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 Detection of SNPWave products with a flanking sizing standard in three consecutive 35 min runs on the MegaBACE 1000. One hundred-plex ligation using 625 ng of genomic DNA of  Arabidopsis  sample Kashmir-2 (N1264), and SNPWave amplification using JOE-labeled
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1) Product Images from "SNPWaveTM: a flexible multiplexed SNP genotyping technology"

Article Title: SNPWaveTM: a flexible multiplexed SNP genotyping technology

Journal: Nucleic Acids Research

doi: 10.1093/nar/gnh045

 Detection of SNPWave products with a flanking sizing standard in three consecutive 35 min runs on the MegaBACE 1000. One hundred-plex ligation using 625 ng of genomic DNA of  Arabidopsis  sample Kashmir-2 (N1264), and SNPWave amplification using JOE-labeled
Figure Legend Snippet: Detection of SNPWave products with a flanking sizing standard in three consecutive 35 min runs on the MegaBACE 1000. One hundred-plex ligation using 625 ng of genomic DNA of Arabidopsis sample Kashmir-2 (N1264), and SNPWave amplification using JOE-labeled

Techniques Used: Ligation, Amplification, Labeling

Related Articles

Clone Assay:

Article Title: Genetic determinants in HIV-1 Gag and Env V3 are related to viral response to combination antiretroviral therapy with a protease inhibitor
Article Snippet: Paragraph title: Amplification, cloning, and sequencing ... Following preparation of amplicon libraries, sequences were generated with DYEnamic ET dye terminator cycle sequencing kit and analyzed on a MegaBACE 1000 (GE Healthcare, Chalfont St. Giles, UK) in the Genome Sequencing Core at the University of Florida.

Centrifugation:

Article Title: SNPWaveTM: a flexible multiplexed SNP genotyping technology
Article Snippet: SNPWave PCR products were desalted over Sephadex G-50 superfine columns in a 96-well plate format prior to detection by capillary electrophoresis on the MegaBACE 1000 (Amersham Biosciences). .. The resin was rinsed twice with 200 µl of Milli-Q water per well and packed by centrifugation for 5 min at 900 g .

Amplification:

Article Title: Charcot-Marie-Tooth neuropathy type 2A: novel mutations in the mitofusin 2 gene (MFN2)
Article Snippet: .. DNA samples showing band shifts in the SSCP analysis were amplified from genomic DNA and cycle sequenced by standard protocols using the Megabace 1000 (Amersham Bioscience, Freiburg, Germany). ..

Article Title: Molecular analysis of holoprosencephaly in South America
Article Snippet: PCR and direct sequencing The coding region and exon-intron boundaries of SHH , SIX3, TGIF , and ZIC2 were amplified as previously described ( , ; ). .. Automated sequencing was performed using MegaBACE 1000 (Amersham Pharmacia Biotech In, London, UK) or ABI Prism 377 (Applied Biosystems, Foster City, CA, USA) DNA sequencing systems.

Article Title: Genetic determinants in HIV-1 Gag and Env V3 are related to viral response to combination antiretroviral therapy with a protease inhibitor
Article Snippet: .. Following preparation of amplicon libraries, sequences were generated with DYEnamic ET dye terminator cycle sequencing kit and analyzed on a MegaBACE 1000 (GE Healthcare, Chalfont St. Giles, UK) in the Genome Sequencing Core at the University of Florida. ..

Article Title: Mutations underlying 3-Hydroxy-3-Methylglutaryl CoA Lyase deficiency in the Saudi population
Article Snippet: .. Genotyping Genotyping of the marker D1S2620 ( < 0.5 cM from HMGCL ) was performed using fluorescently labeled primers (5'-FAM-AAGAGTTGTCCAACCAAATTG-3' and 5'-GAATCTGGGATGGGATGT-3') for PCR amplification (essentially as described above) of alleles which were identified following capillary electrophoresis on a Megabace 1000 and fragment size analysis using Genetic Profiler software (Amersham, Sunnyvale, CA). ..

Article Title: Complexity Reduction of Polymorphic Sequences (CRoPS(TM)): A Novel Approach for Large-Scale Polymorphism Discovery in Complex Genomes
Article Snippet: The amplification profile was 12 min at 94°C, followed by 13 cycles of 30 s at 94°C, 30 s at 65°C with a reduction of 0.7°C per cycle to 56°C in cycle 13, followed by 1 min at 72°C. .. Purification of diluted SNPWave PCR products and subsequent detection on the MegaBACE 1000 (Amersham Biosciences/GE Healthcare Life Sciences) were as described previously .

Article Title: Identification of fungi of the genus Aspergillus section nigri using polyphasic taxonomy
Article Snippet: Paragraph title: DNA amplification and sequencing ... The sequencing reaction was performed by using DYEnamicTM ET dye Terminator Cycle Sequencing Kit (Amersham Pharmacia Biotech, Inc.) on MegaBACE 1000 (Amersham Biosciences).

Article Title: DNA Typing of Mycobacterium bovis Isolates from Badgers (Meles meles) Culled from Areas in Ireland with Different Levels of Tuberculosis Prevalence
Article Snippet: .. The six genomic loci were amplified separately using the primers and polymerase chain reaction (PCR) procedures described by McLernon et al. [ ].When the PCR was complete, the amplified products were stored at −18°C until analysed using the MegaBACE 1000 (GE Healthcare Life Sciences) as described by McLernon et al. [ ]. ..

Article Title: Quaternary climate change drives allo-peripatric speciation and refugial divergence in the Dysosma versipellis-pleiantha complex from different forest types in China
Article Snippet: Amplification of the EST-SSR loci followed the protocol of Guo et al . .. Fluorescently labelled PCR products were supplemented with the internal size standard GS-500 and separated on a MegaBACE 1000 (GE Healthcare Biosciences, Sunnyvale, CA, USA).

Article Title: Effects of Light-Emitting Diode Therapy on Muscle Hypertrophy, Gene Expression, Performance, Damage, and Delayed-Onset Muscle Soreness
Article Snippet: .. Amplified products were detected and separated by capillary electrophoresis using a MegaBACE 1000 (GE Healthcare Bio-Sciences Corp., Pittsburgh, PA). .. Results were analyzed, and allele designations were set automatically using Fragment Profiler software, version 1.2 (GE).

Article Title: A comparative study on genetic effects of artificial and natural habitat fragmentation on Loropetalum chinense (Hamamelidaceae) in Southeast China
Article Snippet: PCR amplification conditions were as follows: initial denaturation at 95 °C for 5 min; 30 cycles of 30 s at 95 °C, 30 s at the optimized annealing temperature, 45 s of elongation at 72 °C; ending with a 10-min extension at 72 °C. .. PCR products were separated on a MegaBACE 1000 (GE Healthcare Biosciences, Pittsburgh, PA, USA).

Article Title: A multigene phylogenetic synthesis for the class Lecanoromycetes (Ascomycota): 1307 fungi representing 1139 infrageneric taxa, 317 genera and 66 families
Article Snippet: Amplification of the target loci used the illustra PuReTaq Ready-To-Go™PCR Beads (GE Healthcare) protocol. .. PCR products were purifiedusing the GFX PCR DNA and Gel Band Purification Kit (GE Healthcare) or Montage SEQ96Sequencing Reaction Cleanup Kit (Millipore) and sequenced on a MegaBACE 1000 sequencer(Amersham).

Article Title: Genetic analysis of historic western Great Lakes region wolf samples reveals early Canis lupus/lycaon hybridization
Article Snippet: A 343–347 bp fragment of the mtDNA control region was amplified using the primers described in and conditions similar to theirs, except that we included 0.1 μg/μl BSA in the reaction and used an annealing temperature of 60°C. .. PCR products were cleaned with ExoSAP-IT (USB Corporation, Cleveland, OH) prior to sequencing on a MegaBACE 1000 (GE Healthcare).

Autoradiography:

Article Title: Charcot-Marie-Tooth neuropathy type 2A: novel mutations in the mitofusin 2 gene (MFN2)
Article Snippet: Gels were evaluated by autoradiography or exposure to a phosphoimager screen, using the corresponding software. .. DNA samples showing band shifts in the SSCP analysis were amplified from genomic DNA and cycle sequenced by standard protocols using the Megabace 1000 (Amersham Bioscience, Freiburg, Germany).

Electrophoresis:

Article Title: Mutations underlying 3-Hydroxy-3-Methylglutaryl CoA Lyase deficiency in the Saudi population
Article Snippet: .. Genotyping Genotyping of the marker D1S2620 ( < 0.5 cM from HMGCL ) was performed using fluorescently labeled primers (5'-FAM-AAGAGTTGTCCAACCAAATTG-3' and 5'-GAATCTGGGATGGGATGT-3') for PCR amplification (essentially as described above) of alleles which were identified following capillary electrophoresis on a Megabace 1000 and fragment size analysis using Genetic Profiler software (Amersham, Sunnyvale, CA). ..

Article Title: Effects of Light-Emitting Diode Therapy on Muscle Hypertrophy, Gene Expression, Performance, Damage, and Delayed-Onset Muscle Soreness
Article Snippet: .. Amplified products were detected and separated by capillary electrophoresis using a MegaBACE 1000 (GE Healthcare Bio-Sciences Corp., Pittsburgh, PA). .. Results were analyzed, and allele designations were set automatically using Fragment Profiler software, version 1.2 (GE).

Article Title: SNPWaveTM: a flexible multiplexed SNP genotyping technology
Article Snippet: .. SNPWave PCR products were desalted over Sephadex G-50 superfine columns in a 96-well plate format prior to detection by capillary electrophoresis on the MegaBACE 1000 (Amersham Biosciences). .. Briefly, dry Sephadex G-50 superfine resin (Amersham Biosciences) was loaded into the wells of a 96-well plate (MultiScreen®-HV, Millipore Corporation, Bedford, MA) using the 45 µl column loader (Millipore), and excess resin removed.

Incubation:

Article Title: SNPWaveTM: a flexible multiplexed SNP genotyping technology
Article Snippet: SNPWave PCR products were desalted over Sephadex G-50 superfine columns in a 96-well plate format prior to detection by capillary electrophoresis on the MegaBACE 1000 (Amersham Biosciences). .. Next, 200 µl of Milli-Q water was added to each well and incubated for 2–3 h to swell the resin.

Hybridization:

Article Title: Complexity Reduction of Polymorphic Sequences (CRoPS(TM)): A Novel Approach for Large-Scale Polymorphism Discovery in Complex Genomes
Article Snippet: Next, 10 cycles of repeated denaturation, probe hybridization and ligation were performed in a Perkin Elmer 9700 thermal cycler (Applied Biosystems) using the following profile: initial denaturation for 2 min at 94°C, followed by 10 cycles of 15 s at 94°C and 60 min at 60°C, and storage at 4°C. .. Purification of diluted SNPWave PCR products and subsequent detection on the MegaBACE 1000 (Amersham Biosciences/GE Healthcare Life Sciences) were as described previously .

Ligation:

Article Title: Complexity Reduction of Polymorphic Sequences (CRoPS(TM)): A Novel Approach for Large-Scale Polymorphism Discovery in Complex Genomes
Article Snippet: Ten µl of diluted ligation reaction was subsequently amplified in a 20 µl mixture containing 1×GeneAmp® PCR buffer (Applied Biosystems), 0.2 mM of each dNTP, 0.4 U AmpliTaq Gold DNA polymerase (Applied Biosystems), and 30 ng unlabeled forward primer (5-GACTGCGTACCAATTC-3) and 30 ng FAM-labeled reverse primer (5-GATGAGTCCTGAGTAA-3). .. Purification of diluted SNPWave PCR products and subsequent detection on the MegaBACE 1000 (Amersham Biosciences/GE Healthcare Life Sciences) were as described previously .

Low Copy Number:

Article Title: Large-Scale Transposon Mutagenesis of Photobacterium profundum SS9 Reveals New Genetic Loci Important for Growth at Low Temperature and High Pressure ▿
Article Snippet: Plasmid DNA was extracted using Qiagen (Valencia, CA) Miniprep (high-copy-number plasmids) and Midiprep (low-copy-number plasmids) kits and following the manufacturer's instructions. .. DNA sequences were determined by thermal cycle fluorescent dideoxy sequencing with a MegaBACE 1000 (Amersham Biosciences, Piscataway, NJ) automated sequencer used as instructed by the manufacturer.

Generated:

Article Title: Genetic determinants in HIV-1 Gag and Env V3 are related to viral response to combination antiretroviral therapy with a protease inhibitor
Article Snippet: .. Following preparation of amplicon libraries, sequences were generated with DYEnamic ET dye terminator cycle sequencing kit and analyzed on a MegaBACE 1000 (GE Healthcare, Chalfont St. Giles, UK) in the Genome Sequencing Core at the University of Florida. ..

DNA Sequencing:

Article Title: Molecular analysis of holoprosencephaly in South America
Article Snippet: .. Automated sequencing was performed using MegaBACE 1000 (Amersham Pharmacia Biotech In, London, UK) or ABI Prism 377 (Applied Biosystems, Foster City, CA, USA) DNA sequencing systems. .. The electropherograms were analyzed using Sequencher software (Gene Codes Corporation, Ann Arbor, MI, USA).

Polymerase Chain Reaction:

Article Title: Diversification in continental island archipelagos: new evidence on the roles of fragmentation, colonization and gene flow on the genetic divergence of Aegean Nigella (Ranunculaceae)
Article Snippet: The selective PCR products were purified using Sephadex G-50 Superfine Resin (GE Healthcare BioSciences, Uppsala, Sweden) following the manufacturer’s instructions. .. AFLP fragments were separated on a MegaBACE™ 1000 (GE Healthcare Biosciences, Pittsburgh, PA, USA), using the ET550-R-Rox-MegaBACE™ sizing standard.

Article Title: Charcot-Marie-Tooth neuropathy type 2A: novel mutations in the mitofusin 2 gene (MFN2)
Article Snippet: In the SSCP analysis the denatured PCR products were separated by polyacrylamide (PAA) gel electrophoresis using two different conditions: 30% PAA (acrylamide/bisacrylamide: 19/1) gel, 1xTBE, and either 10% glycerol or 5% glycerol/1 M urea. .. DNA samples showing band shifts in the SSCP analysis were amplified from genomic DNA and cycle sequenced by standard protocols using the Megabace 1000 (Amersham Bioscience, Freiburg, Germany).

Article Title: Molecular analysis of holoprosencephaly in South America
Article Snippet: Paragraph title: PCR and direct sequencing ... Automated sequencing was performed using MegaBACE 1000 (Amersham Pharmacia Biotech In, London, UK) or ABI Prism 377 (Applied Biosystems, Foster City, CA, USA) DNA sequencing systems.

Article Title: Mutations underlying 3-Hydroxy-3-Methylglutaryl CoA Lyase deficiency in the Saudi population
Article Snippet: .. Genotyping Genotyping of the marker D1S2620 ( < 0.5 cM from HMGCL ) was performed using fluorescently labeled primers (5'-FAM-AAGAGTTGTCCAACCAAATTG-3' and 5'-GAATCTGGGATGGGATGT-3') for PCR amplification (essentially as described above) of alleles which were identified following capillary electrophoresis on a Megabace 1000 and fragment size analysis using Genetic Profiler software (Amersham, Sunnyvale, CA). ..

Article Title: Complexity Reduction of Polymorphic Sequences (CRoPS(TM)): A Novel Approach for Large-Scale Polymorphism Discovery in Complex Genomes
Article Snippet: .. Purification of diluted SNPWave PCR products and subsequent detection on the MegaBACE 1000 (Amersham Biosciences/GE Healthcare Life Sciences) were as described previously . ..

Article Title: Identification of fungi of the genus Aspergillus section nigri using polyphasic taxonomy
Article Snippet: DNA fragments were purified with the Concert TM Rapid PCR Purification System (Gibco BRL, UK). .. The sequencing reaction was performed by using DYEnamicTM ET dye Terminator Cycle Sequencing Kit (Amersham Pharmacia Biotech, Inc.) on MegaBACE 1000 (Amersham Biosciences).

Article Title: DNA Typing of Mycobacterium bovis Isolates from Badgers (Meles meles) Culled from Areas in Ireland with Different Levels of Tuberculosis Prevalence
Article Snippet: .. The six genomic loci were amplified separately using the primers and polymerase chain reaction (PCR) procedures described by McLernon et al. [ ].When the PCR was complete, the amplified products were stored at −18°C until analysed using the MegaBACE 1000 (GE Healthcare Life Sciences) as described by McLernon et al. [ ]. ..

Article Title: Quaternary climate change drives allo-peripatric speciation and refugial divergence in the Dysosma versipellis-pleiantha complex from different forest types in China
Article Snippet: .. Fluorescently labelled PCR products were supplemented with the internal size standard GS-500 and separated on a MegaBACE 1000 (GE Healthcare Biosciences, Sunnyvale, CA, USA). .. Alleles were scored manually in genemarker v2.20 (SoftGenetics, State College, PA, USA).

Article Title: Effects of Light-Emitting Diode Therapy on Muscle Hypertrophy, Gene Expression, Performance, Damage, and Delayed-Onset Muscle Soreness
Article Snippet: Amplified products were detected and separated by capillary electrophoresis using a MegaBACE 1000 (GE Healthcare Bio-Sciences Corp., Pittsburgh, PA). .. Amplified products were detected and separated by capillary electrophoresis using a MegaBACE 1000 (GE Healthcare Bio-Sciences Corp., Pittsburgh, PA).

Article Title: A comparative study on genetic effects of artificial and natural habitat fragmentation on Loropetalum chinense (Hamamelidaceae) in Southeast China
Article Snippet: .. PCR products were separated on a MegaBACE 1000 (GE Healthcare Biosciences, Pittsburgh, PA, USA). .. Alleles were scored manually with the aid of the software GENETIC PROFILER (version 2.2; GE Healthcare Biosciences).

Article Title: A multigene phylogenetic synthesis for the class Lecanoromycetes (Ascomycota): 1307 fungi representing 1139 infrageneric taxa, 317 genera and 66 families
Article Snippet: .. PCR products were purifiedusing the GFX PCR DNA and Gel Band Purification Kit (GE Healthcare) or Montage SEQ96Sequencing Reaction Cleanup Kit (Millipore) and sequenced on a MegaBACE 1000 sequencer(Amersham). .. Sequencing used BigDye® Terminator v1.1 Cycle SequencingKit and the same primers as for amplification with additionnal internal sequencing primerswhen needed ( ).

Article Title: Genetic analysis of historic western Great Lakes region wolf samples reveals early Canis lupus/lycaon hybridization
Article Snippet: .. PCR products were cleaned with ExoSAP-IT (USB Corporation, Cleveland, OH) prior to sequencing on a MegaBACE 1000 (GE Healthcare). .. Amplification of eight nuclear microsatellite loci was attempted for each sample , and homozygous genotypes were confirmed by repeated amplification.

Article Title: SNPWaveTM: a flexible multiplexed SNP genotyping technology
Article Snippet: .. SNPWave PCR products were desalted over Sephadex G-50 superfine columns in a 96-well plate format prior to detection by capillary electrophoresis on the MegaBACE 1000 (Amersham Biosciences). .. Briefly, dry Sephadex G-50 superfine resin (Amersham Biosciences) was loaded into the wells of a 96-well plate (MultiScreen®-HV, Millipore Corporation, Bedford, MA) using the 45 µl column loader (Millipore), and excess resin removed.

DNA Extraction:

Article Title: Large-Scale Transposon Mutagenesis of Photobacterium profundum SS9 Reveals New Genetic Loci Important for Growth at Low Temperature and High Pressure ▿
Article Snippet: Paragraph title: DNA extraction, purification, manipulation, and sequencing. ... DNA sequences were determined by thermal cycle fluorescent dideoxy sequencing with a MegaBACE 1000 (Amersham Biosciences, Piscataway, NJ) automated sequencer used as instructed by the manufacturer.

Article Title: Quaternary climate change drives allo-peripatric speciation and refugial divergence in the Dysosma versipellis-pleiantha complex from different forest types in China
Article Snippet: Paragraph title: DNA extraction, cpDNA sequencing, and EST-SSR genotyping ... Fluorescently labelled PCR products were supplemented with the internal size standard GS-500 and separated on a MegaBACE 1000 (GE Healthcare Biosciences, Sunnyvale, CA, USA).

Nucleic Acid Electrophoresis:

Article Title: Charcot-Marie-Tooth neuropathy type 2A: novel mutations in the mitofusin 2 gene (MFN2)
Article Snippet: In the SSCP analysis the denatured PCR products were separated by polyacrylamide (PAA) gel electrophoresis using two different conditions: 30% PAA (acrylamide/bisacrylamide: 19/1) gel, 1xTBE, and either 10% glycerol or 5% glycerol/1 M urea. .. DNA samples showing band shifts in the SSCP analysis were amplified from genomic DNA and cycle sequenced by standard protocols using the Megabace 1000 (Amersham Bioscience, Freiburg, Germany).

Mutagenesis:

Article Title: Charcot-Marie-Tooth neuropathy type 2A: novel mutations in the mitofusin 2 gene (MFN2)
Article Snippet: Paragraph title: Mutation analysis of MFN2 gene ... DNA samples showing band shifts in the SSCP analysis were amplified from genomic DNA and cycle sequenced by standard protocols using the Megabace 1000 (Amersham Bioscience, Freiburg, Germany).

Article Title: Molecular analysis of holoprosencephaly in South America
Article Snippet: Automated sequencing was performed using MegaBACE 1000 (Amersham Pharmacia Biotech In, London, UK) or ABI Prism 377 (Applied Biosystems, Foster City, CA, USA) DNA sequencing systems. .. The gene mutation nomenclature used in this study was consistent with the recommendations of , and updates are available on the website for the Human Genome Variation Society (HGVS).

Labeling:

Article Title: Mutations underlying 3-Hydroxy-3-Methylglutaryl CoA Lyase deficiency in the Saudi population
Article Snippet: .. Genotyping Genotyping of the marker D1S2620 ( < 0.5 cM from HMGCL ) was performed using fluorescently labeled primers (5'-FAM-AAGAGTTGTCCAACCAAATTG-3' and 5'-GAATCTGGGATGGGATGT-3') for PCR amplification (essentially as described above) of alleles which were identified following capillary electrophoresis on a Megabace 1000 and fragment size analysis using Genetic Profiler software (Amersham, Sunnyvale, CA). ..

Article Title: A comparative study on genetic effects of artificial and natural habitat fragmentation on Loropetalum chinense (Hamamelidaceae) in Southeast China
Article Snippet: Primers were labeled with a fluorescent dye, either HEX or 6-FAM (Applied Biosystems, Foster City, CA, USA), and PCR amplifications were performed on a GeneAmp 9700 DNA Thermal Cycler (Perkin-Elmer, Waltham, MA, USA) using a 10 μl reaction mixture containing 30–50 ng μl–1 of genomic DNA, 0.5 U of Taq polymerase (TaKaRa Biotechnology Co., Ltd, Dalian, China), 1 μl of 10 × PCR buffer with MgCl2 , 1 μl of dNTPs (2.5 m M each) and 0.5 μl of each primer (10 μ M ). .. PCR products were separated on a MegaBACE 1000 (GE Healthcare Biosciences, Pittsburgh, PA, USA).

Purification:

Article Title: Diversification in continental island archipelagos: new evidence on the roles of fragmentation, colonization and gene flow on the genetic divergence of Aegean Nigella (Ranunculaceae)
Article Snippet: The selective PCR products were purified using Sephadex G-50 Superfine Resin (GE Healthcare BioSciences, Uppsala, Sweden) following the manufacturer’s instructions. .. AFLP fragments were separated on a MegaBACE™ 1000 (GE Healthcare Biosciences, Pittsburgh, PA, USA), using the ET550-R-Rox-MegaBACE™ sizing standard.

Article Title: Large-Scale Transposon Mutagenesis of Photobacterium profundum SS9 Reveals New Genetic Loci Important for Growth at Low Temperature and High Pressure ▿
Article Snippet: Paragraph title: DNA extraction, purification, manipulation, and sequencing. ... DNA sequences were determined by thermal cycle fluorescent dideoxy sequencing with a MegaBACE 1000 (Amersham Biosciences, Piscataway, NJ) automated sequencer used as instructed by the manufacturer.

Article Title: Complexity Reduction of Polymorphic Sequences (CRoPS(TM)): A Novel Approach for Large-Scale Polymorphism Discovery in Complex Genomes
Article Snippet: .. Purification of diluted SNPWave PCR products and subsequent detection on the MegaBACE 1000 (Amersham Biosciences/GE Healthcare Life Sciences) were as described previously . ..

Article Title: Identification of fungi of the genus Aspergillus section nigri using polyphasic taxonomy
Article Snippet: DNA fragments were purified with the Concert TM Rapid PCR Purification System (Gibco BRL, UK). .. The sequencing reaction was performed by using DYEnamicTM ET dye Terminator Cycle Sequencing Kit (Amersham Pharmacia Biotech, Inc.) on MegaBACE 1000 (Amersham Biosciences).

Article Title: A multigene phylogenetic synthesis for the class Lecanoromycetes (Ascomycota): 1307 fungi representing 1139 infrageneric taxa, 317 genera and 66 families
Article Snippet: .. PCR products were purifiedusing the GFX PCR DNA and Gel Band Purification Kit (GE Healthcare) or Montage SEQ96Sequencing Reaction Cleanup Kit (Millipore) and sequenced on a MegaBACE 1000 sequencer(Amersham). .. Sequencing used BigDye® Terminator v1.1 Cycle SequencingKit and the same primers as for amplification with additionnal internal sequencing primerswhen needed ( ).

Article Title: SNPWaveTM: a flexible multiplexed SNP genotyping technology
Article Snippet: Paragraph title: Purification of SNPWave reactions ... SNPWave PCR products were desalted over Sephadex G-50 superfine columns in a 96-well plate format prior to detection by capillary electrophoresis on the MegaBACE 1000 (Amersham Biosciences).

Sequencing:

Article Title: Large-Scale Transposon Mutagenesis of Photobacterium profundum SS9 Reveals New Genetic Loci Important for Growth at Low Temperature and High Pressure ▿
Article Snippet: .. DNA sequences were determined by thermal cycle fluorescent dideoxy sequencing with a MegaBACE 1000 (Amersham Biosciences, Piscataway, NJ) automated sequencer used as instructed by the manufacturer. .. Rapid identification of the flanking sequences of the transposon insertions in P. profundum was accomplished by using a rapid arbitrary PCR method similar to the method used by Watnick and Kolter ( ).

Article Title: Molecular analysis of holoprosencephaly in South America
Article Snippet: .. Automated sequencing was performed using MegaBACE 1000 (Amersham Pharmacia Biotech In, London, UK) or ABI Prism 377 (Applied Biosystems, Foster City, CA, USA) DNA sequencing systems. .. The electropherograms were analyzed using Sequencher software (Gene Codes Corporation, Ann Arbor, MI, USA).

Article Title: Genetic determinants in HIV-1 Gag and Env V3 are related to viral response to combination antiretroviral therapy with a protease inhibitor
Article Snippet: .. Following preparation of amplicon libraries, sequences were generated with DYEnamic ET dye terminator cycle sequencing kit and analyzed on a MegaBACE 1000 (GE Healthcare, Chalfont St. Giles, UK) in the Genome Sequencing Core at the University of Florida. ..

Article Title: Identification of fungi of the genus Aspergillus section nigri using polyphasic taxonomy
Article Snippet: .. The sequencing reaction was performed by using DYEnamicTM ET dye Terminator Cycle Sequencing Kit (Amersham Pharmacia Biotech, Inc.) on MegaBACE 1000 (Amersham Biosciences). .. Sequence analysis The quality of the sequences was analyzed using the Phre/Phrap/Consel package.

Article Title: Quaternary climate change drives allo-peripatric speciation and refugial divergence in the Dysosma versipellis-pleiantha complex from different forest types in China
Article Snippet: Paragraph title: DNA extraction, cpDNA sequencing, and EST-SSR genotyping ... Fluorescently labelled PCR products were supplemented with the internal size standard GS-500 and separated on a MegaBACE 1000 (GE Healthcare Biosciences, Sunnyvale, CA, USA).

Article Title: A multigene phylogenetic synthesis for the class Lecanoromycetes (Ascomycota): 1307 fungi representing 1139 infrageneric taxa, 317 genera and 66 families
Article Snippet: PCR products were purifiedusing the GFX PCR DNA and Gel Band Purification Kit (GE Healthcare) or Montage SEQ96Sequencing Reaction Cleanup Kit (Millipore) and sequenced on a MegaBACE 1000 sequencer(Amersham). .. Sequencing used BigDye® Terminator v1.1 Cycle SequencingKit and the same primers as for amplification with additionnal internal sequencing primerswhen needed ( ).

Article Title: Genetic analysis of historic western Great Lakes region wolf samples reveals early Canis lupus/lycaon hybridization
Article Snippet: .. PCR products were cleaned with ExoSAP-IT (USB Corporation, Cleveland, OH) prior to sequencing on a MegaBACE 1000 (GE Healthcare). .. Amplification of eight nuclear microsatellite loci was attempted for each sample , and homozygous genotypes were confirmed by repeated amplification.

Plasmid Preparation:

Article Title: Large-Scale Transposon Mutagenesis of Photobacterium profundum SS9 Reveals New Genetic Loci Important for Growth at Low Temperature and High Pressure ▿
Article Snippet: Plasmid DNA was extracted using Qiagen (Valencia, CA) Miniprep (high-copy-number plasmids) and Midiprep (low-copy-number plasmids) kits and following the manufacturer's instructions. .. DNA sequences were determined by thermal cycle fluorescent dideoxy sequencing with a MegaBACE 1000 (Amersham Biosciences, Piscataway, NJ) automated sequencer used as instructed by the manufacturer.

Software:

Article Title: Diversification in continental island archipelagos: new evidence on the roles of fragmentation, colonization and gene flow on the genetic divergence of Aegean Nigella (Ranunculaceae)
Article Snippet: AFLP fragments were separated on a MegaBACE™ 1000 (GE Healthcare Biosciences, Pittsburgh, PA, USA), using the ET550-R-Rox-MegaBACE™ sizing standard. .. 8.0 (Van Mierlo Software Consultancy, Eindhoven, The Netherlands), polymorphisms were manually scored as presence (1) or absence (0), whereby a fragment was considered polymorphic if at least one individual showed a variant pattern.

Article Title: Charcot-Marie-Tooth neuropathy type 2A: novel mutations in the mitofusin 2 gene (MFN2)
Article Snippet: Gels were evaluated by autoradiography or exposure to a phosphoimager screen, using the corresponding software. .. DNA samples showing band shifts in the SSCP analysis were amplified from genomic DNA and cycle sequenced by standard protocols using the Megabace 1000 (Amersham Bioscience, Freiburg, Germany).

Article Title: Molecular analysis of holoprosencephaly in South America
Article Snippet: Automated sequencing was performed using MegaBACE 1000 (Amersham Pharmacia Biotech In, London, UK) or ABI Prism 377 (Applied Biosystems, Foster City, CA, USA) DNA sequencing systems. .. The electropherograms were analyzed using Sequencher software (Gene Codes Corporation, Ann Arbor, MI, USA).

Article Title: Mutations underlying 3-Hydroxy-3-Methylglutaryl CoA Lyase deficiency in the Saudi population
Article Snippet: .. Genotyping Genotyping of the marker D1S2620 ( < 0.5 cM from HMGCL ) was performed using fluorescently labeled primers (5'-FAM-AAGAGTTGTCCAACCAAATTG-3' and 5'-GAATCTGGGATGGGATGT-3') for PCR amplification (essentially as described above) of alleles which were identified following capillary electrophoresis on a Megabace 1000 and fragment size analysis using Genetic Profiler software (Amersham, Sunnyvale, CA). ..

Article Title: Effects of Light-Emitting Diode Therapy on Muscle Hypertrophy, Gene Expression, Performance, Damage, and Delayed-Onset Muscle Soreness
Article Snippet: Amplified products were detected and separated by capillary electrophoresis using a MegaBACE 1000 (GE Healthcare Bio-Sciences Corp., Pittsburgh, PA). .. Results were analyzed, and allele designations were set automatically using Fragment Profiler software, version 1.2 (GE).

Article Title: A comparative study on genetic effects of artificial and natural habitat fragmentation on Loropetalum chinense (Hamamelidaceae) in Southeast China
Article Snippet: PCR products were separated on a MegaBACE 1000 (GE Healthcare Biosciences, Pittsburgh, PA, USA). .. Alleles were scored manually with the aid of the software GENETIC PROFILER (version 2.2; GE Healthcare Biosciences).

Multiplex Assay:

Article Title: Effects of Light-Emitting Diode Therapy on Muscle Hypertrophy, Gene Expression, Performance, Damage, and Delayed-Onset Muscle Soreness
Article Snippet: Amplified products were detected and separated by capillary electrophoresis using a MegaBACE 1000 (GE Healthcare Bio-Sciences Corp., Pittsburgh, PA). .. Amplified products were detected and separated by capillary electrophoresis using a MegaBACE 1000 (GE Healthcare Bio-Sciences Corp., Pittsburgh, PA).

Ancient DNA Assay:

Article Title: Genetic analysis of historic western Great Lakes region wolf samples reveals early Canis lupus/lycaon hybridization
Article Snippet: We extracted DNA from three historic Canis samples provided by the University of Wisconsin Zoological Museum ( ) using a DNeasy Blood & Tissue Kit (Qiagen Inc., Mississauga, ON) in a dedicated ancient DNA laboratory. .. PCR products were cleaned with ExoSAP-IT (USB Corporation, Cleveland, OH) prior to sequencing on a MegaBACE 1000 (GE Healthcare).

Produced:

Article Title: Diversification in continental island archipelagos: new evidence on the roles of fragmentation, colonization and gene flow on the genetic divergence of Aegean Nigella (Ranunculaceae)
Article Snippet: Based on this, the following primer combinations that produced the best results with respect to polymorphism and clarity of AFLP profiles were chosen for the complete survey (fluorescent dye in parentheses): Eco RI-ACA/ Mse I-CAGC (6-FAM), Eco RI-AGA/ Mse I-CAGA (VIC) and Eco RI-ACC/ Mse I-CTCA (NED). .. AFLP fragments were separated on a MegaBACE™ 1000 (GE Healthcare Biosciences, Pittsburgh, PA, USA), using the ET550-R-Rox-MegaBACE™ sizing standard.

Marker:

Article Title: Mutations underlying 3-Hydroxy-3-Methylglutaryl CoA Lyase deficiency in the Saudi population
Article Snippet: .. Genotyping Genotyping of the marker D1S2620 ( < 0.5 cM from HMGCL ) was performed using fluorescently labeled primers (5'-FAM-AAGAGTTGTCCAACCAAATTG-3' and 5'-GAATCTGGGATGGGATGT-3') for PCR amplification (essentially as described above) of alleles which were identified following capillary electrophoresis on a Megabace 1000 and fragment size analysis using Genetic Profiler software (Amersham, Sunnyvale, CA). ..

Lysis:

Article Title: A multigene phylogenetic synthesis for the class Lecanoromycetes (Ascomycota): 1307 fungi representing 1139 infrageneric taxa, 317 genera and 66 families
Article Snippet: The manufacturer’s protocol was followed, except for the grinding ofthe thallus fragments, which was done in a small amount of lysis buffer instead of liquidnitrogen. .. PCR products were purifiedusing the GFX PCR DNA and Gel Band Purification Kit (GE Healthcare) or Montage SEQ96Sequencing Reaction Cleanup Kit (Millipore) and sequenced on a MegaBACE 1000 sequencer(Amersham).

Variant Assay:

Article Title: Diversification in continental island archipelagos: new evidence on the roles of fragmentation, colonization and gene flow on the genetic divergence of Aegean Nigella (Ranunculaceae)
Article Snippet: AFLP fragments were separated on a MegaBACE™ 1000 (GE Healthcare Biosciences, Pittsburgh, PA, USA), using the ET550-R-Rox-MegaBACE™ sizing standard. .. 8.0 (Van Mierlo Software Consultancy, Eindhoven, The Netherlands), polymorphisms were manually scored as presence (1) or absence (0), whereby a fragment was considered polymorphic if at least one individual showed a variant pattern.

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    GE Healthcare megabace 1000
    RSCA electropherograms . Examples of RSCA electropherograms from the MegaBace™ 1000 for one individual
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    RSCA electropherograms . Examples of RSCA electropherograms from the MegaBace™ 1000 for one individual
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    RSCA electropherograms . Examples of RSCA electropherograms from the MegaBace™ 1000 for one individual
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    RSCA electropherograms . Examples of RSCA electropherograms from the MegaBace™ 1000 for one individual

    Journal: BMC Research Notes

    Article Title: Genotyping of black grouse MHC class II B using reference Strand-Mediated Conformational Analysis (RSCA)

    doi: 10.1186/1756-0500-4-183

    Figure Lengend Snippet: RSCA electropherograms . Examples of RSCA electropherograms from the MegaBace™ 1000 for one individual "Ref26" using all four FLRs, a) FLR-Tete1, b) FLR-Bobo1, c) FLR-Bobo2 and d) FLR-Bobo3. On the x-axis are the migration values in the non-denaturing gel, the y-axis reflects the height of the peaks. The red peaks are the size markers and the blue peaks are the RSCA-peaks. The left most of the blue peaks are the FLR-homoduplex peak. The other blue peaks are used in the RSCA-scoring.

    Article Snippet: After genotyping RSCA in MegaBACE™ 1000, we viewed our electropherograms in the software MegaBACE Fragment Profiler™ version 1.2 (GE Healthcare) and assigned possible alleles (see Figure and Table for an example) for each FLR using the RSCA library and scoring rules.

    Techniques: Migration