polymerase chain reaction clean up kit  (Qiagen)


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    Structured Review

    Qiagen polymerase chain reaction clean up kit
    Polymerase Chain Reaction Clean Up Kit, supplied by Qiagen, used in various techniques. Bioz Stars score: 92/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/polymerase chain reaction clean up kit/product/Qiagen
    Average 92 stars, based on 1 article reviews
    Price from $9.99 to $1999.99
    polymerase chain reaction clean up kit - by Bioz Stars, 2020-04
    92/100 stars

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    Clone Assay:

    Article Title: Analyses of Mitogenome Sequences Revealed that Asian Citrus Psyllids (Diaphorina citri) from California Were Related to Those from Florida
    Article Snippet: The amplified DNA fragments were cut by NucleoSpin® Gel and PCR Clean-up kit (QIAGEN, Valencia, USA). .. PCR products of the respective DNA fragments were cloned into pEASY cloning vectors.

    Centrifugation:

    Article Title: The Staphylococcal Accessory Regulator, SarA, is an RNA-Binding Protein that Modulates the mRNA Turnover Properties of Late-Exponential and Stationary Phase Staphylococcus aureus Cells
    Article Snippet: Columns were washed five times with 1× IP buffer and c-Myc-SarA complexes were eluted in 50 μl of elution buffer (50 mM Tris pH 8.0, 10 mM EDTA, 1% SDS) by first incubating at 65o C for 10 in followed by centrifugation at 4o C to collect eluate. .. For chromatin immunoprecipitation (ChIP-chip) experiments used to detect known SarA-DNA interactions, liberated DNA was purified using a PCR Clean-Up Kit (Qiagen) per manufacturer’s recommendations and hybridized to a GeneChip® and processed as described above.

    Article Title: Bim regulation may determine hippocampal vulnerability after injurious seizures and in temporal lobe epilepsy
    Article Snippet: Samples were cleared by centrifugation (12,000 g ) and then incubated with an antibody against FKHR (Cell Signaling Technology Inc.) overnight at 4°C. .. DNA samples were purified using a PCR clean-up kit (QIAGEN Inc., Valencia, California, USA), and then DNA was subjected to 36 cycles of PCR with primers specific to the FKHR consensus on the bim promoter: sense 5′-TCTCTCAACTGTCCTTCC-3′, antisense 5′-TGTTTACCCTAGTGACTTGG-3′ (accession number ) ( ).

    Amplification:

    Article Title: Melarsoprol Sensitivity Profile of Trypanosoma brucei gambiense Isolates from Cured and Relapsed Sleeping Sickness Patients from the Democratic Republic of the Congo
    Article Snippet: Amplification conditions were: initial denaturation at 95°C for 5 min, 24 cycles of 1 min at 95°C followed by 1 min at 56°C and 2 min at 72°C, final extension at 72°C for 5 min. .. For selected strains, the amplicons were cleaned up and concentrated using a PCR clean-up kit (Qiagen) and sent out for bidirectional direct sequencing at the VIB Genetic Sequencing Facility (Antwerp, Belgium) using the described PCR primers and additional internal primers to cover TbAT1 .

    Article Title: A functional analysis of the CREB signaling pathway using HaloCHIP-chip and high throughput reporter assays
    Article Snippet: Isolated DNA was further purified using a PCR Clean-up kit (Qiagen), and eluted 2 × 50 μl with nuclease-free water, yielding a final volume of 100 μl. .. To prepare sufficient HaloCHIP DNA for downstream amplification steps required for microarrays, an entire 6-well plate was transfected and processed through the HaloCHIP method as recommended.

    Article Title: Analyses of Mitogenome Sequences Revealed that Asian Citrus Psyllids (Diaphorina citri) from California Were Related to Those from Florida
    Article Snippet: .. The amplified DNA fragments were cut by NucleoSpin® Gel and PCR Clean-up kit (QIAGEN, Valencia, USA). .. PCR products of the respective DNA fragments were cloned into pEASY cloning vectors.

    Article Title: The Staphylococcal Accessory Regulator, SarA, is an RNA-Binding Protein that Modulates the mRNA Turnover Properties of Late-Exponential and Stationary Phase Staphylococcus aureus Cells
    Article Snippet: For chromatin immunoprecipitation (ChIP-chip) experiments used to detect known SarA-DNA interactions, liberated DNA was purified using a PCR Clean-Up Kit (Qiagen) per manufacturer’s recommendations and hybridized to a GeneChip® and processed as described above. .. Following IP, bacterial RNA was amplified and reverse-transcribed using a MessageAmp II-Bacteria Prokaryotic RNA Amplification Kit (Ambion).

    Article Title: Melarsoprol Sensitivity Profile of Trypanosoma brucei gambiense Isolates from Cured and Relapsed Sleeping Sickness Patients from the Democratic Republic of the Congo
    Article Snippet: Amplification conditions were: initial denaturation at 95°C for 5 min, 24 cycles of 1 min at 95°C followed by 1 min at 60°C and 4 min at 72°C, final extension at 72°C for 10 min. .. For selected strains, amplicons were cleaned up and concentrated using a PCR clean-up kit (Qiagen) and sent out for bidirectional direct sequencing at the VIB Genetic Sequencing Facility (Antwerp, Belgium) using the described PCR primers and additional internal primers to cover TbAQP2 .

    Article Title: A functional analysis of the CREB signaling pathway using HaloCHIP-chip and high throughput reporter assays
    Article Snippet: .. Isolated DNA was further purified using a PCR Clean-up kit (Qiagen), processed, and amplified using WGA identical as the HaloCHIP samples. .. Quantitative PCR and primers HaloCHIP DNA was analyzed using either Plexor (Promega) or SYBR green (Applied Biosystems) qPCR according to their respective manufacturer's recommendations.

    Whole Genome Amplification:

    Article Title: A functional analysis of the CREB signaling pathway using HaloCHIP-chip and high throughput reporter assays
    Article Snippet: Paragraph title: HaloCHIP Protocol and Whole Genome Amplification ... Isolated DNA was further purified using a PCR Clean-up kit (Qiagen), and eluted 2 × 50 μl with nuclease-free water, yielding a final volume of 100 μl.

    Article Title: A functional analysis of the CREB signaling pathway using HaloCHIP-chip and high throughput reporter assays
    Article Snippet: .. Isolated DNA was further purified using a PCR Clean-up kit (Qiagen), processed, and amplified using WGA identical as the HaloCHIP samples. .. Quantitative PCR and primers HaloCHIP DNA was analyzed using either Plexor (Promega) or SYBR green (Applied Biosystems) qPCR according to their respective manufacturer's recommendations.

    Synthesized:

    Article Title: Bim regulation may determine hippocampal vulnerability after injurious seizures and in temporal lobe epilepsy
    Article Snippet: DNA samples were purified using a PCR clean-up kit (QIAGEN Inc., Valencia, California, USA), and then DNA was subjected to 36 cycles of PCR with primers specific to the FKHR consensus on the bim promoter: sense 5′-TCTCTCAACTGTCCTTCC-3′, antisense 5′-TGTTTACCCTAGTGACTTGG-3′ (accession number ) ( ). .. Antisense oligonucleotides complementary to the bim cDNA sequence were identified and synthesized by Sigma Genosys (Sigma-Aldrich) (antisense 1, 5′-TGGCCAAGCAACCTTCTG-3′; antisense 2, 5′-GTGTGACAGAGAAGGTGG-3′; antisense 3, 5′-TAAGGCAGTCTCAGGAGG-3′; antisense 4, 5′-ATTGCAGCCTGCTGAGAG-3′).

    Construct:

    Article Title: A functional analysis of the CREB signaling pathway using HaloCHIP-chip and high throughput reporter assays
    Article Snippet: After reaching 70-80% confluency, typically 18-24 hours later, cells were transfected with the HaloTag-CREB fusion constructs (experimental sample) or left untransfected (control sample). .. Isolated DNA was further purified using a PCR Clean-up kit (Qiagen), and eluted 2 × 50 μl with nuclease-free water, yielding a final volume of 100 μl.

    SYBR Green Assay:

    Article Title: Autophagy acts through TRAF3 and RELB to regulate gene expression via antagonism of SMAD proteins
    Article Snippet: .. DNA was purified with a Qiagen PCR clean-up kit according to the manufacturer’s instructions, and samples were quantified for specific DNA species by SYBR-green qRT-PCR as described above, using the tabulated primers (Supplementary Table ). .. For re-ChIP assays, following the first immunoprecipitation (as above), beads were washed three times with re-ChIP wash buffer (2 mM EDTA, 200 mM NaCl, 0.1% SDS, 1% NP-40) and twice with Tris-EDTA buffer.

    Incubation:

    Article Title: Specific functions of TET1 and TET2 in regulating mesenchymal cell lineage determination
    Article Snippet: The immunoprecipitation was incubated with magnetic IgG beads for 2 h at 4 °C and washed with IP buffer and then in high salt buffer (10 mM sodium phosphate (pH 7.0), 400 mM NaCl, 0.05% Triton X-100). .. Immunoprecipitated bead–DNA complex was treated with proteinase K for 3 h at 50 °C in elution buffer and hydroxymethylated DNA purified by using the Qiagen PCR clean-up kit (Qiaquick).

    Article Title: The Staphylococcal Accessory Regulator, SarA, is an RNA-Binding Protein that Modulates the mRNA Turnover Properties of Late-Exponential and Stationary Phase Staphylococcus aureus Cells
    Article Snippet: Cells were centrifuged at 3000 RPM for 10 min at 4o C and cell pellets were washed twice in 1 ml ice-cold TBS, resuspended in 350 μl of lysis buffer (10 mM Tris pH 8.0, 10 mM EDTA, 50 mM NaCl, and 1 mM PMSF) and were lysed by the addition 100 μg ml−1 lysostaphin (Ambi; Lawrence, NY) at 37o C for 30 min. Next, an equal volume of 2× immunoprecipitation (IP) buffer (100 mM Tris pH 8.0, 10 mM EDTA, 300 mM NaCl, 2% Triton X-100, 1 mM PMSF) was added and suspensions were incubated for an additional 10 min at 37o C. Nucleic acids were fragmented with a Sonic Dismembrator (Fisher) on ice twice for 15 s using an output setting of one with 15 s rests on ice between each pulse and cell debris was subsequently removed by centrifugation for 10 min at 4o C. Next, 800 μl of the supernatant was mixed with 10 μl of anti-c-Myc agarose (Pierce Biotechnology; Rockford IL) and then added to IP spin columns (Pierce Biotechnology) and incubated overnight at 4o C to collect c-Myc-SarA/RNA and DNA complexes. .. For chromatin immunoprecipitation (ChIP-chip) experiments used to detect known SarA-DNA interactions, liberated DNA was purified using a PCR Clean-Up Kit (Qiagen) per manufacturer’s recommendations and hybridized to a GeneChip® and processed as described above.

    Article Title: Bim regulation may determine hippocampal vulnerability after injurious seizures and in temporal lobe epilepsy
    Article Snippet: Samples were cleared by centrifugation (12,000 g ) and then incubated with an antibody against FKHR (Cell Signaling Technology Inc.) overnight at 4°C. .. DNA samples were purified using a PCR clean-up kit (QIAGEN Inc., Valencia, California, USA), and then DNA was subjected to 36 cycles of PCR with primers specific to the FKHR consensus on the bim promoter: sense 5′-TCTCTCAACTGTCCTTCC-3′, antisense 5′-TGTTTACCCTAGTGACTTGG-3′ (accession number ) ( ).

    Article Title: PRDM9 Drives Evolutionary Erosion of Hotspots in Mus musculus through Haplotype-Specific Initiation of Meiotic Recombination
    Article Snippet: To reverse crosslinks the supernatant was transferred to a new tube, supplemented with 200 mM NaCl, and incubated for 5 hours at 65°C. .. DNA was purified using the Qiagen PCR Clean-up kit (Qiagen).

    Article Title: Autophagy acts through TRAF3 and RELB to regulate gene expression via antagonism of SMAD proteins
    Article Snippet: 200 mM NaCl was added to eluted, precipitated chromatin, or to input samples, and cross-linking was reversed by incubation at 65 °C overnight. .. DNA was purified with a Qiagen PCR clean-up kit according to the manufacturer’s instructions, and samples were quantified for specific DNA species by SYBR-green qRT-PCR as described above, using the tabulated primers (Supplementary Table ).

    Article Title: A functional analysis of the CREB signaling pathway using HaloCHIP-chip and high throughput reporter assays
    Article Snippet: Co-immunoprecipitation was performed using 1 μg of anti-CREB1 antibody (Millipore #06-863) for the experimental sample and 1 μg of anti-IgG antibody (Sigma) for the control sample with incubation at 4°C for 15 hours. .. Isolated DNA was further purified using a PCR Clean-up kit (Qiagen), processed, and amplified using WGA identical as the HaloCHIP samples.

    Expressing:

    Article Title: Bim regulation may determine hippocampal vulnerability after injurious seizures and in temporal lobe epilepsy
    Article Snippet: DNA samples were purified using a PCR clean-up kit (QIAGEN Inc., Valencia, California, USA), and then DNA was subjected to 36 cycles of PCR with primers specific to the FKHR consensus on the bim promoter: sense 5′-TCTCTCAACTGTCCTTCC-3′, antisense 5′-TGTTTACCCTAGTGACTTGG-3′ (accession number ) ( ). .. Bim expression was manipulated in vitro using an antisense approach.

    Modification:

    Article Title: Melarsoprol Sensitivity Profile of Trypanosoma brucei gambiense Isolates from Cured and Relapsed Sleeping Sickness Patients from the Democratic Republic of the Congo
    Article Snippet: PCR for full-length TbAT1 The protocol to amplify the full length TbAT1 gene and its flanking regions was slightly modified from Graf et al. . .. For selected strains, the amplicons were cleaned up and concentrated using a PCR clean-up kit (Qiagen) and sent out for bidirectional direct sequencing at the VIB Genetic Sequencing Facility (Antwerp, Belgium) using the described PCR primers and additional internal primers to cover TbAT1 .

    Western Blot:

    Article Title: The Staphylococcal Accessory Regulator, SarA, is an RNA-Binding Protein that Modulates the mRNA Turnover Properties of Late-Exponential and Stationary Phase Staphylococcus aureus Cells
    Article Snippet: For chromatin immunoprecipitation (ChIP-chip) experiments used to detect known SarA-DNA interactions, liberated DNA was purified using a PCR Clean-Up Kit (Qiagen) per manufacturer’s recommendations and hybridized to a GeneChip® and processed as described above. .. All assays were performed in triplicate for each strain and purification of the c-Myc-SarA protein was confirmed via Western blotting.

    RNA Binding Assay:

    Article Title: The Staphylococcal Accessory Regulator, SarA, is an RNA-Binding Protein that Modulates the mRNA Turnover Properties of Late-Exponential and Stationary Phase Staphylococcus aureus Cells
    Article Snippet: To do so, S. aureus strains UAMS-929 (ΔsarA ; negative control) and KLA43 (ΔsarA /pKLA40::c-Myc-SarA) were grown to mid-exponential phase and RNA-binding proteins were cross-linked to RNA by incubating the cells for 30 min with 1% formaldehyde at room temperature. .. For chromatin immunoprecipitation (ChIP-chip) experiments used to detect known SarA-DNA interactions, liberated DNA was purified using a PCR Clean-Up Kit (Qiagen) per manufacturer’s recommendations and hybridized to a GeneChip® and processed as described above.

    Transfection:

    Article Title: A functional analysis of the CREB signaling pathway using HaloCHIP-chip and high throughput reporter assays
    Article Snippet: After reaching 70-80% confluency, typically 18-24 hours later, cells were transfected with the HaloTag-CREB fusion constructs (experimental sample) or left untransfected (control sample). .. Isolated DNA was further purified using a PCR Clean-up kit (Qiagen), and eluted 2 × 50 μl with nuclease-free water, yielding a final volume of 100 μl.

    Concentration Assay:

    Article Title: A functional analysis of the CREB signaling pathway using HaloCHIP-chip and high throughput reporter assays
    Article Snippet: Twenty four hours post-transfection, cells were crosslinked with formaldehyde (Sigma) at a final concentration of 0.75% for 10 minutes at 22°, quenched with 0.125 M glycine for 10 min. and processed using the HaloCHIP kit (Promega). .. Isolated DNA was further purified using a PCR Clean-up kit (Qiagen), and eluted 2 × 50 μl with nuclease-free water, yielding a final volume of 100 μl.

    Article Title: Autophagy acts through TRAF3 and RELB to regulate gene expression via antagonism of SMAD proteins
    Article Snippet: DNA was purified with a Qiagen PCR clean-up kit according to the manufacturer’s instructions, and samples were quantified for specific DNA species by SYBR-green qRT-PCR as described above, using the tabulated primers (Supplementary Table ). .. Following elution, the supernatant was diluted to a concentration of 0.1% SDS with ChIP dilution buffer (1% Triton-X-100, 2 mM EDTA, 150 mM NaCl, 20 mM Tris-HCl, pH 8.1) supplemented with 50 μg bovine serum albumin and protease inhibitor tablets (Roche).

    Article Title: A functional analysis of the CREB signaling pathway using HaloCHIP-chip and high throughput reporter assays
    Article Snippet: Cells were treated with 10 uM forskolin for 45 minutes at 37°. crosslinked with formaldehyde (Sigma) at a final concentration of 1.0% for 10 minutes at 22°, quenched with 0.125 M glycine for 10 min. and processed using the ChIP Assay Kit (USB). .. Isolated DNA was further purified using a PCR Clean-up kit (Qiagen), processed, and amplified using WGA identical as the HaloCHIP samples.

    Protease Inhibitor:

    Article Title: Bim regulation may determine hippocampal vulnerability after injurious seizures and in temporal lobe epilepsy
    Article Snippet: Hippocampal cultures were treated with paraformaldehyde (2%, 2 minutes) to cross-link proteins to DNA and then lysed and sonicated in buffer containing a protease inhibitor cocktail (Roche Molecular Biochemicals, Indianapolis, Indiana, USA). .. DNA samples were purified using a PCR clean-up kit (QIAGEN Inc., Valencia, California, USA), and then DNA was subjected to 36 cycles of PCR with primers specific to the FKHR consensus on the bim promoter: sense 5′-TCTCTCAACTGTCCTTCC-3′, antisense 5′-TGTTTACCCTAGTGACTTGG-3′ (accession number ) ( ).

    Article Title: Autophagy acts through TRAF3 and RELB to regulate gene expression via antagonism of SMAD proteins
    Article Snippet: DNA was purified with a Qiagen PCR clean-up kit according to the manufacturer’s instructions, and samples were quantified for specific DNA species by SYBR-green qRT-PCR as described above, using the tabulated primers (Supplementary Table ). .. Following elution, the supernatant was diluted to a concentration of 0.1% SDS with ChIP dilution buffer (1% Triton-X-100, 2 mM EDTA, 150 mM NaCl, 20 mM Tris-HCl, pH 8.1) supplemented with 50 μg bovine serum albumin and protease inhibitor tablets (Roche).

    Sequencing:

    Article Title: Melarsoprol Sensitivity Profile of Trypanosoma brucei gambiense Isolates from Cured and Relapsed Sleeping Sickness Patients from the Democratic Republic of the Congo
    Article Snippet: .. For selected strains, the amplicons were cleaned up and concentrated using a PCR clean-up kit (Qiagen) and sent out for bidirectional direct sequencing at the VIB Genetic Sequencing Facility (Antwerp, Belgium) using the described PCR primers and additional internal primers to cover TbAT1 . .. Locus specific PCR for aquaglyceroporin genes The protocols to amplify either the AQP2 locus or the combined AQP2 and AQP3 locus, including the AQP2/3 chimera were slightly modified from Graf et al. .

    Article Title: Analyses of Mitogenome Sequences Revealed that Asian Citrus Psyllids (Diaphorina citri) from California Were Related to Those from Florida
    Article Snippet: Paragraph title: Mitogenome sequencing by MiSeq, assembling and annotation ... The amplified DNA fragments were cut by NucleoSpin® Gel and PCR Clean-up kit (QIAGEN, Valencia, USA).

    Article Title: Melarsoprol Sensitivity Profile of Trypanosoma brucei gambiense Isolates from Cured and Relapsed Sleeping Sickness Patients from the Democratic Republic of the Congo
    Article Snippet: .. For selected strains, amplicons were cleaned up and concentrated using a PCR clean-up kit (Qiagen) and sent out for bidirectional direct sequencing at the VIB Genetic Sequencing Facility (Antwerp, Belgium) using the described PCR primers and additional internal primers to cover TbAQP2 . .. Cloning of aquaglyceroporin variants The full-length ORFs of the AQP2 and AQP2/3 genes were amplified from genomic DNA using a proofreading polymerase (Phusion High-Fidelity DNA Polymerase, Thermo Scientific, Waltham, MA, USA).

    Article Title: Bim regulation may determine hippocampal vulnerability after injurious seizures and in temporal lobe epilepsy
    Article Snippet: DNA samples were purified using a PCR clean-up kit (QIAGEN Inc., Valencia, California, USA), and then DNA was subjected to 36 cycles of PCR with primers specific to the FKHR consensus on the bim promoter: sense 5′-TCTCTCAACTGTCCTTCC-3′, antisense 5′-TGTTTACCCTAGTGACTTGG-3′ (accession number ) ( ). .. Antisense oligonucleotides complementary to the bim cDNA sequence were identified and synthesized by Sigma Genosys (Sigma-Aldrich) (antisense 1, 5′-TGGCCAAGCAACCTTCTG-3′; antisense 2, 5′-GTGTGACAGAGAAGGTGG-3′; antisense 3, 5′-TAAGGCAGTCTCAGGAGG-3′; antisense 4, 5′-ATTGCAGCCTGCTGAGAG-3′).

    Article Title: AAV-Mediated Delivery of Zinc Finger Nucleases Targeting Hepatitis B Virus Inhibits Active Replication
    Article Snippet: .. PCR amplicons were purified with a PCR clean-up kit (QIAgen), pooled together in equimolar ratios, and sequenced by single molecule real time sequencing (SMRT) (Pacific Biosciences) at the University of Washington PacBio Sequencing Services ( https://pacbio.gs.washington.edu/ ). .. 15,437 reads filtered for size and FASTQ quality score (SMRT Portal software, Pacific Biosciences) were aligned to the 10 reference sequences (GeniousPro) in order to detect targeted mutagenesis in the ZFN target sites and potential off-target sites.

    Sonication:

    Article Title: Specific functions of TET1 and TET2 in regulating mesenchymal cell lineage determination
    Article Snippet: Genomic DNA was prepared using the Qiagen genomic DNA isolation kit and then sonicated to generate 200–500 bp fragments. .. Immunoprecipitated bead–DNA complex was treated with proteinase K for 3 h at 50 °C in elution buffer and hydroxymethylated DNA purified by using the Qiagen PCR clean-up kit (Qiaquick).

    Article Title: Bim regulation may determine hippocampal vulnerability after injurious seizures and in temporal lobe epilepsy
    Article Snippet: Hippocampal cultures were treated with paraformaldehyde (2%, 2 minutes) to cross-link proteins to DNA and then lysed and sonicated in buffer containing a protease inhibitor cocktail (Roche Molecular Biochemicals, Indianapolis, Indiana, USA). .. DNA samples were purified using a PCR clean-up kit (QIAGEN Inc., Valencia, California, USA), and then DNA was subjected to 36 cycles of PCR with primers specific to the FKHR consensus on the bim promoter: sense 5′-TCTCTCAACTGTCCTTCC-3′, antisense 5′-TGTTTACCCTAGTGACTTGG-3′ (accession number ) ( ).

    Article Title: A functional analysis of the CREB signaling pathway using HaloCHIP-chip and high throughput reporter assays
    Article Snippet: Chromatin was sheared by sonication using a Misonix MicroTip Probe 418, output of 5.5, with a program of 15 cycles of 5 seconds on and 25 seconds off on ice. .. Isolated DNA was further purified using a PCR Clean-up kit (Qiagen), processed, and amplified using WGA identical as the HaloCHIP samples.

    Recombinant:

    Article Title: Analyses of Mitogenome Sequences Revealed that Asian Citrus Psyllids (Diaphorina citri) from California Were Related to Those from Florida
    Article Snippet: The amplified DNA fragments were cut by NucleoSpin® Gel and PCR Clean-up kit (QIAGEN, Valencia, USA). .. Recombinant plasmid DNAs were purified by a QIAprep Spin Miniprep Kit (Qiagen), and sequenced using ABI 3130 DNA sequencer (ABI, Foster, CA, USA).

    ChIP-chip:

    Article Title: The Staphylococcal Accessory Regulator, SarA, is an RNA-Binding Protein that Modulates the mRNA Turnover Properties of Late-Exponential and Stationary Phase Staphylococcus aureus Cells
    Article Snippet: .. For chromatin immunoprecipitation (ChIP-chip) experiments used to detect known SarA-DNA interactions, liberated DNA was purified using a PCR Clean-Up Kit (Qiagen) per manufacturer’s recommendations and hybridized to a GeneChip® and processed as described above. .. For RIP-chIP experiments, liberated nucleic acid was treated with 17 U of RNase-Free DNase I (Qiagen) and RNA was purified using a Clean and Concentrator Kit (Zymo Research; Orange, CA) according to the manufacturer’s recommendations.

    ChIP-sequencing:

    Article Title: Inappropriate p53 Activation During Development Induces Features of CHARGE Syndrome
    Article Snippet: IP’d DNA was washed, and reverse-crosslinked and isolated using Qiagen PCR clean-up kit. .. Analysis of p53 binding site affinities was based on previously reported ChIP-seq data and a p53-binding site algorithm , .

    DNA Extraction:

    Article Title: Specific functions of TET1 and TET2 in regulating mesenchymal cell lineage determination
    Article Snippet: Genomic DNA was prepared using the Qiagen genomic DNA isolation kit and then sonicated to generate 200–500 bp fragments. .. Immunoprecipitated bead–DNA complex was treated with proteinase K for 3 h at 50 °C in elution buffer and hydroxymethylated DNA purified by using the Qiagen PCR clean-up kit (Qiaquick).

    Mutagenesis:

    Article Title: AAV-Mediated Delivery of Zinc Finger Nucleases Targeting Hepatitis B Virus Inhibits Active Replication
    Article Snippet: PCR amplicons were purified with a PCR clean-up kit (QIAgen), pooled together in equimolar ratios, and sequenced by single molecule real time sequencing (SMRT) (Pacific Biosciences) at the University of Washington PacBio Sequencing Services ( https://pacbio.gs.washington.edu/ ). .. 15,437 reads filtered for size and FASTQ quality score (SMRT Portal software, Pacific Biosciences) were aligned to the 10 reference sequences (GeniousPro) in order to detect targeted mutagenesis in the ZFN target sites and potential off-target sites.

    Isolation:

    Article Title: A functional analysis of the CREB signaling pathway using HaloCHIP-chip and high throughput reporter assays
    Article Snippet: .. Isolated DNA was further purified using a PCR Clean-up kit (Qiagen), and eluted 2 × 50 μl with nuclease-free water, yielding a final volume of 100 μl. .. To prepare sufficient HaloCHIP DNA for downstream amplification steps required for microarrays, an entire 6-well plate was transfected and processed through the HaloCHIP method as recommended.

    Article Title: A functional analysis of the CREB signaling pathway using HaloCHIP-chip and high throughput reporter assays
    Article Snippet: .. Isolated DNA was further purified using a PCR Clean-up kit (Qiagen), processed, and amplified using WGA identical as the HaloCHIP samples. .. Quantitative PCR and primers HaloCHIP DNA was analyzed using either Plexor (Promega) or SYBR green (Applied Biosystems) qPCR according to their respective manufacturer's recommendations.

    Article Title: Inappropriate p53 Activation During Development Induces Features of CHARGE Syndrome
    Article Snippet: .. IP’d DNA was washed, and reverse-crosslinked and isolated using Qiagen PCR clean-up kit. ..

    Purification:

    Article Title: A functional analysis of the CREB signaling pathway using HaloCHIP-chip and high throughput reporter assays
    Article Snippet: .. Isolated DNA was further purified using a PCR Clean-up kit (Qiagen), and eluted 2 × 50 μl with nuclease-free water, yielding a final volume of 100 μl. .. To prepare sufficient HaloCHIP DNA for downstream amplification steps required for microarrays, an entire 6-well plate was transfected and processed through the HaloCHIP method as recommended.

    Article Title: Specific functions of TET1 and TET2 in regulating mesenchymal cell lineage determination
    Article Snippet: .. Immunoprecipitated bead–DNA complex was treated with proteinase K for 3 h at 50 °C in elution buffer and hydroxymethylated DNA purified by using the Qiagen PCR clean-up kit (Qiaquick). ..

    Article Title: Analyses of Mitogenome Sequences Revealed that Asian Citrus Psyllids (Diaphorina citri) from California Were Related to Those from Florida
    Article Snippet: The amplified DNA fragments were cut by NucleoSpin® Gel and PCR Clean-up kit (QIAGEN, Valencia, USA). .. Recombinant plasmid DNAs were purified by a QIAprep Spin Miniprep Kit (Qiagen), and sequenced using ABI 3130 DNA sequencer (ABI, Foster, CA, USA).

    Article Title: The Staphylococcal Accessory Regulator, SarA, is an RNA-Binding Protein that Modulates the mRNA Turnover Properties of Late-Exponential and Stationary Phase Staphylococcus aureus Cells
    Article Snippet: .. For chromatin immunoprecipitation (ChIP-chip) experiments used to detect known SarA-DNA interactions, liberated DNA was purified using a PCR Clean-Up Kit (Qiagen) per manufacturer’s recommendations and hybridized to a GeneChip® and processed as described above. .. For RIP-chIP experiments, liberated nucleic acid was treated with 17 U of RNase-Free DNase I (Qiagen) and RNA was purified using a Clean and Concentrator Kit (Zymo Research; Orange, CA) according to the manufacturer’s recommendations.

    Article Title: Bim regulation may determine hippocampal vulnerability after injurious seizures and in temporal lobe epilepsy
    Article Snippet: .. DNA samples were purified using a PCR clean-up kit (QIAGEN Inc., Valencia, California, USA), and then DNA was subjected to 36 cycles of PCR with primers specific to the FKHR consensus on the bim promoter: sense 5′-TCTCTCAACTGTCCTTCC-3′, antisense 5′-TGTTTACCCTAGTGACTTGG-3′ (accession number ) ( ). .. Amplicons were run on nondenaturing 10% acrylamide gels, stained with ethidium bromide, and viewed under UV light.

    Article Title: PRDM9 Drives Evolutionary Erosion of Hotspots in Mus musculus through Haplotype-Specific Initiation of Meiotic Recombination
    Article Snippet: .. DNA was purified using the Qiagen PCR Clean-up kit (Qiagen). .. High throughput sequencing and data processing Libraries for high-throughput sequencing were prepared using Bioo Scientific's NEXTflex ChIP-Seq Kit without size selection and a 50 ul, 14 cycle, PCR reaction.

    Article Title: Autophagy acts through TRAF3 and RELB to regulate gene expression via antagonism of SMAD proteins
    Article Snippet: .. DNA was purified with a Qiagen PCR clean-up kit according to the manufacturer’s instructions, and samples were quantified for specific DNA species by SYBR-green qRT-PCR as described above, using the tabulated primers (Supplementary Table ). .. For re-ChIP assays, following the first immunoprecipitation (as above), beads were washed three times with re-ChIP wash buffer (2 mM EDTA, 200 mM NaCl, 0.1% SDS, 1% NP-40) and twice with Tris-EDTA buffer.

    Article Title: A functional analysis of the CREB signaling pathway using HaloCHIP-chip and high throughput reporter assays
    Article Snippet: .. Isolated DNA was further purified using a PCR Clean-up kit (Qiagen), processed, and amplified using WGA identical as the HaloCHIP samples. .. Quantitative PCR and primers HaloCHIP DNA was analyzed using either Plexor (Promega) or SYBR green (Applied Biosystems) qPCR according to their respective manufacturer's recommendations.

    Article Title: AAV-Mediated Delivery of Zinc Finger Nucleases Targeting Hepatitis B Virus Inhibits Active Replication
    Article Snippet: .. PCR amplicons were purified with a PCR clean-up kit (QIAgen), pooled together in equimolar ratios, and sequenced by single molecule real time sequencing (SMRT) (Pacific Biosciences) at the University of Washington PacBio Sequencing Services ( https://pacbio.gs.washington.edu/ ). .. 15,437 reads filtered for size and FASTQ quality score (SMRT Portal software, Pacific Biosciences) were aligned to the 10 reference sequences (GeniousPro) in order to detect targeted mutagenesis in the ZFN target sites and potential off-target sites.

    Polymerase Chain Reaction:

    Article Title: Melarsoprol Sensitivity Profile of Trypanosoma brucei gambiense Isolates from Cured and Relapsed Sleeping Sickness Patients from the Democratic Republic of the Congo
    Article Snippet: .. For selected strains, the amplicons were cleaned up and concentrated using a PCR clean-up kit (Qiagen) and sent out for bidirectional direct sequencing at the VIB Genetic Sequencing Facility (Antwerp, Belgium) using the described PCR primers and additional internal primers to cover TbAT1 . .. Locus specific PCR for aquaglyceroporin genes The protocols to amplify either the AQP2 locus or the combined AQP2 and AQP3 locus, including the AQP2/3 chimera were slightly modified from Graf et al. .

    Article Title: A functional analysis of the CREB signaling pathway using HaloCHIP-chip and high throughput reporter assays
    Article Snippet: .. Isolated DNA was further purified using a PCR Clean-up kit (Qiagen), and eluted 2 × 50 μl with nuclease-free water, yielding a final volume of 100 μl. .. To prepare sufficient HaloCHIP DNA for downstream amplification steps required for microarrays, an entire 6-well plate was transfected and processed through the HaloCHIP method as recommended.

    Article Title: Specific functions of TET1 and TET2 in regulating mesenchymal cell lineage determination
    Article Snippet: .. Immunoprecipitated bead–DNA complex was treated with proteinase K for 3 h at 50 °C in elution buffer and hydroxymethylated DNA purified by using the Qiagen PCR clean-up kit (Qiaquick). ..

    Article Title: Analyses of Mitogenome Sequences Revealed that Asian Citrus Psyllids (Diaphorina citri) from California Were Related to Those from Florida
    Article Snippet: .. The amplified DNA fragments were cut by NucleoSpin® Gel and PCR Clean-up kit (QIAGEN, Valencia, USA). .. PCR products of the respective DNA fragments were cloned into pEASY cloning vectors.

    Article Title: The Staphylococcal Accessory Regulator, SarA, is an RNA-Binding Protein that Modulates the mRNA Turnover Properties of Late-Exponential and Stationary Phase Staphylococcus aureus Cells
    Article Snippet: .. For chromatin immunoprecipitation (ChIP-chip) experiments used to detect known SarA-DNA interactions, liberated DNA was purified using a PCR Clean-Up Kit (Qiagen) per manufacturer’s recommendations and hybridized to a GeneChip® and processed as described above. .. For RIP-chIP experiments, liberated nucleic acid was treated with 17 U of RNase-Free DNase I (Qiagen) and RNA was purified using a Clean and Concentrator Kit (Zymo Research; Orange, CA) according to the manufacturer’s recommendations.

    Article Title: Melarsoprol Sensitivity Profile of Trypanosoma brucei gambiense Isolates from Cured and Relapsed Sleeping Sickness Patients from the Democratic Republic of the Congo
    Article Snippet: .. For selected strains, amplicons were cleaned up and concentrated using a PCR clean-up kit (Qiagen) and sent out for bidirectional direct sequencing at the VIB Genetic Sequencing Facility (Antwerp, Belgium) using the described PCR primers and additional internal primers to cover TbAQP2 . .. Cloning of aquaglyceroporin variants The full-length ORFs of the AQP2 and AQP2/3 genes were amplified from genomic DNA using a proofreading polymerase (Phusion High-Fidelity DNA Polymerase, Thermo Scientific, Waltham, MA, USA).

    Article Title: Bim regulation may determine hippocampal vulnerability after injurious seizures and in temporal lobe epilepsy
    Article Snippet: .. DNA samples were purified using a PCR clean-up kit (QIAGEN Inc., Valencia, California, USA), and then DNA was subjected to 36 cycles of PCR with primers specific to the FKHR consensus on the bim promoter: sense 5′-TCTCTCAACTGTCCTTCC-3′, antisense 5′-TGTTTACCCTAGTGACTTGG-3′ (accession number ) ( ). .. Amplicons were run on nondenaturing 10% acrylamide gels, stained with ethidium bromide, and viewed under UV light.

    Article Title: PRDM9 Drives Evolutionary Erosion of Hotspots in Mus musculus through Haplotype-Specific Initiation of Meiotic Recombination
    Article Snippet: .. DNA was purified using the Qiagen PCR Clean-up kit (Qiagen). .. High throughput sequencing and data processing Libraries for high-throughput sequencing were prepared using Bioo Scientific's NEXTflex ChIP-Seq Kit without size selection and a 50 ul, 14 cycle, PCR reaction.

    Article Title: Autophagy acts through TRAF3 and RELB to regulate gene expression via antagonism of SMAD proteins
    Article Snippet: .. DNA was purified with a Qiagen PCR clean-up kit according to the manufacturer’s instructions, and samples were quantified for specific DNA species by SYBR-green qRT-PCR as described above, using the tabulated primers (Supplementary Table ). .. For re-ChIP assays, following the first immunoprecipitation (as above), beads were washed three times with re-ChIP wash buffer (2 mM EDTA, 200 mM NaCl, 0.1% SDS, 1% NP-40) and twice with Tris-EDTA buffer.

    Article Title: A functional analysis of the CREB signaling pathway using HaloCHIP-chip and high throughput reporter assays
    Article Snippet: .. Isolated DNA was further purified using a PCR Clean-up kit (Qiagen), processed, and amplified using WGA identical as the HaloCHIP samples. .. Quantitative PCR and primers HaloCHIP DNA was analyzed using either Plexor (Promega) or SYBR green (Applied Biosystems) qPCR according to their respective manufacturer's recommendations.

    Article Title: AAV-Mediated Delivery of Zinc Finger Nucleases Targeting Hepatitis B Virus Inhibits Active Replication
    Article Snippet: .. PCR amplicons were purified with a PCR clean-up kit (QIAgen), pooled together in equimolar ratios, and sequenced by single molecule real time sequencing (SMRT) (Pacific Biosciences) at the University of Washington PacBio Sequencing Services ( https://pacbio.gs.washington.edu/ ). .. 15,437 reads filtered for size and FASTQ quality score (SMRT Portal software, Pacific Biosciences) were aligned to the 10 reference sequences (GeniousPro) in order to detect targeted mutagenesis in the ZFN target sites and potential off-target sites.

    Article Title: Inappropriate p53 Activation During Development Induces Features of CHARGE Syndrome
    Article Snippet: .. IP’d DNA was washed, and reverse-crosslinked and isolated using Qiagen PCR clean-up kit. ..

    Quantitative RT-PCR:

    Article Title: Autophagy acts through TRAF3 and RELB to regulate gene expression via antagonism of SMAD proteins
    Article Snippet: .. DNA was purified with a Qiagen PCR clean-up kit according to the manufacturer’s instructions, and samples were quantified for specific DNA species by SYBR-green qRT-PCR as described above, using the tabulated primers (Supplementary Table ). .. For re-ChIP assays, following the first immunoprecipitation (as above), beads were washed three times with re-ChIP wash buffer (2 mM EDTA, 200 mM NaCl, 0.1% SDS, 1% NP-40) and twice with Tris-EDTA buffer.

    Staining:

    Article Title: Melarsoprol Sensitivity Profile of Trypanosoma brucei gambiense Isolates from Cured and Relapsed Sleeping Sickness Patients from the Democratic Republic of the Congo
    Article Snippet: Ten µl of the PCR product were electrophorised in a 2% agarose gel for 30 min at 135 V and stained with ethidium bromide for detection of the amplicons. .. For selected strains, the amplicons were cleaned up and concentrated using a PCR clean-up kit (Qiagen) and sent out for bidirectional direct sequencing at the VIB Genetic Sequencing Facility (Antwerp, Belgium) using the described PCR primers and additional internal primers to cover TbAT1 .

    Article Title: Melarsoprol Sensitivity Profile of Trypanosoma brucei gambiense Isolates from Cured and Relapsed Sleeping Sickness Patients from the Democratic Republic of the Congo
    Article Snippet: Ten µl of the PCR product were electrophorised in a 0.8% agarose gel for 30 min at 135 V and stained with ethidium bromide for detection of the amplicons. .. For selected strains, amplicons were cleaned up and concentrated using a PCR clean-up kit (Qiagen) and sent out for bidirectional direct sequencing at the VIB Genetic Sequencing Facility (Antwerp, Belgium) using the described PCR primers and additional internal primers to cover TbAQP2 .

    Article Title: Bim regulation may determine hippocampal vulnerability after injurious seizures and in temporal lobe epilepsy
    Article Snippet: DNA samples were purified using a PCR clean-up kit (QIAGEN Inc., Valencia, California, USA), and then DNA was subjected to 36 cycles of PCR with primers specific to the FKHR consensus on the bim promoter: sense 5′-TCTCTCAACTGTCCTTCC-3′, antisense 5′-TGTTTACCCTAGTGACTTGG-3′ (accession number ) ( ). .. Amplicons were run on nondenaturing 10% acrylamide gels, stained with ethidium bromide, and viewed under UV light.

    Chromatin Immunoprecipitation:

    Article Title: A functional analysis of the CREB signaling pathway using HaloCHIP-chip and high throughput reporter assays
    Article Snippet: Isolated DNA was further purified using a PCR Clean-up kit (Qiagen), and eluted 2 × 50 μl with nuclease-free water, yielding a final volume of 100 μl. .. The concentrated HaloCHIP DNA was then amplified to 2-10 μg using the Whole Genome Amplification kit (Sigma) following the recommended adaptation for ChIP samples [ ].

    Article Title: The Staphylococcal Accessory Regulator, SarA, is an RNA-Binding Protein that Modulates the mRNA Turnover Properties of Late-Exponential and Stationary Phase Staphylococcus aureus Cells
    Article Snippet: .. For chromatin immunoprecipitation (ChIP-chip) experiments used to detect known SarA-DNA interactions, liberated DNA was purified using a PCR Clean-Up Kit (Qiagen) per manufacturer’s recommendations and hybridized to a GeneChip® and processed as described above. .. For RIP-chIP experiments, liberated nucleic acid was treated with 17 U of RNase-Free DNase I (Qiagen) and RNA was purified using a Clean and Concentrator Kit (Zymo Research; Orange, CA) according to the manufacturer’s recommendations.

    Article Title: Bim regulation may determine hippocampal vulnerability after injurious seizures and in temporal lobe epilepsy
    Article Snippet: Paragraph title: In vitro seizure model, chromatin immunoprecipitation assay, and Bim antisense studies. ... DNA samples were purified using a PCR clean-up kit (QIAGEN Inc., Valencia, California, USA), and then DNA was subjected to 36 cycles of PCR with primers specific to the FKHR consensus on the bim promoter: sense 5′-TCTCTCAACTGTCCTTCC-3′, antisense 5′-TGTTTACCCTAGTGACTTGG-3′ (accession number ) ( ).

    Article Title: PRDM9 Drives Evolutionary Erosion of Hotspots in Mus musculus through Haplotype-Specific Initiation of Meiotic Recombination
    Article Snippet: Paragraph title: PRDM9 chromatin immunoprecipitation ... DNA was purified using the Qiagen PCR Clean-up kit (Qiagen).

    Article Title: Autophagy acts through TRAF3 and RELB to regulate gene expression via antagonism of SMAD proteins
    Article Snippet: Paragraph title: Chromatin immunoprecipitation ... DNA was purified with a Qiagen PCR clean-up kit according to the manufacturer’s instructions, and samples were quantified for specific DNA species by SYBR-green qRT-PCR as described above, using the tabulated primers (Supplementary Table ).

    Article Title: A functional analysis of the CREB signaling pathway using HaloCHIP-chip and high throughput reporter assays
    Article Snippet: Paragraph title: ChIP Protocol ... Isolated DNA was further purified using a PCR Clean-up kit (Qiagen), processed, and amplified using WGA identical as the HaloCHIP samples.

    Article Title: Inappropriate p53 Activation During Development Induces Features of CHARGE Syndrome
    Article Snippet: Paragraph title: Chromatin Immunoprecipitation ... IP’d DNA was washed, and reverse-crosslinked and isolated using Qiagen PCR clean-up kit.

    Plasmid Preparation:

    Article Title: Analyses of Mitogenome Sequences Revealed that Asian Citrus Psyllids (Diaphorina citri) from California Were Related to Those from Florida
    Article Snippet: The amplified DNA fragments were cut by NucleoSpin® Gel and PCR Clean-up kit (QIAGEN, Valencia, USA). .. Recombinant plasmid DNAs were purified by a QIAprep Spin Miniprep Kit (Qiagen), and sequenced using ABI 3130 DNA sequencer (ABI, Foster, CA, USA).

    Software:

    Article Title: AAV-Mediated Delivery of Zinc Finger Nucleases Targeting Hepatitis B Virus Inhibits Active Replication
    Article Snippet: PCR amplicons were purified with a PCR clean-up kit (QIAgen), pooled together in equimolar ratios, and sequenced by single molecule real time sequencing (SMRT) (Pacific Biosciences) at the University of Washington PacBio Sequencing Services ( https://pacbio.gs.washington.edu/ ). .. 15,437 reads filtered for size and FASTQ quality score (SMRT Portal software, Pacific Biosciences) were aligned to the 10 reference sequences (GeniousPro) in order to detect targeted mutagenesis in the ZFN target sites and potential off-target sites.

    Negative Control:

    Article Title: The Staphylococcal Accessory Regulator, SarA, is an RNA-Binding Protein that Modulates the mRNA Turnover Properties of Late-Exponential and Stationary Phase Staphylococcus aureus Cells
    Article Snippet: To do so, S. aureus strains UAMS-929 (ΔsarA ; negative control) and KLA43 (ΔsarA /pKLA40::c-Myc-SarA) were grown to mid-exponential phase and RNA-binding proteins were cross-linked to RNA by incubating the cells for 30 min with 1% formaldehyde at room temperature. .. For chromatin immunoprecipitation (ChIP-chip) experiments used to detect known SarA-DNA interactions, liberated DNA was purified using a PCR Clean-Up Kit (Qiagen) per manufacturer’s recommendations and hybridized to a GeneChip® and processed as described above.

    Article Title: Bim regulation may determine hippocampal vulnerability after injurious seizures and in temporal lobe epilepsy
    Article Snippet: A phospho-FKHR antibody was used as a negative control (Cell Signaling Technology Inc.). .. DNA samples were purified using a PCR clean-up kit (QIAGEN Inc., Valencia, California, USA), and then DNA was subjected to 36 cycles of PCR with primers specific to the FKHR consensus on the bim promoter: sense 5′-TCTCTCAACTGTCCTTCC-3′, antisense 5′-TGTTTACCCTAGTGACTTGG-3′ (accession number ) ( ).

    Binding Assay:

    Article Title: Bim regulation may determine hippocampal vulnerability after injurious seizures and in temporal lobe epilepsy
    Article Snippet: Binding of FKHR to the bim promoter site was determined using a chromatin immunoprecipitation assay, as described previously with modifications ( ). .. DNA samples were purified using a PCR clean-up kit (QIAGEN Inc., Valencia, California, USA), and then DNA was subjected to 36 cycles of PCR with primers specific to the FKHR consensus on the bim promoter: sense 5′-TCTCTCAACTGTCCTTCC-3′, antisense 5′-TGTTTACCCTAGTGACTTGG-3′ (accession number ) ( ).

    Article Title: Inappropriate p53 Activation During Development Induces Features of CHARGE Syndrome
    Article Snippet: Chromatin Immunoprecipitation Analysis of p53 binding was performed on Mouse Embryonic Fibroblasts of different genotypes. .. IP’d DNA was washed, and reverse-crosslinked and isolated using Qiagen PCR clean-up kit.

    Agarose Gel Electrophoresis:

    Article Title: Melarsoprol Sensitivity Profile of Trypanosoma brucei gambiense Isolates from Cured and Relapsed Sleeping Sickness Patients from the Democratic Republic of the Congo
    Article Snippet: Ten µl of the PCR product were electrophorised in a 2% agarose gel for 30 min at 135 V and stained with ethidium bromide for detection of the amplicons. .. For selected strains, the amplicons were cleaned up and concentrated using a PCR clean-up kit (Qiagen) and sent out for bidirectional direct sequencing at the VIB Genetic Sequencing Facility (Antwerp, Belgium) using the described PCR primers and additional internal primers to cover TbAT1 .

    Article Title: Melarsoprol Sensitivity Profile of Trypanosoma brucei gambiense Isolates from Cured and Relapsed Sleeping Sickness Patients from the Democratic Republic of the Congo
    Article Snippet: Ten µl of the PCR product were electrophorised in a 0.8% agarose gel for 30 min at 135 V and stained with ethidium bromide for detection of the amplicons. .. For selected strains, amplicons were cleaned up and concentrated using a PCR clean-up kit (Qiagen) and sent out for bidirectional direct sequencing at the VIB Genetic Sequencing Facility (Antwerp, Belgium) using the described PCR primers and additional internal primers to cover TbAQP2 .

    In Vitro:

    Article Title: Bim regulation may determine hippocampal vulnerability after injurious seizures and in temporal lobe epilepsy
    Article Snippet: Paragraph title: In vitro seizure model, chromatin immunoprecipitation assay, and Bim antisense studies. ... DNA samples were purified using a PCR clean-up kit (QIAGEN Inc., Valencia, California, USA), and then DNA was subjected to 36 cycles of PCR with primers specific to the FKHR consensus on the bim promoter: sense 5′-TCTCTCAACTGTCCTTCC-3′, antisense 5′-TGTTTACCCTAGTGACTTGG-3′ (accession number ) ( ).

    Immunoprecipitation:

    Article Title: Specific functions of TET1 and TET2 in regulating mesenchymal cell lineage determination
    Article Snippet: .. Immunoprecipitated bead–DNA complex was treated with proteinase K for 3 h at 50 °C in elution buffer and hydroxymethylated DNA purified by using the Qiagen PCR clean-up kit (Qiaquick). ..

    Article Title: The Staphylococcal Accessory Regulator, SarA, is an RNA-Binding Protein that Modulates the mRNA Turnover Properties of Late-Exponential and Stationary Phase Staphylococcus aureus Cells
    Article Snippet: Paragraph title: Ribonucleoprotein immunoprecipitation (RIP-Chip) ... For chromatin immunoprecipitation (ChIP-chip) experiments used to detect known SarA-DNA interactions, liberated DNA was purified using a PCR Clean-Up Kit (Qiagen) per manufacturer’s recommendations and hybridized to a GeneChip® and processed as described above.

    Article Title: Autophagy acts through TRAF3 and RELB to regulate gene expression via antagonism of SMAD proteins
    Article Snippet: DNA was purified with a Qiagen PCR clean-up kit according to the manufacturer’s instructions, and samples were quantified for specific DNA species by SYBR-green qRT-PCR as described above, using the tabulated primers (Supplementary Table ). .. For re-ChIP assays, following the first immunoprecipitation (as above), beads were washed three times with re-ChIP wash buffer (2 mM EDTA, 200 mM NaCl, 0.1% SDS, 1% NP-40) and twice with Tris-EDTA buffer.

    Article Title: Inappropriate p53 Activation During Development Induces Features of CHARGE Syndrome
    Article Snippet: Chromatin was sheared using Bioruptor sonicator (Diagenode), then immunoprecipitated with anti-p53–Dynabeads complex overnight. .. IP’d DNA was washed, and reverse-crosslinked and isolated using Qiagen PCR clean-up kit.

    Lysis:

    Article Title: The Staphylococcal Accessory Regulator, SarA, is an RNA-Binding Protein that Modulates the mRNA Turnover Properties of Late-Exponential and Stationary Phase Staphylococcus aureus Cells
    Article Snippet: Cells were centrifuged at 3000 RPM for 10 min at 4o C and cell pellets were washed twice in 1 ml ice-cold TBS, resuspended in 350 μl of lysis buffer (10 mM Tris pH 8.0, 10 mM EDTA, 50 mM NaCl, and 1 mM PMSF) and were lysed by the addition 100 μg ml−1 lysostaphin (Ambi; Lawrence, NY) at 37o C for 30 min. Next, an equal volume of 2× immunoprecipitation (IP) buffer (100 mM Tris pH 8.0, 10 mM EDTA, 300 mM NaCl, 2% Triton X-100, 1 mM PMSF) was added and suspensions were incubated for an additional 10 min at 37o C. Nucleic acids were fragmented with a Sonic Dismembrator (Fisher) on ice twice for 15 s using an output setting of one with 15 s rests on ice between each pulse and cell debris was subsequently removed by centrifugation for 10 min at 4o C. Next, 800 μl of the supernatant was mixed with 10 μl of anti-c-Myc agarose (Pierce Biotechnology; Rockford IL) and then added to IP spin columns (Pierce Biotechnology) and incubated overnight at 4o C to collect c-Myc-SarA/RNA and DNA complexes. .. For chromatin immunoprecipitation (ChIP-chip) experiments used to detect known SarA-DNA interactions, liberated DNA was purified using a PCR Clean-Up Kit (Qiagen) per manufacturer’s recommendations and hybridized to a GeneChip® and processed as described above.

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  • 99
    Qiagen pcr clean up kit
    TET1 and TET2 influence 5hmC on osteogenic genes. BMSC were cultured under normal growth conditions and treated with scramble siRNA or siRNA directed to TET1 (siTET1) or TET2 (siTET2) and genomic <t>DNA</t> purified and immunoprecipitated using an antibody to 5hmC. Recruitment of 5hmC to genomic regions was assessed by the hme-DIP analysis and normalised to the genomic input control. a Relative enrichment of 5hmC on RUNX2 transcription start site (TSS) was measured using <t>PCR.</t> b 5hmC on BMP2 TSS was measured as in ( a ). BMSC were cultured under normal growth and genomic DNA purified and immunoprecipitated using an antibody to 5hmC. Recruitment of 5hmc to genomic regions was assessed by the hme-DIP analysis and normalised to the genomic input control. c Cells were cultured under normal and osteogenic conditions. Relative enrichment of 5hmC on RUNX2 transcription start site (TSS), exon and intron regions. d Relative enrichment of 5hmC on BMP2 TSS, exon and intron regions, percentage input. Data represent mean S.E.M., n = 3 BMSC donors, * p ≤ 0.05, one-way ANOVA with multiple comparison analyses
    Pcr Clean Up Kit, supplied by Qiagen, used in various techniques. Bioz Stars score: 99/100, based on 212 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/pcr clean up kit/product/Qiagen
    Average 99 stars, based on 212 article reviews
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    pcr clean up kit - by Bioz Stars, 2020-04
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    88
    Qiagen 96 well plates multichannel pipettor optional pcr clean up kit
    Examples of a saw-tooth pattern in agarose gel analysis of <t>PCR</t> product. PCR mixtures (96 samples) were run on a 1% agarose gel. A primer-ordering algorithm generates a map of oligonucleotide primers in <t>96-well</t> format with alternating expected product
    96 Well Plates Multichannel Pipettor Optional Pcr Clean Up Kit, supplied by Qiagen, used in various techniques. Bioz Stars score: 88/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/96 well plates multichannel pipettor optional pcr clean up kit/product/Qiagen
    Average 88 stars, based on 1 article reviews
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    96 well plates multichannel pipettor optional pcr clean up kit - by Bioz Stars, 2020-04
    88/100 stars
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    TET1 and TET2 influence 5hmC on osteogenic genes. BMSC were cultured under normal growth conditions and treated with scramble siRNA or siRNA directed to TET1 (siTET1) or TET2 (siTET2) and genomic DNA purified and immunoprecipitated using an antibody to 5hmC. Recruitment of 5hmC to genomic regions was assessed by the hme-DIP analysis and normalised to the genomic input control. a Relative enrichment of 5hmC on RUNX2 transcription start site (TSS) was measured using PCR. b 5hmC on BMP2 TSS was measured as in ( a ). BMSC were cultured under normal growth and genomic DNA purified and immunoprecipitated using an antibody to 5hmC. Recruitment of 5hmc to genomic regions was assessed by the hme-DIP analysis and normalised to the genomic input control. c Cells were cultured under normal and osteogenic conditions. Relative enrichment of 5hmC on RUNX2 transcription start site (TSS), exon and intron regions. d Relative enrichment of 5hmC on BMP2 TSS, exon and intron regions, percentage input. Data represent mean S.E.M., n = 3 BMSC donors, * p ≤ 0.05, one-way ANOVA with multiple comparison analyses

    Journal: Epigenetics & Chromatin

    Article Title: Specific functions of TET1 and TET2 in regulating mesenchymal cell lineage determination

    doi: 10.1186/s13072-018-0247-4

    Figure Lengend Snippet: TET1 and TET2 influence 5hmC on osteogenic genes. BMSC were cultured under normal growth conditions and treated with scramble siRNA or siRNA directed to TET1 (siTET1) or TET2 (siTET2) and genomic DNA purified and immunoprecipitated using an antibody to 5hmC. Recruitment of 5hmC to genomic regions was assessed by the hme-DIP analysis and normalised to the genomic input control. a Relative enrichment of 5hmC on RUNX2 transcription start site (TSS) was measured using PCR. b 5hmC on BMP2 TSS was measured as in ( a ). BMSC were cultured under normal growth and genomic DNA purified and immunoprecipitated using an antibody to 5hmC. Recruitment of 5hmc to genomic regions was assessed by the hme-DIP analysis and normalised to the genomic input control. c Cells were cultured under normal and osteogenic conditions. Relative enrichment of 5hmC on RUNX2 transcription start site (TSS), exon and intron regions. d Relative enrichment of 5hmC on BMP2 TSS, exon and intron regions, percentage input. Data represent mean S.E.M., n = 3 BMSC donors, * p ≤ 0.05, one-way ANOVA with multiple comparison analyses

    Article Snippet: Immunoprecipitated bead–DNA complex was treated with proteinase K for 3 h at 50 °C in elution buffer and hydroxymethylated DNA purified by using the Qiagen PCR clean-up kit (Qiaquick).

    Techniques: Cell Culture, Purification, Immunoprecipitation, Polymerase Chain Reaction

    Amplicons generated with TbAT1 -PCR on DNA of the T.b. gambiense strains as listed in Table 1 and of the two T.b. brucei control strains. Lanes 1, 26, 27 and 52 = GeneRuler 100 bp Plus DNA Ladder (Fermentas), lanes 2 to 44 = T.b. gambiense strains isolated from Mbuji-Mayi, lanes 45 to 48 = T.b. gambiense strains isolated from Masi-Manimba, lane 49 = T.b. brucei 427 WT, lane 50 = T.b. brucei 427 AT1/P2 KO, lane 51 = negative PCR control.

    Journal: PLoS Neglected Tropical Diseases

    Article Title: Melarsoprol Sensitivity Profile of Trypanosoma brucei gambiense Isolates from Cured and Relapsed Sleeping Sickness Patients from the Democratic Republic of the Congo

    doi: 10.1371/journal.pntd.0003212

    Figure Lengend Snippet: Amplicons generated with TbAT1 -PCR on DNA of the T.b. gambiense strains as listed in Table 1 and of the two T.b. brucei control strains. Lanes 1, 26, 27 and 52 = GeneRuler 100 bp Plus DNA Ladder (Fermentas), lanes 2 to 44 = T.b. gambiense strains isolated from Mbuji-Mayi, lanes 45 to 48 = T.b. gambiense strains isolated from Masi-Manimba, lane 49 = T.b. brucei 427 WT, lane 50 = T.b. brucei 427 AT1/P2 KO, lane 51 = negative PCR control.

    Article Snippet: For selected strains, amplicons were cleaned up and concentrated using a PCR clean-up kit (Qiagen) and sent out for bidirectional direct sequencing at the VIB Genetic Sequencing Facility (Antwerp, Belgium) using the described PCR primers and additional internal primers to cover TbAQP2 .

    Techniques: Generated, Polymerase Chain Reaction, Isolation

    Amplicons generated with AQP2/3 -PCR on DNA of the T.b. gambiense strains as listed in Table 1 and of the two T.b. brucei control strains. Lanes 1, 26, 27 and 52 = GeneRuler 100 bp Plus DNA Ladder (Fermentas), lanes 2 to 44 = T.b. gambiense strains isolated from Mbuji-Mayi, lanes 45–48 = T.b. gambiense strains isolated from Masi-Manimba, lane 49 = T.b. brucei 427 WT, lane 50 = T.b. brucei 427 AT1/P2 KO, lane 51 = negative PCR control.

    Journal: PLoS Neglected Tropical Diseases

    Article Title: Melarsoprol Sensitivity Profile of Trypanosoma brucei gambiense Isolates from Cured and Relapsed Sleeping Sickness Patients from the Democratic Republic of the Congo

    doi: 10.1371/journal.pntd.0003212

    Figure Lengend Snippet: Amplicons generated with AQP2/3 -PCR on DNA of the T.b. gambiense strains as listed in Table 1 and of the two T.b. brucei control strains. Lanes 1, 26, 27 and 52 = GeneRuler 100 bp Plus DNA Ladder (Fermentas), lanes 2 to 44 = T.b. gambiense strains isolated from Mbuji-Mayi, lanes 45–48 = T.b. gambiense strains isolated from Masi-Manimba, lane 49 = T.b. brucei 427 WT, lane 50 = T.b. brucei 427 AT1/P2 KO, lane 51 = negative PCR control.

    Article Snippet: For selected strains, amplicons were cleaned up and concentrated using a PCR clean-up kit (Qiagen) and sent out for bidirectional direct sequencing at the VIB Genetic Sequencing Facility (Antwerp, Belgium) using the described PCR primers and additional internal primers to cover TbAQP2 .

    Techniques: Generated, Polymerase Chain Reaction, Isolation

    Seizures in vitro increase binding of FKHR to the bim promoter, and Bim antisense is neuroprotective. (A) Representative Western blots from hippocampal neuronal cultures at 24 hours, showing that seizurelike activity in vitro causes FKHR/FKHRL-1 dephosphorylation and increased Bim expression. Immunoblots showing unaffected Bid and α-tubulin levels are included as controls. Immunoblots are representative of two or three independent experiments. (B) Chromatin immunoprecipitation assay demonstrating immunoprecipitation of the bim promoter (pmr) by FKHR. Chromatin fragments were immunoprecipitated using either anti-FKHR or anti–phospho-FKHR followed by PCR with primers specific for the bim -FKHR promoter region. Genomic DNA was subject to PCR as a positive (+) control. Phospho-FKHR did not precipitate the bim promoter. In contrast, FKHR precipitated the bim promoter, and this was increased in cultures subject to seizures and 1 hour of recovery. The image is representative of two independent experiments. (C) Representative Western blots confirming that Bim antisense (AS) reduces Bim levels compared with those in control cultures treated with a scrambled (scram) sequence. Immunoblots showing unaffected Bid and α-tubulin levels are included as controls. Immunoblots are representative of two independent experiments. (D) Graph showing effects of Bim antisense on seizure-induced LDH release. Injury assessment at 24 hours revealed that seizures (seiz) elevated LDH levels to about 275% of control (base-line) levels. Incubation of cultures with the scrambled Bim antisense did not alter seizure-induced LDH release. In contrast, Bim antisense significantly reduced LDH release following seizures. * P

    Journal: Journal of Clinical Investigation

    Article Title: Bim regulation may determine hippocampal vulnerability after injurious seizures and in temporal lobe epilepsy

    doi: 10.1172/JCI200419971

    Figure Lengend Snippet: Seizures in vitro increase binding of FKHR to the bim promoter, and Bim antisense is neuroprotective. (A) Representative Western blots from hippocampal neuronal cultures at 24 hours, showing that seizurelike activity in vitro causes FKHR/FKHRL-1 dephosphorylation and increased Bim expression. Immunoblots showing unaffected Bid and α-tubulin levels are included as controls. Immunoblots are representative of two or three independent experiments. (B) Chromatin immunoprecipitation assay demonstrating immunoprecipitation of the bim promoter (pmr) by FKHR. Chromatin fragments were immunoprecipitated using either anti-FKHR or anti–phospho-FKHR followed by PCR with primers specific for the bim -FKHR promoter region. Genomic DNA was subject to PCR as a positive (+) control. Phospho-FKHR did not precipitate the bim promoter. In contrast, FKHR precipitated the bim promoter, and this was increased in cultures subject to seizures and 1 hour of recovery. The image is representative of two independent experiments. (C) Representative Western blots confirming that Bim antisense (AS) reduces Bim levels compared with those in control cultures treated with a scrambled (scram) sequence. Immunoblots showing unaffected Bid and α-tubulin levels are included as controls. Immunoblots are representative of two independent experiments. (D) Graph showing effects of Bim antisense on seizure-induced LDH release. Injury assessment at 24 hours revealed that seizures (seiz) elevated LDH levels to about 275% of control (base-line) levels. Incubation of cultures with the scrambled Bim antisense did not alter seizure-induced LDH release. In contrast, Bim antisense significantly reduced LDH release following seizures. * P

    Article Snippet: DNA samples were purified using a PCR clean-up kit (QIAGEN Inc., Valencia, California, USA), and then DNA was subjected to 36 cycles of PCR with primers specific to the FKHR consensus on the bim promoter: sense 5′-TCTCTCAACTGTCCTTCC-3′, antisense 5′-TGTTTACCCTAGTGACTTGG-3′ (accession number ) ( ).

    Techniques: In Vitro, Binding Assay, Western Blot, Activity Assay, De-Phosphorylation Assay, Expressing, Chromatin Immunoprecipitation, Immunoprecipitation, Polymerase Chain Reaction, Positive Control, Sequencing, Incubation

    Examples of a saw-tooth pattern in agarose gel analysis of PCR product. PCR mixtures (96 samples) were run on a 1% agarose gel. A primer-ordering algorithm generates a map of oligonucleotide primers in 96-well format with alternating expected product

    Journal: Current protocols in molecular biology / edited by Frederick M. Ausubel ... [et al.]

    Article Title: Recombinational Cloning Using Gateway and In-Fusion Cloning Schemes

    doi: 10.1002/0471142727.mb0320s110

    Figure Lengend Snippet: Examples of a saw-tooth pattern in agarose gel analysis of PCR product. PCR mixtures (96 samples) were run on a 1% agarose gel. A primer-ordering algorithm generates a map of oligonucleotide primers in 96-well format with alternating expected product

    Article Snippet: 10 mM 4dNTPs 100% DMSO 2.0 U/µl Phusion® High-Fidelity DNA polymerase (New England BioLabs (NEB)) ( Most high-fidelity polymerases should be sufficient ) 5× Phusion® HF Buffer (NEB) 2× CloneAmp™ HiFi PCR Premix (Clontech) DNA template: 10 ng/µl first-strand cDNA mix or 1–50 ng/µl plasmid DNA 10 µM gene specific 5′-oligonucleotide primer in sterile H2 O (for primer design see Basic Protocol 1 introduction) 10 µM gene specific 3′-oligonucleotide primer in sterile H2 O (for primer design see Basic Protocol 1 introduction) 100 µM universal 5′-oligonucleotide primer (Gateway® only) 100 µM universal 3′-oligonucleotide primer (Gateway® only) PCR tubes (thin-walled) or 96-well plates Multichannel pipettor (optional) PCR Clean-Up kit (e.g., Qiagen or Macherey Nagel for high-throughput) Centrifuge Thermal cycler Additional reagents and equipment for gel electrophoresis (see unit 2.5A ) and DNA preparation (see unit 1.6 or commercial DNA prep kit).

    Techniques: Agarose Gel Electrophoresis, Polymerase Chain Reaction