repli g single cell kit  (Qiagen)


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    Name:
    REPLI-g Single Cell Kit
    Description:
    For highly uniform whole genome amplification (WGA) from single cells or limited sample material. Kit contents: Qiagen REPLI-g Single Cell Kit, 24 WGA rxns, 2 to 1000 Cells Input Amount, 15 min. Hands-on Time, 8 to 16 hr. Reaction Time, 40g/rxns Yields, MDA Technology, Tube Format, For Highly Uniform Whole Genome Amplification (WGA) from Single Cells or Limited Sample, Includes REPLI-g sc Polymerase, Buffers and Reagents. Benefits: WGA from single cell material with complete genome coverage. Unbiased amplification of genomic loci due to MDA technology. Optimized for use with new technologies, including NGS. Consistent yields of up to 40 µg (average product length >10 kb). Novel tool for cancer research, stem cell research, or metagenomics
    Catalog Number:
    150343
    Price:
    None
    Category:
    REPLI-g Single Cell Kit
    Score:
    85
    Buy from Supplier


    Structured Review

    Qiagen repli g single cell kit
    REPLI-g Single Cell Kit
    For highly uniform whole genome amplification (WGA) from single cells or limited sample material. Kit contents: Qiagen REPLI-g Single Cell Kit, 24 WGA rxns, 2 to 1000 Cells Input Amount, 15 min. Hands-on Time, 8 to 16 hr. Reaction Time, 40g/rxns Yields, MDA Technology, Tube Format, For Highly Uniform Whole Genome Amplification (WGA) from Single Cells or Limited Sample, Includes REPLI-g sc Polymerase, Buffers and Reagents. Benefits: WGA from single cell material with complete genome coverage. Unbiased amplification of genomic loci due to MDA technology. Optimized for use with new technologies, including NGS. Consistent yields of up to 40 µg (average product length >10 kb). Novel tool for cancer research, stem cell research, or metagenomics
    https://www.bioz.com/result/repli g single cell kit/product/Qiagen
    Average 99 stars, based on 33 article reviews
    Price from $9.99 to $1999.99
    repli g single cell kit - by Bioz Stars, 2019-12
    99/100 stars

    Images

    1) Product Images from "Comparative study of whole genome amplification and next generation sequencing performance of single cancer cells"

    Article Title: Comparative study of whole genome amplification and next generation sequencing performance of single cancer cells

    Journal: Oncotarget

    doi: 10.18632/oncotarget.10701

    Plots of CNA profiles along the whole genome (x axis) ( A ) CNA profile of unamplified DNA from unfixed cells. ( B – G ) plots of CNAs in single SK-BR-3 cells, obtained from EDTA-preserved blood. ( H , I ) CNA profiles of individual CTCs, obtained from EDTA-preserved blood of the same breast cancer patient. WGA kits: (B, E) Ampli1; (C, F, H, I) PicoPlex; (D, G) REPLI-g.
    Figure Legend Snippet: Plots of CNA profiles along the whole genome (x axis) ( A ) CNA profile of unamplified DNA from unfixed cells. ( B – G ) plots of CNAs in single SK-BR-3 cells, obtained from EDTA-preserved blood. ( H , I ) CNA profiles of individual CTCs, obtained from EDTA-preserved blood of the same breast cancer patient. WGA kits: (B, E) Ampli1; (C, F, H, I) PicoPlex; (D, G) REPLI-g.

    Techniques Used: Whole Genome Amplification

    Distribution of identified known SNPs between datasets ( A ) Known SNPs identified in single cells, amplified with Ampli1, PicoPlex, and REPLI-g WGA kits and obtained from EDTA-preserved blood in comparison to unamplified DNA. ( B ) Known SNPs identified in single cells, amplified with Ampli1 or PicoPlex and obtained from EDTA- and CellSave-preserved blood in comparison to unamplified DNA from unfixed cells. ( C ) Known SNPs identified in single CTCs, amplified with PicoPlex in comparison to each other.
    Figure Legend Snippet: Distribution of identified known SNPs between datasets ( A ) Known SNPs identified in single cells, amplified with Ampli1, PicoPlex, and REPLI-g WGA kits and obtained from EDTA-preserved blood in comparison to unamplified DNA. ( B ) Known SNPs identified in single cells, amplified with Ampli1 or PicoPlex and obtained from EDTA- and CellSave-preserved blood in comparison to unamplified DNA from unfixed cells. ( C ) Known SNPs identified in single CTCs, amplified with PicoPlex in comparison to each other.

    Techniques Used: Amplification, Whole Genome Amplification

    2) Product Images from "Comparative study of whole genome amplification and next generation sequencing performance of single cancer cells"

    Article Title: Comparative study of whole genome amplification and next generation sequencing performance of single cancer cells

    Journal: Oncotarget

    doi: 10.18632/oncotarget.10701

    Plots of CNA profiles along the whole genome (x axis) ( A ) CNA profile of unamplified DNA from unfixed cells. ( B – G ) plots of CNAs in single SK-BR-3 cells, obtained from EDTA-preserved blood. ( H , I ) CNA profiles of individual CTCs, obtained from EDTA-preserved blood of the same breast cancer patient. WGA kits: (B, E) Ampli1; (C, F, H, I) PicoPlex; (D, G) REPLI-g.
    Figure Legend Snippet: Plots of CNA profiles along the whole genome (x axis) ( A ) CNA profile of unamplified DNA from unfixed cells. ( B – G ) plots of CNAs in single SK-BR-3 cells, obtained from EDTA-preserved blood. ( H , I ) CNA profiles of individual CTCs, obtained from EDTA-preserved blood of the same breast cancer patient. WGA kits: (B, E) Ampli1; (C, F, H, I) PicoPlex; (D, G) REPLI-g.

    Techniques Used: Whole Genome Amplification

    Distribution of identified known SNPs between datasets ( A ) Known SNPs identified in single cells, amplified with Ampli1, PicoPlex, and REPLI-g WGA kits and obtained from EDTA-preserved blood in comparison to unamplified DNA. ( B ) Known SNPs identified in single cells, amplified with Ampli1 or PicoPlex and obtained from EDTA- and CellSave-preserved blood in comparison to unamplified DNA from unfixed cells. ( C ) Known SNPs identified in single CTCs, amplified with PicoPlex in comparison to each other.
    Figure Legend Snippet: Distribution of identified known SNPs between datasets ( A ) Known SNPs identified in single cells, amplified with Ampli1, PicoPlex, and REPLI-g WGA kits and obtained from EDTA-preserved blood in comparison to unamplified DNA. ( B ) Known SNPs identified in single cells, amplified with Ampli1 or PicoPlex and obtained from EDTA- and CellSave-preserved blood in comparison to unamplified DNA from unfixed cells. ( C ) Known SNPs identified in single CTCs, amplified with PicoPlex in comparison to each other.

    Techniques Used: Amplification, Whole Genome Amplification

    Related Articles

    Amplification:

    Article Title: A tripartite survey of hyperparasitic fungi associated with ectoparasitic flies on bats (Mammalia: Chiroptera) in a neotropical cloud forest in Panama
    Article Snippet: Paragraph title: DNA extraction, amplification, phylogenetic analysis ... DNA was extracted from 1-4 Laboulbeniales thalli using a modified REPLI-g Single Cell Kit (Qiagen, Valencia, CA, USA) protocol [ ].

    Article Title: Tracking heavy water (D2O) incorporation for identifying and sorting active microbial cells
    Article Snippet: The REPLI-g Single Cell Kit (Qiagen) was used for cell lysis and MDA according to the manufacturer’s instructions. .. Finally, MDA products were diluted 50-fold in sterile nuclease-free water.

    Article Title: Comparison of variations detection between whole-genome amplification methods used in single-cell resequencing
    Article Snippet: We obtained 29 single cells from the YH cell line (a human lymphoblastoid cell line from first Asian genome donor [ ]) and amplified them using seven commercialized kits. .. The kits tested were: GenomePlex® Single Cell WGA Kit (which we called DOP-1, Sigma-Aldrich, St. Louis, MO, USA); Silicon Biosystem Ampli™ WGA Kit (DOP-2, Silicon Biosystems, Bologna, Italy); NEB Single Cell WGA Kit (DOP-3, New England Biolabs, Ipswich, MA, USA); Qiagen REPLI-g Mini Kit (MDA-1, Qiagen, Düsseldorf, Germany); Qiagen REPLI-g Single Cell Kit (MDA-2, Qiagen, Düsseldorf, Germany); GE Healthcare illustra GenomiPhi V2 DNA Amplification Kit (MDA-3, GE Healthcare, Little Chalfont, Buckinghamshire, England); and Yikon Genomics Single Cell Whole Genome Amplification Kit (MALBAC, Yikon Genomics, China). .. These kits were based on DOP-PCR, MDA, or MALBAC method respectively as indicated by their designations.

    Article Title: Evolution of multiple cell clones over a 29-year period of a CLL patient
    Article Snippet: Single CLL tumour cells are selected by a Micromanipulator (Eppendorf TransferMan NK2) under the inverted fluorescence microscope (Olympus IX-71), and pipetted into PCR tubes that contained 2 μl lysis buffer. .. Single-cell DNA amplification was carried out using the REPLI-g Single Cell Kit (Qiagen), and amplified DNA with positive results for at least six out of eight house-keeping genes were selected for subsequent library construction. .. DNA was fragmented with the Covaris E-210 ultrasonicator with adjusted shearing parameters.

    Article Title: Development of a facile droplet-based single-cell isolation platform for cultivation and genomic analysis in microorganisms
    Article Snippet: Cells were recovered from the droplets as described above and were lysed by adding 1.5 μl of buffer D2 (REPLI-g Single Cell Kit; Qiagen, USA) containing 0.08 mol/L dithiothreitol (DTT) and incubation at 65 o C for 10 minutes, followed by neutralization with 1.5 μl of Stop Solution (REPLI-g Single Cell Kit; Qiagen, USA). .. The volume of droplet after cell lysis in each of the wells was about 5 μl.

    Article Title: Performance of four modern whole genome amplification methods for copy number variant detection in single cells
    Article Snippet: For the bulk DNA sample, DNA was extracted from 5 * 106 cells using the DNeasy Blood & Tissue kit (Qiagen Hilden, Germany). .. Cell lysis and amplification was performed, using the Ampli-1 WGA kit (Silicon Biosystems, Castel Maggiore, Italy), the REPLI-g single cell kit (Qiagen Hilden, Germany) or the DOPlify WGA kit (Reproductive Health Science, Thebarton, Australia) as described in the respective manufacturer’s instructions. .. All samples were purified following the manufacturer’s protocol of the Genomic DNA Clean & Concentrator kit (version 1.0.0, Zymo Research, Irvine, USA) with 5X binding buffer.

    Article Title: Microfluidic-based mini-metagenomics enables discovery of novel microbial lineages from complex environmental samples
    Article Snippet: Paragraph title: Microfluidic genomic DNA amplification on Fluidigm C1 auto prep system ... After alkaline denaturation of DNA, neutralization and MDA were performed (Qiagen REPLI-g single cell kit) ( ).

    Article Title: Precision oncology using a limited number of cells: optimization of whole genome amplification products for sequencing applications
    Article Snippet: Isolated cells were subjected to genomic DNA isolation and WGA using one of the three commercially available single-cell WGA kits according to the manufacturer’s protocol: REPLI-g Single-Cell Kit (Qiagen, California, USA), Multiple Annealing and Looping Based Amplification Cycles (MALBAC) Single-cell WGA Kit (Yikon Genomics, Beijing, China) and PicoPlex Single-Cell WGA Kit (Rubicon, Michigan). .. Isolated cells were subjected to genomic DNA isolation and WGA using one of the three commercially available single-cell WGA kits according to the manufacturer’s protocol: REPLI-g Single-Cell Kit (Qiagen, California, USA), Multiple Annealing and Looping Based Amplification Cycles (MALBAC) Single-cell WGA Kit (Yikon Genomics, Beijing, China) and PicoPlex Single-Cell WGA Kit (Rubicon, Michigan).

    Article Title: A viability-linked metagenomic analysis of cleanroom environments: eukarya, prokaryotes, and viruses
    Article Snippet: All manipulations were performed in a bleach-cleaned biohood, which resided in an ultra-clean laboratory environment (i.e., single-use lab coats, bleached gloves, booties, etc.). .. Each sample was divided into 1 μl aliquots, which were amplified via Multiple Displacement Amplification (MDA) using Repli-g single-cell whole genome amplification kit (Qiagen part #150345) according to the manufacturer’s instructions. .. Reaction mixture consisted of Phi29 Reaction Buffer (1X final concentration), 50 ng in hexamers with phosphoro- thioate modification of the two 3’-terminal nucleo-tides (IDT) [ ], 0.4 mM dNTP, 5 % DMSO (Sigma), 10 mM DTT (Sigma), 100 U Phi29, and 0.5 μM Syto 13 (Invitrogen) in a final volume of 15 μl.

    Article Title: Impact of Contaminating DNA in Whole-Genome Amplification Kits Used for Metagenomic Shotgun Sequencing for Infection Diagnosis
    Article Snippet: Whole-genome amplification (WGA) is a useful tool for amplification of very small quantities of DNA for many uses, including metagenomic shotgun sequencing for infection diagnosis. .. The Illustra V2 Genomiphi, Illustra single cell Genomiphi, and Qiagen REPLI-g single cell kits were used to test identical sonicate fluid samples.

    Article Title: CHROMOTHRIPSIS FROM DNA DAMAGE IN MICRONUCLEI
    Article Snippet: Paragraph title: Multi-strand displacement amplification and library construction of single-cell genomic DNA ... DNA from isolated cells was subject to MDA following lysis using the REPLI-g Single Cell Kit (Qiagen) with minor modification. (Note that we achieved the best overall coverage uniformity with this latest version of REPLI-g from Qiagen as compared to earlier versions of REPLI-g or the RepliPhi enzyme from Epicentre.

    Article Title: FMR1 CGG repeat expansion mutation detection and linked haplotype analysis for reliable and accurate preimplantation genetic diagnosis of fragile X syndrome
    Article Snippet: Single cells isolated from lymphoblastoid cell lines (Coriell Cell Repositories, CCR; Camden, New Jersey, USA) were used to validate the FMR1 TP-PCR and tetradecaplex marker PCR assays for direct CGG repeat and linked multi-marker haplotype analyses, respectively. .. Isolation, lysis and/or whole-genome amplification, using the Genomiphi™ V2 DNA (GE Healthcare, Little Chalfont, UK) or REPLI-g (Qiagen, Hilden, Germany) Amplification Kit, of single lymphoblasts were performed as described (Ref. ). .. This study was approved by the Institutional Review Board of the National University of Singapore (B-15-273E).

    Whole Genome Amplification:

    Article Title: Ultrahigh-throughput functional profiling of microbiota communities
    Article Snippet: The selected MDE droplets were freeze dried and total DNA was isolated using the QIAamp DNA Investigator Kit (Qiagen). .. Whole-genome amplification was performed using the REPLI-g Single Cell Kit (Qiagen). .. For individual strains, genomic DNA (100 ng for each sample) was disrupted into 400- to 550-bp fragments using the Covaris S220 System (Covaris).

    Article Title: Germinal center reentries of BCL2-overexpressing B cells drive follicular lymphoma progression
    Article Snippet: The 50-Mb mouse exome was captured using Agilent SureSelect XT, genome version GRCm38/mm10. .. Capture libraries were constructed from 1 μg of WGA-amplified DNA from GC and post-GC subsets (BCL2-enriched or control empty vector) and germlines (naive) using the REPLI-g Single Cell Kit (QIAGEN). .. Enriched exome libraries were multiplexed and sequenced on the Illumina HiSeq 2000 platform to generate 100-bp paired-end reads.

    Article Title: Comparison of variations detection between whole-genome amplification methods used in single-cell resequencing
    Article Snippet: We obtained 29 single cells from the YH cell line (a human lymphoblastoid cell line from first Asian genome donor [ ]) and amplified them using seven commercialized kits. .. The kits tested were: GenomePlex® Single Cell WGA Kit (which we called DOP-1, Sigma-Aldrich, St. Louis, MO, USA); Silicon Biosystem Ampli™ WGA Kit (DOP-2, Silicon Biosystems, Bologna, Italy); NEB Single Cell WGA Kit (DOP-3, New England Biolabs, Ipswich, MA, USA); Qiagen REPLI-g Mini Kit (MDA-1, Qiagen, Düsseldorf, Germany); Qiagen REPLI-g Single Cell Kit (MDA-2, Qiagen, Düsseldorf, Germany); GE Healthcare illustra GenomiPhi V2 DNA Amplification Kit (MDA-3, GE Healthcare, Little Chalfont, Buckinghamshire, England); and Yikon Genomics Single Cell Whole Genome Amplification Kit (MALBAC, Yikon Genomics, China). .. These kits were based on DOP-PCR, MDA, or MALBAC method respectively as indicated by their designations.

    Article Title: Performance of four modern whole genome amplification methods for copy number variant detection in single cells
    Article Snippet: For the bulk DNA sample, DNA was extracted from 5 * 106 cells using the DNeasy Blood & Tissue kit (Qiagen Hilden, Germany). .. Cell lysis and amplification was performed, using the Ampli-1 WGA kit (Silicon Biosystems, Castel Maggiore, Italy), the REPLI-g single cell kit (Qiagen Hilden, Germany) or the DOPlify WGA kit (Reproductive Health Science, Thebarton, Australia) as described in the respective manufacturer’s instructions. .. All samples were purified following the manufacturer’s protocol of the Genomic DNA Clean & Concentrator kit (version 1.0.0, Zymo Research, Irvine, USA) with 5X binding buffer.

    Article Title: Microfluidic-based mini-metagenomics enables discovery of novel microbial lineages from complex environmental samples
    Article Snippet: Following cell loading, whole genome amplification via MDA was performed on-chip in 96 independent reactions. .. After alkaline denaturation of DNA, neutralization and MDA were performed (Qiagen REPLI-g single cell kit) ( ).

    Article Title: Precision oncology using a limited number of cells: optimization of whole genome amplification products for sequencing applications
    Article Snippet: Cell transfer to the tube cap was confirmed by imaging the cap prior to cap closure using the cap-check function. .. Isolated cells were subjected to genomic DNA isolation and WGA using one of the three commercially available single-cell WGA kits according to the manufacturer’s protocol: REPLI-g Single-Cell Kit (Qiagen, California, USA), Multiple Annealing and Looping Based Amplification Cycles (MALBAC) Single-cell WGA Kit (Yikon Genomics, Beijing, China) and PicoPlex Single-Cell WGA Kit (Rubicon, Michigan). .. WGA products were purified using the QIAquick PCR Purification Kit (Qiagen) and quantified with NanoDrop 2000 (Thermo), in keeping with a previously described CTC molecular analysis methodology [ ].

    Article Title: A viability-linked metagenomic analysis of cleanroom environments: eukarya, prokaryotes, and viruses
    Article Snippet: All manipulations were performed in a bleach-cleaned biohood, which resided in an ultra-clean laboratory environment (i.e., single-use lab coats, bleached gloves, booties, etc.). .. Each sample was divided into 1 μl aliquots, which were amplified via Multiple Displacement Amplification (MDA) using Repli-g single-cell whole genome amplification kit (Qiagen part #150345) according to the manufacturer’s instructions. .. Reaction mixture consisted of Phi29 Reaction Buffer (1X final concentration), 50 ng in hexamers with phosphoro- thioate modification of the two 3’-terminal nucleo-tides (IDT) [ ], 0.4 mM dNTP, 5 % DMSO (Sigma), 10 mM DTT (Sigma), 100 U Phi29, and 0.5 μM Syto 13 (Invitrogen) in a final volume of 15 μl.

    Article Title: Impact of Contaminating DNA in Whole-Genome Amplification Kits Used for Metagenomic Shotgun Sequencing for Infection Diagnosis
    Article Snippet: Three WGA kits were tested for their utility in a metagenomics approach to identify the pathogens in sonicate fluid comprised of biofilms and other materials dislodged from the surfaces of explanted prosthetic joints using sonication. .. The Illustra V2 Genomiphi, Illustra single cell Genomiphi, and Qiagen REPLI-g single cell kits were used to test identical sonicate fluid samples.

    Article Title: CHROMOTHRIPSIS FROM DNA DAMAGE IN MICRONUCLEI
    Article Snippet: DNA from isolated cells was subject to MDA following lysis using the REPLI-g Single Cell Kit (Qiagen) with minor modification. (Note that we achieved the best overall coverage uniformity with this latest version of REPLI-g from Qiagen as compared to earlier versions of REPLI-g or the RepliPhi enzyme from Epicentre. .. DNA from isolated cells was subject to MDA following lysis using the REPLI-g Single Cell Kit (Qiagen) with minor modification. (Note that we achieved the best overall coverage uniformity with this latest version of REPLI-g from Qiagen as compared to earlier versions of REPLI-g or the RepliPhi enzyme from Epicentre.

    Article Title: FMR1 CGG repeat expansion mutation detection and linked haplotype analysis for reliable and accurate preimplantation genetic diagnosis of fragile X syndrome
    Article Snippet: Single cells isolated from lymphoblastoid cell lines (Coriell Cell Repositories, CCR; Camden, New Jersey, USA) were used to validate the FMR1 TP-PCR and tetradecaplex marker PCR assays for direct CGG repeat and linked multi-marker haplotype analyses, respectively. .. Isolation, lysis and/or whole-genome amplification, using the Genomiphi™ V2 DNA (GE Healthcare, Little Chalfont, UK) or REPLI-g (Qiagen, Hilden, Germany) Amplification Kit, of single lymphoblasts were performed as described (Ref. ). .. This study was approved by the Institutional Review Board of the National University of Singapore (B-15-273E).

    Neutralization:

    Article Title: Development of a facile droplet-based single-cell isolation platform for cultivation and genomic analysis in microorganisms
    Article Snippet: Sixty droplets each with a single S. cerevisiae cell and twenty blank droplets were then collected successively in these wells. .. Cells were recovered from the droplets as described above and were lysed by adding 1.5 μl of buffer D2 (REPLI-g Single Cell Kit; Qiagen, USA) containing 0.08 mol/L dithiothreitol (DTT) and incubation at 65 o C for 10 minutes, followed by neutralization with 1.5 μl of Stop Solution (REPLI-g Single Cell Kit; Qiagen, USA). .. The volume of droplet after cell lysis in each of the wells was about 5 μl.

    Article Title: Microfluidic-based mini-metagenomics enables discovery of novel microbial lineages from complex environmental samples
    Article Snippet: A lysozyme (Epicenter) digestion step was added before alkaline denaturation of DNA. .. After alkaline denaturation of DNA, neutralization and MDA were performed (Qiagen REPLI-g single cell kit) ( ). .. Concentrations of all reagents were adjusted to match the 384 well plate-based protocol developed by the single-cell group at DOE’s Joint Genome Institute but adapted for volumes of the Fluidigm C1 IFC ( ).

    Cytometry:

    Article Title: DNA methyltransferase 3b silencing affects locus-specific DNA methylation and inhibits proliferation, migration and invasion in human hepatocellular carcinoma SMMC-7721 and BEL-7402 cells
    Article Snippet: Paragraph title: Cell cycle and apoptosis flow cytometry ... Cell apoptosis and cell cycle distribution were finally evaluated using the Annexin V-FITC/propidium iodide apoptosis detection kit (Qiagen) and cell cycle kit (Qiagen), according to the manufacturer's instructions.

    Construct:

    Article Title: Germinal center reentries of BCL2-overexpressing B cells drive follicular lymphoma progression
    Article Snippet: The 50-Mb mouse exome was captured using Agilent SureSelect XT, genome version GRCm38/mm10. .. Capture libraries were constructed from 1 μg of WGA-amplified DNA from GC and post-GC subsets (BCL2-enriched or control empty vector) and germlines (naive) using the REPLI-g Single Cell Kit (QIAGEN). .. Enriched exome libraries were multiplexed and sequenced on the Illumina HiSeq 2000 platform to generate 100-bp paired-end reads.

    Real-time Polymerase Chain Reaction:

    Article Title: Development of a facile droplet-based single-cell isolation platform for cultivation and genomic analysis in microorganisms
    Article Snippet: Paragraph title: Real-time quantitative PCR (qPCR) of single-cell DNA ... Cells were recovered from the droplets as described above and were lysed by adding 1.5 μl of buffer D2 (REPLI-g Single Cell Kit; Qiagen, USA) containing 0.08 mol/L dithiothreitol (DTT) and incubation at 65 o C for 10 minutes, followed by neutralization with 1.5 μl of Stop Solution (REPLI-g Single Cell Kit; Qiagen, USA).

    Incubation:

    Article Title: Development of a facile droplet-based single-cell isolation platform for cultivation and genomic analysis in microorganisms
    Article Snippet: Sixty droplets each with a single S. cerevisiae cell and twenty blank droplets were then collected successively in these wells. .. Cells were recovered from the droplets as described above and were lysed by adding 1.5 μl of buffer D2 (REPLI-g Single Cell Kit; Qiagen, USA) containing 0.08 mol/L dithiothreitol (DTT) and incubation at 65 o C for 10 minutes, followed by neutralization with 1.5 μl of Stop Solution (REPLI-g Single Cell Kit; Qiagen, USA). .. The volume of droplet after cell lysis in each of the wells was about 5 μl.

    Article Title: CHROMOTHRIPSIS FROM DNA DAMAGE IN MICRONUCLEI
    Article Snippet: DNA from isolated cells was subject to MDA following lysis using the REPLI-g Single Cell Kit (Qiagen) with minor modification. (Note that we achieved the best overall coverage uniformity with this latest version of REPLI-g from Qiagen as compared to earlier versions of REPLI-g or the RepliPhi enzyme from Epicentre. .. DNA from isolated cells was subject to MDA following lysis using the REPLI-g Single Cell Kit (Qiagen) with minor modification. (Note that we achieved the best overall coverage uniformity with this latest version of REPLI-g from Qiagen as compared to earlier versions of REPLI-g or the RepliPhi enzyme from Epicentre.

    Modification:

    Article Title: A tripartite survey of hyperparasitic fungi associated with ectoparasitic flies on bats (Mammalia: Chiroptera) in a neotropical cloud forest in Panama
    Article Snippet: Voucher slides are deposited at Farlow Herbarium (FH; Harvard University, Cambridge, MA, USA) and Herbario de la Universidad Autónoma de Chiriquí (UCH; David, Panamá). .. DNA was extracted from 1-4 Laboulbeniales thalli using a modified REPLI-g Single Cell Kit (Qiagen, Valencia, CA, USA) protocol [ ]. .. Thalli were often manually cut in 2-3 parts (through the perithecium) using a #10 surgical blade on disposable Bard-Parker handle (Aspen Surgical, Caledonia, MI, USA) to ensure successful lysis.

    Article Title: Microfluidic-based mini-metagenomics enables discovery of novel microbial lineages from complex environmental samples
    Article Snippet: The diluted environmental sample was loaded onto the chip using a modified version of the loading protocol where washing was not performed, as the capture sites were too large for microbial cells. .. After alkaline denaturation of DNA, neutralization and MDA were performed (Qiagen REPLI-g single cell kit) ( ).

    Article Title: Precision oncology using a limited number of cells: optimization of whole genome amplification products for sequencing applications
    Article Snippet: Isolated cells were subjected to genomic DNA isolation and WGA using one of the three commercially available single-cell WGA kits according to the manufacturer’s protocol: REPLI-g Single-Cell Kit (Qiagen, California, USA), Multiple Annealing and Looping Based Amplification Cycles (MALBAC) Single-cell WGA Kit (Yikon Genomics, Beijing, China) and PicoPlex Single-Cell WGA Kit (Rubicon, Michigan). .. WGA products were purified using the QIAquick PCR Purification Kit (Qiagen) and quantified with NanoDrop 2000 (Thermo), in keeping with a previously described CTC molecular analysis methodology [ ].

    Article Title: CHROMOTHRIPSIS FROM DNA DAMAGE IN MICRONUCLEI
    Article Snippet: Finally, the high processivity of Phi-29 polymerase consistently generates large amplicons above 10 kb , ; this enables us to perform Sanger sequencing on the MDA product after PCR to generate phasing information of rearrangements and validate their association with the missegregated chromosome, which is crucial in establishing the relationship between chromosomal rearrangements and DNA damage in the micronuclei. .. DNA from isolated cells was subject to MDA following lysis using the REPLI-g Single Cell Kit (Qiagen) with minor modification. (Note that we achieved the best overall coverage uniformity with this latest version of REPLI-g from Qiagen as compared to earlier versions of REPLI-g or the RepliPhi enzyme from Epicentre. .. Comparison of the coverage and uniformity of the single-cell libraries in the current study with previous studies , is summarized in and in Ref.

    Flow Cytometry:

    Article Title: DNA methyltransferase 3b silencing affects locus-specific DNA methylation and inhibits proliferation, migration and invasion in human hepatocellular carcinoma SMMC-7721 and BEL-7402 cells
    Article Snippet: Paragraph title: Cell cycle and apoptosis flow cytometry ... Cell apoptosis and cell cycle distribution were finally evaluated using the Annexin V-FITC/propidium iodide apoptosis detection kit (Qiagen) and cell cycle kit (Qiagen), according to the manufacturer's instructions.

    Gas Chromatography:

    Article Title: Germinal center reentries of BCL2-overexpressing B cells drive follicular lymphoma progression
    Article Snippet: The 50-Mb mouse exome was captured using Agilent SureSelect XT, genome version GRCm38/mm10. .. Capture libraries were constructed from 1 μg of WGA-amplified DNA from GC and post-GC subsets (BCL2-enriched or control empty vector) and germlines (naive) using the REPLI-g Single Cell Kit (QIAGEN). .. Enriched exome libraries were multiplexed and sequenced on the Illumina HiSeq 2000 platform to generate 100-bp paired-end reads.

    Sensitive Assay:

    Article Title: Performance of four modern whole genome amplification methods for copy number variant detection in single cells
    Article Snippet: Cell lysis and amplification was performed, using the Ampli-1 WGA kit (Silicon Biosystems, Castel Maggiore, Italy), the REPLI-g single cell kit (Qiagen Hilden, Germany) or the DOPlify WGA kit (Reproductive Health Science, Thebarton, Australia) as described in the respective manufacturer’s instructions. .. All samples were purified following the manufacturer’s protocol of the Genomic DNA Clean & Concentrator kit (version 1.0.0, Zymo Research, Irvine, USA) with 5X binding buffer.

    Infection:

    Article Title: Impact of Contaminating DNA in Whole-Genome Amplification Kits Used for Metagenomic Shotgun Sequencing for Infection Diagnosis
    Article Snippet: Whole-genome amplification (WGA) is a useful tool for amplification of very small quantities of DNA for many uses, including metagenomic shotgun sequencing for infection diagnosis. .. The Illustra V2 Genomiphi, Illustra single cell Genomiphi, and Qiagen REPLI-g single cell kits were used to test identical sonicate fluid samples.

    DNA Sequencing:

    Article Title: Evolution of multiple cell clones over a 29-year period of a CLL patient
    Article Snippet: Paragraph title: Single-cell DNA sequencing ... Single-cell DNA amplification was carried out using the REPLI-g Single Cell Kit (Qiagen), and amplified DNA with positive results for at least six out of eight house-keeping genes were selected for subsequent library construction.

    Polymerase Chain Reaction:

    Article Title: A tripartite survey of hyperparasitic fungi associated with ectoparasitic flies on bats (Mammalia: Chiroptera) in a neotropical cloud forest in Panama
    Article Snippet: DNA was extracted from 1-4 Laboulbeniales thalli using a modified REPLI-g Single Cell Kit (Qiagen, Valencia, CA, USA) protocol [ ]. .. For the purpose of this survey, we only amplified the nuclear large ribosomal subunit (LSU) using primers LR0R (5’–ACCCGCTGAACTTAAGC–3’) and LR5 (5’–ATCCTGAGGGAAACTTC–3’).

    Article Title: Tracking heavy water (D2O) incorporation for identifying and sorting active microbial cells
    Article Snippet: The REPLI-g Single Cell Kit (Qiagen) was used for cell lysis and MDA according to the manufacturer’s instructions. .. Bacterial 16S rRNA genes were amplified with primers 341F (5′-CCTACGGGNGGCWGCAG-3′) and 785R (5′-GACTACHVGGGTATCTAATCC-3′) ( , ).

    Article Title: Evolution of multiple cell clones over a 29-year period of a CLL patient
    Article Snippet: Single CLL tumour cells are selected by a Micromanipulator (Eppendorf TransferMan NK2) under the inverted fluorescence microscope (Olympus IX-71), and pipetted into PCR tubes that contained 2 μl lysis buffer. .. Single-cell DNA amplification was carried out using the REPLI-g Single Cell Kit (Qiagen), and amplified DNA with positive results for at least six out of eight house-keeping genes were selected for subsequent library construction.

    Article Title: Development of a facile droplet-based single-cell isolation platform for cultivation and genomic analysis in microorganisms
    Article Snippet: Eighty wells of a 96-well PCR plate were each filled with 1 μl of PBS buffer (pH 8.0) before single-cell droplet collection. .. Cells were recovered from the droplets as described above and were lysed by adding 1.5 μl of buffer D2 (REPLI-g Single Cell Kit; Qiagen, USA) containing 0.08 mol/L dithiothreitol (DTT) and incubation at 65 o C for 10 minutes, followed by neutralization with 1.5 μl of Stop Solution (REPLI-g Single Cell Kit; Qiagen, USA).

    Article Title: CHROMOTHRIPSIS FROM DNA DAMAGE IN MICRONUCLEI
    Article Snippet: Finally, the high processivity of Phi-29 polymerase consistently generates large amplicons above 10 kb , ; this enables us to perform Sanger sequencing on the MDA product after PCR to generate phasing information of rearrangements and validate their association with the missegregated chromosome, which is crucial in establishing the relationship between chromosomal rearrangements and DNA damage in the micronuclei. .. DNA from isolated cells was subject to MDA following lysis using the REPLI-g Single Cell Kit (Qiagen) with minor modification. (Note that we achieved the best overall coverage uniformity with this latest version of REPLI-g from Qiagen as compared to earlier versions of REPLI-g or the RepliPhi enzyme from Epicentre.

    Article Title: FMR1 CGG repeat expansion mutation detection and linked haplotype analysis for reliable and accurate preimplantation genetic diagnosis of fragile X syndrome
    Article Snippet: Single cells isolated from lymphoblastoid cell lines (Coriell Cell Repositories, CCR; Camden, New Jersey, USA) were used to validate the FMR1 TP-PCR and tetradecaplex marker PCR assays for direct CGG repeat and linked multi-marker haplotype analyses, respectively. .. Isolation, lysis and/or whole-genome amplification, using the Genomiphi™ V2 DNA (GE Healthcare, Little Chalfont, UK) or REPLI-g (Qiagen, Hilden, Germany) Amplification Kit, of single lymphoblasts were performed as described (Ref. ).

    Sonication:

    Article Title: Impact of Contaminating DNA in Whole-Genome Amplification Kits Used for Metagenomic Shotgun Sequencing for Infection Diagnosis
    Article Snippet: Three WGA kits were tested for their utility in a metagenomics approach to identify the pathogens in sonicate fluid comprised of biofilms and other materials dislodged from the surfaces of explanted prosthetic joints using sonication. .. The Illustra V2 Genomiphi, Illustra single cell Genomiphi, and Qiagen REPLI-g single cell kits were used to test identical sonicate fluid samples.

    DNA Extraction:

    Article Title: A tripartite survey of hyperparasitic fungi associated with ectoparasitic flies on bats (Mammalia: Chiroptera) in a neotropical cloud forest in Panama
    Article Snippet: Paragraph title: DNA extraction, amplification, phylogenetic analysis ... DNA was extracted from 1-4 Laboulbeniales thalli using a modified REPLI-g Single Cell Kit (Qiagen, Valencia, CA, USA) protocol [ ].

    Article Title: Precision oncology using a limited number of cells: optimization of whole genome amplification products for sequencing applications
    Article Snippet: Cell transfer to the tube cap was confirmed by imaging the cap prior to cap closure using the cap-check function. .. Isolated cells were subjected to genomic DNA isolation and WGA using one of the three commercially available single-cell WGA kits according to the manufacturer’s protocol: REPLI-g Single-Cell Kit (Qiagen, California, USA), Multiple Annealing and Looping Based Amplification Cycles (MALBAC) Single-cell WGA Kit (Yikon Genomics, Beijing, China) and PicoPlex Single-Cell WGA Kit (Rubicon, Michigan). .. WGA products were purified using the QIAquick PCR Purification Kit (Qiagen) and quantified with NanoDrop 2000 (Thermo), in keeping with a previously described CTC molecular analysis methodology [ ].

    Article Title: Genomic Comparison of Campylobacter spp. and Their Potential for Zoonotic Transmission between Birds, Primates, and Livestock
    Article Snippet: Paragraph title: DNA extraction, library preparation, and next-generation sequencing. ... DNA was extracted using whole-genome isolation kits (Qiagen, Valencia, CA, USA) with previously published modifications ( ).

    Fluorescence:

    Article Title: Evolution of multiple cell clones over a 29-year period of a CLL patient
    Article Snippet: Single CLL tumour cells are selected by a Micromanipulator (Eppendorf TransferMan NK2) under the inverted fluorescence microscope (Olympus IX-71), and pipetted into PCR tubes that contained 2 μl lysis buffer. .. Single-cell DNA amplification was carried out using the REPLI-g Single Cell Kit (Qiagen), and amplified DNA with positive results for at least six out of eight house-keeping genes were selected for subsequent library construction.

    Multiple Displacement Amplification:

    Article Title: Tracking heavy water (D2O) incorporation for identifying and sorting active microbial cells
    Article Snippet: To wash off any cells that might have stuck to the walls of the capillary, 2 μL of sterile PBS buffer was then added to the capillary piece and the tube was centrifuged again. .. The REPLI-g Single Cell Kit (Qiagen) was used for cell lysis and MDA according to the manufacturer’s instructions. .. MDA was performed for 8 h at 30 °C and inactivated for 3 min at 65 °C.

    Article Title: Comparison of variations detection between whole-genome amplification methods used in single-cell resequencing
    Article Snippet: We obtained 29 single cells from the YH cell line (a human lymphoblastoid cell line from first Asian genome donor [ ]) and amplified them using seven commercialized kits. .. The kits tested were: GenomePlex® Single Cell WGA Kit (which we called DOP-1, Sigma-Aldrich, St. Louis, MO, USA); Silicon Biosystem Ampli™ WGA Kit (DOP-2, Silicon Biosystems, Bologna, Italy); NEB Single Cell WGA Kit (DOP-3, New England Biolabs, Ipswich, MA, USA); Qiagen REPLI-g Mini Kit (MDA-1, Qiagen, Düsseldorf, Germany); Qiagen REPLI-g Single Cell Kit (MDA-2, Qiagen, Düsseldorf, Germany); GE Healthcare illustra GenomiPhi V2 DNA Amplification Kit (MDA-3, GE Healthcare, Little Chalfont, Buckinghamshire, England); and Yikon Genomics Single Cell Whole Genome Amplification Kit (MALBAC, Yikon Genomics, China). .. These kits were based on DOP-PCR, MDA, or MALBAC method respectively as indicated by their designations.

    Article Title: Microfluidic-based mini-metagenomics enables discovery of novel microbial lineages from complex environmental samples
    Article Snippet: A lysozyme (Epicenter) digestion step was added before alkaline denaturation of DNA. .. After alkaline denaturation of DNA, neutralization and MDA were performed (Qiagen REPLI-g single cell kit) ( ). .. Concentrations of all reagents were adjusted to match the 384 well plate-based protocol developed by the single-cell group at DOE’s Joint Genome Institute but adapted for volumes of the Fluidigm C1 IFC ( ).

    Article Title: Precision oncology using a limited number of cells: optimization of whole genome amplification products for sequencing applications
    Article Snippet: Isolated cells were subjected to genomic DNA isolation and WGA using one of the three commercially available single-cell WGA kits according to the manufacturer’s protocol: REPLI-g Single-Cell Kit (Qiagen, California, USA), Multiple Annealing and Looping Based Amplification Cycles (MALBAC) Single-cell WGA Kit (Yikon Genomics, Beijing, China) and PicoPlex Single-Cell WGA Kit (Rubicon, Michigan). .. Isolated cells were subjected to genomic DNA isolation and WGA using one of the three commercially available single-cell WGA kits according to the manufacturer’s protocol: REPLI-g Single-Cell Kit (Qiagen, California, USA), Multiple Annealing and Looping Based Amplification Cycles (MALBAC) Single-cell WGA Kit (Yikon Genomics, Beijing, China) and PicoPlex Single-Cell WGA Kit (Rubicon, Michigan).

    Article Title: A viability-linked metagenomic analysis of cleanroom environments: eukarya, prokaryotes, and viruses
    Article Snippet: All manipulations were performed in a bleach-cleaned biohood, which resided in an ultra-clean laboratory environment (i.e., single-use lab coats, bleached gloves, booties, etc.). .. Each sample was divided into 1 μl aliquots, which were amplified via Multiple Displacement Amplification (MDA) using Repli-g single-cell whole genome amplification kit (Qiagen part #150345) according to the manufacturer’s instructions. .. Reaction mixture consisted of Phi29 Reaction Buffer (1X final concentration), 50 ng in hexamers with phosphoro- thioate modification of the two 3’-terminal nucleo-tides (IDT) [ ], 0.4 mM dNTP, 5 % DMSO (Sigma), 10 mM DTT (Sigma), 100 U Phi29, and 0.5 μM Syto 13 (Invitrogen) in a final volume of 15 μl.

    Article Title: CHROMOTHRIPSIS FROM DNA DAMAGE IN MICRONUCLEI
    Article Snippet: Finally, the high processivity of Phi-29 polymerase consistently generates large amplicons above 10 kb , ; this enables us to perform Sanger sequencing on the MDA product after PCR to generate phasing information of rearrangements and validate their association with the missegregated chromosome, which is crucial in establishing the relationship between chromosomal rearrangements and DNA damage in the micronuclei. .. DNA from isolated cells was subject to MDA following lysis using the REPLI-g Single Cell Kit (Qiagen) with minor modification. (Note that we achieved the best overall coverage uniformity with this latest version of REPLI-g from Qiagen as compared to earlier versions of REPLI-g or the RepliPhi enzyme from Epicentre. .. Comparison of the coverage and uniformity of the single-cell libraries in the current study with previous studies , is summarized in and in Ref.

    Isolation:

    Article Title: Ultrahigh-throughput functional profiling of microbiota communities
    Article Snippet: The selected MDE droplets were freeze dried and total DNA was isolated using the QIAamp DNA Investigator Kit (Qiagen). .. Whole-genome amplification was performed using the REPLI-g Single Cell Kit (Qiagen).

    Article Title: Precision oncology using a limited number of cells: optimization of whole genome amplification products for sequencing applications
    Article Snippet: Cell transfer to the tube cap was confirmed by imaging the cap prior to cap closure using the cap-check function. .. Isolated cells were subjected to genomic DNA isolation and WGA using one of the three commercially available single-cell WGA kits according to the manufacturer’s protocol: REPLI-g Single-Cell Kit (Qiagen, California, USA), Multiple Annealing and Looping Based Amplification Cycles (MALBAC) Single-cell WGA Kit (Yikon Genomics, Beijing, China) and PicoPlex Single-Cell WGA Kit (Rubicon, Michigan). .. WGA products were purified using the QIAquick PCR Purification Kit (Qiagen) and quantified with NanoDrop 2000 (Thermo), in keeping with a previously described CTC molecular analysis methodology [ ].

    Article Title: CHROMOTHRIPSIS FROM DNA DAMAGE IN MICRONUCLEI
    Article Snippet: Finally, the high processivity of Phi-29 polymerase consistently generates large amplicons above 10 kb , ; this enables us to perform Sanger sequencing on the MDA product after PCR to generate phasing information of rearrangements and validate their association with the missegregated chromosome, which is crucial in establishing the relationship between chromosomal rearrangements and DNA damage in the micronuclei. .. DNA from isolated cells was subject to MDA following lysis using the REPLI-g Single Cell Kit (Qiagen) with minor modification. (Note that we achieved the best overall coverage uniformity with this latest version of REPLI-g from Qiagen as compared to earlier versions of REPLI-g or the RepliPhi enzyme from Epicentre. .. Comparison of the coverage and uniformity of the single-cell libraries in the current study with previous studies , is summarized in and in Ref.

    Article Title: FMR1 CGG repeat expansion mutation detection and linked haplotype analysis for reliable and accurate preimplantation genetic diagnosis of fragile X syndrome
    Article Snippet: Single cells isolated from lymphoblastoid cell lines (Coriell Cell Repositories, CCR; Camden, New Jersey, USA) were used to validate the FMR1 TP-PCR and tetradecaplex marker PCR assays for direct CGG repeat and linked multi-marker haplotype analyses, respectively. .. Isolation, lysis and/or whole-genome amplification, using the Genomiphi™ V2 DNA (GE Healthcare, Little Chalfont, UK) or REPLI-g (Qiagen, Hilden, Germany) Amplification Kit, of single lymphoblasts were performed as described (Ref. ). .. This study was approved by the Institutional Review Board of the National University of Singapore (B-15-273E).

    Article Title: Genomic Comparison of Campylobacter spp. and Their Potential for Zoonotic Transmission between Birds, Primates, and Livestock
    Article Snippet: High-molecular-weight genomic DNA (gDNA) was isolated from bacterial colonies grown on 5% SBA plates (UC Davis Vet Med Biological Services) at 37°C in microaerophilic conditions (as described above). .. DNA was extracted using whole-genome isolation kits (Qiagen, Valencia, CA, USA) with previously published modifications ( ). .. The bacterial cells were processed using the protocols of the 100K Pathogen Genome Project (UC Davis, Weimer laboratory) as previously described ( , ).

    Microscopy:

    Article Title: Evolution of multiple cell clones over a 29-year period of a CLL patient
    Article Snippet: Single CLL tumour cells are selected by a Micromanipulator (Eppendorf TransferMan NK2) under the inverted fluorescence microscope (Olympus IX-71), and pipetted into PCR tubes that contained 2 μl lysis buffer. .. Single-cell DNA amplification was carried out using the REPLI-g Single Cell Kit (Qiagen), and amplified DNA with positive results for at least six out of eight house-keeping genes were selected for subsequent library construction.

    Purification:

    Article Title: A tripartite survey of hyperparasitic fungi associated with ectoparasitic flies on bats (Mammalia: Chiroptera) in a neotropical cloud forest in Panama
    Article Snippet: DNA was extracted from 1-4 Laboulbeniales thalli using a modified REPLI-g Single Cell Kit (Qiagen, Valencia, CA, USA) protocol [ ]. .. DNA was extracted from 1-4 Laboulbeniales thalli using a modified REPLI-g Single Cell Kit (Qiagen, Valencia, CA, USA) protocol [ ].

    Article Title: Evolution of multiple cell clones over a 29-year period of a CLL patient
    Article Snippet: Single-cell DNA amplification was carried out using the REPLI-g Single Cell Kit (Qiagen), and amplified DNA with positive results for at least six out of eight house-keeping genes were selected for subsequent library construction. .. Single-cell DNA amplification was carried out using the REPLI-g Single Cell Kit (Qiagen), and amplified DNA with positive results for at least six out of eight house-keeping genes were selected for subsequent library construction.

    Article Title: Search for a Prion-Specific Nucleic Acid
    Article Snippet: The plates were irradiated at 4°C at 10 cm from the UV light source with an E max of 254 nm. .. The P3′SS vector was irradiated with 19.5 J/m2 (15 s) and 39 J/m2 (30 s), after which it was purified using the QIAGEN genomic purification kit. .. DNA was incubated with T4 den V to cleave UV photoproducts.

    Article Title: Genomic Comparison of Campylobacter spp. and Their Potential for Zoonotic Transmission between Birds, Primates, and Livestock
    Article Snippet: DNA was extracted using whole-genome isolation kits (Qiagen, Valencia, CA, USA) with previously published modifications ( ). .. DNA was extracted using whole-genome isolation kits (Qiagen, Valencia, CA, USA) with previously published modifications ( ).

    Sequencing:

    Article Title: Ultrahigh-throughput functional profiling of microbiota communities
    Article Snippet: Paragraph title: NGS Sequencing. ... Whole-genome amplification was performed using the REPLI-g Single Cell Kit (Qiagen).

    Article Title: Germinal center reentries of BCL2-overexpressing B cells drive follicular lymphoma progression
    Article Snippet: Paragraph title: Whole-exome mouse sequencing and analysis. ... Capture libraries were constructed from 1 μg of WGA-amplified DNA from GC and post-GC subsets (BCL2-enriched or control empty vector) and germlines (naive) using the REPLI-g Single Cell Kit (QIAGEN).

    Article Title: Comparison of variations detection between whole-genome amplification methods used in single-cell resequencing
    Article Snippet: The kits tested were: GenomePlex® Single Cell WGA Kit (which we called DOP-1, Sigma-Aldrich, St. Louis, MO, USA); Silicon Biosystem Ampli™ WGA Kit (DOP-2, Silicon Biosystems, Bologna, Italy); NEB Single Cell WGA Kit (DOP-3, New England Biolabs, Ipswich, MA, USA); Qiagen REPLI-g Mini Kit (MDA-1, Qiagen, Düsseldorf, Germany); Qiagen REPLI-g Single Cell Kit (MDA-2, Qiagen, Düsseldorf, Germany); GE Healthcare illustra GenomiPhi V2 DNA Amplification Kit (MDA-3, GE Healthcare, Little Chalfont, Buckinghamshire, England); and Yikon Genomics Single Cell Whole Genome Amplification Kit (MALBAC, Yikon Genomics, China). .. We performed several experimental replicates for each kit, and sequenced the WGA product of each single cell a mean depth of ~0.5X (Additional file : Table S1 and Additional file : Table S2).

    Article Title: Evolution of multiple cell clones over a 29-year period of a CLL patient
    Article Snippet: Single-cell DNA amplification was carried out using the REPLI-g Single Cell Kit (Qiagen), and amplified DNA with positive results for at least six out of eight house-keeping genes were selected for subsequent library construction. .. We purified the DNA fragments, blunted the ends, added A tails and ligated them with adaptors to prepare Hiseq libraries.

    Article Title: A viability-linked metagenomic analysis of cleanroom environments: eukarya, prokaryotes, and viruses
    Article Snippet: Paragraph title: Metagenomic sequencing ... Each sample was divided into 1 μl aliquots, which were amplified via Multiple Displacement Amplification (MDA) using Repli-g single-cell whole genome amplification kit (Qiagen part #150345) according to the manufacturer’s instructions.

    Article Title: CHROMOTHRIPSIS FROM DNA DAMAGE IN MICRONUCLEI
    Article Snippet: Finally, the high processivity of Phi-29 polymerase consistently generates large amplicons above 10 kb , ; this enables us to perform Sanger sequencing on the MDA product after PCR to generate phasing information of rearrangements and validate their association with the missegregated chromosome, which is crucial in establishing the relationship between chromosomal rearrangements and DNA damage in the micronuclei. .. DNA from isolated cells was subject to MDA following lysis using the REPLI-g Single Cell Kit (Qiagen) with minor modification. (Note that we achieved the best overall coverage uniformity with this latest version of REPLI-g from Qiagen as compared to earlier versions of REPLI-g or the RepliPhi enzyme from Epicentre.

    Blocking Assay:

    Article Title: Microfluidic-based mini-metagenomics enables discovery of novel microbial lineages from complex environmental samples
    Article Snippet: Priming the C1 IFC involved filling all microfluidic control channels with C1 Harvest Reagent, all capture sites with C1 Blocking Reagent, and the input multiplexer with C1 Preloading Reagent. .. After alkaline denaturation of DNA, neutralization and MDA were performed (Qiagen REPLI-g single cell kit) ( ).

    Shotgun Sequencing:

    Article Title: Impact of Contaminating DNA in Whole-Genome Amplification Kits Used for Metagenomic Shotgun Sequencing for Infection Diagnosis
    Article Snippet: Whole-genome amplification (WGA) is a useful tool for amplification of very small quantities of DNA for many uses, including metagenomic shotgun sequencing for infection diagnosis. .. The Illustra V2 Genomiphi, Illustra single cell Genomiphi, and Qiagen REPLI-g single cell kits were used to test identical sonicate fluid samples.

    Chromatin Immunoprecipitation:

    Article Title: Microfluidic-based mini-metagenomics enables discovery of novel microbial lineages from complex environmental samples
    Article Snippet: The diluted environmental sample was loaded onto the chip using a modified version of the loading protocol where washing was not performed, as the capture sites were too large for microbial cells. .. After alkaline denaturation of DNA, neutralization and MDA were performed (Qiagen REPLI-g single cell kit) ( ).

    Plasmid Preparation:

    Article Title: Germinal center reentries of BCL2-overexpressing B cells drive follicular lymphoma progression
    Article Snippet: The 50-Mb mouse exome was captured using Agilent SureSelect XT, genome version GRCm38/mm10. .. Capture libraries were constructed from 1 μg of WGA-amplified DNA from GC and post-GC subsets (BCL2-enriched or control empty vector) and germlines (naive) using the REPLI-g Single Cell Kit (QIAGEN). .. Enriched exome libraries were multiplexed and sequenced on the Illumina HiSeq 2000 platform to generate 100-bp paired-end reads.

    Article Title: Search for a Prion-Specific Nucleic Acid
    Article Snippet: The plates were irradiated at 4°C at 10 cm from the UV light source with an E max of 254 nm. .. The P3′SS vector was irradiated with 19.5 J/m2 (15 s) and 39 J/m2 (30 s), after which it was purified using the QIAGEN genomic purification kit. .. DNA was incubated with T4 den V to cleave UV photoproducts.

    Irradiation:

    Article Title: Search for a Prion-Specific Nucleic Acid
    Article Snippet: The plates were irradiated at 4°C at 10 cm from the UV light source with an E max of 254 nm. .. The P3′SS vector was irradiated with 19.5 J/m2 (15 s) and 39 J/m2 (30 s), after which it was purified using the QIAGEN genomic purification kit. .. DNA was incubated with T4 den V to cleave UV photoproducts.

    Selection:

    Article Title: Impact of Contaminating DNA in Whole-Genome Amplification Kits Used for Metagenomic Shotgun Sequencing for Infection Diagnosis
    Article Snippet: The Illustra V2 Genomiphi, Illustra single cell Genomiphi, and Qiagen REPLI-g single cell kits were used to test identical sonicate fluid samples. .. The Illustra V2 Genomiphi, Illustra single cell Genomiphi, and Qiagen REPLI-g single cell kits were used to test identical sonicate fluid samples.

    Next-Generation Sequencing:

    Article Title: Ultrahigh-throughput functional profiling of microbiota communities
    Article Snippet: Paragraph title: NGS Sequencing. ... Whole-genome amplification was performed using the REPLI-g Single Cell Kit (Qiagen).

    Article Title: Genomic Comparison of Campylobacter spp. and Their Potential for Zoonotic Transmission between Birds, Primates, and Livestock
    Article Snippet: Paragraph title: DNA extraction, library preparation, and next-generation sequencing. ... DNA was extracted using whole-genome isolation kits (Qiagen, Valencia, CA, USA) with previously published modifications ( ).

    Multiple Annealing and Looping–Based Amplification Cycles:

    Article Title: Comparison of variations detection between whole-genome amplification methods used in single-cell resequencing
    Article Snippet: We obtained 29 single cells from the YH cell line (a human lymphoblastoid cell line from first Asian genome donor [ ]) and amplified them using seven commercialized kits. .. The kits tested were: GenomePlex® Single Cell WGA Kit (which we called DOP-1, Sigma-Aldrich, St. Louis, MO, USA); Silicon Biosystem Ampli™ WGA Kit (DOP-2, Silicon Biosystems, Bologna, Italy); NEB Single Cell WGA Kit (DOP-3, New England Biolabs, Ipswich, MA, USA); Qiagen REPLI-g Mini Kit (MDA-1, Qiagen, Düsseldorf, Germany); Qiagen REPLI-g Single Cell Kit (MDA-2, Qiagen, Düsseldorf, Germany); GE Healthcare illustra GenomiPhi V2 DNA Amplification Kit (MDA-3, GE Healthcare, Little Chalfont, Buckinghamshire, England); and Yikon Genomics Single Cell Whole Genome Amplification Kit (MALBAC, Yikon Genomics, China). .. These kits were based on DOP-PCR, MDA, or MALBAC method respectively as indicated by their designations.

    Article Title: Precision oncology using a limited number of cells: optimization of whole genome amplification products for sequencing applications
    Article Snippet: Cell transfer to the tube cap was confirmed by imaging the cap prior to cap closure using the cap-check function. .. Isolated cells were subjected to genomic DNA isolation and WGA using one of the three commercially available single-cell WGA kits according to the manufacturer’s protocol: REPLI-g Single-Cell Kit (Qiagen, California, USA), Multiple Annealing and Looping Based Amplification Cycles (MALBAC) Single-cell WGA Kit (Yikon Genomics, Beijing, China) and PicoPlex Single-Cell WGA Kit (Rubicon, Michigan). .. WGA products were purified using the QIAquick PCR Purification Kit (Qiagen) and quantified with NanoDrop 2000 (Thermo), in keeping with a previously described CTC molecular analysis methodology [ ].

    Article Title: CHROMOTHRIPSIS FROM DNA DAMAGE IN MICRONUCLEI
    Article Snippet: We chose to amplify single-cell genomes by multi-strand displacement amplification (MDA) with the Phi-29 polymerase for four main reasons: First, MDA gives better overall genome coverage than PCR-based methods and also gives comparable uniformity - to other methods such as MALBAC ; this is required for the detection of chromosomal rearrangements. .. DNA from isolated cells was subject to MDA following lysis using the REPLI-g Single Cell Kit (Qiagen) with minor modification. (Note that we achieved the best overall coverage uniformity with this latest version of REPLI-g from Qiagen as compared to earlier versions of REPLI-g or the RepliPhi enzyme from Epicentre.

    Concentration Assay:

    Article Title: Performance of four modern whole genome amplification methods for copy number variant detection in single cells
    Article Snippet: Cell lysis and amplification was performed, using the Ampli-1 WGA kit (Silicon Biosystems, Castel Maggiore, Italy), the REPLI-g single cell kit (Qiagen Hilden, Germany) or the DOPlify WGA kit (Reproductive Health Science, Thebarton, Australia) as described in the respective manufacturer’s instructions. .. All samples were purified following the manufacturer’s protocol of the Genomic DNA Clean & Concentrator kit (version 1.0.0, Zymo Research, Irvine, USA) with 5X binding buffer.

    Marker:

    Article Title: FMR1 CGG repeat expansion mutation detection and linked haplotype analysis for reliable and accurate preimplantation genetic diagnosis of fragile X syndrome
    Article Snippet: Single cells isolated from lymphoblastoid cell lines (Coriell Cell Repositories, CCR; Camden, New Jersey, USA) were used to validate the FMR1 TP-PCR and tetradecaplex marker PCR assays for direct CGG repeat and linked multi-marker haplotype analyses, respectively. .. Isolation, lysis and/or whole-genome amplification, using the Genomiphi™ V2 DNA (GE Healthcare, Little Chalfont, UK) or REPLI-g (Qiagen, Hilden, Germany) Amplification Kit, of single lymphoblasts were performed as described (Ref. ).

    Lysis:

    Article Title: Tracking heavy water (D2O) incorporation for identifying and sorting active microbial cells
    Article Snippet: To wash off any cells that might have stuck to the walls of the capillary, 2 μL of sterile PBS buffer was then added to the capillary piece and the tube was centrifuged again. .. The REPLI-g Single Cell Kit (Qiagen) was used for cell lysis and MDA according to the manufacturer’s instructions. .. MDA was performed for 8 h at 30 °C and inactivated for 3 min at 65 °C.

    Article Title: Evolution of multiple cell clones over a 29-year period of a CLL patient
    Article Snippet: Single CLL tumour cells are selected by a Micromanipulator (Eppendorf TransferMan NK2) under the inverted fluorescence microscope (Olympus IX-71), and pipetted into PCR tubes that contained 2 μl lysis buffer. .. Single-cell DNA amplification was carried out using the REPLI-g Single Cell Kit (Qiagen), and amplified DNA with positive results for at least six out of eight house-keeping genes were selected for subsequent library construction.

    Article Title: Performance of four modern whole genome amplification methods for copy number variant detection in single cells
    Article Snippet: For the bulk DNA sample, DNA was extracted from 5 * 106 cells using the DNeasy Blood & Tissue kit (Qiagen Hilden, Germany). .. Cell lysis and amplification was performed, using the Ampli-1 WGA kit (Silicon Biosystems, Castel Maggiore, Italy), the REPLI-g single cell kit (Qiagen Hilden, Germany) or the DOPlify WGA kit (Reproductive Health Science, Thebarton, Australia) as described in the respective manufacturer’s instructions. .. All samples were purified following the manufacturer’s protocol of the Genomic DNA Clean & Concentrator kit (version 1.0.0, Zymo Research, Irvine, USA) with 5X binding buffer.

    Article Title: Precision oncology using a limited number of cells: optimization of whole genome amplification products for sequencing applications
    Article Snippet: Isolated cells were subjected to genomic DNA isolation and WGA using one of the three commercially available single-cell WGA kits according to the manufacturer’s protocol: REPLI-g Single-Cell Kit (Qiagen, California, USA), Multiple Annealing and Looping Based Amplification Cycles (MALBAC) Single-cell WGA Kit (Yikon Genomics, Beijing, China) and PicoPlex Single-Cell WGA Kit (Rubicon, Michigan). .. Isolated cells were subjected to genomic DNA isolation and WGA using one of the three commercially available single-cell WGA kits according to the manufacturer’s protocol: REPLI-g Single-Cell Kit (Qiagen, California, USA), Multiple Annealing and Looping Based Amplification Cycles (MALBAC) Single-cell WGA Kit (Yikon Genomics, Beijing, China) and PicoPlex Single-Cell WGA Kit (Rubicon, Michigan).

    Article Title: A viability-linked metagenomic analysis of cleanroom environments: eukarya, prokaryotes, and viruses
    Article Snippet: Each sample was divided into 1 μl aliquots, which were amplified via Multiple Displacement Amplification (MDA) using Repli-g single-cell whole genome amplification kit (Qiagen part #150345) according to the manufacturer’s instructions. .. Each sample was divided into 1 μl aliquots, which were amplified via Multiple Displacement Amplification (MDA) using Repli-g single-cell whole genome amplification kit (Qiagen part #150345) according to the manufacturer’s instructions.

    Article Title: CHROMOTHRIPSIS FROM DNA DAMAGE IN MICRONUCLEI
    Article Snippet: Finally, the high processivity of Phi-29 polymerase consistently generates large amplicons above 10 kb , ; this enables us to perform Sanger sequencing on the MDA product after PCR to generate phasing information of rearrangements and validate their association with the missegregated chromosome, which is crucial in establishing the relationship between chromosomal rearrangements and DNA damage in the micronuclei. .. DNA from isolated cells was subject to MDA following lysis using the REPLI-g Single Cell Kit (Qiagen) with minor modification. (Note that we achieved the best overall coverage uniformity with this latest version of REPLI-g from Qiagen as compared to earlier versions of REPLI-g or the RepliPhi enzyme from Epicentre. .. Comparison of the coverage and uniformity of the single-cell libraries in the current study with previous studies , is summarized in and in Ref.

    Article Title: FMR1 CGG repeat expansion mutation detection and linked haplotype analysis for reliable and accurate preimplantation genetic diagnosis of fragile X syndrome
    Article Snippet: Single cells isolated from lymphoblastoid cell lines (Coriell Cell Repositories, CCR; Camden, New Jersey, USA) were used to validate the FMR1 TP-PCR and tetradecaplex marker PCR assays for direct CGG repeat and linked multi-marker haplotype analyses, respectively. .. Isolation, lysis and/or whole-genome amplification, using the Genomiphi™ V2 DNA (GE Healthcare, Little Chalfont, UK) or REPLI-g (Qiagen, Hilden, Germany) Amplification Kit, of single lymphoblasts were performed as described (Ref. ). .. This study was approved by the Institutional Review Board of the National University of Singapore (B-15-273E).

    Variant Assay:

    Article Title: Germinal center reentries of BCL2-overexpressing B cells drive follicular lymphoma progression
    Article Snippet: Capture libraries were constructed from 1 μg of WGA-amplified DNA from GC and post-GC subsets (BCL2-enriched or control empty vector) and germlines (naive) using the REPLI-g Single Cell Kit (QIAGEN). .. The DNA sequence was aligned to the mouse genome (UCSC mm10; Dec 2011 release; Genome Reference Consortium GRCh38) using Bowtie2, version 2.1.0 (SourceForge).

    Environmental Sampling:

    Article Title: Microfluidic-based mini-metagenomics enables discovery of novel microbial lineages from complex environmental samples
    Article Snippet: The diluted environmental sample was loaded onto the chip using a modified version of the loading protocol where washing was not performed, as the capture sites were too large for microbial cells. .. After alkaline denaturation of DNA, neutralization and MDA were performed (Qiagen REPLI-g single cell kit) ( ).

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    Qiagen repli g single cell kit
    Whole genome amplification by using GenomePlex (WGA4) and <t>REPLI-g.</t> a Comparison of two whole genome amplification methods: GenomePlex (WGA4) and REPLI-g. b Workflow of GenomePlex (WGA4) and REPLI-g kits. c Whole Genome Amplified DNA products. GenomePlex (WGA4) or REPLI-g WGA was performed on DNA from both fresh and fixed HCT116 cells following the vendor’s manuals. The amplified DNA was checked using agarose gel electrophoresis. d DNA yield comparison. GenomePlex (WGA4) or REPLI-g WGA was performed on both fresh and fixed HCT116 cells following the vendor’s manuals. The amplified DNA amount was measured using the Qubit. (*: standard protocol. **: increased DNA volume protocol)
    Repli G Single Cell Kit, supplied by Qiagen, used in various techniques. Bioz Stars score: 99/100, based on 29 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Whole genome amplification by using GenomePlex (WGA4) and REPLI-g. a Comparison of two whole genome amplification methods: GenomePlex (WGA4) and REPLI-g. b Workflow of GenomePlex (WGA4) and REPLI-g kits. c Whole Genome Amplified DNA products. GenomePlex (WGA4) or REPLI-g WGA was performed on DNA from both fresh and fixed HCT116 cells following the vendor’s manuals. The amplified DNA was checked using agarose gel electrophoresis. d DNA yield comparison. GenomePlex (WGA4) or REPLI-g WGA was performed on both fresh and fixed HCT116 cells following the vendor’s manuals. The amplified DNA amount was measured using the Qubit. (*: standard protocol. **: increased DNA volume protocol)

    Journal: NPJ Genomic Medicine

    Article Title: Workflow optimization of whole genome amplification and targeted panel sequencing for CTC mutation detection

    doi: 10.1038/s41525-017-0034-3

    Figure Lengend Snippet: Whole genome amplification by using GenomePlex (WGA4) and REPLI-g. a Comparison of two whole genome amplification methods: GenomePlex (WGA4) and REPLI-g. b Workflow of GenomePlex (WGA4) and REPLI-g kits. c Whole Genome Amplified DNA products. GenomePlex (WGA4) or REPLI-g WGA was performed on DNA from both fresh and fixed HCT116 cells following the vendor’s manuals. The amplified DNA was checked using agarose gel electrophoresis. d DNA yield comparison. GenomePlex (WGA4) or REPLI-g WGA was performed on both fresh and fixed HCT116 cells following the vendor’s manuals. The amplified DNA amount was measured using the Qubit. (*: standard protocol. **: increased DNA volume protocol)

    Article Snippet: Hou et al. performed a thorough study to compare these different strategies and showed that QIAGEN REPLI-g Single Cell Kit had the highest mean genome coverage (8.84%) and significantly higher genome recovery sensitivity (~84%) compared to DOP-PCR (~6%) and MALBAC (~52%).

    Techniques: Whole Genome Amplification, Amplification, Agarose Gel Electrophoresis

    Sequencing comparison in WGA amplified and non-amplified DNA samples. a Mutation detection comparison for REPLI-g WGA. REPLI-g amplified or non-amplified DNA from both fresh and fixed HCT116 cells were subjected to the CRC targeted NGS. The blue color highlights the true mutations detected, while the number inside each cell represents the MAF of the mutation. The light red color highlights the false mutations called. b Gene coverage comparison for WGA. The coverage was compared among the following samples: ① Fresh cells; ② Fixed cells; ③ Fresh cells + REPLI-g; ④ Fixed cells + REPLI-g. ⑤ Fixed cells+WGA4. The reads were aligned using BWA-MEM and coverage was computed using GATK’s DepthOfCoverage and in-house scripts. The percentage of bases covered by at least 10 reads with minimum base quality score Q30 (%_bases_above_10) was calculated using data obtained from DepthOfCoverage and in-house scripts and summarized in the table. (*) In the case of GenomePlex (WGA4), the plotted data was trimmed of 10 bp at the beginning and 40 bp at the end because of a primer/adapter contamination

    Journal: NPJ Genomic Medicine

    Article Title: Workflow optimization of whole genome amplification and targeted panel sequencing for CTC mutation detection

    doi: 10.1038/s41525-017-0034-3

    Figure Lengend Snippet: Sequencing comparison in WGA amplified and non-amplified DNA samples. a Mutation detection comparison for REPLI-g WGA. REPLI-g amplified or non-amplified DNA from both fresh and fixed HCT116 cells were subjected to the CRC targeted NGS. The blue color highlights the true mutations detected, while the number inside each cell represents the MAF of the mutation. The light red color highlights the false mutations called. b Gene coverage comparison for WGA. The coverage was compared among the following samples: ① Fresh cells; ② Fixed cells; ③ Fresh cells + REPLI-g; ④ Fixed cells + REPLI-g. ⑤ Fixed cells+WGA4. The reads were aligned using BWA-MEM and coverage was computed using GATK’s DepthOfCoverage and in-house scripts. The percentage of bases covered by at least 10 reads with minimum base quality score Q30 (%_bases_above_10) was calculated using data obtained from DepthOfCoverage and in-house scripts and summarized in the table. (*) In the case of GenomePlex (WGA4), the plotted data was trimmed of 10 bp at the beginning and 40 bp at the end because of a primer/adapter contamination

    Article Snippet: Hou et al. performed a thorough study to compare these different strategies and showed that QIAGEN REPLI-g Single Cell Kit had the highest mean genome coverage (8.84%) and significantly higher genome recovery sensitivity (~84%) compared to DOP-PCR (~6%) and MALBAC (~52%).

    Techniques: Sequencing, Whole Genome Amplification, Amplification, Mutagenesis, Next-Generation Sequencing

    Workflow optimization for biopsy genomic profiling, tissue and CTCs. Qiagen QIAamp Micro Kit and GeneRead DNAseq targeted panel sequencing were applied on all types of cell samples. This overall workflow performs well when DNA amount is sufficient, i.e., from whole blood and tissue biopsy. For rare cells, DNA input is insufficient for targeted NGS, leading to a bias and the need for an extra step of Whole Genome Amplification (WGA). Two WGA kits were evaluated (WGA4 from Sigma and REPLI-g from Qiagen) and obtained low coverage for fixed cells, while REPLI-g was identified as optimal for fresh rare cells and used for a final validation on patient CTCs

    Journal: NPJ Genomic Medicine

    Article Title: Workflow optimization of whole genome amplification and targeted panel sequencing for CTC mutation detection

    doi: 10.1038/s41525-017-0034-3

    Figure Lengend Snippet: Workflow optimization for biopsy genomic profiling, tissue and CTCs. Qiagen QIAamp Micro Kit and GeneRead DNAseq targeted panel sequencing were applied on all types of cell samples. This overall workflow performs well when DNA amount is sufficient, i.e., from whole blood and tissue biopsy. For rare cells, DNA input is insufficient for targeted NGS, leading to a bias and the need for an extra step of Whole Genome Amplification (WGA). Two WGA kits were evaluated (WGA4 from Sigma and REPLI-g from Qiagen) and obtained low coverage for fixed cells, while REPLI-g was identified as optimal for fresh rare cells and used for a final validation on patient CTCs

    Article Snippet: Hou et al. performed a thorough study to compare these different strategies and showed that QIAGEN REPLI-g Single Cell Kit had the highest mean genome coverage (8.84%) and significantly higher genome recovery sensitivity (~84%) compared to DOP-PCR (~6%) and MALBAC (~52%).

    Techniques: Sequencing, Next-Generation Sequencing, Whole Genome Amplification