snp rs28416813 Search Results


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    ATCC hela cells
    The alleles at rs28416813-rev and rs71356849-rev affect NFκB binding in EMSA. A) The distal region nucleotide sequence of the IL28B promoter is shown along with the two SNP positions (italics, underlined) and the non-consensus NFκB-binding site (underlined) identified by Osterlund et al. (2007) [21] . The start codon is underlined and is in italics. The numbering is with respect to TSS. Note that the naming is on the opposite DNA strand to that used for naming SNPs in dbSNP, hence the SNPs have a “rev” notation. B) The oligonucleotides used for EMSA and pull-down experiment. The consensus NF-κB binding sequence is underlined in the competitor oligonucleotide. C) Autoradiograph of EMSA carried out from nuclear extracts prepared from <t>HeLa</t> cells after stimulation for NF-κB signaling and overexpression. Increasing concentrations of the extracts (0, 2, 4 and 6 µl respectively in lanes 1–4 and 5–8) were used at a constant concentration of the probe. The arrow indicates a likely NF-κB dimer. The fold-change in binding at the band positions (arrow) for the two probes G-T and C-C are shown below each lane. D) EMSA with recombinant p50. Arrow indicates the shifted probe position due to binding with p50. C-oligo- competitor oligo. E) Pull-down assay and western blot. The streptavidin-bound biotin labeled probes were incubated with nuclear extracts from HEK293T cells <t>overexpressed</t> with activated NF-κB. The bound proteins were probed with antibodies against p65 (Abcam).
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    Thermo Fisher applied biosystems thermocycler
    The alleles at rs28416813-rev and rs71356849-rev affect NFκB binding in EMSA. A) The distal region nucleotide sequence of the IL28B promoter is shown along with the two SNP positions (italics, underlined) and the non-consensus NFκB-binding site (underlined) identified by Osterlund et al. (2007) [21] . The start codon is underlined and is in italics. The numbering is with respect to TSS. Note that the naming is on the opposite DNA strand to that used for naming SNPs in dbSNP, hence the SNPs have a “rev” notation. B) The oligonucleotides used for EMSA and pull-down experiment. The consensus NF-κB binding sequence is underlined in the competitor oligonucleotide. C) Autoradiograph of EMSA carried out from nuclear extracts prepared from <t>HeLa</t> cells after stimulation for NF-κB signaling and overexpression. Increasing concentrations of the extracts (0, 2, 4 and 6 µl respectively in lanes 1–4 and 5–8) were used at a constant concentration of the probe. The arrow indicates a likely NF-κB dimer. The fold-change in binding at the band positions (arrow) for the two probes G-T and C-C are shown below each lane. D) EMSA with recombinant p50. Arrow indicates the shifted probe position due to binding with p50. C-oligo- competitor oligo. E) Pull-down assay and western blot. The streptavidin-bound biotin labeled probes were incubated with nuclear extracts from HEK293T cells <t>overexpressed</t> with activated NF-κB. The bound proteins were probed with antibodies against p65 (Abcam).
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    85
    Thermo Fisher custom assays on demand
    The alleles at rs28416813-rev and rs71356849-rev affect NFκB binding in EMSA. A) The distal region nucleotide sequence of the IL28B promoter is shown along with the two SNP positions (italics, underlined) and the non-consensus NFκB-binding site (underlined) identified by Osterlund et al. (2007) [21] . The start codon is underlined and is in italics. The numbering is with respect to TSS. Note that the naming is on the opposite DNA strand to that used for naming SNPs in dbSNP, hence the SNPs have a “rev” notation. B) The oligonucleotides used for EMSA and pull-down experiment. The consensus NF-κB binding sequence is underlined in the competitor oligonucleotide. C) Autoradiograph of EMSA carried out from nuclear extracts prepared from <t>HeLa</t> cells after stimulation for NF-κB signaling and overexpression. Increasing concentrations of the extracts (0, 2, 4 and 6 µl respectively in lanes 1–4 and 5–8) were used at a constant concentration of the probe. The arrow indicates a likely NF-κB dimer. The fold-change in binding at the band positions (arrow) for the two probes G-T and C-C are shown below each lane. D) EMSA with recombinant p50. Arrow indicates the shifted probe position due to binding with p50. C-oligo- competitor oligo. E) Pull-down assay and western blot. The streptavidin-bound biotin labeled probes were incubated with nuclear extracts from HEK293T cells <t>overexpressed</t> with activated NF-κB. The bound proteins were probed with antibodies against p65 (Abcam).
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    99
    Qiagen long range pcr kit
    rs28416813 is in LD with rs12979860. A) EtBr-stained gel of the <t>PCR</t> products that were amplified from the IL28A and IL28B promoters that included the <t>SNP</t> rs28416813 by the same set of primers because of high homology between the two genes at their 5′ ends [35] . The ∼2 kb fragment specific to IL28B was excised from gels purified and subject to DNA sequencing to genotype the SNP rs28416813. 1 and 2 are samples from two different patients. Ma-DNA Mol. Wt. marker. B) Pairwise LD plots for the three SNPs genotyped from a cohort of patients with chronic HCV infections in India (n = 20) (top) and LD plots for the SNPs from genotype data of a CEU population available from the 1000 genomes project database (bottom). The plots were generated using LDHeatmap [20] .
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    91
    Thermo Fisher taqman allelic discrimination
    Primer pair optimization for the pre-amplification step. Because discordant results were obtained by genotyping and resequencing, several primer combinations were tested for the pre-amplification step preceding the genotyping. The arrows show the different PCR products amplified for the pre-amplification step. Arrows with dashed lines indicate discordant results for a given SNP (heterozygous by resequencing and homozygous by the <t>TaqMan</t> assay), whereas arrows with solid lines indicate concordant results for a given SNP (heterozygous by both resequencing and TaqMan assay). A primer combination containing a forward primer located upstream of position g.-520G yielded discordant results in up to 19.5% of the individuals (for rs8103142). The red triangles show the location of the four genotyped <t>SNPs.</t>
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    Thermo Fisher tag snp rs12979860
    Primer pair optimization for the pre-amplification step. Because discordant results were obtained by genotyping and resequencing, several primer combinations were tested for the pre-amplification step preceding the genotyping. The arrows show the different PCR products amplified for the pre-amplification step. Arrows with dashed lines indicate discordant results for a given SNP (heterozygous by resequencing and homozygous by the <t>TaqMan</t> assay), whereas arrows with solid lines indicate concordant results for a given SNP (heterozygous by both resequencing and TaqMan assay). A primer combination containing a forward primer located upstream of position g.-520G yielded discordant results in up to 19.5% of the individuals (for rs8103142). The red triangles show the location of the four genotyped <t>SNPs.</t>
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    Thermo Fisher snp ifnl3 c 11710096 10
    Primer pair optimization for the pre-amplification step. Because discordant results were obtained by genotyping and resequencing, several primer combinations were tested for the pre-amplification step preceding the genotyping. The arrows show the different PCR products amplified for the pre-amplification step. Arrows with dashed lines indicate discordant results for a given SNP (heterozygous by resequencing and homozygous by the <t>TaqMan</t> assay), whereas arrows with solid lines indicate concordant results for a given SNP (heterozygous by both resequencing and TaqMan assay). A primer combination containing a forward primer located upstream of position g.-520G yielded discordant results in up to 19.5% of the individuals (for rs8103142). The red triangles show the location of the four genotyped <t>SNPs.</t>
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    91
    Sequenom primer design software
    Primer pair optimization for the pre-amplification step. Because discordant results were obtained by genotyping and resequencing, several primer combinations were tested for the pre-amplification step preceding the genotyping. The arrows show the different PCR products amplified for the pre-amplification step. Arrows with dashed lines indicate discordant results for a given SNP (heterozygous by resequencing and homozygous by the <t>TaqMan</t> assay), whereas arrows with solid lines indicate concordant results for a given SNP (heterozygous by both resequencing and TaqMan assay). A primer combination containing a forward primer located upstream of position g.-520G yielded discordant results in up to 19.5% of the individuals (for rs8103142). The red triangles show the location of the four genotyped <t>SNPs.</t>
    Primer Design Software, supplied by Sequenom, used in various techniques. Bioz Stars score: 91/100, based on 16 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Thermo Fisher assays on demand
    Primer pair optimization for the pre-amplification step. Because discordant results were obtained by genotyping and resequencing, several primer combinations were tested for the pre-amplification step preceding the genotyping. The arrows show the different PCR products amplified for the pre-amplification step. Arrows with dashed lines indicate discordant results for a given SNP (heterozygous by resequencing and homozygous by the <t>TaqMan</t> assay), whereas arrows with solid lines indicate concordant results for a given SNP (heterozygous by both resequencing and TaqMan assay). A primer combination containing a forward primer located upstream of position g.-520G yielded discordant results in up to 19.5% of the individuals (for rs8103142). The red triangles show the location of the four genotyped <t>SNPs.</t>
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    Thermo Fisher custom taqman assay
    Primer pair optimization for the pre-amplification step. Because discordant results were obtained by genotyping and resequencing, several primer combinations were tested for the pre-amplification step preceding the genotyping. The arrows show the different PCR products amplified for the pre-amplification step. Arrows with dashed lines indicate discordant results for a given <t>SNP</t> (heterozygous by resequencing and homozygous by the <t>TaqMan</t> assay), whereas arrows with solid lines indicate concordant results for a given SNP (heterozygous by both resequencing and TaqMan assay). A primer combination containing a forward primer located upstream of position g.-520G yielded discordant results in up to 19.5% of the individuals (for rs8103142). The red triangles show the location of the four genotyped SNPs.
    Custom Taqman Assay, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 99/100, based on 351 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Image Search Results


    The alleles at rs28416813-rev and rs71356849-rev affect NFκB binding in EMSA. A) The distal region nucleotide sequence of the IL28B promoter is shown along with the two SNP positions (italics, underlined) and the non-consensus NFκB-binding site (underlined) identified by Osterlund et al. (2007) [21] . The start codon is underlined and is in italics. The numbering is with respect to TSS. Note that the naming is on the opposite DNA strand to that used for naming SNPs in dbSNP, hence the SNPs have a “rev” notation. B) The oligonucleotides used for EMSA and pull-down experiment. The consensus NF-κB binding sequence is underlined in the competitor oligonucleotide. C) Autoradiograph of EMSA carried out from nuclear extracts prepared from HeLa cells after stimulation for NF-κB signaling and overexpression. Increasing concentrations of the extracts (0, 2, 4 and 6 µl respectively in lanes 1–4 and 5–8) were used at a constant concentration of the probe. The arrow indicates a likely NF-κB dimer. The fold-change in binding at the band positions (arrow) for the two probes G-T and C-C are shown below each lane. D) EMSA with recombinant p50. Arrow indicates the shifted probe position due to binding with p50. C-oligo- competitor oligo. E) Pull-down assay and western blot. The streptavidin-bound biotin labeled probes were incubated with nuclear extracts from HEK293T cells overexpressed with activated NF-κB. The bound proteins were probed with antibodies against p65 (Abcam).

    Journal: PLoS ONE

    Article Title: A Single Nucleotide Polymorphism Associated with Hepatitis C Virus Infections Located in the Distal Region of the IL28B Promoter Influences NF-?B-Mediated Gene Transcription

    doi: 10.1371/journal.pone.0075495

    Figure Lengend Snippet: The alleles at rs28416813-rev and rs71356849-rev affect NFκB binding in EMSA. A) The distal region nucleotide sequence of the IL28B promoter is shown along with the two SNP positions (italics, underlined) and the non-consensus NFκB-binding site (underlined) identified by Osterlund et al. (2007) [21] . The start codon is underlined and is in italics. The numbering is with respect to TSS. Note that the naming is on the opposite DNA strand to that used for naming SNPs in dbSNP, hence the SNPs have a “rev” notation. B) The oligonucleotides used for EMSA and pull-down experiment. The consensus NF-κB binding sequence is underlined in the competitor oligonucleotide. C) Autoradiograph of EMSA carried out from nuclear extracts prepared from HeLa cells after stimulation for NF-κB signaling and overexpression. Increasing concentrations of the extracts (0, 2, 4 and 6 µl respectively in lanes 1–4 and 5–8) were used at a constant concentration of the probe. The arrow indicates a likely NF-κB dimer. The fold-change in binding at the band positions (arrow) for the two probes G-T and C-C are shown below each lane. D) EMSA with recombinant p50. Arrow indicates the shifted probe position due to binding with p50. C-oligo- competitor oligo. E) Pull-down assay and western blot. The streptavidin-bound biotin labeled probes were incubated with nuclear extracts from HEK293T cells overexpressed with activated NF-κB. The bound proteins were probed with antibodies against p65 (Abcam).

    Article Snippet: Nuclear extracts (NE) prepared from HeLa cells containing overexpressed and activated NF-κB were used in the assay at increasing concentrations. shows that both the radiolabeled probes G-T and C-C bound to nuclear proteins and at least two distinct bands were visible at the three concentrations of the NE used.

    Techniques: Binding Assay, Sequencing, Autoradiography, Over Expression, Concentration Assay, Recombinant, Pull Down Assay, Western Blot, Labeling, Incubation

    rs28416813 is in LD with rs12979860. A) EtBr-stained gel of the PCR products that were amplified from the IL28A and IL28B promoters that included the SNP rs28416813 by the same set of primers because of high homology between the two genes at their 5′ ends [35] . The ∼2 kb fragment specific to IL28B was excised from gels purified and subject to DNA sequencing to genotype the SNP rs28416813. 1 and 2 are samples from two different patients. Ma-DNA Mol. Wt. marker. B) Pairwise LD plots for the three SNPs genotyped from a cohort of patients with chronic HCV infections in India (n = 20) (top) and LD plots for the SNPs from genotype data of a CEU population available from the 1000 genomes project database (bottom). The plots were generated using LDHeatmap [20] .

    Journal: PLoS ONE

    Article Title: A Single Nucleotide Polymorphism Associated with Hepatitis C Virus Infections Located in the Distal Region of the IL28B Promoter Influences NF-?B-Mediated Gene Transcription

    doi: 10.1371/journal.pone.0075495

    Figure Lengend Snippet: rs28416813 is in LD with rs12979860. A) EtBr-stained gel of the PCR products that were amplified from the IL28A and IL28B promoters that included the SNP rs28416813 by the same set of primers because of high homology between the two genes at their 5′ ends [35] . The ∼2 kb fragment specific to IL28B was excised from gels purified and subject to DNA sequencing to genotype the SNP rs28416813. 1 and 2 are samples from two different patients. Ma-DNA Mol. Wt. marker. B) Pairwise LD plots for the three SNPs genotyped from a cohort of patients with chronic HCV infections in India (n = 20) (top) and LD plots for the SNPs from genotype data of a CEU population available from the 1000 genomes project database (bottom). The plots were generated using LDHeatmap [20] .

    Article Snippet: The SNP rs28416813 was amplified with the Long-range PCR kit from Qiagen by using: Forward primer 1.9kbrs813KpnIFor2 (5′GATATCGGTACCTGCATTGTACGACCCTCCAAC-3′) and reverse primer: 1.9kbil28b12aaHIIIREV1 (5′GATATCAAGCTTCAGCACTGCGGCCATCAG-3′).

    Techniques: Staining, Polymerase Chain Reaction, Amplification, Purification, DNA Sequencing, Marker, Generated

    Primer pair optimization for the pre-amplification step. Because discordant results were obtained by genotyping and resequencing, several primer combinations were tested for the pre-amplification step preceding the genotyping. The arrows show the different PCR products amplified for the pre-amplification step. Arrows with dashed lines indicate discordant results for a given SNP (heterozygous by resequencing and homozygous by the TaqMan assay), whereas arrows with solid lines indicate concordant results for a given SNP (heterozygous by both resequencing and TaqMan assay). A primer combination containing a forward primer located upstream of position g.-520G yielded discordant results in up to 19.5% of the individuals (for rs8103142). The red triangles show the location of the four genotyped SNPs.

    Journal: Hepatology (Baltimore, Md.)

    Article Title: Estimating the Net Contribution of Interleukin-28B Variation to Spontaneous Hepatitis C Virus Clearance

    doi: 10.1002/hep.24263

    Figure Lengend Snippet: Primer pair optimization for the pre-amplification step. Because discordant results were obtained by genotyping and resequencing, several primer combinations were tested for the pre-amplification step preceding the genotyping. The arrows show the different PCR products amplified for the pre-amplification step. Arrows with dashed lines indicate discordant results for a given SNP (heterozygous by resequencing and homozygous by the TaqMan assay), whereas arrows with solid lines indicate concordant results for a given SNP (heterozygous by both resequencing and TaqMan assay). A primer combination containing a forward primer located upstream of position g.-520G yielded discordant results in up to 19.5% of the individuals (for rs8103142). The red triangles show the location of the four genotyped SNPs.

    Article Snippet: On the basis of our previous work on the resequencing of the IL-28B locus, the genotyping of four candidate causal SNPs (rs4803219, rs28416813, rs8103142, and rs4803217) was performed by TaqMan allelic discrimination (ABI-Prism 7000 SDS software, Applied Biosystems) with custom Assays-on-Demand products from Applied Biosystems; this was preceded by a pre-amplification step.

    Techniques: Amplification, Polymerase Chain Reaction, TaqMan Assay

    Primer pair optimization for the pre-amplification step. Because discordant results were obtained by genotyping and resequencing, several primer combinations were tested for the pre-amplification step preceding the genotyping. The arrows show the different PCR products amplified for the pre-amplification step. Arrows with dashed lines indicate discordant results for a given SNP (heterozygous by resequencing and homozygous by the TaqMan assay), whereas arrows with solid lines indicate concordant results for a given SNP (heterozygous by both resequencing and TaqMan assay). A primer combination containing a forward primer located upstream of position g.-520G yielded discordant results in up to 19.5% of the individuals (for rs8103142). The red triangles show the location of the four genotyped SNPs.

    Journal: Hepatology (Baltimore, Md.)

    Article Title: Estimating the Net Contribution of Interleukin-28B Variation to Spontaneous Hepatitis C Virus Clearance

    doi: 10.1002/hep.24263

    Figure Lengend Snippet: Primer pair optimization for the pre-amplification step. Because discordant results were obtained by genotyping and resequencing, several primer combinations were tested for the pre-amplification step preceding the genotyping. The arrows show the different PCR products amplified for the pre-amplification step. Arrows with dashed lines indicate discordant results for a given SNP (heterozygous by resequencing and homozygous by the TaqMan assay), whereas arrows with solid lines indicate concordant results for a given SNP (heterozygous by both resequencing and TaqMan assay). A primer combination containing a forward primer located upstream of position g.-520G yielded discordant results in up to 19.5% of the individuals (for rs8103142). The red triangles show the location of the four genotyped SNPs.

    Article Snippet: In addition, the tag SNP rs12979860 was assessed with a custom TaqMan assay designed by Ge et al., and the tag SNP rs8099917 was genotyped with an Assays-on-Demand product provided by Applied Biosystems (C__11710096_10).

    Techniques: Amplification, Polymerase Chain Reaction, TaqMan Assay