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  • 94
    New England Biolabs nspi
    Diagram of tGBS. Digestion . Genomic <t>DNA</t> is digested with two REs: <t>NspI</t> leaves a 3′overhang and BfuCI leaves a 5′ overhang. Ligation . Two distinct oligos are ligated to the complementary 3′ and 5′ overhangs. The oligo matching the 3′ overhang contains a sample-specific internal barcode sequence for sample identification. The oligo matching the 5′ overhang is universal and present in every reaction for later amplification. Selective PCR . Target sites are selected using a selective primer with variable selective bases (‘CA’) that match selected sequences in the digested genome fragments and a non-selective primer. When properly amplified, the selected sequence is complementary to the selective bases. Final PCR . Primers matching the amplification primer and the selective primer which contain the full Proton adaptor sequence are used for amplification of the final library. Final on-target sequence . The final sequence contains the 5′ Proton adaptor sequence, an internal barcode, the NspI RE site, the target molecule, selective bases, the BfuCI RE site and the 3′ Proton adaptor sequence. It is possible to adapt the tGBS protocol for sequencing on an Illumina instrument by redesigning the ligation oligos and PCR primers.
    Nspi, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 94/100, based on 186 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/nspi/product/New England Biolabs
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    nspi - by Bioz Stars, 2020-09
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    99
    New England Biolabs t4 dna ligase
    Diagram of tGBS. Digestion . Genomic <t>DNA</t> is digested with two REs: <t>NspI</t> leaves a 3′overhang and BfuCI leaves a 5′ overhang. Ligation . Two distinct oligos are ligated to the complementary 3′ and 5′ overhangs. The oligo matching the 3′ overhang contains a sample-specific internal barcode sequence for sample identification. The oligo matching the 5′ overhang is universal and present in every reaction for later amplification. Selective PCR . Target sites are selected using a selective primer with variable selective bases (‘CA’) that match selected sequences in the digested genome fragments and a non-selective primer. When properly amplified, the selected sequence is complementary to the selective bases. Final PCR . Primers matching the amplification primer and the selective primer which contain the full Proton adaptor sequence are used for amplification of the final library. Final on-target sequence . The final sequence contains the 5′ Proton adaptor sequence, an internal barcode, the NspI RE site, the target molecule, selective bases, the BfuCI RE site and the 3′ Proton adaptor sequence. It is possible to adapt the tGBS protocol for sequencing on an Illumina instrument by redesigning the ligation oligos and PCR primers.
    T4 Dna Ligase, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 99/100, based on 49373 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Average 99 stars, based on 49373 article reviews
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    t4 dna ligase - by Bioz Stars, 2020-09
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    92
    New England Biolabs styi
    Diagram of tGBS. Digestion . Genomic <t>DNA</t> is digested with two REs: <t>NspI</t> leaves a 3′overhang and BfuCI leaves a 5′ overhang. Ligation . Two distinct oligos are ligated to the complementary 3′ and 5′ overhangs. The oligo matching the 3′ overhang contains a sample-specific internal barcode sequence for sample identification. The oligo matching the 5′ overhang is universal and present in every reaction for later amplification. Selective PCR . Target sites are selected using a selective primer with variable selective bases (‘CA’) that match selected sequences in the digested genome fragments and a non-selective primer. When properly amplified, the selected sequence is complementary to the selective bases. Final PCR . Primers matching the amplification primer and the selective primer which contain the full Proton adaptor sequence are used for amplification of the final library. Final on-target sequence . The final sequence contains the 5′ Proton adaptor sequence, an internal barcode, the NspI RE site, the target molecule, selective bases, the BfuCI RE site and the 3′ Proton adaptor sequence. It is possible to adapt the tGBS protocol for sequencing on an Illumina instrument by redesigning the ligation oligos and PCR primers.
    Styi, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 92/100, based on 112 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    99
    Qiagen dneasy tissue kit
    Diagram of tGBS. Digestion . Genomic <t>DNA</t> is digested with two REs: <t>NspI</t> leaves a 3′overhang and BfuCI leaves a 5′ overhang. Ligation . Two distinct oligos are ligated to the complementary 3′ and 5′ overhangs. The oligo matching the 3′ overhang contains a sample-specific internal barcode sequence for sample identification. The oligo matching the 5′ overhang is universal and present in every reaction for later amplification. Selective PCR . Target sites are selected using a selective primer with variable selective bases (‘CA’) that match selected sequences in the digested genome fragments and a non-selective primer. When properly amplified, the selected sequence is complementary to the selective bases. Final PCR . Primers matching the amplification primer and the selective primer which contain the full Proton adaptor sequence are used for amplification of the final library. Final on-target sequence . The final sequence contains the 5′ Proton adaptor sequence, an internal barcode, the NspI RE site, the target molecule, selective bases, the BfuCI RE site and the 3′ Proton adaptor sequence. It is possible to adapt the tGBS protocol for sequencing on an Illumina instrument by redesigning the ligation oligos and PCR primers.
    Dneasy Tissue Kit, supplied by Qiagen, used in various techniques. Bioz Stars score: 99/100, based on 19017 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/dneasy tissue kit/product/Qiagen
    Average 99 stars, based on 19017 article reviews
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    99
    New England Biolabs hindiii
    Copy number variation at APOL1 locus. a. Sequence coverage analysis of samples from 1000 Genomes Project. Grey lines are used to depict coverage of each of 2,527 samples at genomic loci to which sequence reads map. Red lines indicate coverage for 8 samples with apparent duplication. The black line depicts median coverage for all samples showing elevated coverage over a region of this locus, including APOL1, suggesting duplication. Coordinates of the genome are plotted on the X-axis against normalized read depth on the Y-axis. Coordinates of APOL1 gene are chr22: 36,649,117–36,663,571 (hg19). b. Pictorial representation of the duplication event. An approximately 100kb region of chromosome 22, beginning from a region adjacent to APOL2, and involving all of APOL1 and part of MYH9 is duplicated (chr22:36,612,938–36,714,262, hg19). c. Gel electrophoresis (3% agarose) of the PCR product of the qualitative PCR assay used for detection of duplication. The PCR assay amplifies sequence across the junction between the duplicated segments, and results in a 291 bp size product, if present. Lane 1 corresponds to 100 bp ladder with size of each fragment indicated. Lanes 2 and 3 represent samples from individuals of European ancestry, who are negative for duplication. Lanes 4, 5 and 6 show a band of the expected size and indicate the presence of a duplication in these three unrelated African American individuals. Lanes 7, 8 and 9 show the absence of a PCR product in three other African American individuals. One of these three (lane 7) showed 3 copies using the Taqman copy number assay, indicating an insertional variant of different structure. Lane 10 is a non-template control reaction. d. Allelic discrimination digest assay: Gel electrophoresis of the PCR products obtained during allelic discrimination assay. Lane 1 shows a 100 bp ladder. Lane 2 (a, b and c) corresponds to sample NA 19701, Lane 3 (a, b and c) corresponds to sample NA 19372, Lane 4 (a, b and c) corresponds to sample NA 19700 and lane 5 corresponds to sample NA 19702. The band in the lanes 2a, 3a, 4a and 5a represent PCR products not subjected to any digestion (314 bp in size). Lanes 2b, 3b, 4b and 5b represent PCR products after digestion with <t>HindIII.</t> Lanes 2c, 3c, 4c and 5c represent PCR products after digestion with NspI. Since sample NA 19700 is homozygous for G0, there are only 2 bands in lane 4b and 1 band in lane 4c. Of note, with HindIII digestion, which cleaves the PCR product only if G0 allele is present, bands are expected to be 100 bp and 214 bp in size. With NspI, which cleaves the PCR product only in the presence of I384M G1 allele, the bands are expected to be 228 and 86 bp in size.
    Hindiii, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 99/100, based on 8137 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/hindiii/product/New England Biolabs
    Average 99 stars, based on 8137 article reviews
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    99
    New England Biolabs quick ligation kit
    Copy number variation at APOL1 locus. a. Sequence coverage analysis of samples from 1000 Genomes Project. Grey lines are used to depict coverage of each of 2,527 samples at genomic loci to which sequence reads map. Red lines indicate coverage for 8 samples with apparent duplication. The black line depicts median coverage for all samples showing elevated coverage over a region of this locus, including APOL1, suggesting duplication. Coordinates of the genome are plotted on the X-axis against normalized read depth on the Y-axis. Coordinates of APOL1 gene are chr22: 36,649,117–36,663,571 (hg19). b. Pictorial representation of the duplication event. An approximately 100kb region of chromosome 22, beginning from a region adjacent to APOL2, and involving all of APOL1 and part of MYH9 is duplicated (chr22:36,612,938–36,714,262, hg19). c. Gel electrophoresis (3% agarose) of the PCR product of the qualitative PCR assay used for detection of duplication. The PCR assay amplifies sequence across the junction between the duplicated segments, and results in a 291 bp size product, if present. Lane 1 corresponds to 100 bp ladder with size of each fragment indicated. Lanes 2 and 3 represent samples from individuals of European ancestry, who are negative for duplication. Lanes 4, 5 and 6 show a band of the expected size and indicate the presence of a duplication in these three unrelated African American individuals. Lanes 7, 8 and 9 show the absence of a PCR product in three other African American individuals. One of these three (lane 7) showed 3 copies using the Taqman copy number assay, indicating an insertional variant of different structure. Lane 10 is a non-template control reaction. d. Allelic discrimination digest assay: Gel electrophoresis of the PCR products obtained during allelic discrimination assay. Lane 1 shows a 100 bp ladder. Lane 2 (a, b and c) corresponds to sample NA 19701, Lane 3 (a, b and c) corresponds to sample NA 19372, Lane 4 (a, b and c) corresponds to sample NA 19700 and lane 5 corresponds to sample NA 19702. The band in the lanes 2a, 3a, 4a and 5a represent PCR products not subjected to any digestion (314 bp in size). Lanes 2b, 3b, 4b and 5b represent PCR products after digestion with <t>HindIII.</t> Lanes 2c, 3c, 4c and 5c represent PCR products after digestion with NspI. Since sample NA 19700 is homozygous for G0, there are only 2 bands in lane 4b and 1 band in lane 4c. Of note, with HindIII digestion, which cleaves the PCR product only if G0 allele is present, bands are expected to be 100 bp and 214 bp in size. With NspI, which cleaves the PCR product only in the presence of I384M G1 allele, the bands are expected to be 228 and 86 bp in size.
    Quick Ligation Kit, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 99/100, based on 4509 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/quick ligation kit/product/New England Biolabs
    Average 99 stars, based on 4509 article reviews
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    quick ligation kit - by Bioz Stars, 2020-09
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    99
    Qiagen genomic dna
    Copy number variation at APOL1 locus. a. Sequence coverage analysis of samples from 1000 Genomes Project. Grey lines are used to depict coverage of each of 2,527 samples at genomic loci to which sequence reads map. Red lines indicate coverage for 8 samples with apparent duplication. The black line depicts median coverage for all samples showing elevated coverage over a region of this locus, including APOL1, suggesting duplication. Coordinates of the genome are plotted on the X-axis against normalized read depth on the Y-axis. Coordinates of APOL1 gene are chr22: 36,649,117–36,663,571 (hg19). b. Pictorial representation of the duplication event. An approximately 100kb region of chromosome 22, beginning from a region adjacent to APOL2, and involving all of APOL1 and part of MYH9 is duplicated (chr22:36,612,938–36,714,262, hg19). c. Gel electrophoresis (3% agarose) of the PCR product of the qualitative PCR assay used for detection of duplication. The PCR assay amplifies sequence across the junction between the duplicated segments, and results in a 291 bp size product, if present. Lane 1 corresponds to 100 bp ladder with size of each fragment indicated. Lanes 2 and 3 represent samples from individuals of European ancestry, who are negative for duplication. Lanes 4, 5 and 6 show a band of the expected size and indicate the presence of a duplication in these three unrelated African American individuals. Lanes 7, 8 and 9 show the absence of a PCR product in three other African American individuals. One of these three (lane 7) showed 3 copies using the Taqman copy number assay, indicating an insertional variant of different structure. Lane 10 is a non-template control reaction. d. Allelic discrimination digest assay: Gel electrophoresis of the PCR products obtained during allelic discrimination assay. Lane 1 shows a 100 bp ladder. Lane 2 (a, b and c) corresponds to sample NA 19701, Lane 3 (a, b and c) corresponds to sample NA 19372, Lane 4 (a, b and c) corresponds to sample NA 19700 and lane 5 corresponds to sample NA 19702. The band in the lanes 2a, 3a, 4a and 5a represent PCR products not subjected to any digestion (314 bp in size). Lanes 2b, 3b, 4b and 5b represent PCR products after digestion with <t>HindIII.</t> Lanes 2c, 3c, 4c and 5c represent PCR products after digestion with NspI. Since sample NA 19700 is homozygous for G0, there are only 2 bands in lane 4b and 1 band in lane 4c. Of note, with HindIII digestion, which cleaves the PCR product only if G0 allele is present, bands are expected to be 100 bp and 214 bp in size. With NspI, which cleaves the PCR product only in the presence of I384M G1 allele, the bands are expected to be 228 and 86 bp in size.
    Genomic Dna, supplied by Qiagen, used in various techniques. Bioz Stars score: 99/100, based on 127055 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    85
    Thermo Fisher genome wide human snp nsp sty assay kit
    Copy number variation at APOL1 locus. a. Sequence coverage analysis of samples from 1000 Genomes Project. Grey lines are used to depict coverage of each of 2,527 samples at genomic loci to which sequence reads map. Red lines indicate coverage for 8 samples with apparent duplication. The black line depicts median coverage for all samples showing elevated coverage over a region of this locus, including APOL1, suggesting duplication. Coordinates of the genome are plotted on the X-axis against normalized read depth on the Y-axis. Coordinates of APOL1 gene are chr22: 36,649,117–36,663,571 (hg19). b. Pictorial representation of the duplication event. An approximately 100kb region of chromosome 22, beginning from a region adjacent to APOL2, and involving all of APOL1 and part of MYH9 is duplicated (chr22:36,612,938–36,714,262, hg19). c. Gel electrophoresis (3% agarose) of the PCR product of the qualitative PCR assay used for detection of duplication. The PCR assay amplifies sequence across the junction between the duplicated segments, and results in a 291 bp size product, if present. Lane 1 corresponds to 100 bp ladder with size of each fragment indicated. Lanes 2 and 3 represent samples from individuals of European ancestry, who are negative for duplication. Lanes 4, 5 and 6 show a band of the expected size and indicate the presence of a duplication in these three unrelated African American individuals. Lanes 7, 8 and 9 show the absence of a PCR product in three other African American individuals. One of these three (lane 7) showed 3 copies using the Taqman copy number assay, indicating an insertional variant of different structure. Lane 10 is a non-template control reaction. d. Allelic discrimination digest assay: Gel electrophoresis of the PCR products obtained during allelic discrimination assay. Lane 1 shows a 100 bp ladder. Lane 2 (a, b and c) corresponds to sample NA 19701, Lane 3 (a, b and c) corresponds to sample NA 19372, Lane 4 (a, b and c) corresponds to sample NA 19700 and lane 5 corresponds to sample NA 19702. The band in the lanes 2a, 3a, 4a and 5a represent PCR products not subjected to any digestion (314 bp in size). Lanes 2b, 3b, 4b and 5b represent PCR products after digestion with <t>HindIII.</t> Lanes 2c, 3c, 4c and 5c represent PCR products after digestion with NspI. Since sample NA 19700 is homozygous for G0, there are only 2 bands in lane 4b and 1 band in lane 4c. Of note, with HindIII digestion, which cleaves the PCR product only if G0 allele is present, bands are expected to be 100 bp and 214 bp in size. With NspI, which cleaves the PCR product only in the presence of I384M G1 allele, the bands are expected to be 228 and 86 bp in size.
    Genome Wide Human Snp Nsp Sty Assay Kit, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 85/100, based on 31 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    99
    New England Biolabs restriction endonuclease nspi
    Copy number variation at APOL1 locus. a. Sequence coverage analysis of samples from 1000 Genomes Project. Grey lines are used to depict coverage of each of 2,527 samples at genomic loci to which sequence reads map. Red lines indicate coverage for 8 samples with apparent duplication. The black line depicts median coverage for all samples showing elevated coverage over a region of this locus, including APOL1, suggesting duplication. Coordinates of the genome are plotted on the X-axis against normalized read depth on the Y-axis. Coordinates of APOL1 gene are chr22: 36,649,117–36,663,571 (hg19). b. Pictorial representation of the duplication event. An approximately 100kb region of chromosome 22, beginning from a region adjacent to APOL2, and involving all of APOL1 and part of MYH9 is duplicated (chr22:36,612,938–36,714,262, hg19). c. Gel electrophoresis (3% agarose) of the PCR product of the qualitative PCR assay used for detection of duplication. The PCR assay amplifies sequence across the junction between the duplicated segments, and results in a 291 bp size product, if present. Lane 1 corresponds to 100 bp ladder with size of each fragment indicated. Lanes 2 and 3 represent samples from individuals of European ancestry, who are negative for duplication. Lanes 4, 5 and 6 show a band of the expected size and indicate the presence of a duplication in these three unrelated African American individuals. Lanes 7, 8 and 9 show the absence of a PCR product in three other African American individuals. One of these three (lane 7) showed 3 copies using the Taqman copy number assay, indicating an insertional variant of different structure. Lane 10 is a non-template control reaction. d. Allelic discrimination digest assay: Gel electrophoresis of the PCR products obtained during allelic discrimination assay. Lane 1 shows a 100 bp ladder. Lane 2 (a, b and c) corresponds to sample NA 19701, Lane 3 (a, b and c) corresponds to sample NA 19372, Lane 4 (a, b and c) corresponds to sample NA 19700 and lane 5 corresponds to sample NA 19702. The band in the lanes 2a, 3a, 4a and 5a represent PCR products not subjected to any digestion (314 bp in size). Lanes 2b, 3b, 4b and 5b represent PCR products after digestion with <t>HindIII.</t> Lanes 2c, 3c, 4c and 5c represent PCR products after digestion with NspI. Since sample NA 19700 is homozygous for G0, there are only 2 bands in lane 4b and 1 band in lane 4c. Of note, with HindIII digestion, which cleaves the PCR product only if G0 allele is present, bands are expected to be 100 bp and 214 bp in size. With NspI, which cleaves the PCR product only in the presence of I384M G1 allele, the bands are expected to be 228 and 86 bp in size.
    Restriction Endonuclease Nspi, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 99/100, based on 4 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    99
    TaKaRa titanium taq dna polymerase
    Copy number variation at APOL1 locus. a. Sequence coverage analysis of samples from 1000 Genomes Project. Grey lines are used to depict coverage of each of 2,527 samples at genomic loci to which sequence reads map. Red lines indicate coverage for 8 samples with apparent duplication. The black line depicts median coverage for all samples showing elevated coverage over a region of this locus, including APOL1, suggesting duplication. Coordinates of the genome are plotted on the X-axis against normalized read depth on the Y-axis. Coordinates of APOL1 gene are chr22: 36,649,117–36,663,571 (hg19). b. Pictorial representation of the duplication event. An approximately 100kb region of chromosome 22, beginning from a region adjacent to APOL2, and involving all of APOL1 and part of MYH9 is duplicated (chr22:36,612,938–36,714,262, hg19). c. Gel electrophoresis (3% agarose) of the PCR product of the qualitative PCR assay used for detection of duplication. The PCR assay amplifies sequence across the junction between the duplicated segments, and results in a 291 bp size product, if present. Lane 1 corresponds to 100 bp ladder with size of each fragment indicated. Lanes 2 and 3 represent samples from individuals of European ancestry, who are negative for duplication. Lanes 4, 5 and 6 show a band of the expected size and indicate the presence of a duplication in these three unrelated African American individuals. Lanes 7, 8 and 9 show the absence of a PCR product in three other African American individuals. One of these three (lane 7) showed 3 copies using the Taqman copy number assay, indicating an insertional variant of different structure. Lane 10 is a non-template control reaction. d. Allelic discrimination digest assay: Gel electrophoresis of the PCR products obtained during allelic discrimination assay. Lane 1 shows a 100 bp ladder. Lane 2 (a, b and c) corresponds to sample NA 19701, Lane 3 (a, b and c) corresponds to sample NA 19372, Lane 4 (a, b and c) corresponds to sample NA 19700 and lane 5 corresponds to sample NA 19702. The band in the lanes 2a, 3a, 4a and 5a represent PCR products not subjected to any digestion (314 bp in size). Lanes 2b, 3b, 4b and 5b represent PCR products after digestion with <t>HindIII.</t> Lanes 2c, 3c, 4c and 5c represent PCR products after digestion with NspI. Since sample NA 19700 is homozygous for G0, there are only 2 bands in lane 4b and 1 band in lane 4c. Of note, with HindIII digestion, which cleaves the PCR product only if G0 allele is present, bands are expected to be 100 bp and 214 bp in size. With NspI, which cleaves the PCR product only in the presence of I384M G1 allele, the bands are expected to be 228 and 86 bp in size.
    Titanium Taq Dna Polymerase, supplied by TaKaRa, used in various techniques. Bioz Stars score: 99/100, based on 1649 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    90
    TaKaRa adaptor ligated dna fragments
    Copy number variation at APOL1 locus. a. Sequence coverage analysis of samples from 1000 Genomes Project. Grey lines are used to depict coverage of each of 2,527 samples at genomic loci to which sequence reads map. Red lines indicate coverage for 8 samples with apparent duplication. The black line depicts median coverage for all samples showing elevated coverage over a region of this locus, including APOL1, suggesting duplication. Coordinates of the genome are plotted on the X-axis against normalized read depth on the Y-axis. Coordinates of APOL1 gene are chr22: 36,649,117–36,663,571 (hg19). b. Pictorial representation of the duplication event. An approximately 100kb region of chromosome 22, beginning from a region adjacent to APOL2, and involving all of APOL1 and part of MYH9 is duplicated (chr22:36,612,938–36,714,262, hg19). c. Gel electrophoresis (3% agarose) of the PCR product of the qualitative PCR assay used for detection of duplication. The PCR assay amplifies sequence across the junction between the duplicated segments, and results in a 291 bp size product, if present. Lane 1 corresponds to 100 bp ladder with size of each fragment indicated. Lanes 2 and 3 represent samples from individuals of European ancestry, who are negative for duplication. Lanes 4, 5 and 6 show a band of the expected size and indicate the presence of a duplication in these three unrelated African American individuals. Lanes 7, 8 and 9 show the absence of a PCR product in three other African American individuals. One of these three (lane 7) showed 3 copies using the Taqman copy number assay, indicating an insertional variant of different structure. Lane 10 is a non-template control reaction. d. Allelic discrimination digest assay: Gel electrophoresis of the PCR products obtained during allelic discrimination assay. Lane 1 shows a 100 bp ladder. Lane 2 (a, b and c) corresponds to sample NA 19701, Lane 3 (a, b and c) corresponds to sample NA 19372, Lane 4 (a, b and c) corresponds to sample NA 19700 and lane 5 corresponds to sample NA 19702. The band in the lanes 2a, 3a, 4a and 5a represent PCR products not subjected to any digestion (314 bp in size). Lanes 2b, 3b, 4b and 5b represent PCR products after digestion with <t>HindIII.</t> Lanes 2c, 3c, 4c and 5c represent PCR products after digestion with NspI. Since sample NA 19700 is homozygous for G0, there are only 2 bands in lane 4b and 1 band in lane 4c. Of note, with HindIII digestion, which cleaves the PCR product only if G0 allele is present, bands are expected to be 100 bp and 214 bp in size. With NspI, which cleaves the PCR product only in the presence of I384M G1 allele, the bands are expected to be 228 and 86 bp in size.
    Adaptor Ligated Dna Fragments, supplied by TaKaRa, used in various techniques. Bioz Stars score: 90/100, based on 29 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    94
    New England Biolabs afliii
    Copy number variation at APOL1 locus. a. Sequence coverage analysis of samples from 1000 Genomes Project. Grey lines are used to depict coverage of each of 2,527 samples at genomic loci to which sequence reads map. Red lines indicate coverage for 8 samples with apparent duplication. The black line depicts median coverage for all samples showing elevated coverage over a region of this locus, including APOL1, suggesting duplication. Coordinates of the genome are plotted on the X-axis against normalized read depth on the Y-axis. Coordinates of APOL1 gene are chr22: 36,649,117–36,663,571 (hg19). b. Pictorial representation of the duplication event. An approximately 100kb region of chromosome 22, beginning from a region adjacent to APOL2, and involving all of APOL1 and part of MYH9 is duplicated (chr22:36,612,938–36,714,262, hg19). c. Gel electrophoresis (3% agarose) of the PCR product of the qualitative PCR assay used for detection of duplication. The PCR assay amplifies sequence across the junction between the duplicated segments, and results in a 291 bp size product, if present. Lane 1 corresponds to 100 bp ladder with size of each fragment indicated. Lanes 2 and 3 represent samples from individuals of European ancestry, who are negative for duplication. Lanes 4, 5 and 6 show a band of the expected size and indicate the presence of a duplication in these three unrelated African American individuals. Lanes 7, 8 and 9 show the absence of a PCR product in three other African American individuals. One of these three (lane 7) showed 3 copies using the Taqman copy number assay, indicating an insertional variant of different structure. Lane 10 is a non-template control reaction. d. Allelic discrimination digest assay: Gel electrophoresis of the PCR products obtained during allelic discrimination assay. Lane 1 shows a 100 bp ladder. Lane 2 (a, b and c) corresponds to sample NA 19701, Lane 3 (a, b and c) corresponds to sample NA 19372, Lane 4 (a, b and c) corresponds to sample NA 19700 and lane 5 corresponds to sample NA 19702. The band in the lanes 2a, 3a, 4a and 5a represent PCR products not subjected to any digestion (314 bp in size). Lanes 2b, 3b, 4b and 5b represent PCR products after digestion with <t>HindIII.</t> Lanes 2c, 3c, 4c and 5c represent PCR products after digestion with NspI. Since sample NA 19700 is homozygous for G0, there are only 2 bands in lane 4b and 1 band in lane 4c. Of note, with HindIII digestion, which cleaves the PCR product only if G0 allele is present, bands are expected to be 100 bp and 214 bp in size. With NspI, which cleaves the PCR product only in the presence of I384M G1 allele, the bands are expected to be 228 and 86 bp in size.
    Afliii, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 94/100, based on 176 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/afliii/product/New England Biolabs
    Average 94 stars, based on 176 article reviews
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    afliii - by Bioz Stars, 2020-09
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    88
    Thermo Fisher amplitag gold
    Copy number variation at APOL1 locus. a. Sequence coverage analysis of samples from 1000 Genomes Project. Grey lines are used to depict coverage of each of 2,527 samples at genomic loci to which sequence reads map. Red lines indicate coverage for 8 samples with apparent duplication. The black line depicts median coverage for all samples showing elevated coverage over a region of this locus, including APOL1, suggesting duplication. Coordinates of the genome are plotted on the X-axis against normalized read depth on the Y-axis. Coordinates of APOL1 gene are chr22: 36,649,117–36,663,571 (hg19). b. Pictorial representation of the duplication event. An approximately 100kb region of chromosome 22, beginning from a region adjacent to APOL2, and involving all of APOL1 and part of MYH9 is duplicated (chr22:36,612,938–36,714,262, hg19). c. Gel electrophoresis (3% agarose) of the PCR product of the qualitative PCR assay used for detection of duplication. The PCR assay amplifies sequence across the junction between the duplicated segments, and results in a 291 bp size product, if present. Lane 1 corresponds to 100 bp ladder with size of each fragment indicated. Lanes 2 and 3 represent samples from individuals of European ancestry, who are negative for duplication. Lanes 4, 5 and 6 show a band of the expected size and indicate the presence of a duplication in these three unrelated African American individuals. Lanes 7, 8 and 9 show the absence of a PCR product in three other African American individuals. One of these three (lane 7) showed 3 copies using the Taqman copy number assay, indicating an insertional variant of different structure. Lane 10 is a non-template control reaction. d. Allelic discrimination digest assay: Gel electrophoresis of the PCR products obtained during allelic discrimination assay. Lane 1 shows a 100 bp ladder. Lane 2 (a, b and c) corresponds to sample NA 19701, Lane 3 (a, b and c) corresponds to sample NA 19372, Lane 4 (a, b and c) corresponds to sample NA 19700 and lane 5 corresponds to sample NA 19702. The band in the lanes 2a, 3a, 4a and 5a represent PCR products not subjected to any digestion (314 bp in size). Lanes 2b, 3b, 4b and 5b represent PCR products after digestion with <t>HindIII.</t> Lanes 2c, 3c, 4c and 5c represent PCR products after digestion with NspI. Since sample NA 19700 is homozygous for G0, there are only 2 bands in lane 4b and 1 band in lane 4c. Of note, with HindIII digestion, which cleaves the PCR product only if G0 allele is present, bands are expected to be 100 bp and 214 bp in size. With NspI, which cleaves the PCR product only in the presence of I384M G1 allele, the bands are expected to be 228 and 86 bp in size.
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    New England Biolabs apoi
    Copy number variation at APOL1 locus. a. Sequence coverage analysis of samples from 1000 Genomes Project. Grey lines are used to depict coverage of each of 2,527 samples at genomic loci to which sequence reads map. Red lines indicate coverage for 8 samples with apparent duplication. The black line depicts median coverage for all samples showing elevated coverage over a region of this locus, including APOL1, suggesting duplication. Coordinates of the genome are plotted on the X-axis against normalized read depth on the Y-axis. Coordinates of APOL1 gene are chr22: 36,649,117–36,663,571 (hg19). b. Pictorial representation of the duplication event. An approximately 100kb region of chromosome 22, beginning from a region adjacent to APOL2, and involving all of APOL1 and part of MYH9 is duplicated (chr22:36,612,938–36,714,262, hg19). c. Gel electrophoresis (3% agarose) of the PCR product of the qualitative PCR assay used for detection of duplication. The PCR assay amplifies sequence across the junction between the duplicated segments, and results in a 291 bp size product, if present. Lane 1 corresponds to 100 bp ladder with size of each fragment indicated. Lanes 2 and 3 represent samples from individuals of European ancestry, who are negative for duplication. Lanes 4, 5 and 6 show a band of the expected size and indicate the presence of a duplication in these three unrelated African American individuals. Lanes 7, 8 and 9 show the absence of a PCR product in three other African American individuals. One of these three (lane 7) showed 3 copies using the Taqman copy number assay, indicating an insertional variant of different structure. Lane 10 is a non-template control reaction. d. Allelic discrimination digest assay: Gel electrophoresis of the PCR products obtained during allelic discrimination assay. Lane 1 shows a 100 bp ladder. Lane 2 (a, b and c) corresponds to sample NA 19701, Lane 3 (a, b and c) corresponds to sample NA 19372, Lane 4 (a, b and c) corresponds to sample NA 19700 and lane 5 corresponds to sample NA 19702. The band in the lanes 2a, 3a, 4a and 5a represent PCR products not subjected to any digestion (314 bp in size). Lanes 2b, 3b, 4b and 5b represent PCR products after digestion with <t>HindIII.</t> Lanes 2c, 3c, 4c and 5c represent PCR products after digestion with NspI. Since sample NA 19700 is homozygous for G0, there are only 2 bands in lane 4b and 1 band in lane 4c. Of note, with HindIII digestion, which cleaves the PCR product only if G0 allele is present, bands are expected to be 100 bp and 214 bp in size. With NspI, which cleaves the PCR product only in the presence of I384M G1 allele, the bands are expected to be 228 and 86 bp in size.
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    96
    New England Biolabs avaii
    Copy number variation at APOL1 locus. a. Sequence coverage analysis of samples from 1000 Genomes Project. Grey lines are used to depict coverage of each of 2,527 samples at genomic loci to which sequence reads map. Red lines indicate coverage for 8 samples with apparent duplication. The black line depicts median coverage for all samples showing elevated coverage over a region of this locus, including APOL1, suggesting duplication. Coordinates of the genome are plotted on the X-axis against normalized read depth on the Y-axis. Coordinates of APOL1 gene are chr22: 36,649,117–36,663,571 (hg19). b. Pictorial representation of the duplication event. An approximately 100kb region of chromosome 22, beginning from a region adjacent to APOL2, and involving all of APOL1 and part of MYH9 is duplicated (chr22:36,612,938–36,714,262, hg19). c. Gel electrophoresis (3% agarose) of the PCR product of the qualitative PCR assay used for detection of duplication. The PCR assay amplifies sequence across the junction between the duplicated segments, and results in a 291 bp size product, if present. Lane 1 corresponds to 100 bp ladder with size of each fragment indicated. Lanes 2 and 3 represent samples from individuals of European ancestry, who are negative for duplication. Lanes 4, 5 and 6 show a band of the expected size and indicate the presence of a duplication in these three unrelated African American individuals. Lanes 7, 8 and 9 show the absence of a PCR product in three other African American individuals. One of these three (lane 7) showed 3 copies using the Taqman copy number assay, indicating an insertional variant of different structure. Lane 10 is a non-template control reaction. d. Allelic discrimination digest assay: Gel electrophoresis of the PCR products obtained during allelic discrimination assay. Lane 1 shows a 100 bp ladder. Lane 2 (a, b and c) corresponds to sample NA 19701, Lane 3 (a, b and c) corresponds to sample NA 19372, Lane 4 (a, b and c) corresponds to sample NA 19700 and lane 5 corresponds to sample NA 19702. The band in the lanes 2a, 3a, 4a and 5a represent PCR products not subjected to any digestion (314 bp in size). Lanes 2b, 3b, 4b and 5b represent PCR products after digestion with <t>HindIII.</t> Lanes 2c, 3c, 4c and 5c represent PCR products after digestion with NspI. Since sample NA 19700 is homozygous for G0, there are only 2 bands in lane 4b and 1 band in lane 4c. Of note, with HindIII digestion, which cleaves the PCR product only if G0 allele is present, bands are expected to be 100 bp and 214 bp in size. With NspI, which cleaves the PCR product only in the presence of I384M G1 allele, the bands are expected to be 228 and 86 bp in size.
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    89
    Santa Cruz Biotechnology anti nfatc1 antibody
    Copy number variation at APOL1 locus. a. Sequence coverage analysis of samples from 1000 Genomes Project. Grey lines are used to depict coverage of each of 2,527 samples at genomic loci to which sequence reads map. Red lines indicate coverage for 8 samples with apparent duplication. The black line depicts median coverage for all samples showing elevated coverage over a region of this locus, including APOL1, suggesting duplication. Coordinates of the genome are plotted on the X-axis against normalized read depth on the Y-axis. Coordinates of APOL1 gene are chr22: 36,649,117–36,663,571 (hg19). b. Pictorial representation of the duplication event. An approximately 100kb region of chromosome 22, beginning from a region adjacent to APOL2, and involving all of APOL1 and part of MYH9 is duplicated (chr22:36,612,938–36,714,262, hg19). c. Gel electrophoresis (3% agarose) of the PCR product of the qualitative PCR assay used for detection of duplication. The PCR assay amplifies sequence across the junction between the duplicated segments, and results in a 291 bp size product, if present. Lane 1 corresponds to 100 bp ladder with size of each fragment indicated. Lanes 2 and 3 represent samples from individuals of European ancestry, who are negative for duplication. Lanes 4, 5 and 6 show a band of the expected size and indicate the presence of a duplication in these three unrelated African American individuals. Lanes 7, 8 and 9 show the absence of a PCR product in three other African American individuals. One of these three (lane 7) showed 3 copies using the Taqman copy number assay, indicating an insertional variant of different structure. Lane 10 is a non-template control reaction. d. Allelic discrimination digest assay: Gel electrophoresis of the PCR products obtained during allelic discrimination assay. Lane 1 shows a 100 bp ladder. Lane 2 (a, b and c) corresponds to sample NA 19701, Lane 3 (a, b and c) corresponds to sample NA 19372, Lane 4 (a, b and c) corresponds to sample NA 19700 and lane 5 corresponds to sample NA 19702. The band in the lanes 2a, 3a, 4a and 5a represent PCR products not subjected to any digestion (314 bp in size). Lanes 2b, 3b, 4b and 5b represent PCR products after digestion with <t>HindIII.</t> Lanes 2c, 3c, 4c and 5c represent PCR products after digestion with NspI. Since sample NA 19700 is homozygous for G0, there are only 2 bands in lane 4b and 1 band in lane 4c. Of note, with HindIII digestion, which cleaves the PCR product only if G0 allele is present, bands are expected to be 100 bp and 214 bp in size. With NspI, which cleaves the PCR product only in the presence of I384M G1 allele, the bands are expected to be 228 and 86 bp in size.
    Anti Nfatc1 Antibody, supplied by Santa Cruz Biotechnology, used in various techniques. Bioz Stars score: 89/100, based on 84 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Santa Cruz Biotechnology anti nf κb p65 antibody
    Copy number variation at APOL1 locus. a. Sequence coverage analysis of samples from 1000 Genomes Project. Grey lines are used to depict coverage of each of 2,527 samples at genomic loci to which sequence reads map. Red lines indicate coverage for 8 samples with apparent duplication. The black line depicts median coverage for all samples showing elevated coverage over a region of this locus, including APOL1, suggesting duplication. Coordinates of the genome are plotted on the X-axis against normalized read depth on the Y-axis. Coordinates of APOL1 gene are chr22: 36,649,117–36,663,571 (hg19). b. Pictorial representation of the duplication event. An approximately 100kb region of chromosome 22, beginning from a region adjacent to APOL2, and involving all of APOL1 and part of MYH9 is duplicated (chr22:36,612,938–36,714,262, hg19). c. Gel electrophoresis (3% agarose) of the PCR product of the qualitative PCR assay used for detection of duplication. The PCR assay amplifies sequence across the junction between the duplicated segments, and results in a 291 bp size product, if present. Lane 1 corresponds to 100 bp ladder with size of each fragment indicated. Lanes 2 and 3 represent samples from individuals of European ancestry, who are negative for duplication. Lanes 4, 5 and 6 show a band of the expected size and indicate the presence of a duplication in these three unrelated African American individuals. Lanes 7, 8 and 9 show the absence of a PCR product in three other African American individuals. One of these three (lane 7) showed 3 copies using the Taqman copy number assay, indicating an insertional variant of different structure. Lane 10 is a non-template control reaction. d. Allelic discrimination digest assay: Gel electrophoresis of the PCR products obtained during allelic discrimination assay. Lane 1 shows a 100 bp ladder. Lane 2 (a, b and c) corresponds to sample NA 19701, Lane 3 (a, b and c) corresponds to sample NA 19372, Lane 4 (a, b and c) corresponds to sample NA 19700 and lane 5 corresponds to sample NA 19702. The band in the lanes 2a, 3a, 4a and 5a represent PCR products not subjected to any digestion (314 bp in size). Lanes 2b, 3b, 4b and 5b represent PCR products after digestion with <t>HindIII.</t> Lanes 2c, 3c, 4c and 5c represent PCR products after digestion with NspI. Since sample NA 19700 is homozygous for G0, there are only 2 bands in lane 4b and 1 band in lane 4c. Of note, with HindIII digestion, which cleaves the PCR product only if G0 allele is present, bands are expected to be 100 bp and 214 bp in size. With NspI, which cleaves the PCR product only in the presence of I384M G1 allele, the bands are expected to be 228 and 86 bp in size.
    Anti Nf κb P65 Antibody, supplied by Santa Cruz Biotechnology, used in various techniques. Bioz Stars score: 92/100, based on 246 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    88
    Thermo Fisher affymetrix 100k
    Heat map visualization of the genome-wide copy number results for (A) 30 primary and 6 recurrent central nervous system primitive neuroectodermal tumors (CNS PNETs) and (B) 6 primary and 2 recurrent pineoblastomas (PBs) using <t>Affymetrix</t> <t>100K</t> and 500K
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    Image Search Results


    Diagram of tGBS. Digestion . Genomic DNA is digested with two REs: NspI leaves a 3′overhang and BfuCI leaves a 5′ overhang. Ligation . Two distinct oligos are ligated to the complementary 3′ and 5′ overhangs. The oligo matching the 3′ overhang contains a sample-specific internal barcode sequence for sample identification. The oligo matching the 5′ overhang is universal and present in every reaction for later amplification. Selective PCR . Target sites are selected using a selective primer with variable selective bases (‘CA’) that match selected sequences in the digested genome fragments and a non-selective primer. When properly amplified, the selected sequence is complementary to the selective bases. Final PCR . Primers matching the amplification primer and the selective primer which contain the full Proton adaptor sequence are used for amplification of the final library. Final on-target sequence . The final sequence contains the 5′ Proton adaptor sequence, an internal barcode, the NspI RE site, the target molecule, selective bases, the BfuCI RE site and the 3′ Proton adaptor sequence. It is possible to adapt the tGBS protocol for sequencing on an Illumina instrument by redesigning the ligation oligos and PCR primers.

    Journal: Nucleic Acids Research

    Article Title: tGBS® genotyping-by-sequencing enables reliable genotyping of heterozygous loci

    doi: 10.1093/nar/gkx853

    Figure Lengend Snippet: Diagram of tGBS. Digestion . Genomic DNA is digested with two REs: NspI leaves a 3′overhang and BfuCI leaves a 5′ overhang. Ligation . Two distinct oligos are ligated to the complementary 3′ and 5′ overhangs. The oligo matching the 3′ overhang contains a sample-specific internal barcode sequence for sample identification. The oligo matching the 5′ overhang is universal and present in every reaction for later amplification. Selective PCR . Target sites are selected using a selective primer with variable selective bases (‘CA’) that match selected sequences in the digested genome fragments and a non-selective primer. When properly amplified, the selected sequence is complementary to the selective bases. Final PCR . Primers matching the amplification primer and the selective primer which contain the full Proton adaptor sequence are used for amplification of the final library. Final on-target sequence . The final sequence contains the 5′ Proton adaptor sequence, an internal barcode, the NspI RE site, the target molecule, selective bases, the BfuCI RE site and the 3′ Proton adaptor sequence. It is possible to adapt the tGBS protocol for sequencing on an Illumina instrument by redesigning the ligation oligos and PCR primers.

    Article Snippet: tGBS procedure Approximately 120 ng of genomic DNA from each sample was digested with 100 units of NspI [New England Biolabs (Beverly, MA, USA), No. R0602L] and 400 units of BfuCI [New England Biolabs (Beverly, MA, USA), No. R0636L] in NEB CutSmart Buffer 4 in a 30-μl volume at 37°C for 1.5 h following the manufacturer’s protocol.

    Techniques: Ligation, Sequencing, Amplification, Polymerase Chain Reaction

    Nsp I site analysis of the WASP alternate promoter fragment. Lane 1; 700 ng 100 bp marker (Gibco BRL); lanes 1–3, 5, 9, and 12 homozygous Nsp I−; lanes 4 and 8 hemizygous Nsp I+; and lanes 6, 7, 10, and 11 heterozygous Nsp I+/ Nsp I− carrier females within this XPID pedigree.

    Journal: American Journal of Human Genetics

    Article Title: X-Linked Syndrome of Polyendocrinopathy, Immune Dysfunction, and Diarrhea Maps to Xp11.23-Xq13.3

    doi:

    Figure Lengend Snippet: Nsp I site analysis of the WASP alternate promoter fragment. Lane 1; 700 ng 100 bp marker (Gibco BRL); lanes 1–3, 5, 9, and 12 homozygous Nsp I−; lanes 4 and 8 hemizygous Nsp I+; and lanes 6, 7, 10, and 11 heterozygous Nsp I+/ Nsp I− carrier females within this XPID pedigree.

    Article Snippet: Digestion reactions consisted of ∼500 ng of the DNA fragment discussed above, 5 U Nsp I (NE Biolabs), 2 μl 10× digestion buffer, and H2 O double-distilled to 20 μl, incubated for 3 h prior to heat denaturation at 65°C for 20 min.

    Techniques: Marker

    Copy number variation at APOL1 locus. a. Sequence coverage analysis of samples from 1000 Genomes Project. Grey lines are used to depict coverage of each of 2,527 samples at genomic loci to which sequence reads map. Red lines indicate coverage for 8 samples with apparent duplication. The black line depicts median coverage for all samples showing elevated coverage over a region of this locus, including APOL1, suggesting duplication. Coordinates of the genome are plotted on the X-axis against normalized read depth on the Y-axis. Coordinates of APOL1 gene are chr22: 36,649,117–36,663,571 (hg19). b. Pictorial representation of the duplication event. An approximately 100kb region of chromosome 22, beginning from a region adjacent to APOL2, and involving all of APOL1 and part of MYH9 is duplicated (chr22:36,612,938–36,714,262, hg19). c. Gel electrophoresis (3% agarose) of the PCR product of the qualitative PCR assay used for detection of duplication. The PCR assay amplifies sequence across the junction between the duplicated segments, and results in a 291 bp size product, if present. Lane 1 corresponds to 100 bp ladder with size of each fragment indicated. Lanes 2 and 3 represent samples from individuals of European ancestry, who are negative for duplication. Lanes 4, 5 and 6 show a band of the expected size and indicate the presence of a duplication in these three unrelated African American individuals. Lanes 7, 8 and 9 show the absence of a PCR product in three other African American individuals. One of these three (lane 7) showed 3 copies using the Taqman copy number assay, indicating an insertional variant of different structure. Lane 10 is a non-template control reaction. d. Allelic discrimination digest assay: Gel electrophoresis of the PCR products obtained during allelic discrimination assay. Lane 1 shows a 100 bp ladder. Lane 2 (a, b and c) corresponds to sample NA 19701, Lane 3 (a, b and c) corresponds to sample NA 19372, Lane 4 (a, b and c) corresponds to sample NA 19700 and lane 5 corresponds to sample NA 19702. The band in the lanes 2a, 3a, 4a and 5a represent PCR products not subjected to any digestion (314 bp in size). Lanes 2b, 3b, 4b and 5b represent PCR products after digestion with HindIII. Lanes 2c, 3c, 4c and 5c represent PCR products after digestion with NspI. Since sample NA 19700 is homozygous for G0, there are only 2 bands in lane 4b and 1 band in lane 4c. Of note, with HindIII digestion, which cleaves the PCR product only if G0 allele is present, bands are expected to be 100 bp and 214 bp in size. With NspI, which cleaves the PCR product only in the presence of I384M G1 allele, the bands are expected to be 228 and 86 bp in size.

    Journal: PLoS ONE

    Article Title: Copy Number Variation at the APOL1 Locus

    doi: 10.1371/journal.pone.0125410

    Figure Lengend Snippet: Copy number variation at APOL1 locus. a. Sequence coverage analysis of samples from 1000 Genomes Project. Grey lines are used to depict coverage of each of 2,527 samples at genomic loci to which sequence reads map. Red lines indicate coverage for 8 samples with apparent duplication. The black line depicts median coverage for all samples showing elevated coverage over a region of this locus, including APOL1, suggesting duplication. Coordinates of the genome are plotted on the X-axis against normalized read depth on the Y-axis. Coordinates of APOL1 gene are chr22: 36,649,117–36,663,571 (hg19). b. Pictorial representation of the duplication event. An approximately 100kb region of chromosome 22, beginning from a region adjacent to APOL2, and involving all of APOL1 and part of MYH9 is duplicated (chr22:36,612,938–36,714,262, hg19). c. Gel electrophoresis (3% agarose) of the PCR product of the qualitative PCR assay used for detection of duplication. The PCR assay amplifies sequence across the junction between the duplicated segments, and results in a 291 bp size product, if present. Lane 1 corresponds to 100 bp ladder with size of each fragment indicated. Lanes 2 and 3 represent samples from individuals of European ancestry, who are negative for duplication. Lanes 4, 5 and 6 show a band of the expected size and indicate the presence of a duplication in these three unrelated African American individuals. Lanes 7, 8 and 9 show the absence of a PCR product in three other African American individuals. One of these three (lane 7) showed 3 copies using the Taqman copy number assay, indicating an insertional variant of different structure. Lane 10 is a non-template control reaction. d. Allelic discrimination digest assay: Gel electrophoresis of the PCR products obtained during allelic discrimination assay. Lane 1 shows a 100 bp ladder. Lane 2 (a, b and c) corresponds to sample NA 19701, Lane 3 (a, b and c) corresponds to sample NA 19372, Lane 4 (a, b and c) corresponds to sample NA 19700 and lane 5 corresponds to sample NA 19702. The band in the lanes 2a, 3a, 4a and 5a represent PCR products not subjected to any digestion (314 bp in size). Lanes 2b, 3b, 4b and 5b represent PCR products after digestion with HindIII. Lanes 2c, 3c, 4c and 5c represent PCR products after digestion with NspI. Since sample NA 19700 is homozygous for G0, there are only 2 bands in lane 4b and 1 band in lane 4c. Of note, with HindIII digestion, which cleaves the PCR product only if G0 allele is present, bands are expected to be 100 bp and 214 bp in size. With NspI, which cleaves the PCR product only in the presence of I384M G1 allele, the bands are expected to be 228 and 86 bp in size.

    Article Snippet: 10 μL of each PCR product was digested with HindIII or NspI (cleaving G0 at S342G and G1 at I384M, respectively) according to manufacturer’s directions (New England Biolabs) for 3–4 hrs at 37C.

    Techniques: Sequencing, Nucleic Acid Electrophoresis, Polymerase Chain Reaction, TaqMan Copy Number Assay, Variant Assay

    Heat map visualization of the genome-wide copy number results for (A) 30 primary and 6 recurrent central nervous system primitive neuroectodermal tumors (CNS PNETs) and (B) 6 primary and 2 recurrent pineoblastomas (PBs) using Affymetrix 100K and 500K

    Journal: Neuro-Oncology

    Article Title: Genome-wide molecular characterization of central nervous system primitive neuroectodermal tumor and pineoblastoma

    doi: 10.1093/neuonc/nor070

    Figure Lengend Snippet: Heat map visualization of the genome-wide copy number results for (A) 30 primary and 6 recurrent central nervous system primitive neuroectodermal tumors (CNS PNETs) and (B) 6 primary and 2 recurrent pineoblastomas (PBs) using Affymetrix 100K and 500K

    Article Snippet: DNA digestion, labeling, and hybridization were performed on the basis of the Affymetrix 100K or 500K SNP array protocols., In brief, 250 ng of DNA was digested (with either Xba1 or HindIII [New England Biolabs] for each 50K SNP array and NspI or StyI [New England Biolabs] for each 250K SNP array).

    Techniques: Genome Wide