end fragments pcr Search Results


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  • 99
    New England Biolabs dna fragments
    Dna Fragments, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 99/100, based on 11859 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/dna fragments/product/New England Biolabs
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    97
    Thermo Fisher bglii sali ended pcr fragment
    Bglii Sali Ended Pcr Fragment, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 97/100, based on 8 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Average 97 stars, based on 8 article reviews
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    90
    Eurofins bp cy5 end labeled fragment
    PHF13 binds to DNA and recombinant nucleosomes. ( A ) Schematic of the putative domain structure of PHF13. ( B ) Mononucleosome EMSA using recombinant mononucleosomes reconstituted on a 200 bp DNA fragment (20 nM) and increasing concentrations of GST (150 nM, 1200 nM), GST-ISWI (28 nM, 226 nM) and GST-PHF13 (70 nM, 140 nM, 280 nM, 560 nM). ( C ) Mononucleosome EMSA using recombinant mononucleosomes reconstituted on a 151 bp fragment (20 nM) and increasing concentrations (80, 160, 320 nM) of GST-1-100, GST-101-200, GST-201-300, GST-PHD and PWWP (positive control). ( D ) EMSA: 248 fM of P 32 radioactively labeled 248 bp DNA with increasing concentrations of GST (37.5, 150, 300 nM) GST-PHF13 (17, 34, 68, 102 and 135 nM) and GST-ΔPHD (18.5, 37, 74, 111, 148 nM) and ACF1 (10.5, 21, 31.5 and 42 nM). ACF1 served as a positive control. ( E ) EMSA: 10 nM <t>Cy5</t> labeled 40 bp DNA with increasing concentrations (40, 80, 160 nM) of GST, GST-1-100, GST-101-200, GST-201-300, GST-PHD and GST-PWWP (positive control). The input DNA and mononucleosomes are indicated in B–E . DOI: http://dx.doi.org/10.7554/eLife.10607.003
    Bp Cy5 End Labeled Fragment, supplied by Eurofins, used in various techniques. Bioz Stars score: 90/100, based on 8 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Average 90 stars, based on 8 article reviews
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    93
    Illumina Inc blunt ended dna fragments
    PHF13 binds to DNA and recombinant nucleosomes. ( A ) Schematic of the putative domain structure of PHF13. ( B ) Mononucleosome EMSA using recombinant mononucleosomes reconstituted on a 200 bp DNA fragment (20 nM) and increasing concentrations of GST (150 nM, 1200 nM), GST-ISWI (28 nM, 226 nM) and GST-PHF13 (70 nM, 140 nM, 280 nM, 560 nM). ( C ) Mononucleosome EMSA using recombinant mononucleosomes reconstituted on a 151 bp fragment (20 nM) and increasing concentrations (80, 160, 320 nM) of GST-1-100, GST-101-200, GST-201-300, GST-PHD and PWWP (positive control). ( D ) EMSA: 248 fM of P 32 radioactively labeled 248 bp DNA with increasing concentrations of GST (37.5, 150, 300 nM) GST-PHF13 (17, 34, 68, 102 and 135 nM) and GST-ΔPHD (18.5, 37, 74, 111, 148 nM) and ACF1 (10.5, 21, 31.5 and 42 nM). ACF1 served as a positive control. ( E ) EMSA: 10 nM <t>Cy5</t> labeled 40 bp DNA with increasing concentrations (40, 80, 160 nM) of GST, GST-1-100, GST-101-200, GST-201-300, GST-PHD and GST-PWWP (positive control). The input DNA and mononucleosomes are indicated in B–E . DOI: http://dx.doi.org/10.7554/eLife.10607.003
    Blunt Ended Dna Fragments, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 93/100, based on 37 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    99
    New England Biolabs end repair reaction buffer klenow fragment
    PHF13 binds to DNA and recombinant nucleosomes. ( A ) Schematic of the putative domain structure of PHF13. ( B ) Mononucleosome EMSA using recombinant mononucleosomes reconstituted on a 200 bp DNA fragment (20 nM) and increasing concentrations of GST (150 nM, 1200 nM), GST-ISWI (28 nM, 226 nM) and GST-PHF13 (70 nM, 140 nM, 280 nM, 560 nM). ( C ) Mononucleosome EMSA using recombinant mononucleosomes reconstituted on a 151 bp fragment (20 nM) and increasing concentrations (80, 160, 320 nM) of GST-1-100, GST-101-200, GST-201-300, GST-PHD and PWWP (positive control). ( D ) EMSA: 248 fM of P 32 radioactively labeled 248 bp DNA with increasing concentrations of GST (37.5, 150, 300 nM) GST-PHF13 (17, 34, 68, 102 and 135 nM) and GST-ΔPHD (18.5, 37, 74, 111, 148 nM) and ACF1 (10.5, 21, 31.5 and 42 nM). ACF1 served as a positive control. ( E ) EMSA: 10 nM <t>Cy5</t> labeled 40 bp DNA with increasing concentrations (40, 80, 160 nM) of GST, GST-1-100, GST-101-200, GST-201-300, GST-PHD and GST-PWWP (positive control). The input DNA and mononucleosomes are indicated in B–E . DOI: http://dx.doi.org/10.7554/eLife.10607.003
    End Repair Reaction Buffer Klenow Fragment, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 99/100, based on 14 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    99
    New England Biolabs nebnext end repair reaction buffer klenow fragment
    PHF13 binds to DNA and recombinant nucleosomes. ( A ) Schematic of the putative domain structure of PHF13. ( B ) Mononucleosome EMSA using recombinant mononucleosomes reconstituted on a 200 bp DNA fragment (20 nM) and increasing concentrations of GST (150 nM, 1200 nM), GST-ISWI (28 nM, 226 nM) and GST-PHF13 (70 nM, 140 nM, 280 nM, 560 nM). ( C ) Mononucleosome EMSA using recombinant mononucleosomes reconstituted on a 151 bp fragment (20 nM) and increasing concentrations (80, 160, 320 nM) of GST-1-100, GST-101-200, GST-201-300, GST-PHD and PWWP (positive control). ( D ) EMSA: 248 fM of P 32 radioactively labeled 248 bp DNA with increasing concentrations of GST (37.5, 150, 300 nM) GST-PHF13 (17, 34, 68, 102 and 135 nM) and GST-ΔPHD (18.5, 37, 74, 111, 148 nM) and ACF1 (10.5, 21, 31.5 and 42 nM). ACF1 served as a positive control. ( E ) EMSA: 10 nM <t>Cy5</t> labeled 40 bp DNA with increasing concentrations (40, 80, 160 nM) of GST, GST-1-100, GST-101-200, GST-201-300, GST-PHD and GST-PWWP (positive control). The input DNA and mononucleosomes are indicated in B–E . DOI: http://dx.doi.org/10.7554/eLife.10607.003
    Nebnext End Repair Reaction Buffer Klenow Fragment, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 99/100, based on 5 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    91
    Millipore pcr core kit
    PHF13 binds to DNA and recombinant nucleosomes. ( A ) Schematic of the putative domain structure of PHF13. ( B ) Mononucleosome EMSA using recombinant mononucleosomes reconstituted on a 200 bp DNA fragment (20 nM) and increasing concentrations of GST (150 nM, 1200 nM), GST-ISWI (28 nM, 226 nM) and GST-PHF13 (70 nM, 140 nM, 280 nM, 560 nM). ( C ) Mononucleosome EMSA using recombinant mononucleosomes reconstituted on a 151 bp fragment (20 nM) and increasing concentrations (80, 160, 320 nM) of GST-1-100, GST-101-200, GST-201-300, GST-PHD and PWWP (positive control). ( D ) EMSA: 248 fM of P 32 radioactively labeled 248 bp DNA with increasing concentrations of GST (37.5, 150, 300 nM) GST-PHF13 (17, 34, 68, 102 and 135 nM) and GST-ΔPHD (18.5, 37, 74, 111, 148 nM) and ACF1 (10.5, 21, 31.5 and 42 nM). ACF1 served as a positive control. ( E ) EMSA: 10 nM <t>Cy5</t> labeled 40 bp DNA with increasing concentrations (40, 80, 160 nM) of GST, GST-1-100, GST-101-200, GST-201-300, GST-PHD and GST-PWWP (positive control). The input DNA and mononucleosomes are indicated in B–E . DOI: http://dx.doi.org/10.7554/eLife.10607.003
    Pcr Core Kit, supplied by Millipore, used in various techniques. Bioz Stars score: 91/100, based on 32 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Qiagen qiaquick pcr purification kit
    PHF13 binds to DNA and recombinant nucleosomes. ( A ) Schematic of the putative domain structure of PHF13. ( B ) Mononucleosome EMSA using recombinant mononucleosomes reconstituted on a 200 bp DNA fragment (20 nM) and increasing concentrations of GST (150 nM, 1200 nM), GST-ISWI (28 nM, 226 nM) and GST-PHF13 (70 nM, 140 nM, 280 nM, 560 nM). ( C ) Mononucleosome EMSA using recombinant mononucleosomes reconstituted on a 151 bp fragment (20 nM) and increasing concentrations (80, 160, 320 nM) of GST-1-100, GST-101-200, GST-201-300, GST-PHD and PWWP (positive control). ( D ) EMSA: 248 fM of P 32 radioactively labeled 248 bp DNA with increasing concentrations of GST (37.5, 150, 300 nM) GST-PHF13 (17, 34, 68, 102 and 135 nM) and GST-ΔPHD (18.5, 37, 74, 111, 148 nM) and ACF1 (10.5, 21, 31.5 and 42 nM). ACF1 served as a positive control. ( E ) EMSA: 10 nM <t>Cy5</t> labeled 40 bp DNA with increasing concentrations (40, 80, 160 nM) of GST, GST-1-100, GST-101-200, GST-201-300, GST-PHD and GST-PWWP (positive control). The input DNA and mononucleosomes are indicated in B–E . DOI: http://dx.doi.org/10.7554/eLife.10607.003
    Qiaquick Pcr Purification Kit, supplied by Qiagen, used in various techniques. Bioz Stars score: 99/100, based on 137129 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    92
    Illumina Inc pcr primer cocktail
    PHF13 binds to DNA and recombinant nucleosomes. ( A ) Schematic of the putative domain structure of PHF13. ( B ) Mononucleosome EMSA using recombinant mononucleosomes reconstituted on a 200 bp DNA fragment (20 nM) and increasing concentrations of GST (150 nM, 1200 nM), GST-ISWI (28 nM, 226 nM) and GST-PHF13 (70 nM, 140 nM, 280 nM, 560 nM). ( C ) Mononucleosome EMSA using recombinant mononucleosomes reconstituted on a 151 bp fragment (20 nM) and increasing concentrations (80, 160, 320 nM) of GST-1-100, GST-101-200, GST-201-300, GST-PHD and PWWP (positive control). ( D ) EMSA: 248 fM of P 32 radioactively labeled 248 bp DNA with increasing concentrations of GST (37.5, 150, 300 nM) GST-PHF13 (17, 34, 68, 102 and 135 nM) and GST-ΔPHD (18.5, 37, 74, 111, 148 nM) and ACF1 (10.5, 21, 31.5 and 42 nM). ACF1 served as a positive control. ( E ) EMSA: 10 nM <t>Cy5</t> labeled 40 bp DNA with increasing concentrations (40, 80, 160 nM) of GST, GST-1-100, GST-101-200, GST-201-300, GST-PHD and GST-PWWP (positive control). The input DNA and mononucleosomes are indicated in B–E . DOI: http://dx.doi.org/10.7554/eLife.10607.003
    Pcr Primer Cocktail, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 92/100, based on 1051 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Qiagen pcr purification kit
    PHF13 binds to DNA and recombinant nucleosomes. ( A ) Schematic of the putative domain structure of PHF13. ( B ) Mononucleosome EMSA using recombinant mononucleosomes reconstituted on a 200 bp DNA fragment (20 nM) and increasing concentrations of GST (150 nM, 1200 nM), GST-ISWI (28 nM, 226 nM) and GST-PHF13 (70 nM, 140 nM, 280 nM, 560 nM). ( C ) Mononucleosome EMSA using recombinant mononucleosomes reconstituted on a 151 bp fragment (20 nM) and increasing concentrations (80, 160, 320 nM) of GST-1-100, GST-101-200, GST-201-300, GST-PHD and PWWP (positive control). ( D ) EMSA: 248 fM of P 32 radioactively labeled 248 bp DNA with increasing concentrations of GST (37.5, 150, 300 nM) GST-PHF13 (17, 34, 68, 102 and 135 nM) and GST-ΔPHD (18.5, 37, 74, 111, 148 nM) and ACF1 (10.5, 21, 31.5 and 42 nM). ACF1 served as a positive control. ( E ) EMSA: 10 nM <t>Cy5</t> labeled 40 bp DNA with increasing concentrations (40, 80, 160 nM) of GST, GST-1-100, GST-101-200, GST-201-300, GST-PHD and GST-PWWP (positive control). The input DNA and mononucleosomes are indicated in B–E . DOI: http://dx.doi.org/10.7554/eLife.10607.003
    Pcr Purification Kit, supplied by Qiagen, used in various techniques. Bioz Stars score: 99/100, based on 42554 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    89
    Illumina Inc paired end pcr primers
    PHF13 binds to DNA and recombinant nucleosomes. ( A ) Schematic of the putative domain structure of PHF13. ( B ) Mononucleosome EMSA using recombinant mononucleosomes reconstituted on a 200 bp DNA fragment (20 nM) and increasing concentrations of GST (150 nM, 1200 nM), GST-ISWI (28 nM, 226 nM) and GST-PHF13 (70 nM, 140 nM, 280 nM, 560 nM). ( C ) Mononucleosome EMSA using recombinant mononucleosomes reconstituted on a 151 bp fragment (20 nM) and increasing concentrations (80, 160, 320 nM) of GST-1-100, GST-101-200, GST-201-300, GST-PHD and PWWP (positive control). ( D ) EMSA: 248 fM of P 32 radioactively labeled 248 bp DNA with increasing concentrations of GST (37.5, 150, 300 nM) GST-PHF13 (17, 34, 68, 102 and 135 nM) and GST-ΔPHD (18.5, 37, 74, 111, 148 nM) and ACF1 (10.5, 21, 31.5 and 42 nM). ACF1 served as a positive control. ( E ) EMSA: 10 nM <t>Cy5</t> labeled 40 bp DNA with increasing concentrations (40, 80, 160 nM) of GST, GST-1-100, GST-101-200, GST-201-300, GST-PHD and GST-PWWP (positive control). The input DNA and mononucleosomes are indicated in B–E . DOI: http://dx.doi.org/10.7554/eLife.10607.003
    Paired End Pcr Primers, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 89/100, based on 150 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/paired end pcr primers/product/Illumina Inc
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    Thermo Fisher instaclone pcr cloning kit
    PHF13 binds to DNA and recombinant nucleosomes. ( A ) Schematic of the putative domain structure of PHF13. ( B ) Mononucleosome EMSA using recombinant mononucleosomes reconstituted on a 200 bp DNA fragment (20 nM) and increasing concentrations of GST (150 nM, 1200 nM), GST-ISWI (28 nM, 226 nM) and GST-PHF13 (70 nM, 140 nM, 280 nM, 560 nM). ( C ) Mononucleosome EMSA using recombinant mononucleosomes reconstituted on a 151 bp fragment (20 nM) and increasing concentrations (80, 160, 320 nM) of GST-1-100, GST-101-200, GST-201-300, GST-PHD and PWWP (positive control). ( D ) EMSA: 248 fM of P 32 radioactively labeled 248 bp DNA with increasing concentrations of GST (37.5, 150, 300 nM) GST-PHF13 (17, 34, 68, 102 and 135 nM) and GST-ΔPHD (18.5, 37, 74, 111, 148 nM) and ACF1 (10.5, 21, 31.5 and 42 nM). ACF1 served as a positive control. ( E ) EMSA: 10 nM <t>Cy5</t> labeled 40 bp DNA with increasing concentrations (40, 80, 160 nM) of GST, GST-1-100, GST-101-200, GST-201-300, GST-PHD and GST-PWWP (positive control). The input DNA and mononucleosomes are indicated in B–E . DOI: http://dx.doi.org/10.7554/eLife.10607.003
    Instaclone Pcr Cloning Kit, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 98/100, based on 2664 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/instaclone pcr cloning kit/product/Thermo Fisher
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    92
    Addgene inc pcr reaction
    PHF13 binds to DNA and recombinant nucleosomes. ( A ) Schematic of the putative domain structure of PHF13. ( B ) Mononucleosome EMSA using recombinant mononucleosomes reconstituted on a 200 bp DNA fragment (20 nM) and increasing concentrations of GST (150 nM, 1200 nM), GST-ISWI (28 nM, 226 nM) and GST-PHF13 (70 nM, 140 nM, 280 nM, 560 nM). ( C ) Mononucleosome EMSA using recombinant mononucleosomes reconstituted on a 151 bp fragment (20 nM) and increasing concentrations (80, 160, 320 nM) of GST-1-100, GST-101-200, GST-201-300, GST-PHD and PWWP (positive control). ( D ) EMSA: 248 fM of P 32 radioactively labeled 248 bp DNA with increasing concentrations of GST (37.5, 150, 300 nM) GST-PHF13 (17, 34, 68, 102 and 135 nM) and GST-ΔPHD (18.5, 37, 74, 111, 148 nM) and ACF1 (10.5, 21, 31.5 and 42 nM). ACF1 served as a positive control. ( E ) EMSA: 10 nM <t>Cy5</t> labeled 40 bp DNA with increasing concentrations (40, 80, 160 nM) of GST, GST-1-100, GST-101-200, GST-201-300, GST-PHD and GST-PWWP (positive control). The input DNA and mononucleosomes are indicated in B–E . DOI: http://dx.doi.org/10.7554/eLife.10607.003
    Pcr Reaction, supplied by Addgene inc, used in various techniques. Bioz Stars score: 92/100, based on 150 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/pcr reaction/product/Addgene inc
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    93
    Bioo Scientific nextflex pcr free barcodes adapters
    PHF13 binds to DNA and recombinant nucleosomes. ( A ) Schematic of the putative domain structure of PHF13. ( B ) Mononucleosome EMSA using recombinant mononucleosomes reconstituted on a 200 bp DNA fragment (20 nM) and increasing concentrations of GST (150 nM, 1200 nM), GST-ISWI (28 nM, 226 nM) and GST-PHF13 (70 nM, 140 nM, 280 nM, 560 nM). ( C ) Mononucleosome EMSA using recombinant mononucleosomes reconstituted on a 151 bp fragment (20 nM) and increasing concentrations (80, 160, 320 nM) of GST-1-100, GST-101-200, GST-201-300, GST-PHD and PWWP (positive control). ( D ) EMSA: 248 fM of P 32 radioactively labeled 248 bp DNA with increasing concentrations of GST (37.5, 150, 300 nM) GST-PHF13 (17, 34, 68, 102 and 135 nM) and GST-ΔPHD (18.5, 37, 74, 111, 148 nM) and ACF1 (10.5, 21, 31.5 and 42 nM). ACF1 served as a positive control. ( E ) EMSA: 10 nM <t>Cy5</t> labeled 40 bp DNA with increasing concentrations (40, 80, 160 nM) of GST, GST-1-100, GST-101-200, GST-201-300, GST-PHD and GST-PWWP (positive control). The input DNA and mononucleosomes are indicated in B–E . DOI: http://dx.doi.org/10.7554/eLife.10607.003
    Nextflex Pcr Free Barcodes Adapters, supplied by Bioo Scientific, used in various techniques. Bioz Stars score: 93/100, based on 61 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    93
    Roche emulsion pcr
    PHF13 binds to DNA and recombinant nucleosomes. ( A ) Schematic of the putative domain structure of PHF13. ( B ) Mononucleosome EMSA using recombinant mononucleosomes reconstituted on a 200 bp DNA fragment (20 nM) and increasing concentrations of GST (150 nM, 1200 nM), GST-ISWI (28 nM, 226 nM) and GST-PHF13 (70 nM, 140 nM, 280 nM, 560 nM). ( C ) Mononucleosome EMSA using recombinant mononucleosomes reconstituted on a 151 bp fragment (20 nM) and increasing concentrations (80, 160, 320 nM) of GST-1-100, GST-101-200, GST-201-300, GST-PHD and PWWP (positive control). ( D ) EMSA: 248 fM of P 32 radioactively labeled 248 bp DNA with increasing concentrations of GST (37.5, 150, 300 nM) GST-PHF13 (17, 34, 68, 102 and 135 nM) and GST-ΔPHD (18.5, 37, 74, 111, 148 nM) and ACF1 (10.5, 21, 31.5 and 42 nM). ACF1 served as a positive control. ( E ) EMSA: 10 nM <t>Cy5</t> labeled 40 bp DNA with increasing concentrations (40, 80, 160 nM) of GST, GST-1-100, GST-101-200, GST-201-300, GST-PHD and GST-PWWP (positive control). The input DNA and mononucleosomes are indicated in B–E . DOI: http://dx.doi.org/10.7554/eLife.10607.003
    Emulsion Pcr, supplied by Roche, used in various techniques. Bioz Stars score: 93/100, based on 3899 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    92
    Illumina Inc pcr fragments
    Structural comparison of SERV from different Vero sublines and different <t>SVL.</t> (a) Validation of Vero cell-specific SVL by genomic <t>PCR.</t> Nested PCR experiments were performed using genomic DNA from the three Vero cell sublines and AGM PBMC as described in the Methods. A schematic picture of nested PCR with the primer-binding sites is shown at the top. SVL IDs are specified under the panel. The black arrowheads indicate SERV-integrated PCR fragments, and the white arrowheads SERV-unintegrated PCR fragments. The arrow indicates an unknown band. Note that the sizes of smaller bands are consistent with the sizes expected for SERV-unintegrated genome sequences. 1st rd: 1st round PCR, 2nd rd: 2nd round PCR. All gel images shown include full-length without grouping. (b) A comparative analysis among twelve Vero cell-specific SVL regions. The colored bars show that the homologous region had at least 80% identity between the consensus SERV sequence found in the Vero 0111 genome (GenBank: AB935214) and each SERV region. Genetic features including mutations for respective SVLs are shown on the right side. Identity with 5′-LTR and 3′-LTR sequences of the AB935214 reference in the BLASTN homology search are: 94.3 and 73.4% for SVL13c, 72.0 and 99.0% for SVL15f, 95.4 and 74.0% for SVL22e, and 94.7 and 74.2% for SVL26, respectively. Due to the high identities with both LTRs of the reference, both 5′- and 3′-LTR regions of these SVL integrations are depicted in the panel, although the SVLs with no intervening sequence (13c, 15f, 22e, and 26) are the solo LTRs as highlighted on the right side of the panel.
    Pcr Fragments, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 92/100, based on 486 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/pcr fragments/product/Illumina Inc
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    95
    Millipore readymix taq pcr mix
    Structural comparison of SERV from different Vero sublines and different <t>SVL.</t> (a) Validation of Vero cell-specific SVL by genomic <t>PCR.</t> Nested PCR experiments were performed using genomic DNA from the three Vero cell sublines and AGM PBMC as described in the Methods. A schematic picture of nested PCR with the primer-binding sites is shown at the top. SVL IDs are specified under the panel. The black arrowheads indicate SERV-integrated PCR fragments, and the white arrowheads SERV-unintegrated PCR fragments. The arrow indicates an unknown band. Note that the sizes of smaller bands are consistent with the sizes expected for SERV-unintegrated genome sequences. 1st rd: 1st round PCR, 2nd rd: 2nd round PCR. All gel images shown include full-length without grouping. (b) A comparative analysis among twelve Vero cell-specific SVL regions. The colored bars show that the homologous region had at least 80% identity between the consensus SERV sequence found in the Vero 0111 genome (GenBank: AB935214) and each SERV region. Genetic features including mutations for respective SVLs are shown on the right side. Identity with 5′-LTR and 3′-LTR sequences of the AB935214 reference in the BLASTN homology search are: 94.3 and 73.4% for SVL13c, 72.0 and 99.0% for SVL15f, 95.4 and 74.0% for SVL22e, and 94.7 and 74.2% for SVL26, respectively. Due to the high identities with both LTRs of the reference, both 5′- and 3′-LTR regions of these SVL integrations are depicted in the panel, although the SVLs with no intervening sequence (13c, 15f, 22e, and 26) are the solo LTRs as highlighted on the right side of the panel.
    Readymix Taq Pcr Mix, supplied by Millipore, used in various techniques. Bioz Stars score: 95/100, based on 75 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    99
    Thermo Fisher blunt ended ecori ecorib fragment
    Structural comparison of SERV from different Vero sublines and different <t>SVL.</t> (a) Validation of Vero cell-specific SVL by genomic <t>PCR.</t> Nested PCR experiments were performed using genomic DNA from the three Vero cell sublines and AGM PBMC as described in the Methods. A schematic picture of nested PCR with the primer-binding sites is shown at the top. SVL IDs are specified under the panel. The black arrowheads indicate SERV-integrated PCR fragments, and the white arrowheads SERV-unintegrated PCR fragments. The arrow indicates an unknown band. Note that the sizes of smaller bands are consistent with the sizes expected for SERV-unintegrated genome sequences. 1st rd: 1st round PCR, 2nd rd: 2nd round PCR. All gel images shown include full-length without grouping. (b) A comparative analysis among twelve Vero cell-specific SVL regions. The colored bars show that the homologous region had at least 80% identity between the consensus SERV sequence found in the Vero 0111 genome (GenBank: AB935214) and each SERV region. Genetic features including mutations for respective SVLs are shown on the right side. Identity with 5′-LTR and 3′-LTR sequences of the AB935214 reference in the BLASTN homology search are: 94.3 and 73.4% for SVL13c, 72.0 and 99.0% for SVL15f, 95.4 and 74.0% for SVL22e, and 94.7 and 74.2% for SVL26, respectively. Due to the high identities with both LTRs of the reference, both 5′- and 3′-LTR regions of these SVL integrations are depicted in the panel, although the SVLs with no intervening sequence (13c, 15f, 22e, and 26) are the solo LTRs as highlighted on the right side of the panel.
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    Structural comparison of SERV from different Vero sublines and different <t>SVL.</t> (a) Validation of Vero cell-specific SVL by genomic <t>PCR.</t> Nested PCR experiments were performed using genomic DNA from the three Vero cell sublines and AGM PBMC as described in the Methods. A schematic picture of nested PCR with the primer-binding sites is shown at the top. SVL IDs are specified under the panel. The black arrowheads indicate SERV-integrated PCR fragments, and the white arrowheads SERV-unintegrated PCR fragments. The arrow indicates an unknown band. Note that the sizes of smaller bands are consistent with the sizes expected for SERV-unintegrated genome sequences. 1st rd: 1st round PCR, 2nd rd: 2nd round PCR. All gel images shown include full-length without grouping. (b) A comparative analysis among twelve Vero cell-specific SVL regions. The colored bars show that the homologous region had at least 80% identity between the consensus SERV sequence found in the Vero 0111 genome (GenBank: AB935214) and each SERV region. Genetic features including mutations for respective SVLs are shown on the right side. Identity with 5′-LTR and 3′-LTR sequences of the AB935214 reference in the BLASTN homology search are: 94.3 and 73.4% for SVL13c, 72.0 and 99.0% for SVL15f, 95.4 and 74.0% for SVL22e, and 94.7 and 74.2% for SVL26, respectively. Due to the high identities with both LTRs of the reference, both 5′- and 3′-LTR regions of these SVL integrations are depicted in the panel, although the SVLs with no intervening sequence (13c, 15f, 22e, and 26) are the solo LTRs as highlighted on the right side of the panel.
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    Structural comparison of SERV from different Vero sublines and different <t>SVL.</t> (a) Validation of Vero cell-specific SVL by genomic <t>PCR.</t> Nested PCR experiments were performed using genomic DNA from the three Vero cell sublines and AGM PBMC as described in the Methods. A schematic picture of nested PCR with the primer-binding sites is shown at the top. SVL IDs are specified under the panel. The black arrowheads indicate SERV-integrated PCR fragments, and the white arrowheads SERV-unintegrated PCR fragments. The arrow indicates an unknown band. Note that the sizes of smaller bands are consistent with the sizes expected for SERV-unintegrated genome sequences. 1st rd: 1st round PCR, 2nd rd: 2nd round PCR. All gel images shown include full-length without grouping. (b) A comparative analysis among twelve Vero cell-specific SVL regions. The colored bars show that the homologous region had at least 80% identity between the consensus SERV sequence found in the Vero 0111 genome (GenBank: AB935214) and each SERV region. Genetic features including mutations for respective SVLs are shown on the right side. Identity with 5′-LTR and 3′-LTR sequences of the AB935214 reference in the BLASTN homology search are: 94.3 and 73.4% for SVL13c, 72.0 and 99.0% for SVL15f, 95.4 and 74.0% for SVL22e, and 94.7 and 74.2% for SVL26, respectively. Due to the high identities with both LTRs of the reference, both 5′- and 3′-LTR regions of these SVL integrations are depicted in the panel, although the SVLs with no intervening sequence (13c, 15f, 22e, and 26) are the solo LTRs as highlighted on the right side of the panel.
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    TaKaRa race pcr
    Structural comparison of SERV from different Vero sublines and different <t>SVL.</t> (a) Validation of Vero cell-specific SVL by genomic <t>PCR.</t> Nested PCR experiments were performed using genomic DNA from the three Vero cell sublines and AGM PBMC as described in the Methods. A schematic picture of nested PCR with the primer-binding sites is shown at the top. SVL IDs are specified under the panel. The black arrowheads indicate SERV-integrated PCR fragments, and the white arrowheads SERV-unintegrated PCR fragments. The arrow indicates an unknown band. Note that the sizes of smaller bands are consistent with the sizes expected for SERV-unintegrated genome sequences. 1st rd: 1st round PCR, 2nd rd: 2nd round PCR. All gel images shown include full-length without grouping. (b) A comparative analysis among twelve Vero cell-specific SVL regions. The colored bars show that the homologous region had at least 80% identity between the consensus SERV sequence found in the Vero 0111 genome (GenBank: AB935214) and each SERV region. Genetic features including mutations for respective SVLs are shown on the right side. Identity with 5′-LTR and 3′-LTR sequences of the AB935214 reference in the BLASTN homology search are: 94.3 and 73.4% for SVL13c, 72.0 and 99.0% for SVL15f, 95.4 and 74.0% for SVL22e, and 94.7 and 74.2% for SVL26, respectively. Due to the high identities with both LTRs of the reference, both 5′- and 3′-LTR regions of these SVL integrations are depicted in the panel, although the SVLs with no intervening sequence (13c, 15f, 22e, and 26) are the solo LTRs as highlighted on the right side of the panel.
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    Structural comparison of SERV from different Vero sublines and different <t>SVL.</t> (a) Validation of Vero cell-specific SVL by genomic <t>PCR.</t> Nested PCR experiments were performed using genomic DNA from the three Vero cell sublines and AGM PBMC as described in the Methods. A schematic picture of nested PCR with the primer-binding sites is shown at the top. SVL IDs are specified under the panel. The black arrowheads indicate SERV-integrated PCR fragments, and the white arrowheads SERV-unintegrated PCR fragments. The arrow indicates an unknown band. Note that the sizes of smaller bands are consistent with the sizes expected for SERV-unintegrated genome sequences. 1st rd: 1st round PCR, 2nd rd: 2nd round PCR. All gel images shown include full-length without grouping. (b) A comparative analysis among twelve Vero cell-specific SVL regions. The colored bars show that the homologous region had at least 80% identity between the consensus SERV sequence found in the Vero 0111 genome (GenBank: AB935214) and each SERV region. Genetic features including mutations for respective SVLs are shown on the right side. Identity with 5′-LTR and 3′-LTR sequences of the AB935214 reference in the BLASTN homology search are: 94.3 and 73.4% for SVL13c, 72.0 and 99.0% for SVL15f, 95.4 and 74.0% for SVL22e, and 94.7 and 74.2% for SVL26, respectively. Due to the high identities with both LTRs of the reference, both 5′- and 3′-LTR regions of these SVL integrations are depicted in the panel, although the SVLs with no intervening sequence (13c, 15f, 22e, and 26) are the solo LTRs as highlighted on the right side of the panel.
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    Structural comparison of SERV from different Vero sublines and different <t>SVL.</t> (a) Validation of Vero cell-specific SVL by genomic <t>PCR.</t> Nested PCR experiments were performed using genomic DNA from the three Vero cell sublines and AGM PBMC as described in the Methods. A schematic picture of nested PCR with the primer-binding sites is shown at the top. SVL IDs are specified under the panel. The black arrowheads indicate SERV-integrated PCR fragments, and the white arrowheads SERV-unintegrated PCR fragments. The arrow indicates an unknown band. Note that the sizes of smaller bands are consistent with the sizes expected for SERV-unintegrated genome sequences. 1st rd: 1st round PCR, 2nd rd: 2nd round PCR. All gel images shown include full-length without grouping. (b) A comparative analysis among twelve Vero cell-specific SVL regions. The colored bars show that the homologous region had at least 80% identity between the consensus SERV sequence found in the Vero 0111 genome (GenBank: AB935214) and each SERV region. Genetic features including mutations for respective SVLs are shown on the right side. Identity with 5′-LTR and 3′-LTR sequences of the AB935214 reference in the BLASTN homology search are: 94.3 and 73.4% for SVL13c, 72.0 and 99.0% for SVL15f, 95.4 and 74.0% for SVL22e, and 94.7 and 74.2% for SVL26, respectively. Due to the high identities with both LTRs of the reference, both 5′- and 3′-LTR regions of these SVL integrations are depicted in the panel, although the SVLs with no intervening sequence (13c, 15f, 22e, and 26) are the solo LTRs as highlighted on the right side of the panel.
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    Structural comparison of SERV from different Vero sublines and different <t>SVL.</t> (a) Validation of Vero cell-specific SVL by genomic <t>PCR.</t> Nested PCR experiments were performed using genomic DNA from the three Vero cell sublines and AGM PBMC as described in the Methods. A schematic picture of nested PCR with the primer-binding sites is shown at the top. SVL IDs are specified under the panel. The black arrowheads indicate SERV-integrated PCR fragments, and the white arrowheads SERV-unintegrated PCR fragments. The arrow indicates an unknown band. Note that the sizes of smaller bands are consistent with the sizes expected for SERV-unintegrated genome sequences. 1st rd: 1st round PCR, 2nd rd: 2nd round PCR. All gel images shown include full-length without grouping. (b) A comparative analysis among twelve Vero cell-specific SVL regions. The colored bars show that the homologous region had at least 80% identity between the consensus SERV sequence found in the Vero 0111 genome (GenBank: AB935214) and each SERV region. Genetic features including mutations for respective SVLs are shown on the right side. Identity with 5′-LTR and 3′-LTR sequences of the AB935214 reference in the BLASTN homology search are: 94.3 and 73.4% for SVL13c, 72.0 and 99.0% for SVL15f, 95.4 and 74.0% for SVL22e, and 94.7 and 74.2% for SVL26, respectively. Due to the high identities with both LTRs of the reference, both 5′- and 3′-LTR regions of these SVL integrations are depicted in the panel, although the SVLs with no intervening sequence (13c, 15f, 22e, and 26) are the solo LTRs as highlighted on the right side of the panel.
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    Structural comparison of SERV from different Vero sublines and different <t>SVL.</t> (a) Validation of Vero cell-specific SVL by genomic <t>PCR.</t> Nested PCR experiments were performed using genomic DNA from the three Vero cell sublines and AGM PBMC as described in the Methods. A schematic picture of nested PCR with the primer-binding sites is shown at the top. SVL IDs are specified under the panel. The black arrowheads indicate SERV-integrated PCR fragments, and the white arrowheads SERV-unintegrated PCR fragments. The arrow indicates an unknown band. Note that the sizes of smaller bands are consistent with the sizes expected for SERV-unintegrated genome sequences. 1st rd: 1st round PCR, 2nd rd: 2nd round PCR. All gel images shown include full-length without grouping. (b) A comparative analysis among twelve Vero cell-specific SVL regions. The colored bars show that the homologous region had at least 80% identity between the consensus SERV sequence found in the Vero 0111 genome (GenBank: AB935214) and each SERV region. Genetic features including mutations for respective SVLs are shown on the right side. Identity with 5′-LTR and 3′-LTR sequences of the AB935214 reference in the BLASTN homology search are: 94.3 and 73.4% for SVL13c, 72.0 and 99.0% for SVL15f, 95.4 and 74.0% for SVL22e, and 94.7 and 74.2% for SVL26, respectively. Due to the high identities with both LTRs of the reference, both 5′- and 3′-LTR regions of these SVL integrations are depicted in the panel, although the SVLs with no intervening sequence (13c, 15f, 22e, and 26) are the solo LTRs as highlighted on the right side of the panel.
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    Image Search Results


    PHF13 binds to DNA and recombinant nucleosomes. ( A ) Schematic of the putative domain structure of PHF13. ( B ) Mononucleosome EMSA using recombinant mononucleosomes reconstituted on a 200 bp DNA fragment (20 nM) and increasing concentrations of GST (150 nM, 1200 nM), GST-ISWI (28 nM, 226 nM) and GST-PHF13 (70 nM, 140 nM, 280 nM, 560 nM). ( C ) Mononucleosome EMSA using recombinant mononucleosomes reconstituted on a 151 bp fragment (20 nM) and increasing concentrations (80, 160, 320 nM) of GST-1-100, GST-101-200, GST-201-300, GST-PHD and PWWP (positive control). ( D ) EMSA: 248 fM of P 32 radioactively labeled 248 bp DNA with increasing concentrations of GST (37.5, 150, 300 nM) GST-PHF13 (17, 34, 68, 102 and 135 nM) and GST-ΔPHD (18.5, 37, 74, 111, 148 nM) and ACF1 (10.5, 21, 31.5 and 42 nM). ACF1 served as a positive control. ( E ) EMSA: 10 nM Cy5 labeled 40 bp DNA with increasing concentrations (40, 80, 160 nM) of GST, GST-1-100, GST-101-200, GST-201-300, GST-PHD and GST-PWWP (positive control). The input DNA and mononucleosomes are indicated in B–E . DOI: http://dx.doi.org/10.7554/eLife.10607.003

    Journal: eLife

    Article Title: PHF13 is a molecular reader and transcriptional co-regulator of H3K4me2/3

    doi: 10.7554/eLife.10607

    Figure Lengend Snippet: PHF13 binds to DNA and recombinant nucleosomes. ( A ) Schematic of the putative domain structure of PHF13. ( B ) Mononucleosome EMSA using recombinant mononucleosomes reconstituted on a 200 bp DNA fragment (20 nM) and increasing concentrations of GST (150 nM, 1200 nM), GST-ISWI (28 nM, 226 nM) and GST-PHF13 (70 nM, 140 nM, 280 nM, 560 nM). ( C ) Mononucleosome EMSA using recombinant mononucleosomes reconstituted on a 151 bp fragment (20 nM) and increasing concentrations (80, 160, 320 nM) of GST-1-100, GST-101-200, GST-201-300, GST-PHD and PWWP (positive control). ( D ) EMSA: 248 fM of P 32 radioactively labeled 248 bp DNA with increasing concentrations of GST (37.5, 150, 300 nM) GST-PHF13 (17, 34, 68, 102 and 135 nM) and GST-ΔPHD (18.5, 37, 74, 111, 148 nM) and ACF1 (10.5, 21, 31.5 and 42 nM). ACF1 served as a positive control. ( E ) EMSA: 10 nM Cy5 labeled 40 bp DNA with increasing concentrations (40, 80, 160 nM) of GST, GST-1-100, GST-101-200, GST-201-300, GST-PHD and GST-PWWP (positive control). The input DNA and mononucleosomes are indicated in B–E . DOI: http://dx.doi.org/10.7554/eLife.10607.003

    Article Snippet: EMSA and nucleosome shift assays DNA EMSA reactions were performed using a 248 bp DNA fragment radio-labeled by PCR, as previously described ( ) or a 40 bp Cy5-end labeled fragment (5'-Cy5-CCTGGAGAATCCCGGTGCCGAGGCCGCTCAATTGGTCGTA-3'; Eurofins MWG).

    Techniques: Recombinant, Positive Control, Labeling

    Structural comparison of SERV from different Vero sublines and different SVL. (a) Validation of Vero cell-specific SVL by genomic PCR. Nested PCR experiments were performed using genomic DNA from the three Vero cell sublines and AGM PBMC as described in the Methods. A schematic picture of nested PCR with the primer-binding sites is shown at the top. SVL IDs are specified under the panel. The black arrowheads indicate SERV-integrated PCR fragments, and the white arrowheads SERV-unintegrated PCR fragments. The arrow indicates an unknown band. Note that the sizes of smaller bands are consistent with the sizes expected for SERV-unintegrated genome sequences. 1st rd: 1st round PCR, 2nd rd: 2nd round PCR. All gel images shown include full-length without grouping. (b) A comparative analysis among twelve Vero cell-specific SVL regions. The colored bars show that the homologous region had at least 80% identity between the consensus SERV sequence found in the Vero 0111 genome (GenBank: AB935214) and each SERV region. Genetic features including mutations for respective SVLs are shown on the right side. Identity with 5′-LTR and 3′-LTR sequences of the AB935214 reference in the BLASTN homology search are: 94.3 and 73.4% for SVL13c, 72.0 and 99.0% for SVL15f, 95.4 and 74.0% for SVL22e, and 94.7 and 74.2% for SVL26, respectively. Due to the high identities with both LTRs of the reference, both 5′- and 3′-LTR regions of these SVL integrations are depicted in the panel, although the SVLs with no intervening sequence (13c, 15f, 22e, and 26) are the solo LTRs as highlighted on the right side of the panel.

    Journal: Scientific Reports

    Article Title: Novel endogenous simian retroviral integrations in Vero cells: implications for quality control of a human vaccine cell substrate

    doi: 10.1038/s41598-017-18934-2

    Figure Lengend Snippet: Structural comparison of SERV from different Vero sublines and different SVL. (a) Validation of Vero cell-specific SVL by genomic PCR. Nested PCR experiments were performed using genomic DNA from the three Vero cell sublines and AGM PBMC as described in the Methods. A schematic picture of nested PCR with the primer-binding sites is shown at the top. SVL IDs are specified under the panel. The black arrowheads indicate SERV-integrated PCR fragments, and the white arrowheads SERV-unintegrated PCR fragments. The arrow indicates an unknown band. Note that the sizes of smaller bands are consistent with the sizes expected for SERV-unintegrated genome sequences. 1st rd: 1st round PCR, 2nd rd: 2nd round PCR. All gel images shown include full-length without grouping. (b) A comparative analysis among twelve Vero cell-specific SVL regions. The colored bars show that the homologous region had at least 80% identity between the consensus SERV sequence found in the Vero 0111 genome (GenBank: AB935214) and each SERV region. Genetic features including mutations for respective SVLs are shown on the right side. Identity with 5′-LTR and 3′-LTR sequences of the AB935214 reference in the BLASTN homology search are: 94.3 and 73.4% for SVL13c, 72.0 and 99.0% for SVL15f, 95.4 and 74.0% for SVL22e, and 94.7 and 74.2% for SVL26, respectively. Due to the high identities with both LTRs of the reference, both 5′- and 3′-LTR regions of these SVL integrations are depicted in the panel, although the SVLs with no intervening sequence (13c, 15f, 22e, and 26) are the solo LTRs as highlighted on the right side of the panel.

    Article Snippet: Paired-end libraries of the PCR fragments from SVL integrations (SVL ID; 3b, 4e, 6a, 10b, 20d, 21b, 21e, and 27b) were prepared for MiniSeq sequencing using the Nextera XT DNA Library Preparation Kit (Illumina) and sequenced with the MiniSeq Mid Output Kit (Illumina).

    Techniques: Polymerase Chain Reaction, Nested PCR, Binding Assay, Sequencing