origin of replication, the Gateway cassette containing attR sites flanking the ccdB gene, and the CAMR gene.

    Article Title: FibroChip, a Functional DNA Microarray to Monitor Cellulolytic and Hemicellulolytic Activities of Rumen Microbiota
    Article Snippet: Amplification steps were: initial denaturation (94°C, 2 min), 35 cycles comprising denaturation (95°C, 30 s), hybridization (50°C, 30 s), elongation (72°C, 60 s), and final elongation (72°C, 5 min). .. PCR products were gel-purified using the QIAquick Gel extraction Kit (Qiagen, Hilden, Germany) according to the supplier instructions.

    Article Title: PCR Biases Distort Bacterial and Archaeal Community Structure in Pyrosequencing Datasets
    Article Snippet: Paragraph title: PCR Amplification and Sample Preparation for Sequencing ... The bands corresponding to 600–700 bp for bacteria and 600–900 bp for archaea were excised and purified using a Qiaquick Gel Extraction kit (Qiagen, Valencia, CA).

    Article Title: Evaluating the Ribosomal Internal Transcribed Spacer (ITS) as a Candidate Dinoflagellate Barcode Marker
    Article Snippet: PCR amplification reaction was carried out on 25–100 ng of DNA using PuReTaq Ready-to-Go beads (GE Lifesciences, NJ, USA) at 94°C for 31minutes followed by 35 cycles of 94°C for 30 seconds, 47°C for 30 seconds and 72°C for 45 seconds, ending with a 72°C extension step for 7 minutes, resulting in products ranging from 500–600 bp. .. Single PCR products were diluted to 30 ng/µl or purified by gel extraction using the QIAquick Gel Extraction kit (Qiagen, Mississauga, ON, Canada), according to manufacturer's instructions and were either sent to Canadian Centre of DNA Barcoding, Guelph, ON for DNA sequencing or were sequenced directly using BigDye v3.1 reagents and sent to NAPS unit at University of British Columbia, BC for capillary electrophoresis.

    Article Title: Mutations in Escherichia coli aceE and ribB Genes Allow Survival of Strains Defective in the First Step of the Isoprenoid Biosynthesis Pathway
    Article Snippet: Fragments of 2–4 kb were gel-purified using the Qiaquick (Qiagen) system and ligated into the Bam HI site of pUC19. .. Fragments of 2–4 kb were gel-purified using the Qiaquick (Qiagen) system and ligated into the Bam HI site of pUC19.

    Synthesized:

    Article Title: Genome-wide identification of new reference genes for RT-qPCR normalization in CGMMV-infected Lagenaria siceraria
    Article Snippet: To check the specificity of all primers, the cDNA of each sample was amplified by PCR, and the amplified products were separated by electrophoresis on 3% agarose gel and purified using a QIAquick Gel Extraction Kit (Qiagen, Hilden, Germany) according to the manufacturer’s instructions, and cloned into pEASY-Blunt zero (Transgen, Beijing, China) followed by sequencing. .. To check the specificity of all primers, the cDNA of each sample was amplified by PCR, and the amplified products were separated by electrophoresis on 3% agarose gel and purified using a QIAquick Gel Extraction Kit (Qiagen, Hilden, Germany) according to the manufacturer’s instructions, and cloned into pEASY-Blunt zero (Transgen, Beijing, China) followed by sequencing.

    Construct:

    Article Title: Differential genome-wide profiling of alternative polyadenylation sites in nasopharyngeal carcinoma by high-throughput sequencing
    Article Snippet: The SAPAS sequencing libraries were constructed as described previously [ , ]. .. PAGE gel-excision was carried out to select the PCR products with the fragments of 300-500 bp with a QIAquick Gel Extraction Kit (Qiagen, Valencia, CA).

    Article Title: Inhibitor of intramembrane protease RseP blocks the σE response causing lethal accumulation of unfolded outer membrane proteins
    Article Snippet: The purified product obtained after isolation with the QIAquick Gel Extraction Kit (Qiagen) was used as template to amplify a variable allele library of rseP . .. Briefly, using the Clontech Diversify PCR Random Mutagenesis Kit under conditions yielding 2.3 mutations per 1,000 bp (160 µM MnSO4 and 40 mM dGTP), 50 ng of purified rseP template was amplified with primers rseP_5′ and rseP_3′ and was gel purified.

    Article Title: Amino Acid Substitutions within HLA-B*27-Restricted T Cell Epitopes Prevent Recognition by Hepatitis Delta Virus-Specific CD8+ T Cells
    Article Snippet: A maximum-likelihood phylogenetic tree was constructed under the Tamura-Nei substitution model using MEGA software v6 ( ). .. The amplicons had a length of 515 bp and were isolated from 0.9% agarose gels with the QIAquick extraction kit (QIAquick spin handbook; Qiagen, Hilden, Germany) and quantified using Quan-iTPicogreens DNA reagent (Invitrogen).

    Electrophoresis:

    Article Title: Taxonomic and Functional Metagenomic Profile of Sediment From a Commercial Catfish Pond in Mississippi
    Article Snippet: Briefly, genomic DNA was sheared by sonication and separated by electrophoresis on a 1% agarose gel. .. Gel slices corresponding to ∼300 and ∼500 bp were excised and purified using QIAquick Gel Extraction Kit (Qiagen).

    Article Title: Genome-wide identification of new reference genes for RT-qPCR normalization in CGMMV-infected Lagenaria siceraria
    Article Snippet: All primers were synthesized by a commercial supplier (Biosune, Hangzhou, China). .. To check the specificity of all primers, the cDNA of each sample was amplified by PCR, and the amplified products were separated by electrophoresis on 3% agarose gel and purified using a QIAquick Gel Extraction Kit (Qiagen, Hilden, Germany) according to the manufacturer’s instructions, and cloned into pEASY-Blunt zero (Transgen, Beijing, China) followed by sequencing. .. The quantification cycle (Cq) values obtained by qRT-PCR on a standard curve generated from a fourfold dilution series of one sample at six dilution points for three technical replicates were used to draw the standard curve to get R2 and slope values.

    Article Title: Evaluating the Ribosomal Internal Transcribed Spacer (ITS) as a Candidate Dinoflagellate Barcode Marker
    Article Snippet: All culture collection ITS amplicons were sequenced directly. .. Single PCR products were diluted to 30 ng/µl or purified by gel extraction using the QIAquick Gel Extraction kit (Qiagen, Mississauga, ON, Canada), according to manufacturer's instructions and were either sent to Canadian Centre of DNA Barcoding, Guelph, ON for DNA sequencing or were sequenced directly using BigDye v3.1 reagents and sent to NAPS unit at University of British Columbia, BC for capillary electrophoresis. .. All sequences generated from this study are listed in with Genbank accession numbers) and on the BOLD database in DAITS project at http://www.barcodinglife.org/views/projectlist.php?

    IA:

    Article Title: Antibiotic Treatments for Clostridium difficile Infection Are Associated with Distinct Bacterial and Fungal Community Structures
    Article Snippet: Pooled PCR products were gel purified with a QIAquick gel extraction kit (Qiagen, Frederick, MD) and quantified with a Qubit 2.0 fluorometer (Life Technologies, Inc., Carlsbad, CA). .. Before submission for sequencing, libraries were quality checked with the 2100 Bioanalyzer DNA 1000 chip (Agilent Technologies, Santa Clara, CA).

    Incubation:

    Article Title: Whole-Genome Sequencing and Bioinformatic Analysis of Isolates from Foodborne Illness Outbreaks of Campylobacter jejuni and Salmonella enterica
    Article Snippet: Plates were incubated overnight at 42°C under microaerophilic conditions created in a 2.5-liter jar with 5% O2 , 10% CO2 , and 85% N2 produced by an Oxoid CampyGen sachet (Thermo Fisher Scientific). .. For isolates that could not be recovered from frozen cultures, DNA was extracted directly from the PFGE plugs with the QIAquick gel extraction kit (Qiagen).

    Article Title: Epstein-Barr virus nuclear antigen EBNA-LP is essential for transforming naïve B cells, and facilitates recruitment of transcription factors to the viral genome
    Article Snippet: Precleared chromatin, using 45μl protein A agarose beads was diluted with ChIP dilution buffer and incubated overnight with primary antibodies against EBNA 2 (Abcam ab90543), EBF1 (Millipore AB10523), RBPJk (Abcam ab25949) or an IgG control (Sigma). .. After proteinase K treatment for 2 hours at 50 degrees, DNA was then purified using the Qiagen QIAQuick gel extraction kit, and eluted in 120 μl water.

    Hybridization:

    Article Title: FibroChip, a Functional DNA Microarray to Monitor Cellulolytic and Hemicellulolytic Activities of Rumen Microbiota
    Article Snippet: Amplification steps were: initial denaturation (94°C, 2 min), 35 cycles comprising denaturation (95°C, 30 s), hybridization (50°C, 30 s), elongation (72°C, 60 s), and final elongation (72°C, 5 min). .. PCR products were gel-purified using the QIAquick Gel extraction Kit (Qiagen, Hilden, Germany) according to the supplier instructions.

    Low Copy Number:

    Article Title: Inhibitor of intramembrane protease RseP blocks the σE response causing lethal accumulation of unfolded outer membrane proteins
    Article Snippet: The purified product obtained after isolation with the QIAquick Gel Extraction Kit (Qiagen) was used as template to amplify a variable allele library of rseP . .. Briefly, using the Clontech Diversify PCR Random Mutagenesis Kit under conditions yielding 2.3 mutations per 1,000 bp (160 µM MnSO4 and 40 mM dGTP), 50 ng of purified rseP template was amplified with primers rseP_5′ and rseP_3′ and was gel purified.

    Infection:

    Article Title: Epstein-Barr virus nuclear antigen EBNA-LP is essential for transforming naïve B cells, and facilitates recruitment of transcription factors to the viral genome
    Article Snippet: Briefly, 2x106 infected B cells were fixed for 10 minutes in 1% formaldehyde and neutralised with glycine. .. After proteinase K treatment for 2 hours at 50 degrees, DNA was then purified using the Qiagen QIAQuick gel extraction kit, and eluted in 120 μl water.

    Generated:

    Article Title: Feeding and growth of the marine heterotrophic nanoflagellates, Procryptobia sorokini and Paraphysomonas imperforata on a bacterium, Pseudoalteromonas sp. with an inducible defence against grazing
    Article Snippet: PCR products were generated in 50 μL reaction volumes containing 0,02 U Phusion™ High-Fidelity DNA Polymerase (Thermo Scientific, USA), 1× HF Green Buffer, 200 μM dNTP mix, and 0.5 μM forward and 0.5 μM reverse primer. .. PCR products were subsequently purified with either the QIAquick PCR Purification Kit (Qiagen, Germany) or the QIAquick Gel Extraction Kit (Qiagen, Germany) and outsourced for sequencing at Eurofins Genomics (Eurofins, Germany).

    Article Title: Differential genome-wide profiling of alternative polyadenylation sites in nasopharyngeal carcinoma by high-throughput sequencing
    Article Snippet: The first strand cDNA was generated by a template-switch reverse transcription (RT) reaction, in which contains an anchored oligo d(T) primer, a 5′ template switching adaptor, and Super-Script II kits (Invitrogen Life Technologies, Karlsruhe, Germany). .. PAGE gel-excision was carried out to select the PCR products with the fragments of 300-500 bp with a QIAquick Gel Extraction Kit (Qiagen, Valencia, CA).

    Article Title: Epstein-Barr virus nuclear antigen EBNA-LP is essential for transforming naïve B cells, and facilitates recruitment of transcription factors to the viral genome
    Article Snippet: After proteinase K treatment for 2 hours at 50 degrees, DNA was then purified using the Qiagen QIAQuick gel extraction kit, and eluted in 120 μl water. .. Chromatin was quantified by qPCR using the Kapa qPCR SYBR kit (low Rox) on a QuantStudio7 real time PCR machine (Applied Biosystems).

    Article Title: PCR Biases Distort Bacterial and Archaeal Community Structure in Pyrosequencing Datasets
    Article Snippet: Two different PCR product pools were generated, one each for bacteria and archaea. .. The bands corresponding to 600–700 bp for bacteria and 600–900 bp for archaea were excised and purified using a Qiaquick Gel Extraction kit (Qiagen, Valencia, CA).

    Polymerase Chain Reaction:

    Article Title: Feeding and growth of the marine heterotrophic nanoflagellates, Procryptobia sorokini and Paraphysomonas imperforata on a bacterium, Pseudoalteromonas sp. with an inducible defence against grazing
    Article Snippet: PCR products were generated in 50 μL reaction volumes containing 0,02 U Phusion™ High-Fidelity DNA Polymerase (Thermo Scientific, USA), 1× HF Green Buffer, 200 μM dNTP mix, and 0.5 μM forward and 0.5 μM reverse primer. .. PCR products were subsequently purified with either the QIAquick PCR Purification Kit (Qiagen, Germany) or the QIAquick Gel Extraction Kit (Qiagen, Germany) and outsourced for sequencing at Eurofins Genomics (Eurofins, Germany). .. A blastN analysis was performed against the non-redundant database at NCBI to identify the relevant taxa [ ].

    Article Title: Composition and richness of the serum microbiome differ by age and link to systemic inflammation
    Article Snippet: Paragraph title: Microbiome analyses—16S PCR amplification ... The band was excised and purified from the agarose using Qiagen QIAquick Gel Extraction Kit according to the manufacturer’s instructions.

    Article Title: Haplotyping of Cornus florida and C. kousa chloroplasts: Insights into species-level differences and patterns of plastic DNA variation in cultivars
    Article Snippet: The cpDNA01, 02, and 03 regions from samples of other Cornus species[ ], belonging to three phylogenetic groups as previously described[ ], were also amplified, and their sequences included in the study ( ). .. PCR products were purified for sequencing using the QIAquick Gel Extraction Kit (Qiagen) or ExoSap-It kit (Affymetrix, Cleveland, OH, USA). .. Analytical sequencing was completed at the UT Genomics Core (Knoxville, TN, USA) and McLab (South San Francisco, CA, USA).

    Article Title: Tackling critical parameters in metazoan meta-barcoding experiments: a preliminary study based on coxI DNA barcode
    Article Snippet: PCR products along with 100 bp DNA Ladder (Fermentas Life Sciences, Waltham, MA, USA) were visualized on a 1% agarose gel stained with 0.005% of ethidium bromide. .. PCR products were subsequently gel purified using QIAquick Gel Extraction Kit (Qiagen, Hilden, Germany). .. The coxI barcode region was sequenced singularly for each Carabidae organism by Sanger method.

    Article Title: Taxonomic and Functional Metagenomic Profile of Sediment From a Commercial Catfish Pond in Mississippi
    Article Snippet: Gel slices corresponding to ∼300 and ∼500 bp were excised and purified using QIAquick Gel Extraction Kit (Qiagen). .. Sheared DNA was ligated to sequence adapters.

    Article Title: Genome-wide identification of new reference genes for RT-qPCR normalization in CGMMV-infected Lagenaria siceraria
    Article Snippet: All primers were synthesized by a commercial supplier (Biosune, Hangzhou, China). .. To check the specificity of all primers, the cDNA of each sample was amplified by PCR, and the amplified products were separated by electrophoresis on 3% agarose gel and purified using a QIAquick Gel Extraction Kit (Qiagen, Hilden, Germany) according to the manufacturer’s instructions, and cloned into pEASY-Blunt zero (Transgen, Beijing, China) followed by sequencing. .. The quantification cycle (Cq) values obtained by qRT-PCR on a standard curve generated from a fourfold dilution series of one sample at six dilution points for three technical replicates were used to draw the standard curve to get R2 and slope values.

    Article Title: Prognostic significance of CD117 expression and TP53 missense mutations in triple-negative breast cancer
    Article Snippet: PCR was performed using a Mastercycler gradient PCR machine (Eppendorf, Hamburg, Germany) under the following amplification conditions: 94°C for 10 min; 40 cycles of 94°C for 45 sec, 61°C for 45 sec, and 72°C for 45 sec; with a final extension at 72°C for 7 min. .. The PCR products were purified using a QIAquick Gel Extraction kit (Qiagen GmbH) and were prepared for sequencing via a 3500Dx genetic analyzer (Applied Biosystems; Thermo Fisher Scientific, Inc., Waltham, MA, USA) with a BigDye Terminator Cycle Sequencing Ready Reaction kit (Applied Biosystems; Thermo Fisher Scientific, Inc.). .. The cycling conditions were: 94°C for 1 min; 24 cycles of 94°C for 10 sec, 50°C for 5 sec, and 60°C for 1 min; and final extension at 72°C for 5 min.

    Article Title: Antibiotic Treatments for Clostridium difficile Infection Are Associated with Distinct Bacterial and Fungal Community Structures
    Article Snippet: Each PCR was carried out with an MJ Research PTC-200 thermocycler (Bio-Rad, Hercules, CA). .. Pooled PCR products were gel purified with a QIAquick gel extraction kit (Qiagen, Frederick, MD) and quantified with a Qubit 2.0 fluorometer (Life Technologies, Inc., Carlsbad, CA). .. Before submission for sequencing, libraries were quality checked with the 2100 Bioanalyzer DNA 1000 chip (Agilent Technologies, Santa Clara, CA).

    Article Title: Integrative genomic and transcriptomic analysis of leiomyosarcoma
    Article Snippet: Amplifications were carried out using Taq DNA Polymerase (Qiagen) according to the manufacturer’s instructions. .. PCR products were visualized in 1% agarose gels and purified using the QIAquick PCR Purification Kit or the QIAquick Gel Extraction Kit (Qiagen). .. Direct sequencing was performed with the forward or reverse primer of the respective amplification.

    Article Title: Blood parasites infecting the Hoatzin (Opisthocomus hoazin), a unique neotropical folivorous bird
    Article Snippet: The PCR conditions were a partial denaturation at 94 °C for 1 min and 30 cycles with 30 s at 94 °C and 7 min at 68 °C and a final extension of 10 min at 72 °C. .. Then, we excised two independent PCR products (50 ul) from the gel (bands of approximately 6 kbp) and purified using QIAquick® Gel extraction kit (Qiagen, GmbH, Hilden, Germany). .. We cloned at least two independent PCR products using pGEM® -T Easy Vector Systems (Promega, Madison, WI, USA), and we sequenced four clones from each individual.

    Article Title: FibroChip, a Functional DNA Microarray to Monitor Cellulolytic and Hemicellulolytic Activities of Rumen Microbiota
    Article Snippet: Several secondary PCR reactions were realized in order to obtain enough PCR products for sequencing. .. PCR products were gel-purified using the QIAquick Gel extraction Kit (Qiagen, Hilden, Germany) according to the supplier instructions. .. Finally purified PCR products were concentrated with the MinElute PCR Purification Kit (Qiagen, Hilden, Germany) and sequenced by the MWG Company (Mulhouse, France) using primers of the secondary PCR reaction.

    Article Title: PCR Biases Distort Bacterial and Archaeal Community Structure in Pyrosequencing Datasets
    Article Snippet: Paragraph title: PCR Amplification and Sample Preparation for Sequencing ... The bands corresponding to 600–700 bp for bacteria and 600–900 bp for archaea were excised and purified using a Qiaquick Gel Extraction kit (Qiagen, Valencia, CA).

    Article Title: Evaluating the Ribosomal Internal Transcribed Spacer (ITS) as a Candidate Dinoflagellate Barcode Marker
    Article Snippet: All culture collection ITS amplicons were sequenced directly. .. Single PCR products were diluted to 30 ng/µl or purified by gel extraction using the QIAquick Gel Extraction kit (Qiagen, Mississauga, ON, Canada), according to manufacturer's instructions and were either sent to Canadian Centre of DNA Barcoding, Guelph, ON for DNA sequencing or were sequenced directly using BigDye v3.1 reagents and sent to NAPS unit at University of British Columbia, BC for capillary electrophoresis. .. All sequences generated from this study are listed in with Genbank accession numbers) and on the BOLD database in DAITS project at http://www.barcodinglife.org/views/projectlist.php?

    Article Title: Amino Acid Substitutions within HLA-B*27-Restricted T Cell Epitopes Prevent Recognition by Hepatitis Delta Virus-Specific CD8+ T Cells
    Article Snippet: Finally, the PCR products were purified via QIAquick gel extraction (Qiagen) and directly sequenced on an ABI 3730xl DNA analyzer using internal primers 912-F and 1674-R. HDV sequences from this study and NCBI GenBank were aligned using ClustalX2 software ( ). .. The amplicons had a length of 515 bp and were isolated from 0.9% agarose gels with the QIAquick extraction kit (QIAquick spin handbook; Qiagen, Hilden, Germany) and quantified using Quan-iTPicogreens DNA reagent (Invitrogen).

    Article Title: Prevalence of Yersinia Species in the Ileum of Crohn's Disease Patients and Controls
    Article Snippet: PCR products were then analyzed on 1.5% agarose gels and stained with SYBR-safe (Invitrogen). .. Sequencing was subsequently performed on all gel-purified PCR products (QIAquick extraction kit, Qiagen). .. Bi-allelic direct DNA sequencing was applied using BigDye Terminator v1.1 reagent (Applied Biosystems, USA), on an ABI 3730 automated genetic analyzer and analyzed using the 4peaks software.

    Article Title: Mutations in Escherichia coli aceE and ribB Genes Allow Survival of Strains Defective in the First Step of the Isoprenoid Biosynthesis Pathway
    Article Snippet: Fragments of 2–4 kb were gel-purified using the Qiaquick (Qiagen) system and ligated into the Bam HI site of pUC19. .. Fragments of 2–4 kb were gel-purified using the Qiaquick (Qiagen) system and ligated into the Bam HI site of pUC19.

    DNA Sequencing:

    Article Title: Evaluating the Ribosomal Internal Transcribed Spacer (ITS) as a Candidate Dinoflagellate Barcode Marker
    Article Snippet: All culture collection ITS amplicons were sequenced directly. .. Single PCR products were diluted to 30 ng/µl or purified by gel extraction using the QIAquick Gel Extraction kit (Qiagen, Mississauga, ON, Canada), according to manufacturer's instructions and were either sent to Canadian Centre of DNA Barcoding, Guelph, ON for DNA sequencing or were sequenced directly using BigDye v3.1 reagents and sent to NAPS unit at University of British Columbia, BC for capillary electrophoresis. .. All sequences generated from this study are listed in with Genbank accession numbers) and on the BOLD database in DAITS project at http://www.barcodinglife.org/views/projectlist.php?

    Sequencing:

    Article Title: Feeding and growth of the marine heterotrophic nanoflagellates, Procryptobia sorokini and Paraphysomonas imperforata on a bacterium, Pseudoalteromonas sp. with an inducible defence against grazing
    Article Snippet: PCR products were generated in 50 μL reaction volumes containing 0,02 U Phusion™ High-Fidelity DNA Polymerase (Thermo Scientific, USA), 1× HF Green Buffer, 200 μM dNTP mix, and 0.5 μM forward and 0.5 μM reverse primer. .. PCR products were subsequently purified with either the QIAquick PCR Purification Kit (Qiagen, Germany) or the QIAquick Gel Extraction Kit (Qiagen, Germany) and outsourced for sequencing at Eurofins Genomics (Eurofins, Germany). .. A blastN analysis was performed against the non-redundant database at NCBI to identify the relevant taxa [ ].

    Article Title: Composition and richness of the serum microbiome differ by age and link to systemic inflammation
    Article Snippet: The band was excised and purified from the agarose using Qiagen QIAquick Gel Extraction Kit according to the manufacturer’s instructions. .. The band was excised and purified from the agarose using Qiagen QIAquick Gel Extraction Kit according to the manufacturer’s instructions.

    Article Title: Haplotyping of Cornus florida and C. kousa chloroplasts: Insights into species-level differences and patterns of plastic DNA variation in cultivars
    Article Snippet: The cpDNA01, 02, and 03 regions from samples of other Cornus species[ ], belonging to three phylogenetic groups as previously described[ ], were also amplified, and their sequences included in the study ( ). .. PCR products were purified for sequencing using the QIAquick Gel Extraction Kit (Qiagen) or ExoSap-It kit (Affymetrix, Cleveland, OH, USA). .. Analytical sequencing was completed at the UT Genomics Core (Knoxville, TN, USA) and McLab (South San Francisco, CA, USA).

    Article Title: Taxonomic and Functional Metagenomic Profile of Sediment From a Commercial Catfish Pond in Mississippi
    Article Snippet: Paragraph title: Sediment Sampling, DNA Extraction, and Sequencing ... Gel slices corresponding to ∼300 and ∼500 bp were excised and purified using QIAquick Gel Extraction Kit (Qiagen).

    Article Title: Differential genome-wide profiling of alternative polyadenylation sites in nasopharyngeal carcinoma by high-throughput sequencing
    Article Snippet: The SAPAS sequencing libraries were constructed as described previously [ , ]. .. PAGE gel-excision was carried out to select the PCR products with the fragments of 300-500 bp with a QIAquick Gel Extraction Kit (Qiagen, Valencia, CA).

    Article Title: Genome-wide identification of new reference genes for RT-qPCR normalization in CGMMV-infected Lagenaria siceraria
    Article Snippet: All primers were synthesized by a commercial supplier (Biosune, Hangzhou, China). .. To check the specificity of all primers, the cDNA of each sample was amplified by PCR, and the amplified products were separated by electrophoresis on 3% agarose gel and purified using a QIAquick Gel Extraction Kit (Qiagen, Hilden, Germany) according to the manufacturer’s instructions, and cloned into pEASY-Blunt zero (Transgen, Beijing, China) followed by sequencing. .. The quantification cycle (Cq) values obtained by qRT-PCR on a standard curve generated from a fourfold dilution series of one sample at six dilution points for three technical replicates were used to draw the standard curve to get R2 and slope values.

    Article Title: Prognostic significance of CD117 expression and TP53 missense mutations in triple-negative breast cancer
    Article Snippet: PCR was performed using a Mastercycler gradient PCR machine (Eppendorf, Hamburg, Germany) under the following amplification conditions: 94°C for 10 min; 40 cycles of 94°C for 45 sec, 61°C for 45 sec, and 72°C for 45 sec; with a final extension at 72°C for 7 min. .. The PCR products were purified using a QIAquick Gel Extraction kit (Qiagen GmbH) and were prepared for sequencing via a 3500Dx genetic analyzer (Applied Biosystems; Thermo Fisher Scientific, Inc., Waltham, MA, USA) with a BigDye Terminator Cycle Sequencing Ready Reaction kit (Applied Biosystems; Thermo Fisher Scientific, Inc.). .. The cycling conditions were: 94°C for 1 min; 24 cycles of 94°C for 10 sec, 50°C for 5 sec, and 60°C for 1 min; and final extension at 72°C for 5 min.

    Article Title: Antibiotic Treatments for Clostridium difficile Infection Are Associated with Distinct Bacterial and Fungal Community Structures
    Article Snippet: Pooled PCR products were gel purified with a QIAquick gel extraction kit (Qiagen, Frederick, MD) and quantified with a Qubit 2.0 fluorometer (Life Technologies, Inc., Carlsbad, CA). .. Pooled PCR products were gel purified with a QIAquick gel extraction kit (Qiagen, Frederick, MD) and quantified with a Qubit 2.0 fluorometer (Life Technologies, Inc., Carlsbad, CA).

    Article Title: Integrative genomic and transcriptomic analysis of leiomyosarcoma
    Article Snippet: PCR products were visualized in 1% agarose gels and purified using the QIAquick PCR Purification Kit or the QIAquick Gel Extraction Kit (Qiagen). .. PCR products were visualized in 1% agarose gels and purified using the QIAquick PCR Purification Kit or the QIAquick Gel Extraction Kit (Qiagen).

    Article Title: Inhibitor of intramembrane protease RseP blocks the σE response causing lethal accumulation of unfolded outer membrane proteins
    Article Snippet: Primers rseP_5′ and rseP_3′, both of which incorporate overhangs complementary to the sequence flanking the cloning site in pCDFG (described below), were used to amplify rseP from BW25113 E. coli using Phusion High-Fidelity DNA polymerase. .. The purified product obtained after isolation with the QIAquick Gel Extraction Kit (Qiagen) was used as template to amplify a variable allele library of rseP .

    Article Title: FibroChip, a Functional DNA Microarray to Monitor Cellulolytic and Hemicellulolytic Activities of Rumen Microbiota
    Article Snippet: Several secondary PCR reactions were realized in order to obtain enough PCR products for sequencing. .. PCR products were gel-purified using the QIAquick Gel extraction Kit (Qiagen, Hilden, Germany) according to the supplier instructions.

    Article Title: PCR Biases Distort Bacterial and Archaeal Community Structure in Pyrosequencing Datasets
    Article Snippet: Paragraph title: PCR Amplification and Sample Preparation for Sequencing ... The bands corresponding to 600–700 bp for bacteria and 600–900 bp for archaea were excised and purified using a Qiaquick Gel Extraction kit (Qiagen, Valencia, CA).

    Article Title: Evaluating the Ribosomal Internal Transcribed Spacer (ITS) as a Candidate Dinoflagellate Barcode Marker
    Article Snippet: Paragraph title: PCR and Sequencing ... Single PCR products were diluted to 30 ng/µl or purified by gel extraction using the QIAquick Gel Extraction kit (Qiagen, Mississauga, ON, Canada), according to manufacturer's instructions and were either sent to Canadian Centre of DNA Barcoding, Guelph, ON for DNA sequencing or were sequenced directly using BigDye v3.1 reagents and sent to NAPS unit at University of British Columbia, BC for capillary electrophoresis.

    Article Title: Prevalence of Yersinia Species in the Ileum of Crohn's Disease Patients and Controls
    Article Snippet: PCR products were then analyzed on 1.5% agarose gels and stained with SYBR-safe (Invitrogen). .. Sequencing was subsequently performed on all gel-purified PCR products (QIAquick extraction kit, Qiagen). .. Bi-allelic direct DNA sequencing was applied using BigDye Terminator v1.1 reagent (Applied Biosystems, USA), on an ABI 3730 automated genetic analyzer and analyzed using the 4peaks software.

    Article Title: Mutations in Escherichia coli aceE and ribB Genes Allow Survival of Strains Defective in the First Step of the Isoprenoid Biosynthesis Pathway
    Article Snippet: Fragments of 2–4 kb were gel-purified using the Qiaquick (Qiagen) system and ligated into the Bam HI site of pUC19. .. Fragments of 2–4 kb were gel-purified using the Qiaquick (Qiagen) system and ligated into the Bam HI site of pUC19.

    Sonication:

    Article Title: Taxonomic and Functional Metagenomic Profile of Sediment From a Commercial Catfish Pond in Mississippi
    Article Snippet: Briefly, genomic DNA was sheared by sonication and separated by electrophoresis on a 1% agarose gel. .. Gel slices corresponding to ∼300 and ∼500 bp were excised and purified using QIAquick Gel Extraction Kit (Qiagen).

    Article Title: Epstein-Barr virus nuclear antigen EBNA-LP is essential for transforming naïve B cells, and facilitates recruitment of transcription factors to the viral genome
    Article Snippet: After two PBS washes, cells were lysed with SDS Lysis buffer on ice for 10 minutes and sonicated using the Diagenode UCD-200 Bioruptor for 15 minutes. .. After proteinase K treatment for 2 hours at 50 degrees, DNA was then purified using the Qiagen QIAQuick gel extraction kit, and eluted in 120 μl water.

    Binding Assay:

    Article Title: Integrative genomic and transcriptomic analysis of leiomyosarcoma
    Article Snippet: Breakpoint-spanning primers were designed manually and examined for secondary structures using mfold and off-target binding using Primer-BLAST. .. PCR products were visualized in 1% agarose gels and purified using the QIAquick PCR Purification Kit or the QIAquick Gel Extraction Kit (Qiagen).

    Staining:

    Article Title: Tackling critical parameters in metazoan meta-barcoding experiments: a preliminary study based on coxI DNA barcode
    Article Snippet: PCR products along with 100 bp DNA Ladder (Fermentas Life Sciences, Waltham, MA, USA) were visualized on a 1% agarose gel stained with 0.005% of ethidium bromide. .. PCR products were subsequently gel purified using QIAquick Gel Extraction Kit (Qiagen, Hilden, Germany).

    Article Title: Prevalence of Yersinia Species in the Ileum of Crohn's Disease Patients and Controls
    Article Snippet: PCR products were then analyzed on 1.5% agarose gels and stained with SYBR-safe (Invitrogen). .. Sequencing was subsequently performed on all gel-purified PCR products (QIAquick extraction kit, Qiagen).

    DNA Extraction:

    Article Title: Tackling critical parameters in metazoan meta-barcoding experiments: a preliminary study based on coxI DNA barcode
    Article Snippet: Paragraph title: DNA extraction and amplification of coxI barcode ... PCR products were subsequently gel purified using QIAquick Gel Extraction Kit (Qiagen, Hilden, Germany).

    Article Title: Whole-Genome Sequencing and Bioinformatic Analysis of Isolates from Foodborne Illness Outbreaks of Campylobacter jejuni and Salmonella enterica
    Article Snippet: Paragraph title: Campylobacter jejuni DNA isolation. ... For isolates that could not be recovered from frozen cultures, DNA was extracted directly from the PFGE plugs with the QIAquick gel extraction kit (Qiagen).

    Article Title: Taxonomic and Functional Metagenomic Profile of Sediment From a Commercial Catfish Pond in Mississippi
    Article Snippet: Paragraph title: Sediment Sampling, DNA Extraction, and Sequencing ... Gel slices corresponding to ∼300 and ∼500 bp were excised and purified using QIAquick Gel Extraction Kit (Qiagen).

    Article Title: Antibiotic Treatments for Clostridium difficile Infection Are Associated with Distinct Bacterial and Fungal Community Structures
    Article Snippet: DNA was extracted from approximately 680 μl of a homogenized fecal solution ( n = 176) with a Mo Bio PowerFecal DNA extraction kit in accordance with the manufacturer’s instructions (Mo Bio Laboratories, Carlsbad, CA). .. Pooled PCR products were gel purified with a QIAquick gel extraction kit (Qiagen, Frederick, MD) and quantified with a Qubit 2.0 fluorometer (Life Technologies, Inc., Carlsbad, CA).

    RNA Sequencing Assay:

    Article Title: Genome-wide identification of new reference genes for RT-qPCR normalization in CGMMV-infected Lagenaria siceraria
    Article Snippet: Specific primers for the candidate RGs from our RNA-sequencing data were designed using Primer 3 ( ) ( ). .. To check the specificity of all primers, the cDNA of each sample was amplified by PCR, and the amplified products were separated by electrophoresis on 3% agarose gel and purified using a QIAquick Gel Extraction Kit (Qiagen, Hilden, Germany) according to the manufacturer’s instructions, and cloned into pEASY-Blunt zero (Transgen, Beijing, China) followed by sequencing.

    Mutagenesis:

    Article Title: Prognostic significance of CD117 expression and TP53 missense mutations in triple-negative breast cancer
    Article Snippet: Paragraph title: TP53 mutation analysis ... The PCR products were purified using a QIAquick Gel Extraction kit (Qiagen GmbH) and were prepared for sequencing via a 3500Dx genetic analyzer (Applied Biosystems; Thermo Fisher Scientific, Inc., Waltham, MA, USA) with a BigDye Terminator Cycle Sequencing Ready Reaction kit (Applied Biosystems; Thermo Fisher Scientific, Inc.).

    Article Title: Inhibitor of intramembrane protease RseP blocks the σE response causing lethal accumulation of unfolded outer membrane proteins
    Article Snippet: Paragraph title: RseP Cloning, Deletion, and Mutagenesis. ... The purified product obtained after isolation with the QIAquick Gel Extraction Kit (Qiagen) was used as template to amplify a variable allele library of rseP .

    Article Title: Mutations in Escherichia coli aceE and ribB Genes Allow Survival of Strains Defective in the First Step of the Isoprenoid Biosynthesis Pathway
    Article Snippet: Fragments of 2–4 kb were gel-purified using the Qiaquick (Qiagen) system and ligated into the Bam HI site of pUC19. .. Plasmid DNA isolated from these transformants was used to transform new EcAB4-2 cells to confirm that it conferred the ability to grow in the absence of MVA.

    Isolation:

    Article Title: Inhibitor of intramembrane protease RseP blocks the σE response causing lethal accumulation of unfolded outer membrane proteins
    Article Snippet: Primers rseP_5′ and rseP_3′, both of which incorporate overhangs complementary to the sequence flanking the cloning site in pCDFG (described below), were used to amplify rseP from BW25113 E. coli using Phusion High-Fidelity DNA polymerase. .. The purified product obtained after isolation with the QIAquick Gel Extraction Kit (Qiagen) was used as template to amplify a variable allele library of rseP . .. Briefly, using the Clontech Diversify PCR Random Mutagenesis Kit under conditions yielding 2.3 mutations per 1,000 bp (160 µM MnSO4 and 40 mM dGTP), 50 ng of purified rseP template was amplified with primers rseP_5′ and rseP_3′ and was gel purified.

    Article Title: FibroChip, a Functional DNA Microarray to Monitor Cellulolytic and Hemicellulolytic Activities of Rumen Microbiota
    Article Snippet: Paragraph title: Isolation of a GH11 Transcript of Piromyces communis from Total Rumen Content ... PCR products were gel-purified using the QIAquick Gel extraction Kit (Qiagen, Hilden, Germany) according to the supplier instructions.

    Article Title: Amino Acid Substitutions within HLA-B*27-Restricted T Cell Epitopes Prevent Recognition by Hepatitis Delta Virus-Specific CD8+ T Cells
    Article Snippet: Next-generation sequencing was performed in 11 selected samples to identify variations at a detection level of 0.1% and to pin down variations in the region flanked by nucleotide positions 956 to 1,360 by ultradeep pyrosequencing (UDPS) (primer sequences are listed in ). .. The amplicons had a length of 515 bp and were isolated from 0.9% agarose gels with the QIAquick extraction kit (QIAquick spin handbook; Qiagen, Hilden, Germany) and quantified using Quan-iTPicogreens DNA reagent (Invitrogen). .. UDPS was performed with the 454/GS-Junior platform (Roche, Branford, CT, USA) using titanium chemistry (GS-Junior titanium sequencing kit).

    Article Title: Mutations in Escherichia coli aceE and ribB Genes Allow Survival of Strains Defective in the First Step of the Isoprenoid Biosynthesis Pathway
    Article Snippet: Genomic DNA from suppressor mutants was isolated as described , and partially digested with Sau 3A. .. Fragments of 2–4 kb were gel-purified using the Qiaquick (Qiagen) system and ligated into the Bam HI site of pUC19.

    Size-exclusion Chromatography:

    Article Title: Prognostic significance of CD117 expression and TP53 missense mutations in triple-negative breast cancer
    Article Snippet: PCR was performed using a Mastercycler gradient PCR machine (Eppendorf, Hamburg, Germany) under the following amplification conditions: 94°C for 10 min; 40 cycles of 94°C for 45 sec, 61°C for 45 sec, and 72°C for 45 sec; with a final extension at 72°C for 7 min. .. The PCR products were purified using a QIAquick Gel Extraction kit (Qiagen GmbH) and were prepared for sequencing via a 3500Dx genetic analyzer (Applied Biosystems; Thermo Fisher Scientific, Inc., Waltham, MA, USA) with a BigDye Terminator Cycle Sequencing Ready Reaction kit (Applied Biosystems; Thermo Fisher Scientific, Inc.).

    Purification:

    Article Title: Feeding and growth of the marine heterotrophic nanoflagellates, Procryptobia sorokini and Paraphysomonas imperforata on a bacterium, Pseudoalteromonas sp. with an inducible defence against grazing
    Article Snippet: PCR products were generated in 50 μL reaction volumes containing 0,02 U Phusion™ High-Fidelity DNA Polymerase (Thermo Scientific, USA), 1× HF Green Buffer, 200 μM dNTP mix, and 0.5 μM forward and 0.5 μM reverse primer. .. PCR products were subsequently purified with either the QIAquick PCR Purification Kit (Qiagen, Germany) or the QIAquick Gel Extraction Kit (Qiagen, Germany) and outsourced for sequencing at Eurofins Genomics (Eurofins, Germany). .. A blastN analysis was performed against the non-redundant database at NCBI to identify the relevant taxa [ ].

    Article Title: Composition and richness of the serum microbiome differ by age and link to systemic inflammation
    Article Snippet: The PCR product (approximately 250 base pairs) was visualized by UV illumination. .. The band was excised and purified from the agarose using Qiagen QIAquick Gel Extraction Kit according to the manufacturer’s instructions. .. The PCR products were then sequenced using the Illumina MiSeq platform (Kumar et al. ).

    Article Title: Haplotyping of Cornus florida and C. kousa chloroplasts: Insights into species-level differences and patterns of plastic DNA variation in cultivars
    Article Snippet: The cpDNA01, 02, and 03 regions from samples of other Cornus species[ ], belonging to three phylogenetic groups as previously described[ ], were also amplified, and their sequences included in the study ( ). .. PCR products were purified for sequencing using the QIAquick Gel Extraction Kit (Qiagen) or ExoSap-It kit (Affymetrix, Cleveland, OH, USA). .. Analytical sequencing was completed at the UT Genomics Core (Knoxville, TN, USA) and McLab (South San Francisco, CA, USA).

    Article Title: Tackling critical parameters in metazoan meta-barcoding experiments: a preliminary study based on coxI DNA barcode
    Article Snippet: PCR products along with 100 bp DNA Ladder (Fermentas Life Sciences, Waltham, MA, USA) were visualized on a 1% agarose gel stained with 0.005% of ethidium bromide. .. PCR products were subsequently gel purified using QIAquick Gel Extraction Kit (Qiagen, Hilden, Germany). .. The coxI barcode region was sequenced singularly for each Carabidae organism by Sanger method.

    Article Title: Taxonomic and Functional Metagenomic Profile of Sediment From a Commercial Catfish Pond in Mississippi
    Article Snippet: Briefly, genomic DNA was sheared by sonication and separated by electrophoresis on a 1% agarose gel. .. Gel slices corresponding to ∼300 and ∼500 bp were excised and purified using QIAquick Gel Extraction Kit (Qiagen). .. The blunt-ended DNA fragments were A-tailed using the Quick Blunting Kit (New England BioLabs) and purified.

    Article Title: Genome-wide identification of new reference genes for RT-qPCR normalization in CGMMV-infected Lagenaria siceraria
    Article Snippet: All primers were synthesized by a commercial supplier (Biosune, Hangzhou, China). .. To check the specificity of all primers, the cDNA of each sample was amplified by PCR, and the amplified products were separated by electrophoresis on 3% agarose gel and purified using a QIAquick Gel Extraction Kit (Qiagen, Hilden, Germany) according to the manufacturer’s instructions, and cloned into pEASY-Blunt zero (Transgen, Beijing, China) followed by sequencing. .. The quantification cycle (Cq) values obtained by qRT-PCR on a standard curve generated from a fourfold dilution series of one sample at six dilution points for three technical replicates were used to draw the standard curve to get R2 and slope values.

    Article Title: Prognostic significance of CD117 expression and TP53 missense mutations in triple-negative breast cancer
    Article Snippet: PCR was performed using a Mastercycler gradient PCR machine (Eppendorf, Hamburg, Germany) under the following amplification conditions: 94°C for 10 min; 40 cycles of 94°C for 45 sec, 61°C for 45 sec, and 72°C for 45 sec; with a final extension at 72°C for 7 min. .. The PCR products were purified using a QIAquick Gel Extraction kit (Qiagen GmbH) and were prepared for sequencing via a 3500Dx genetic analyzer (Applied Biosystems; Thermo Fisher Scientific, Inc., Waltham, MA, USA) with a BigDye Terminator Cycle Sequencing Ready Reaction kit (Applied Biosystems; Thermo Fisher Scientific, Inc.). .. The cycling conditions were: 94°C for 1 min; 24 cycles of 94°C for 10 sec, 50°C for 5 sec, and 60°C for 1 min; and final extension at 72°C for 5 min.

    Article Title: Antibiotic Treatments for Clostridium difficile Infection Are Associated with Distinct Bacterial and Fungal Community Structures
    Article Snippet: Each PCR was carried out with an MJ Research PTC-200 thermocycler (Bio-Rad, Hercules, CA). .. Pooled PCR products were gel purified with a QIAquick gel extraction kit (Qiagen, Frederick, MD) and quantified with a Qubit 2.0 fluorometer (Life Technologies, Inc., Carlsbad, CA). .. Before submission for sequencing, libraries were quality checked with the 2100 Bioanalyzer DNA 1000 chip (Agilent Technologies, Santa Clara, CA).

    Article Title: Integrative genomic and transcriptomic analysis of leiomyosarcoma
    Article Snippet: Amplifications were carried out using Taq DNA Polymerase (Qiagen) according to the manufacturer’s instructions. .. PCR products were visualized in 1% agarose gels and purified using the QIAquick PCR Purification Kit or the QIAquick Gel Extraction Kit (Qiagen). .. Direct sequencing was performed with the forward or reverse primer of the respective amplification.

    Article Title: Blood parasites infecting the Hoatzin (Opisthocomus hoazin), a unique neotropical folivorous bird
    Article Snippet: The PCR conditions were a partial denaturation at 94 °C for 1 min and 30 cycles with 30 s at 94 °C and 7 min at 68 °C and a final extension of 10 min at 72 °C. .. Then, we excised two independent PCR products (50 ul) from the gel (bands of approximately 6 kbp) and purified using QIAquick® Gel extraction kit (Qiagen, GmbH, Hilden, Germany). .. We cloned at least two independent PCR products using pGEM® -T Easy Vector Systems (Promega, Madison, WI, USA), and we sequenced four clones from each individual.

    Article Title: Epstein-Barr virus nuclear antigen EBNA-LP is essential for transforming naïve B cells, and facilitates recruitment of transcription factors to the viral genome
    Article Snippet: The immune complexes were eluted from the beads using elution buffer and left overnight at 65 degrees. .. After proteinase K treatment for 2 hours at 50 degrees, DNA was then purified using the Qiagen QIAQuick gel extraction kit, and eluted in 120 μl water. .. Chromatin was quantified by qPCR using the Kapa qPCR SYBR kit (low Rox) on a QuantStudio7 real time PCR machine (Applied Biosystems).

    Article Title: Inhibitor of intramembrane protease RseP blocks the σE response causing lethal accumulation of unfolded outer membrane proteins
    Article Snippet: Primers rseP_5′ and rseP_3′, both of which incorporate overhangs complementary to the sequence flanking the cloning site in pCDFG (described below), were used to amplify rseP from BW25113 E. coli using Phusion High-Fidelity DNA polymerase. .. The purified product obtained after isolation with the QIAquick Gel Extraction Kit (Qiagen) was used as template to amplify a variable allele library of rseP . .. Briefly, using the Clontech Diversify PCR Random Mutagenesis Kit under conditions yielding 2.3 mutations per 1,000 bp (160 µM MnSO4 and 40 mM dGTP), 50 ng of purified rseP template was amplified with primers rseP_5′ and rseP_3′ and was gel purified.

    Article Title: PCR Biases Distort Bacterial and Archaeal Community Structure in Pyrosequencing Datasets
    Article Snippet: Both PCR product pools were then run on 2% agarose gel at 50 Volts for 60 min. .. The bands corresponding to 600–700 bp for bacteria and 600–900 bp for archaea were excised and purified using a Qiaquick Gel Extraction kit (Qiagen, Valencia, CA). .. A larger range of amplicon sizes was extracted for archaea as the V3–V5 region of C. maquilingensis is 733 bp in size.

    Article Title: Evaluating the Ribosomal Internal Transcribed Spacer (ITS) as a Candidate Dinoflagellate Barcode Marker
    Article Snippet: All culture collection ITS amplicons were sequenced directly. .. Single PCR products were diluted to 30 ng/µl or purified by gel extraction using the QIAquick Gel Extraction kit (Qiagen, Mississauga, ON, Canada), according to manufacturer's instructions and were either sent to Canadian Centre of DNA Barcoding, Guelph, ON for DNA sequencing or were sequenced directly using BigDye v3.1 reagents and sent to NAPS unit at University of British Columbia, BC for capillary electrophoresis. .. All sequences generated from this study are listed in with Genbank accession numbers) and on the BOLD database in DAITS project at http://www.barcodinglife.org/views/projectlist.php?

    Article Title: Amino Acid Substitutions within HLA-B*27-Restricted T Cell Epitopes Prevent Recognition by Hepatitis Delta Virus-Specific CD8+ T Cells
    Article Snippet: Finally, the PCR products were purified via QIAquick gel extraction (Qiagen) and directly sequenced on an ABI 3730xl DNA analyzer using internal primers 912-F and 1674-R. HDV sequences from this study and NCBI GenBank were aligned using ClustalX2 software ( ). .. The amplicons had a length of 515 bp and were isolated from 0.9% agarose gels with the QIAquick extraction kit (QIAquick spin handbook; Qiagen, Hilden, Germany) and quantified using Quan-iTPicogreens DNA reagent (Invitrogen).

    Reverse Transcription Polymerase Chain Reaction:

    Article Title: Integrative genomic and transcriptomic analysis of leiomyosarcoma
    Article Snippet: PCR products were visualized in 1% agarose gels and purified using the QIAquick PCR Purification Kit or the QIAquick Gel Extraction Kit (Qiagen). .. PCR products were visualized in 1% agarose gels and purified using the QIAquick PCR Purification Kit or the QIAquick Gel Extraction Kit (Qiagen).

    Polyacrylamide Gel Electrophoresis:

    Article Title: Differential genome-wide profiling of alternative polyadenylation sites in nasopharyngeal carcinoma by high-throughput sequencing
    Article Snippet: The sequences of all primers were consistent with previous studies [ , ]. .. PAGE gel-excision was carried out to select the PCR products with the fragments of 300-500 bp with a QIAquick Gel Extraction Kit (Qiagen, Valencia, CA). .. The final pooled fragments were sequenced from their 3’end on the Illumina HiSeq 2000 system in dark cycle mode.

    Lysis:

    Article Title: Epstein-Barr virus nuclear antigen EBNA-LP is essential for transforming naïve B cells, and facilitates recruitment of transcription factors to the viral genome
    Article Snippet: After two PBS washes, cells were lysed with SDS Lysis buffer on ice for 10 minutes and sonicated using the Diagenode UCD-200 Bioruptor for 15 minutes. .. After proteinase K treatment for 2 hours at 50 degrees, DNA was then purified using the Qiagen QIAQuick gel extraction kit, and eluted in 120 μl water.

    Nested PCR:

    Article Title: Blood parasites infecting the Hoatzin (Opisthocomus hoazin), a unique neotropical folivorous bird
    Article Snippet: For those samples that were positive using the cytb PCR protocol, we amplified between 5,515 to 5,838 bp of the parasite mitochondrial genomes (mtDNA) using a nested PCR with Takara LA Taq™ Polymerase (TaKaRa Takara Mirus Bio) following manufacturers’ directions. .. Then, we excised two independent PCR products (50 ul) from the gel (bands of approximately 6 kbp) and purified using QIAquick® Gel extraction kit (Qiagen, GmbH, Hilden, Germany).

    Article Title: FibroChip, a Functional DNA Microarray to Monitor Cellulolytic and Hemicellulolytic Activities of Rumen Microbiota
    Article Snippet: Then a secondary nested PCR was achieved with 1.5 μl of the first PCR reaction used as PCR template. .. PCR products were gel-purified using the QIAquick Gel extraction Kit (Qiagen, Hilden, Germany) according to the supplier instructions.

    Agarose Gel Electrophoresis:

    Article Title: Tackling critical parameters in metazoan meta-barcoding experiments: a preliminary study based on coxI DNA barcode
    Article Snippet: PCR products along with 100 bp DNA Ladder (Fermentas Life Sciences, Waltham, MA, USA) were visualized on a 1% agarose gel stained with 0.005% of ethidium bromide. .. PCR products were subsequently gel purified using QIAquick Gel Extraction Kit (Qiagen, Hilden, Germany).

    Article Title: Taxonomic and Functional Metagenomic Profile of Sediment From a Commercial Catfish Pond in Mississippi
    Article Snippet: Briefly, genomic DNA was sheared by sonication and separated by electrophoresis on a 1% agarose gel. .. Gel slices corresponding to ∼300 and ∼500 bp were excised and purified using QIAquick Gel Extraction Kit (Qiagen).

    Article Title: Genome-wide identification of new reference genes for RT-qPCR normalization in CGMMV-infected Lagenaria siceraria
    Article Snippet: All primers were synthesized by a commercial supplier (Biosune, Hangzhou, China). .. To check the specificity of all primers, the cDNA of each sample was amplified by PCR, and the amplified products were separated by electrophoresis on 3% agarose gel and purified using a QIAquick Gel Extraction Kit (Qiagen, Hilden, Germany) according to the manufacturer’s instructions, and cloned into pEASY-Blunt zero (Transgen, Beijing, China) followed by sequencing. .. The quantification cycle (Cq) values obtained by qRT-PCR on a standard curve generated from a fourfold dilution series of one sample at six dilution points for three technical replicates were used to draw the standard curve to get R2 and slope values.

    Article Title: PCR Biases Distort Bacterial and Archaeal Community Structure in Pyrosequencing Datasets
    Article Snippet: Both PCR product pools were then run on 2% agarose gel at 50 Volts for 60 min. .. The bands corresponding to 600–700 bp for bacteria and 600–900 bp for archaea were excised and purified using a Qiaquick Gel Extraction kit (Qiagen, Valencia, CA).

    Chromatin Immunoprecipitation:

    Article Title: Epstein-Barr virus nuclear antigen EBNA-LP is essential for transforming naïve B cells, and facilitates recruitment of transcription factors to the viral genome
    Article Snippet: Paragraph title: Chromatin immunoprecipitation (ChIP) ... After proteinase K treatment for 2 hours at 50 degrees, DNA was then purified using the Qiagen QIAQuick gel extraction kit, and eluted in 120 μl water.

    Plasmid Preparation:

    Article Title: Inhibitor of intramembrane protease RseP blocks the σE response causing lethal accumulation of unfolded outer membrane proteins
    Article Snippet: The purified product obtained after isolation with the QIAquick Gel Extraction Kit (Qiagen) was used as template to amplify a variable allele library of rseP . .. The purified product obtained after isolation with the QIAquick Gel Extraction Kit (Qiagen) was used as template to amplify a variable allele library of rseP .

    Article Title: Mutations in Escherichia coli aceE and ribB Genes Allow Survival of Strains Defective in the First Step of the Isoprenoid Biosynthesis Pathway
    Article Snippet: Fragments of 2–4 kb were gel-purified using the Qiaquick (Qiagen) system and ligated into the Bam HI site of pUC19. .. After amplification of the genomic library in TOP10 cells, EcAB4-2 competent cells were transformed with aliquots of the library, and transformants resistant to kanamycin, chloramphenicol, and 100 µg/ml ampicillin that were able to grow without MVA were selected.

    Software:

    Article Title: Prognostic significance of CD117 expression and TP53 missense mutations in triple-negative breast cancer
    Article Snippet: The PCR products were purified using a QIAquick Gel Extraction kit (Qiagen GmbH) and were prepared for sequencing via a 3500Dx genetic analyzer (Applied Biosystems; Thermo Fisher Scientific, Inc., Waltham, MA, USA) with a BigDye Terminator Cycle Sequencing Ready Reaction kit (Applied Biosystems; Thermo Fisher Scientific, Inc.). .. The PCR products were purified using a QIAquick Gel Extraction kit (Qiagen GmbH) and were prepared for sequencing via a 3500Dx genetic analyzer (Applied Biosystems; Thermo Fisher Scientific, Inc., Waltham, MA, USA) with a BigDye Terminator Cycle Sequencing Ready Reaction kit (Applied Biosystems; Thermo Fisher Scientific, Inc.).

    Article Title: Amino Acid Substitutions within HLA-B*27-Restricted T Cell Epitopes Prevent Recognition by Hepatitis Delta Virus-Specific CD8+ T Cells
    Article Snippet: A maximum-likelihood phylogenetic tree was constructed under the Tamura-Nei substitution model using MEGA software v6 ( ). .. The amplicons had a length of 515 bp and were isolated from 0.9% agarose gels with the QIAquick extraction kit (QIAquick spin handbook; Qiagen, Hilden, Germany) and quantified using Quan-iTPicogreens DNA reagent (Invitrogen).

    Real-time Polymerase Chain Reaction:

    Article Title: Epstein-Barr virus nuclear antigen EBNA-LP is essential for transforming naïve B cells, and facilitates recruitment of transcription factors to the viral genome
    Article Snippet: After proteinase K treatment for 2 hours at 50 degrees, DNA was then purified using the Qiagen QIAQuick gel extraction kit, and eluted in 120 μl water. .. Absolute quantity (relative to input) was calculated from standard curves generated from input DNA that was serially diluted 1:4, four times.

    Selection:

    Article Title: Haplotyping of Cornus florida and C. kousa chloroplasts: Insights into species-level differences and patterns of plastic DNA variation in cultivars
    Article Snippet: To extend the chlorotyping panel ( i . e ., the number of informative nucleotide substitutions), the cpDNA01, 02, and 03 regions of six C . kousa cultivars, four C . florida cultivars, and one C . florida breeding selection ( ) were selected for sequencing. .. PCR products were purified for sequencing using the QIAquick Gel Extraction Kit (Qiagen) or ExoSap-It kit (Affymetrix, Cleveland, OH, USA).

    Sample Prep:

    Article Title: PCR Biases Distort Bacterial and Archaeal Community Structure in Pyrosequencing Datasets
    Article Snippet: Paragraph title: PCR Amplification and Sample Preparation for Sequencing ... The bands corresponding to 600–700 bp for bacteria and 600–900 bp for archaea were excised and purified using a Qiaquick Gel Extraction kit (Qiagen, Valencia, CA).

    Next-Generation Sequencing:

    Article Title: Amino Acid Substitutions within HLA-B*27-Restricted T Cell Epitopes Prevent Recognition by Hepatitis Delta Virus-Specific CD8+ T Cells
    Article Snippet: Next-generation sequencing was performed in 11 selected samples to identify variations at a detection level of 0.1% and to pin down variations in the region flanked by nucleotide positions 956 to 1,360 by ultradeep pyrosequencing (UDPS) (primer sequences are listed in ). .. The amplicons had a length of 515 bp and were isolated from 0.9% agarose gels with the QIAquick extraction kit (QIAquick spin handbook; Qiagen, Hilden, Germany) and quantified using Quan-iTPicogreens DNA reagent (Invitrogen).

    dsDNA Assay:

    Article Title: PCR Biases Distort Bacterial and Archaeal Community Structure in Pyrosequencing Datasets
    Article Snippet: The amount of PCR product from each sample was quantified in triplicate using Quant-iT dsDNA assay kit (Invitrogen, Carlsbad, CA) on a Nanodrop 3300 (Thermo Scientific, Wilmington, DE). .. The bands corresponding to 600–700 bp for bacteria and 600–900 bp for archaea were excised and purified using a Qiaquick Gel Extraction kit (Qiagen, Valencia, CA).

    Sampling:

    Article Title: Taxonomic and Functional Metagenomic Profile of Sediment From a Commercial Catfish Pond in Mississippi
    Article Snippet: Paragraph title: Sediment Sampling, DNA Extraction, and Sequencing ... Gel slices corresponding to ∼300 and ∼500 bp were excised and purified using QIAquick Gel Extraction Kit (Qiagen).

    Produced:

    Article Title: Whole-Genome Sequencing and Bioinformatic Analysis of Isolates from Foodborne Illness Outbreaks of Campylobacter jejuni and Salmonella enterica
    Article Snippet: Plates were incubated overnight at 42°C under microaerophilic conditions created in a 2.5-liter jar with 5% O2 , 10% CO2 , and 85% N2 produced by an Oxoid CampyGen sachet (Thermo Fisher Scientific). .. For isolates that could not be recovered from frozen cultures, DNA was extracted directly from the PFGE plugs with the QIAquick gel extraction kit (Qiagen).

    Concentration Assay:

    Article Title: Composition and richness of the serum microbiome differ by age and link to systemic inflammation
    Article Snippet: The band was excised and purified from the agarose using Qiagen QIAquick Gel Extraction Kit according to the manufacturer’s instructions. .. The band was excised and purified from the agarose using Qiagen QIAquick Gel Extraction Kit according to the manufacturer’s instructions.

    Article Title: Antibiotic Treatments for Clostridium difficile Infection Are Associated with Distinct Bacterial and Fungal Community Structures
    Article Snippet: Illumina iTag PCR mixtures (25 μl) contained approximately 5 to 10 ng of template DNA with a final concentration of 1× PCR buffer, 0.8 mM deoxynucleoside triphosphates, 0.625 U of Taq polymerase, 0.2 μM barcoded 515F forward primer, and 0.2 μM Illumina 806R reverse primer per reaction mixture ( ). .. Pooled PCR products were gel purified with a QIAquick gel extraction kit (Qiagen, Frederick, MD) and quantified with a Qubit 2.0 fluorometer (Life Technologies, Inc., Carlsbad, CA).

    Gel Extraction:

    Article Title: Feeding and growth of the marine heterotrophic nanoflagellates, Procryptobia sorokini and Paraphysomonas imperforata on a bacterium, Pseudoalteromonas sp. with an inducible defence against grazing
    Article Snippet: PCR products were generated in 50 μL reaction volumes containing 0,02 U Phusion™ High-Fidelity DNA Polymerase (Thermo Scientific, USA), 1× HF Green Buffer, 200 μM dNTP mix, and 0.5 μM forward and 0.5 μM reverse primer. .. PCR products were subsequently purified with either the QIAquick PCR Purification Kit (Qiagen, Germany) or the QIAquick Gel Extraction Kit (Qiagen, Germany) and outsourced for sequencing at Eurofins Genomics (Eurofins, Germany). .. A blastN analysis was performed against the non-redundant database at NCBI to identify the relevant taxa [ ].

    Article Title: Composition and richness of the serum microbiome differ by age and link to systemic inflammation
    Article Snippet: The PCR product (approximately 250 base pairs) was visualized by UV illumination. .. The band was excised and purified from the agarose using Qiagen QIAquick Gel Extraction Kit according to the manufacturer’s instructions. .. The PCR products were then sequenced using the Illumina MiSeq platform (Kumar et al. ).

    Article Title: Haplotyping of Cornus florida and C. kousa chloroplasts: Insights into species-level differences and patterns of plastic DNA variation in cultivars
    Article Snippet: The cpDNA01, 02, and 03 regions from samples of other Cornus species[ ], belonging to three phylogenetic groups as previously described[ ], were also amplified, and their sequences included in the study ( ). .. PCR products were purified for sequencing using the QIAquick Gel Extraction Kit (Qiagen) or ExoSap-It kit (Affymetrix, Cleveland, OH, USA). .. Analytical sequencing was completed at the UT Genomics Core (Knoxville, TN, USA) and McLab (South San Francisco, CA, USA).

    Article Title: Tackling critical parameters in metazoan meta-barcoding experiments: a preliminary study based on coxI DNA barcode
    Article Snippet: PCR products along with 100 bp DNA Ladder (Fermentas Life Sciences, Waltham, MA, USA) were visualized on a 1% agarose gel stained with 0.005% of ethidium bromide. .. PCR products were subsequently gel purified using QIAquick Gel Extraction Kit (Qiagen, Hilden, Germany). .. The coxI barcode region was sequenced singularly for each Carabidae organism by Sanger method.

    Article Title: Whole-Genome Sequencing and Bioinformatic Analysis of Isolates from Foodborne Illness Outbreaks of Campylobacter jejuni and Salmonella enterica
    Article Snippet: The supernatant was removed, and the pelleted bacteria were used for DNA extraction using the DNeasy blood and tissue kit (Qiagen). .. For isolates that could not be recovered from frozen cultures, DNA was extracted directly from the PFGE plugs with the QIAquick gel extraction kit (Qiagen). .. DNA in the final eluate was quantified by using a Qubit 3.0 fluorometer (Thermo Fisher Scientific).

    Article Title: Taxonomic and Functional Metagenomic Profile of Sediment From a Commercial Catfish Pond in Mississippi
    Article Snippet: Briefly, genomic DNA was sheared by sonication and separated by electrophoresis on a 1% agarose gel. .. Gel slices corresponding to ∼300 and ∼500 bp were excised and purified using QIAquick Gel Extraction Kit (Qiagen). .. The blunt-ended DNA fragments were A-tailed using the Quick Blunting Kit (New England BioLabs) and purified.

    Article Title: Genome-wide identification of new reference genes for RT-qPCR normalization in CGMMV-infected Lagenaria siceraria
    Article Snippet: All primers were synthesized by a commercial supplier (Biosune, Hangzhou, China). .. To check the specificity of all primers, the cDNA of each sample was amplified by PCR, and the amplified products were separated by electrophoresis on 3% agarose gel and purified using a QIAquick Gel Extraction Kit (Qiagen, Hilden, Germany) according to the manufacturer’s instructions, and cloned into pEASY-Blunt zero (Transgen, Beijing, China) followed by sequencing. .. The quantification cycle (Cq) values obtained by qRT-PCR on a standard curve generated from a fourfold dilution series of one sample at six dilution points for three technical replicates were used to draw the standard curve to get R2 and slope values.

    Article Title: Prognostic significance of CD117 expression and TP53 missense mutations in triple-negative breast cancer
    Article Snippet: PCR was performed using a Mastercycler gradient PCR machine (Eppendorf, Hamburg, Germany) under the following amplification conditions: 94°C for 10 min; 40 cycles of 94°C for 45 sec, 61°C for 45 sec, and 72°C for 45 sec; with a final extension at 72°C for 7 min. .. The PCR products were purified using a QIAquick Gel Extraction kit (Qiagen GmbH) and were prepared for sequencing via a 3500Dx genetic analyzer (Applied Biosystems; Thermo Fisher Scientific, Inc., Waltham, MA, USA) with a BigDye Terminator Cycle Sequencing Ready Reaction kit (Applied Biosystems; Thermo Fisher Scientific, Inc.). .. The cycling conditions were: 94°C for 1 min; 24 cycles of 94°C for 10 sec, 50°C for 5 sec, and 60°C for 1 min; and final extension at 72°C for 5 min.

    Article Title: Antibiotic Treatments for Clostridium difficile Infection Are Associated with Distinct Bacterial and Fungal Community Structures
    Article Snippet: Each PCR was carried out with an MJ Research PTC-200 thermocycler (Bio-Rad, Hercules, CA). .. Pooled PCR products were gel purified with a QIAquick gel extraction kit (Qiagen, Frederick, MD) and quantified with a Qubit 2.0 fluorometer (Life Technologies, Inc., Carlsbad, CA). .. Before submission for sequencing, libraries were quality checked with the 2100 Bioanalyzer DNA 1000 chip (Agilent Technologies, Santa Clara, CA).

    Article Title: Integrative genomic and transcriptomic analysis of leiomyosarcoma
    Article Snippet: Amplifications were carried out using Taq DNA Polymerase (Qiagen) according to the manufacturer’s instructions. .. PCR products were visualized in 1% agarose gels and purified using the QIAquick PCR Purification Kit or the QIAquick Gel Extraction Kit (Qiagen). .. Direct sequencing was performed with the forward or reverse primer of the respective amplification.

    Article Title: Blood parasites infecting the Hoatzin (Opisthocomus hoazin), a unique neotropical folivorous bird
    Article Snippet: The PCR conditions were a partial denaturation at 94 °C for 1 min and 30 cycles with 30 s at 94 °C and 7 min at 68 °C and a final extension of 10 min at 72 °C. .. Then, we excised two independent PCR products (50 ul) from the gel (bands of approximately 6 kbp) and purified using QIAquick® Gel extraction kit (Qiagen, GmbH, Hilden, Germany). .. We cloned at least two independent PCR products using pGEM® -T Easy Vector Systems (Promega, Madison, WI, USA), and we sequenced four clones from each individual.

    Article Title: Epstein-Barr virus nuclear antigen EBNA-LP is essential for transforming naïve B cells, and facilitates recruitment of transcription factors to the viral genome
    Article Snippet: The immune complexes were eluted from the beads using elution buffer and left overnight at 65 degrees. .. After proteinase K treatment for 2 hours at 50 degrees, DNA was then purified using the Qiagen QIAQuick gel extraction kit, and eluted in 120 μl water. .. Chromatin was quantified by qPCR using the Kapa qPCR SYBR kit (low Rox) on a QuantStudio7 real time PCR machine (Applied Biosystems).

    Article Title: Inhibitor of intramembrane protease RseP blocks the σE response causing lethal accumulation of unfolded outer membrane proteins
    Article Snippet: Primers rseP_5′ and rseP_3′, both of which incorporate overhangs complementary to the sequence flanking the cloning site in pCDFG (described below), were used to amplify rseP from BW25113 E. coli using Phusion High-Fidelity DNA polymerase. .. The purified product obtained after isolation with the QIAquick Gel Extraction Kit (Qiagen) was used as template to amplify a variable allele library of rseP . .. Briefly, using the Clontech Diversify PCR Random Mutagenesis Kit under conditions yielding 2.3 mutations per 1,000 bp (160 µM MnSO4 and 40 mM dGTP), 50 ng of purified rseP template was amplified with primers rseP_5′ and rseP_3′ and was gel purified.

    Article Title: FibroChip, a Functional DNA Microarray to Monitor Cellulolytic and Hemicellulolytic Activities of Rumen Microbiota
    Article Snippet: Several secondary PCR reactions were realized in order to obtain enough PCR products for sequencing. .. PCR products were gel-purified using the QIAquick Gel extraction Kit (Qiagen, Hilden, Germany) according to the supplier instructions. .. Finally purified PCR products were concentrated with the MinElute PCR Purification Kit (Qiagen, Hilden, Germany) and sequenced by the MWG Company (Mulhouse, France) using primers of the secondary PCR reaction.

    Article Title: PCR Biases Distort Bacterial and Archaeal Community Structure in Pyrosequencing Datasets
    Article Snippet: Both PCR product pools were then run on 2% agarose gel at 50 Volts for 60 min. .. The bands corresponding to 600–700 bp for bacteria and 600–900 bp for archaea were excised and purified using a Qiaquick Gel Extraction kit (Qiagen, Valencia, CA). .. A larger range of amplicon sizes was extracted for archaea as the V3–V5 region of C. maquilingensis is 733 bp in size.

    Article Title: Evaluating the Ribosomal Internal Transcribed Spacer (ITS) as a Candidate Dinoflagellate Barcode Marker
    Article Snippet: All culture collection ITS amplicons were sequenced directly. .. Single PCR products were diluted to 30 ng/µl or purified by gel extraction using the QIAquick Gel Extraction kit (Qiagen, Mississauga, ON, Canada), according to manufacturer's instructions and were either sent to Canadian Centre of DNA Barcoding, Guelph, ON for DNA sequencing or were sequenced directly using BigDye v3.1 reagents and sent to NAPS unit at University of British Columbia, BC for capillary electrophoresis. .. All sequences generated from this study are listed in with Genbank accession numbers) and on the BOLD database in DAITS project at http://www.barcodinglife.org/views/projectlist.php?

    Article Title: Amino Acid Substitutions within HLA-B*27-Restricted T Cell Epitopes Prevent Recognition by Hepatitis Delta Virus-Specific CD8+ T Cells
    Article Snippet: Finally, the PCR products were purified via QIAquick gel extraction (Qiagen) and directly sequenced on an ABI 3730xl DNA analyzer using internal primers 912-F and 1674-R. HDV sequences from this study and NCBI GenBank were aligned using ClustalX2 software ( ). .. The amplicons had a length of 515 bp and were isolated from 0.9% agarose gels with the QIAquick extraction kit (QIAquick spin handbook; Qiagen, Hilden, Germany) and quantified using Quan-iTPicogreens DNA reagent (Invitrogen).

    Environmental Sampling:

    Article Title: PCR Biases Distort Bacterial and Archaeal Community Structure in Pyrosequencing Datasets
    Article Snippet: The bands corresponding to 600–700 bp for bacteria and 600–900 bp for archaea were excised and purified using a Qiaquick Gel Extraction kit (Qiagen, Valencia, CA). .. The bands corresponding to 600–700 bp for bacteria and 600–900 bp for archaea were excised and purified using a Qiaquick Gel Extraction kit (Qiagen, Valencia, CA).

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    Qiagen sgrnas
    Comparison of selected treatments on the visualization of RPA-generated amplicons. a Results using primer pair TYL828F/TYL834R from crude extracts prepared in 0.5 N NaOH from Tomato yellow leaf curl virus (TYLCV)-infected tomato leaves and cleaned by heating to 65 °C for 15 min. Lane M: 50 bp ladder MW standard, size is indicated in kilobases (kb); Lane 1 fresh tissue; Lane 2 tissue kept frozen at −20 °C for 5 months; Lane 3 tissue kept frozen at −80 °C for 3 months; Lane 4 desiccated tissue maintained at room temperature for 15 years; Lane 5 non-inoculated tissue kept frozen at −80 °C for 3 months. b Detection of TYLCV from crude extracts prepared in 0.5 N NaOH and cleaned as follows: Lane 1 untreated; Lane 2 <t>QIAquick</t> PCR purification column; Lane 3 heated at 65 °C for 10 min; Lane 4 heated at 95 °C for 10 min; Lane 5 amplicon loading buffer contained 5 % SDS; Lane 6 amplicon loading buffer contained 10 % SDS; Lane 7 amplicon loading buffer contained 5 % formamide; Lane 8 amplicon loading buffer contained 15 % formamide. Ten μl of amplified product were loaded into each lane of the 1.5 % agarose gels and stained with ethidium bromide
    Sgrnas, supplied by Qiagen, used in various techniques. Bioz Stars score: 99/100, based on 40 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Comparison of selected treatments on the visualization of RPA-generated amplicons. a Results using primer pair TYL828F/TYL834R from crude extracts prepared in 0.5 N NaOH from Tomato yellow leaf curl virus (TYLCV)-infected tomato leaves and cleaned by heating to 65 °C for 15 min. Lane M: 50 bp ladder MW standard, size is indicated in kilobases (kb); Lane 1 fresh tissue; Lane 2 tissue kept frozen at −20 °C for 5 months; Lane 3 tissue kept frozen at −80 °C for 3 months; Lane 4 desiccated tissue maintained at room temperature for 15 years; Lane 5 non-inoculated tissue kept frozen at −80 °C for 3 months. b Detection of TYLCV from crude extracts prepared in 0.5 N NaOH and cleaned as follows: Lane 1 untreated; Lane 2 QIAquick PCR purification column; Lane 3 heated at 65 °C for 10 min; Lane 4 heated at 95 °C for 10 min; Lane 5 amplicon loading buffer contained 5 % SDS; Lane 6 amplicon loading buffer contained 10 % SDS; Lane 7 amplicon loading buffer contained 5 % formamide; Lane 8 amplicon loading buffer contained 15 % formamide. Ten μl of amplified product were loaded into each lane of the 1.5 % agarose gels and stained with ethidium bromide

    Journal: Virology Journal

    Article Title: Evaluation of recombinase polymerase amplification for detection of begomoviruses by plant diagnostic clinics

    doi: 10.1186/s12985-016-0504-8

    Figure Lengend Snippet: Comparison of selected treatments on the visualization of RPA-generated amplicons. a Results using primer pair TYL828F/TYL834R from crude extracts prepared in 0.5 N NaOH from Tomato yellow leaf curl virus (TYLCV)-infected tomato leaves and cleaned by heating to 65 °C for 15 min. Lane M: 50 bp ladder MW standard, size is indicated in kilobases (kb); Lane 1 fresh tissue; Lane 2 tissue kept frozen at −20 °C for 5 months; Lane 3 tissue kept frozen at −80 °C for 3 months; Lane 4 desiccated tissue maintained at room temperature for 15 years; Lane 5 non-inoculated tissue kept frozen at −80 °C for 3 months. b Detection of TYLCV from crude extracts prepared in 0.5 N NaOH and cleaned as follows: Lane 1 untreated; Lane 2 QIAquick PCR purification column; Lane 3 heated at 65 °C for 10 min; Lane 4 heated at 95 °C for 10 min; Lane 5 amplicon loading buffer contained 5 % SDS; Lane 6 amplicon loading buffer contained 10 % SDS; Lane 7 amplicon loading buffer contained 5 % formamide; Lane 8 amplicon loading buffer contained 15 % formamide. Ten μl of amplified product were loaded into each lane of the 1.5 % agarose gels and stained with ethidium bromide

    Article Snippet: The amplicons were cleaned using one of these methods: QIAquick columns according to the manufacturer’s instructions (Qiagen, Valencia, CA); incubation at 65 °C for 10 min; incubation at 95 °C for 10 min; addition of SDS to the loading buffer to a final concentration of 5 % w/v; addition of SDS to a final concentration of 10 % w/v %; or addition of formamide to a final concentration of 15 %.

    Techniques: Recombinase Polymerase Amplification, Generated, Infection, Polymerase Chain Reaction, Purification, Amplification, Staining

    CRISPR/Cas9 mutagenesis of lamc3 causes defects in parachordal chain (PAC) development. ( A ) Design of sgRNAs targeted to exon1 of the lamc3 gene. Each sgRNA targets a restriction endonuclease site used for genotyping and is upstream of a protospacer adjustment motif (PAM). ( B – D ) Cas9/sgRNA injected embryos (as labelled) at 50 hpf. ( B – D ) Brightfield images show no developmental defects or developmental delay. ( B′ – D′ ) Whole embryo images of Tg( fli1a :egfp) fluorescence area indicated by white dotted line is enlarged in ( B′′ – D′′ ) the PAC in each hemisegment is indicated with a red asterisk. ( E ) Quantification of Tg( fli1a :egfp) embryos at 50 hpf with PAC defects. P-values determined by Fisher’s exact Two-tailed test compared to Cas9 alone controls. ( F – I ) 2% agarose genotyping gels with 100 bp ladder. ( F ) Schematic diagram of the region amplified by PCR contains two SphI sites (orange), which would digest into three fragments of 83, 164 and 263 bp in length. Predicted mutation of one of these sites will produce two bands of 83 and 427 bp in length. A natural variant contains a SNP in the second SphI site, complete digestion of this variant would produce two bands of 164 and 346 bp in length. Mutation of the target SphI site would prevent digestion of the fragment. Digestion of the amplicon with Taq α I (blue) in wild type embryos will yield two fragments of 204 and 306 bp in size. ( G ) Restriction endonuclease digest of target region shows undigested mutant products (black asterisk) at a size of 427/510 bp in sgRNA1-injected embryos. ( H ) Fewer undigested mutant products (510 bp) were observed in sgRNA2-injected embryos. ( I ) Brightfield images sgRNA1/Cas9 injected embryo at 5 dpf shows severe oedema. ( J ) Genotyping of 3-month adult fish. A, anterior; b/bp, base pairs; d, days post fertilisation; D, dorsal; kb, kilobases; mpf, months post fertilisation; n, number of embryos; PAC, parachordal chain; PAM, protospacer adjustment motif; SBMO, splice-blocking morpholino; sgRNA, short guide RNA; U, undigested control;.

    Journal: Wellcome Open Research

    Article Title: Knockdown of Laminin gamma-3 (Lamc3) impairs motoneuron guidance in the zebrafish embryo

    doi: 10.12688/wellcomeopenres.12394.1

    Figure Lengend Snippet: CRISPR/Cas9 mutagenesis of lamc3 causes defects in parachordal chain (PAC) development. ( A ) Design of sgRNAs targeted to exon1 of the lamc3 gene. Each sgRNA targets a restriction endonuclease site used for genotyping and is upstream of a protospacer adjustment motif (PAM). ( B – D ) Cas9/sgRNA injected embryos (as labelled) at 50 hpf. ( B – D ) Brightfield images show no developmental defects or developmental delay. ( B′ – D′ ) Whole embryo images of Tg( fli1a :egfp) fluorescence area indicated by white dotted line is enlarged in ( B′′ – D′′ ) the PAC in each hemisegment is indicated with a red asterisk. ( E ) Quantification of Tg( fli1a :egfp) embryos at 50 hpf with PAC defects. P-values determined by Fisher’s exact Two-tailed test compared to Cas9 alone controls. ( F – I ) 2% agarose genotyping gels with 100 bp ladder. ( F ) Schematic diagram of the region amplified by PCR contains two SphI sites (orange), which would digest into three fragments of 83, 164 and 263 bp in length. Predicted mutation of one of these sites will produce two bands of 83 and 427 bp in length. A natural variant contains a SNP in the second SphI site, complete digestion of this variant would produce two bands of 164 and 346 bp in length. Mutation of the target SphI site would prevent digestion of the fragment. Digestion of the amplicon with Taq α I (blue) in wild type embryos will yield two fragments of 204 and 306 bp in size. ( G ) Restriction endonuclease digest of target region shows undigested mutant products (black asterisk) at a size of 427/510 bp in sgRNA1-injected embryos. ( H ) Fewer undigested mutant products (510 bp) were observed in sgRNA2-injected embryos. ( I ) Brightfield images sgRNA1/Cas9 injected embryo at 5 dpf shows severe oedema. ( J ) Genotyping of 3-month adult fish. A, anterior; b/bp, base pairs; d, days post fertilisation; D, dorsal; kb, kilobases; mpf, months post fertilisation; n, number of embryos; PAC, parachordal chain; PAM, protospacer adjustment motif; SBMO, splice-blocking morpholino; sgRNA, short guide RNA; U, undigested control;.

    Article Snippet: PCR products were gel purified (28706, Qiagen) and sgRNAs were transcribed using T7 MegaShortScript transcription kits (AM1354, Ambion) and purified using RNeasy Mini kits (74104, Qiagen) according to the manufacturers’ instructions. sgRNA quality was checked by running on a 2% agarose gel, quantified using a Nanodrop spectrophotometer and stored in aliquots at -80°C.

    Techniques: CRISPR, Mutagenesis, Injection, Fluorescence, Two Tailed Test, Amplification, Polymerase Chain Reaction, Variant Assay, Fluorescence In Situ Hybridization, Blocking Assay

    (A) PCR analysis of pShuttle-CMV-p27. 1: DNA marker; 2–5: pShuttle-CMV-p27. (B) Analysis of agarose gel electrophoresis for plasmid pAd-p27. 1: DNA marker, 2–7: electrophoresis photographs of pAd-p27. The positive clones include 2, 5, 6, and 7.

    Journal: Acta Pharmacologica Sinica

    Article Title: Adenovirus-mediated delivery of p27KIP1 to prevent wound healing after experimental glaucoma filtration surgery

    doi: 10.1038/aps.2009.23

    Figure Lengend Snippet: (A) PCR analysis of pShuttle-CMV-p27. 1: DNA marker; 2–5: pShuttle-CMV-p27. (B) Analysis of agarose gel electrophoresis for plasmid pAd-p27. 1: DNA marker, 2–7: electrophoresis photographs of pAd-p27. The positive clones include 2, 5, 6, and 7.

    Article Snippet: After verifying amplification by agarose gel electrophoresis, the PCR products were purified using a Plasmid DNA Extraction Kit (Qiagen Co, Germany).

    Techniques: Polymerase Chain Reaction, Marker, Agarose Gel Electrophoresis, Plasmid Preparation, Electrophoresis, Clone Assay

    Recovery of nucleic acids and polyphosphate (polyP) using various purification methods. Known quantities of bacteriophage lambda DNA (DNA, striped bars), polyG (RNA, white bars), or long-chain polyP (black bars) were processed for nucleic acid purification using Qiaquick, DNeasy, or TRIzol kits, following the manufacturer’s instructions, or with phenol/chloroform extraction. Nucleic acid recovery was quantified using A 260 and polyP recovery by digestion with PPX1 and PiBlue assay. Results are plotted as percent of the input amount in each experiment. For all experiments except the Qiaquick kits, the three samples were: (A) DNA alone (5 µg lambda DNA); (B) RNA alone (5 µg polyG); (C) 5 µg polyP alone; (D) a mixture of 5 µg polyP plus 5 µg of DNA; or (E) 5 µg polyP plus 5 µg of RNA (E) . Experiments with the Qiaquick kit employed 2.5 µg of polyP and/or nucleic acid. Data are mean ± SEM ( n = 3).

    Journal: Frontiers in Medicine

    Article Title: Ability of Polyphosphate and Nucleic Acids to Trigger Blood Clotting: Some Observations and Caveats

    doi: 10.3389/fmed.2018.00107

    Figure Lengend Snippet: Recovery of nucleic acids and polyphosphate (polyP) using various purification methods. Known quantities of bacteriophage lambda DNA (DNA, striped bars), polyG (RNA, white bars), or long-chain polyP (black bars) were processed for nucleic acid purification using Qiaquick, DNeasy, or TRIzol kits, following the manufacturer’s instructions, or with phenol/chloroform extraction. Nucleic acid recovery was quantified using A 260 and polyP recovery by digestion with PPX1 and PiBlue assay. Results are plotted as percent of the input amount in each experiment. For all experiments except the Qiaquick kits, the three samples were: (A) DNA alone (5 µg lambda DNA); (B) RNA alone (5 µg polyG); (C) 5 µg polyP alone; (D) a mixture of 5 µg polyP plus 5 µg of DNA; or (E) 5 µg polyP plus 5 µg of RNA (E) . Experiments with the Qiaquick kit employed 2.5 µg of polyP and/or nucleic acid. Data are mean ± SEM ( n = 3).

    Article Snippet: In these experiments, known quantities of purified bacteriophage lambda DNA or a synthetic RNA homopolymer, polyG, either alone or mixed with long-chain polyP, were purified using phenol/chloroform extraction or Qiaquick kits (Qiagen), DNeasy kits (Qiagen), RNeasy Miniprep kits (Qiagen), or TRIzol kits (Thermo Fisher), following the manufacturers’ instructions.

    Techniques: Purification, Lambda DNA Preparation, Nucleic Acid Purification