pcr amplicon sequencing Search Results


premium pcr sequencing  (Plasmidsaurus)
99
Plasmidsaurus premium pcr sequencing
A , Schematic of 3 methods reading out reporter expression (2 methods of library preparation and 2 <t>sequencing</t> methods) from an upstream MPRA assay used to identify confounders. “BC only prep” is the typical readout, uses a splice junction-spanning <t>PCR</t> primer to enrich for spliced transcripts, and only reads out the barcode sequence. “Full transcript prep” uses a template switch oligo to add a primer handle to the 5’-end of the cDNA allowing for amplification of the full-length transcript, which can then be sequenced at just the 5’-end or the whole transcript with long-read sequencing. B , Schematic of all potential intended and confounding RNA species produced from an upstream reporter design, along with which are both captured in the reporter transcript preparation method (“captured”) and distinguishable from the method of sequencing readout (“distinguish”) by the 3 methods of library preparation and sequencing. For example, the BC only prep “captures” properly spliced transcripts whether they initiate within the promoter or enhancer but cannot distinguish the two types of transcripts because only the BC is sequenced. Alternatively spliced (“alt-spliced”) or unspliced transcripts are rarer but undistinguishable even by full transcript prep with 5’-end sequencing. These species can cause even more unexpected, pathological confounding. C, Expression of each E-P pair of the 21E x 26P library in the upstream integrated design where each E-P pair is colored by whether the 5’-end mapping short reads predominantly (>90%) align to the intended promoter TSS (red if yes and black if no). Gray points indicate E-P pairs with too few 5’ TSO PCR reads were detected and/or alignment quality. E-P pairs with the “seq14780” enhancer are outlined in blue. D , Expression of E-P pairs in the 21E x 26P library by the BC only short read readout (y-axis) versus the 5’-end mapping short read readout (x-axis). Off-diagonal E-P pairs are due to additional, alternatively spliced reporter transcripts illustrated in B that confound expression from the reporter but are undetectable by typical BC only readouts. Examples of a few of the alternatively spliced (“alt-spliced”) transcripts that led to the discrepancy were identified through long read sequencing of the full-length transcripts rather than 5’-end short read sequencing only. E , Enhancer effects and enhancer activity computed from upstream integrated assay after filtering out enhancer-promoter pairs confounded by upstream enhancer transcripts. FTH1, MRPS23, JUNB, and LYL1 promoter sequences are genomic in origin, and the endogenous gene is highly expressed. Similar to and . F , Histogram the fraction of 5’-end mapping short reads aligning to the promoter for the larger 203E x 78P and 21E x 500P library promoters after first removing seq14780 from the set of enhancer-promoter pairs to analyze. A cutoff of 90% (red dashed line) was used for determining promoter suitable for enhancer activation quantification. G, Promoter activity versus apparent enhancer activity of the enhancer sequences in the 203E library. Promoter activity is quantified by the expression of each enhancer with negative control sequence (noTFBS) in the promoter position (BC only short reads). “Apparent” enhancer activity is the average log2FC relative to basal promoter activity of the enhancer over the set of promoters preliminarily kept after filtering in panel F , which could still be confounded by autonomous promoter activity of some enhancer sequences. Enhancer sequences “chr3:128134842-128135106-enhancer” and its reverse complement “chr3:128134842-128135106-enhancer_rc” are labeled only with genome coordinates for brevity. Generally, stronger enhancers had more promoter activity. Enhancers with promoter activity greater than -1 were filtered out before further E-P activation quantification.
Premium Pcr Sequencing, supplied by Plasmidsaurus, used in various techniques. Bioz Stars score: 99/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
https://www.bioz.com/product/pcr+amplicon+sequencing/Premium+PCR/bio_rxiv__64898__2026__06__25__734173-362-11-9
Average 99 stars, based on 1 article reviews
premium pcr sequencing - by Bioz Stars, 2026-10
99/100 stars
  Buy from Supplier
sanger sequencing of pcr amplicons  (Source BioScience plc)
90
Source BioScience plc sanger sequencing of pcr amplicons
A , Schematic of 3 methods reading out reporter expression (2 methods of library preparation and 2 <t>sequencing</t> methods) from an upstream MPRA assay used to identify confounders. “BC only prep” is the typical readout, uses a splice junction-spanning <t>PCR</t> primer to enrich for spliced transcripts, and only reads out the barcode sequence. “Full transcript prep” uses a template switch oligo to add a primer handle to the 5’-end of the cDNA allowing for amplification of the full-length transcript, which can then be sequenced at just the 5’-end or the whole transcript with long-read sequencing. B , Schematic of all potential intended and confounding RNA species produced from an upstream reporter design, along with which are both captured in the reporter transcript preparation method (“captured”) and distinguishable from the method of sequencing readout (“distinguish”) by the 3 methods of library preparation and sequencing. For example, the BC only prep “captures” properly spliced transcripts whether they initiate within the promoter or enhancer but cannot distinguish the two types of transcripts because only the BC is sequenced. Alternatively spliced (“alt-spliced”) or unspliced transcripts are rarer but undistinguishable even by full transcript prep with 5’-end sequencing. These species can cause even more unexpected, pathological confounding. C, Expression of each E-P pair of the 21E x 26P library in the upstream integrated design where each E-P pair is colored by whether the 5’-end mapping short reads predominantly (>90%) align to the intended promoter TSS (red if yes and black if no). Gray points indicate E-P pairs with too few 5’ TSO PCR reads were detected and/or alignment quality. E-P pairs with the “seq14780” enhancer are outlined in blue. D , Expression of E-P pairs in the 21E x 26P library by the BC only short read readout (y-axis) versus the 5’-end mapping short read readout (x-axis). Off-diagonal E-P pairs are due to additional, alternatively spliced reporter transcripts illustrated in B that confound expression from the reporter but are undetectable by typical BC only readouts. Examples of a few of the alternatively spliced (“alt-spliced”) transcripts that led to the discrepancy were identified through long read sequencing of the full-length transcripts rather than 5’-end short read sequencing only. E , Enhancer effects and enhancer activity computed from upstream integrated assay after filtering out enhancer-promoter pairs confounded by upstream enhancer transcripts. FTH1, MRPS23, JUNB, and LYL1 promoter sequences are genomic in origin, and the endogenous gene is highly expressed. Similar to and . F , Histogram the fraction of 5’-end mapping short reads aligning to the promoter for the larger 203E x 78P and 21E x 500P library promoters after first removing seq14780 from the set of enhancer-promoter pairs to analyze. A cutoff of 90% (red dashed line) was used for determining promoter suitable for enhancer activation quantification. G, Promoter activity versus apparent enhancer activity of the enhancer sequences in the 203E library. Promoter activity is quantified by the expression of each enhancer with negative control sequence (noTFBS) in the promoter position (BC only short reads). “Apparent” enhancer activity is the average log2FC relative to basal promoter activity of the enhancer over the set of promoters preliminarily kept after filtering in panel F , which could still be confounded by autonomous promoter activity of some enhancer sequences. Enhancer sequences “chr3:128134842-128135106-enhancer” and its reverse complement “chr3:128134842-128135106-enhancer_rc” are labeled only with genome coordinates for brevity. Generally, stronger enhancers had more promoter activity. Enhancers with promoter activity greater than -1 were filtered out before further E-P activation quantification.
Sanger Sequencing Of Pcr Amplicons, supplied by Source BioScience plc, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
https://www.bioz.com/product/pcr+amplicon+sequencing/sanger+sequencing+of+pcr+amplicons/pmc05016526-63-14-18
Average 90 stars, based on 1 article reviews
sanger sequencing of pcr amplicons - by Bioz Stars, 2026-10
90/100 stars
  Buy from Supplier
pcr amplicon sequencing on the oxford-nanopore minion platform  (Oxford Nanopore)
90
Oxford Nanopore pcr amplicon sequencing on the oxford-nanopore minion platform
A , Schematic of 3 methods reading out reporter expression (2 methods of library preparation and 2 <t>sequencing</t> methods) from an upstream MPRA assay used to identify confounders. “BC only prep” is the typical readout, uses a splice junction-spanning <t>PCR</t> primer to enrich for spliced transcripts, and only reads out the barcode sequence. “Full transcript prep” uses a template switch oligo to add a primer handle to the 5’-end of the cDNA allowing for amplification of the full-length transcript, which can then be sequenced at just the 5’-end or the whole transcript with long-read sequencing. B , Schematic of all potential intended and confounding RNA species produced from an upstream reporter design, along with which are both captured in the reporter transcript preparation method (“captured”) and distinguishable from the method of sequencing readout (“distinguish”) by the 3 methods of library preparation and sequencing. For example, the BC only prep “captures” properly spliced transcripts whether they initiate within the promoter or enhancer but cannot distinguish the two types of transcripts because only the BC is sequenced. Alternatively spliced (“alt-spliced”) or unspliced transcripts are rarer but undistinguishable even by full transcript prep with 5’-end sequencing. These species can cause even more unexpected, pathological confounding. C, Expression of each E-P pair of the 21E x 26P library in the upstream integrated design where each E-P pair is colored by whether the 5’-end mapping short reads predominantly (>90%) align to the intended promoter TSS (red if yes and black if no). Gray points indicate E-P pairs with too few 5’ TSO PCR reads were detected and/or alignment quality. E-P pairs with the “seq14780” enhancer are outlined in blue. D , Expression of E-P pairs in the 21E x 26P library by the BC only short read readout (y-axis) versus the 5’-end mapping short read readout (x-axis). Off-diagonal E-P pairs are due to additional, alternatively spliced reporter transcripts illustrated in B that confound expression from the reporter but are undetectable by typical BC only readouts. Examples of a few of the alternatively spliced (“alt-spliced”) transcripts that led to the discrepancy were identified through long read sequencing of the full-length transcripts rather than 5’-end short read sequencing only. E , Enhancer effects and enhancer activity computed from upstream integrated assay after filtering out enhancer-promoter pairs confounded by upstream enhancer transcripts. FTH1, MRPS23, JUNB, and LYL1 promoter sequences are genomic in origin, and the endogenous gene is highly expressed. Similar to and . F , Histogram the fraction of 5’-end mapping short reads aligning to the promoter for the larger 203E x 78P and 21E x 500P library promoters after first removing seq14780 from the set of enhancer-promoter pairs to analyze. A cutoff of 90% (red dashed line) was used for determining promoter suitable for enhancer activation quantification. G, Promoter activity versus apparent enhancer activity of the enhancer sequences in the 203E library. Promoter activity is quantified by the expression of each enhancer with negative control sequence (noTFBS) in the promoter position (BC only short reads). “Apparent” enhancer activity is the average log2FC relative to basal promoter activity of the enhancer over the set of promoters preliminarily kept after filtering in panel F , which could still be confounded by autonomous promoter activity of some enhancer sequences. Enhancer sequences “chr3:128134842-128135106-enhancer” and its reverse complement “chr3:128134842-128135106-enhancer_rc” are labeled only with genome coordinates for brevity. Generally, stronger enhancers had more promoter activity. Enhancers with promoter activity greater than -1 were filtered out before further E-P activation quantification.
Pcr Amplicon Sequencing On The Oxford Nanopore Minion Platform, supplied by Oxford Nanopore, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
https://www.bioz.com/product/pcr+amplicon+sequencing/oxford+nanopore+technology+based+rep+pcr+amplicon+sequencing/pm33262485-1116-6-6
Average 90 stars, based on 1 article reviews
pcr amplicon sequencing on the oxford-nanopore minion platform - by Bioz Stars, 2026-10
90/100 stars
  Buy from Supplier
pcr amplicons sequencing  (LGC Genomics GmbH)
90
LGC Genomics GmbH pcr amplicons sequencing
A , Schematic of 3 methods reading out reporter expression (2 methods of library preparation and 2 <t>sequencing</t> methods) from an upstream MPRA assay used to identify confounders. “BC only prep” is the typical readout, uses a splice junction-spanning <t>PCR</t> primer to enrich for spliced transcripts, and only reads out the barcode sequence. “Full transcript prep” uses a template switch oligo to add a primer handle to the 5’-end of the cDNA allowing for amplification of the full-length transcript, which can then be sequenced at just the 5’-end or the whole transcript with long-read sequencing. B , Schematic of all potential intended and confounding RNA species produced from an upstream reporter design, along with which are both captured in the reporter transcript preparation method (“captured”) and distinguishable from the method of sequencing readout (“distinguish”) by the 3 methods of library preparation and sequencing. For example, the BC only prep “captures” properly spliced transcripts whether they initiate within the promoter or enhancer but cannot distinguish the two types of transcripts because only the BC is sequenced. Alternatively spliced (“alt-spliced”) or unspliced transcripts are rarer but undistinguishable even by full transcript prep with 5’-end sequencing. These species can cause even more unexpected, pathological confounding. C, Expression of each E-P pair of the 21E x 26P library in the upstream integrated design where each E-P pair is colored by whether the 5’-end mapping short reads predominantly (>90%) align to the intended promoter TSS (red if yes and black if no). Gray points indicate E-P pairs with too few 5’ TSO PCR reads were detected and/or alignment quality. E-P pairs with the “seq14780” enhancer are outlined in blue. D , Expression of E-P pairs in the 21E x 26P library by the BC only short read readout (y-axis) versus the 5’-end mapping short read readout (x-axis). Off-diagonal E-P pairs are due to additional, alternatively spliced reporter transcripts illustrated in B that confound expression from the reporter but are undetectable by typical BC only readouts. Examples of a few of the alternatively spliced (“alt-spliced”) transcripts that led to the discrepancy were identified through long read sequencing of the full-length transcripts rather than 5’-end short read sequencing only. E , Enhancer effects and enhancer activity computed from upstream integrated assay after filtering out enhancer-promoter pairs confounded by upstream enhancer transcripts. FTH1, MRPS23, JUNB, and LYL1 promoter sequences are genomic in origin, and the endogenous gene is highly expressed. Similar to and . F , Histogram the fraction of 5’-end mapping short reads aligning to the promoter for the larger 203E x 78P and 21E x 500P library promoters after first removing seq14780 from the set of enhancer-promoter pairs to analyze. A cutoff of 90% (red dashed line) was used for determining promoter suitable for enhancer activation quantification. G, Promoter activity versus apparent enhancer activity of the enhancer sequences in the 203E library. Promoter activity is quantified by the expression of each enhancer with negative control sequence (noTFBS) in the promoter position (BC only short reads). “Apparent” enhancer activity is the average log2FC relative to basal promoter activity of the enhancer over the set of promoters preliminarily kept after filtering in panel F , which could still be confounded by autonomous promoter activity of some enhancer sequences. Enhancer sequences “chr3:128134842-128135106-enhancer” and its reverse complement “chr3:128134842-128135106-enhancer_rc” are labeled only with genome coordinates for brevity. Generally, stronger enhancers had more promoter activity. Enhancers with promoter activity greater than -1 were filtered out before further E-P activation quantification.
Pcr Amplicons Sequencing, supplied by LGC Genomics GmbH, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
https://www.bioz.com/product/pcr+amplicon+sequencing/pcr+amplicons+sequencing/pmc05764319-65-0-5
Average 90 stars, based on 1 article reviews
pcr amplicons sequencing - by Bioz Stars, 2026-10
90/100 stars
  Buy from Supplier
pcr amplicons sequencing  (GATC Biotech)
90
GATC Biotech pcr amplicons sequencing
A , Schematic of 3 methods reading out reporter expression (2 methods of library preparation and 2 <t>sequencing</t> methods) from an upstream MPRA assay used to identify confounders. “BC only prep” is the typical readout, uses a splice junction-spanning <t>PCR</t> primer to enrich for spliced transcripts, and only reads out the barcode sequence. “Full transcript prep” uses a template switch oligo to add a primer handle to the 5’-end of the cDNA allowing for amplification of the full-length transcript, which can then be sequenced at just the 5’-end or the whole transcript with long-read sequencing. B , Schematic of all potential intended and confounding RNA species produced from an upstream reporter design, along with which are both captured in the reporter transcript preparation method (“captured”) and distinguishable from the method of sequencing readout (“distinguish”) by the 3 methods of library preparation and sequencing. For example, the BC only prep “captures” properly spliced transcripts whether they initiate within the promoter or enhancer but cannot distinguish the two types of transcripts because only the BC is sequenced. Alternatively spliced (“alt-spliced”) or unspliced transcripts are rarer but undistinguishable even by full transcript prep with 5’-end sequencing. These species can cause even more unexpected, pathological confounding. C, Expression of each E-P pair of the 21E x 26P library in the upstream integrated design where each E-P pair is colored by whether the 5’-end mapping short reads predominantly (>90%) align to the intended promoter TSS (red if yes and black if no). Gray points indicate E-P pairs with too few 5’ TSO PCR reads were detected and/or alignment quality. E-P pairs with the “seq14780” enhancer are outlined in blue. D , Expression of E-P pairs in the 21E x 26P library by the BC only short read readout (y-axis) versus the 5’-end mapping short read readout (x-axis). Off-diagonal E-P pairs are due to additional, alternatively spliced reporter transcripts illustrated in B that confound expression from the reporter but are undetectable by typical BC only readouts. Examples of a few of the alternatively spliced (“alt-spliced”) transcripts that led to the discrepancy were identified through long read sequencing of the full-length transcripts rather than 5’-end short read sequencing only. E , Enhancer effects and enhancer activity computed from upstream integrated assay after filtering out enhancer-promoter pairs confounded by upstream enhancer transcripts. FTH1, MRPS23, JUNB, and LYL1 promoter sequences are genomic in origin, and the endogenous gene is highly expressed. Similar to and . F , Histogram the fraction of 5’-end mapping short reads aligning to the promoter for the larger 203E x 78P and 21E x 500P library promoters after first removing seq14780 from the set of enhancer-promoter pairs to analyze. A cutoff of 90% (red dashed line) was used for determining promoter suitable for enhancer activation quantification. G, Promoter activity versus apparent enhancer activity of the enhancer sequences in the 203E library. Promoter activity is quantified by the expression of each enhancer with negative control sequence (noTFBS) in the promoter position (BC only short reads). “Apparent” enhancer activity is the average log2FC relative to basal promoter activity of the enhancer over the set of promoters preliminarily kept after filtering in panel F , which could still be confounded by autonomous promoter activity of some enhancer sequences. Enhancer sequences “chr3:128134842-128135106-enhancer” and its reverse complement “chr3:128134842-128135106-enhancer_rc” are labeled only with genome coordinates for brevity. Generally, stronger enhancers had more promoter activity. Enhancers with promoter activity greater than -1 were filtered out before further E-P activation quantification.
Pcr Amplicons Sequencing, supplied by GATC Biotech, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
https://www.bioz.com/product/pcr+amplicon+sequencing/pcr+amplicons+sequencing/10__1016_slash_j__ejbas__2015__06__002-71-1-6
Average 90 stars, based on 1 article reviews
pcr amplicons sequencing - by Bioz Stars, 2026-10
90/100 stars
  Buy from Supplier
pcr amplicon sequencing  (Scisco Genetics)
90
Scisco Genetics pcr amplicon sequencing
A , Schematic of 3 methods reading out reporter expression (2 methods of library preparation and 2 <t>sequencing</t> methods) from an upstream MPRA assay used to identify confounders. “BC only prep” is the typical readout, uses a splice junction-spanning <t>PCR</t> primer to enrich for spliced transcripts, and only reads out the barcode sequence. “Full transcript prep” uses a template switch oligo to add a primer handle to the 5’-end of the cDNA allowing for amplification of the full-length transcript, which can then be sequenced at just the 5’-end or the whole transcript with long-read sequencing. B , Schematic of all potential intended and confounding RNA species produced from an upstream reporter design, along with which are both captured in the reporter transcript preparation method (“captured”) and distinguishable from the method of sequencing readout (“distinguish”) by the 3 methods of library preparation and sequencing. For example, the BC only prep “captures” properly spliced transcripts whether they initiate within the promoter or enhancer but cannot distinguish the two types of transcripts because only the BC is sequenced. Alternatively spliced (“alt-spliced”) or unspliced transcripts are rarer but undistinguishable even by full transcript prep with 5’-end sequencing. These species can cause even more unexpected, pathological confounding. C, Expression of each E-P pair of the 21E x 26P library in the upstream integrated design where each E-P pair is colored by whether the 5’-end mapping short reads predominantly (>90%) align to the intended promoter TSS (red if yes and black if no). Gray points indicate E-P pairs with too few 5’ TSO PCR reads were detected and/or alignment quality. E-P pairs with the “seq14780” enhancer are outlined in blue. D , Expression of E-P pairs in the 21E x 26P library by the BC only short read readout (y-axis) versus the 5’-end mapping short read readout (x-axis). Off-diagonal E-P pairs are due to additional, alternatively spliced reporter transcripts illustrated in B that confound expression from the reporter but are undetectable by typical BC only readouts. Examples of a few of the alternatively spliced (“alt-spliced”) transcripts that led to the discrepancy were identified through long read sequencing of the full-length transcripts rather than 5’-end short read sequencing only. E , Enhancer effects and enhancer activity computed from upstream integrated assay after filtering out enhancer-promoter pairs confounded by upstream enhancer transcripts. FTH1, MRPS23, JUNB, and LYL1 promoter sequences are genomic in origin, and the endogenous gene is highly expressed. Similar to and . F , Histogram the fraction of 5’-end mapping short reads aligning to the promoter for the larger 203E x 78P and 21E x 500P library promoters after first removing seq14780 from the set of enhancer-promoter pairs to analyze. A cutoff of 90% (red dashed line) was used for determining promoter suitable for enhancer activation quantification. G, Promoter activity versus apparent enhancer activity of the enhancer sequences in the 203E library. Promoter activity is quantified by the expression of each enhancer with negative control sequence (noTFBS) in the promoter position (BC only short reads). “Apparent” enhancer activity is the average log2FC relative to basal promoter activity of the enhancer over the set of promoters preliminarily kept after filtering in panel F , which could still be confounded by autonomous promoter activity of some enhancer sequences. Enhancer sequences “chr3:128134842-128135106-enhancer” and its reverse complement “chr3:128134842-128135106-enhancer_rc” are labeled only with genome coordinates for brevity. Generally, stronger enhancers had more promoter activity. Enhancers with promoter activity greater than -1 were filtered out before further E-P activation quantification.
Pcr Amplicon Sequencing, supplied by Scisco Genetics, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
https://www.bioz.com/product/pcr+amplicon+sequencing/pcr+amplicon+sequencing/pmc08986086-226-4-8
Average 90 stars, based on 1 article reviews
pcr amplicon sequencing - by Bioz Stars, 2026-10
90/100 stars
  Buy from Supplier
pcr amplicons sequenced bi-directionally  (Cogenics Inc)
90
Cogenics Inc pcr amplicons sequenced bi-directionally
A , Schematic of 3 methods reading out reporter expression (2 methods of library preparation and 2 <t>sequencing</t> methods) from an upstream MPRA assay used to identify confounders. “BC only prep” is the typical readout, uses a splice junction-spanning <t>PCR</t> primer to enrich for spliced transcripts, and only reads out the barcode sequence. “Full transcript prep” uses a template switch oligo to add a primer handle to the 5’-end of the cDNA allowing for amplification of the full-length transcript, which can then be sequenced at just the 5’-end or the whole transcript with long-read sequencing. B , Schematic of all potential intended and confounding RNA species produced from an upstream reporter design, along with which are both captured in the reporter transcript preparation method (“captured”) and distinguishable from the method of sequencing readout (“distinguish”) by the 3 methods of library preparation and sequencing. For example, the BC only prep “captures” properly spliced transcripts whether they initiate within the promoter or enhancer but cannot distinguish the two types of transcripts because only the BC is sequenced. Alternatively spliced (“alt-spliced”) or unspliced transcripts are rarer but undistinguishable even by full transcript prep with 5’-end sequencing. These species can cause even more unexpected, pathological confounding. C, Expression of each E-P pair of the 21E x 26P library in the upstream integrated design where each E-P pair is colored by whether the 5’-end mapping short reads predominantly (>90%) align to the intended promoter TSS (red if yes and black if no). Gray points indicate E-P pairs with too few 5’ TSO PCR reads were detected and/or alignment quality. E-P pairs with the “seq14780” enhancer are outlined in blue. D , Expression of E-P pairs in the 21E x 26P library by the BC only short read readout (y-axis) versus the 5’-end mapping short read readout (x-axis). Off-diagonal E-P pairs are due to additional, alternatively spliced reporter transcripts illustrated in B that confound expression from the reporter but are undetectable by typical BC only readouts. Examples of a few of the alternatively spliced (“alt-spliced”) transcripts that led to the discrepancy were identified through long read sequencing of the full-length transcripts rather than 5’-end short read sequencing only. E , Enhancer effects and enhancer activity computed from upstream integrated assay after filtering out enhancer-promoter pairs confounded by upstream enhancer transcripts. FTH1, MRPS23, JUNB, and LYL1 promoter sequences are genomic in origin, and the endogenous gene is highly expressed. Similar to and . F , Histogram the fraction of 5’-end mapping short reads aligning to the promoter for the larger 203E x 78P and 21E x 500P library promoters after first removing seq14780 from the set of enhancer-promoter pairs to analyze. A cutoff of 90% (red dashed line) was used for determining promoter suitable for enhancer activation quantification. G, Promoter activity versus apparent enhancer activity of the enhancer sequences in the 203E library. Promoter activity is quantified by the expression of each enhancer with negative control sequence (noTFBS) in the promoter position (BC only short reads). “Apparent” enhancer activity is the average log2FC relative to basal promoter activity of the enhancer over the set of promoters preliminarily kept after filtering in panel F , which could still be confounded by autonomous promoter activity of some enhancer sequences. Enhancer sequences “chr3:128134842-128135106-enhancer” and its reverse complement “chr3:128134842-128135106-enhancer_rc” are labeled only with genome coordinates for brevity. Generally, stronger enhancers had more promoter activity. Enhancers with promoter activity greater than -1 were filtered out before further E-P activation quantification.
Pcr Amplicons Sequenced Bi Directionally, supplied by Cogenics Inc, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
https://www.bioz.com/product/pcr+amplicon+sequencing/pcr+amplicons+sequenced+bi+directionally/pmc02920856-219-0-6
Average 90 stars, based on 1 article reviews
pcr amplicons sequenced bi-directionally - by Bioz Stars, 2026-10
90/100 stars
  Buy from Supplier
multiplex reverse transcription–pcr amplicon sequencing  (Oxford Nanopore)
90
Oxford Nanopore multiplex reverse transcription–pcr amplicon sequencing
A , Schematic of 3 methods reading out reporter expression (2 methods of library preparation and 2 <t>sequencing</t> methods) from an upstream MPRA assay used to identify confounders. “BC only prep” is the typical readout, uses a splice junction-spanning <t>PCR</t> primer to enrich for spliced transcripts, and only reads out the barcode sequence. “Full transcript prep” uses a template switch oligo to add a primer handle to the 5’-end of the cDNA allowing for amplification of the full-length transcript, which can then be sequenced at just the 5’-end or the whole transcript with long-read sequencing. B , Schematic of all potential intended and confounding RNA species produced from an upstream reporter design, along with which are both captured in the reporter transcript preparation method (“captured”) and distinguishable from the method of sequencing readout (“distinguish”) by the 3 methods of library preparation and sequencing. For example, the BC only prep “captures” properly spliced transcripts whether they initiate within the promoter or enhancer but cannot distinguish the two types of transcripts because only the BC is sequenced. Alternatively spliced (“alt-spliced”) or unspliced transcripts are rarer but undistinguishable even by full transcript prep with 5’-end sequencing. These species can cause even more unexpected, pathological confounding. C, Expression of each E-P pair of the 21E x 26P library in the upstream integrated design where each E-P pair is colored by whether the 5’-end mapping short reads predominantly (>90%) align to the intended promoter TSS (red if yes and black if no). Gray points indicate E-P pairs with too few 5’ TSO PCR reads were detected and/or alignment quality. E-P pairs with the “seq14780” enhancer are outlined in blue. D , Expression of E-P pairs in the 21E x 26P library by the BC only short read readout (y-axis) versus the 5’-end mapping short read readout (x-axis). Off-diagonal E-P pairs are due to additional, alternatively spliced reporter transcripts illustrated in B that confound expression from the reporter but are undetectable by typical BC only readouts. Examples of a few of the alternatively spliced (“alt-spliced”) transcripts that led to the discrepancy were identified through long read sequencing of the full-length transcripts rather than 5’-end short read sequencing only. E , Enhancer effects and enhancer activity computed from upstream integrated assay after filtering out enhancer-promoter pairs confounded by upstream enhancer transcripts. FTH1, MRPS23, JUNB, and LYL1 promoter sequences are genomic in origin, and the endogenous gene is highly expressed. Similar to and . F , Histogram the fraction of 5’-end mapping short reads aligning to the promoter for the larger 203E x 78P and 21E x 500P library promoters after first removing seq14780 from the set of enhancer-promoter pairs to analyze. A cutoff of 90% (red dashed line) was used for determining promoter suitable for enhancer activation quantification. G, Promoter activity versus apparent enhancer activity of the enhancer sequences in the 203E library. Promoter activity is quantified by the expression of each enhancer with negative control sequence (noTFBS) in the promoter position (BC only short reads). “Apparent” enhancer activity is the average log2FC relative to basal promoter activity of the enhancer over the set of promoters preliminarily kept after filtering in panel F , which could still be confounded by autonomous promoter activity of some enhancer sequences. Enhancer sequences “chr3:128134842-128135106-enhancer” and its reverse complement “chr3:128134842-128135106-enhancer_rc” are labeled only with genome coordinates for brevity. Generally, stronger enhancers had more promoter activity. Enhancers with promoter activity greater than -1 were filtered out before further E-P activation quantification.
Multiplex Reverse Transcription–Pcr Amplicon Sequencing, supplied by Oxford Nanopore, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
https://www.bioz.com/product/pcr+amplicon+sequencing/multiplex+reverse+transcription+pcr+amplicon+sequencing/pmc08750003-196-5-12
Average 90 stars, based on 1 article reviews
multiplex reverse transcription–pcr amplicon sequencing - by Bioz Stars, 2026-10
90/100 stars
  Buy from Supplier
pcr amplicons sequenced by lgc genomics  (LGC Genomics GmbH)
90
LGC Genomics GmbH pcr amplicons sequenced by lgc genomics
A , Schematic of 3 methods reading out reporter expression (2 methods of library preparation and 2 <t>sequencing</t> methods) from an upstream MPRA assay used to identify confounders. “BC only prep” is the typical readout, uses a splice junction-spanning <t>PCR</t> primer to enrich for spliced transcripts, and only reads out the barcode sequence. “Full transcript prep” uses a template switch oligo to add a primer handle to the 5’-end of the cDNA allowing for amplification of the full-length transcript, which can then be sequenced at just the 5’-end or the whole transcript with long-read sequencing. B , Schematic of all potential intended and confounding RNA species produced from an upstream reporter design, along with which are both captured in the reporter transcript preparation method (“captured”) and distinguishable from the method of sequencing readout (“distinguish”) by the 3 methods of library preparation and sequencing. For example, the BC only prep “captures” properly spliced transcripts whether they initiate within the promoter or enhancer but cannot distinguish the two types of transcripts because only the BC is sequenced. Alternatively spliced (“alt-spliced”) or unspliced transcripts are rarer but undistinguishable even by full transcript prep with 5’-end sequencing. These species can cause even more unexpected, pathological confounding. C, Expression of each E-P pair of the 21E x 26P library in the upstream integrated design where each E-P pair is colored by whether the 5’-end mapping short reads predominantly (>90%) align to the intended promoter TSS (red if yes and black if no). Gray points indicate E-P pairs with too few 5’ TSO PCR reads were detected and/or alignment quality. E-P pairs with the “seq14780” enhancer are outlined in blue. D , Expression of E-P pairs in the 21E x 26P library by the BC only short read readout (y-axis) versus the 5’-end mapping short read readout (x-axis). Off-diagonal E-P pairs are due to additional, alternatively spliced reporter transcripts illustrated in B that confound expression from the reporter but are undetectable by typical BC only readouts. Examples of a few of the alternatively spliced (“alt-spliced”) transcripts that led to the discrepancy were identified through long read sequencing of the full-length transcripts rather than 5’-end short read sequencing only. E , Enhancer effects and enhancer activity computed from upstream integrated assay after filtering out enhancer-promoter pairs confounded by upstream enhancer transcripts. FTH1, MRPS23, JUNB, and LYL1 promoter sequences are genomic in origin, and the endogenous gene is highly expressed. Similar to and . F , Histogram the fraction of 5’-end mapping short reads aligning to the promoter for the larger 203E x 78P and 21E x 500P library promoters after first removing seq14780 from the set of enhancer-promoter pairs to analyze. A cutoff of 90% (red dashed line) was used for determining promoter suitable for enhancer activation quantification. G, Promoter activity versus apparent enhancer activity of the enhancer sequences in the 203E library. Promoter activity is quantified by the expression of each enhancer with negative control sequence (noTFBS) in the promoter position (BC only short reads). “Apparent” enhancer activity is the average log2FC relative to basal promoter activity of the enhancer over the set of promoters preliminarily kept after filtering in panel F , which could still be confounded by autonomous promoter activity of some enhancer sequences. Enhancer sequences “chr3:128134842-128135106-enhancer” and its reverse complement “chr3:128134842-128135106-enhancer_rc” are labeled only with genome coordinates for brevity. Generally, stronger enhancers had more promoter activity. Enhancers with promoter activity greater than -1 were filtered out before further E-P activation quantification.
Pcr Amplicons Sequenced By Lgc Genomics, supplied by LGC Genomics GmbH, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
https://www.bioz.com/product/pcr+amplicon+sequencing/pcr+amplicons+sequenced+by+lgc+genomics/pmc05581456-176-0-5
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pcr amplicons sequenced by lgc genomics - by Bioz Stars, 2026-10
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oxford nanopore long-read sequencing rt-pcr amplicons (exons 13–17)  (Oxford Nanopore)
90
Oxford Nanopore oxford nanopore long-read sequencing rt-pcr amplicons (exons 13–17)
Investigation of RNA variants in SMGs using transactivation of HDFs (A) Illustration of USH2A mRNA expression (red) in human adult tissues as reported by the Human Protein Atlas (HPA). (B) Diagram depicts the USH2A variant under investigation. Sashimi plots report USH2A mRNA splicing. Data derived from Oxford Nanopore long read <t>sequencing</t> of RT-PCR <t>amplicons</t> (exons 13–16) produced using RNA isolated following transactivation of USH2A in HDFs derived from healthy control and affected individuals in the presence and absence of cycloheximide (CHX). Arrows in the sashimi plots specify the reads coming from the alleles with pathogenic variant and allele with VUS as segregated by allelic phasing. (C) Illustration of SCN1A mRNA expression (red) in human adult tissues (HPA). (D) Diagram depicts the SCN1A variant under investigation. Sashimi plots report SCN1A mRNA splicing. Data derived from Oxford Nanopore long-read sequencing RT-PCR amplicons (exons 13–17) produced from RNA isolated following transactivation of SCN1A in HDFs derived from healthy control and affected individuals in the presence and absence of CHX. Arrows on the sashimi plot indicates the position of the pathogenic variant. (E) Illustration of DMD mRNA expression (red) in human adult tissues (HPA). (F) Diagram depicts the DMD variant under investigation. Graphs represent relative read depth of reported across DMD exons 2–5 as determined using long read sequencing of RT-PCR amplicons produced from RNA isolated following transactivation of DMD in HDFs derived from healthy control and affected individuals in the presence and absence of CHX. Note read depth is 1.8 times greater (∼double) in exons 3– and 4 only in samples from the affected individual and is not influenced by CHX.
Oxford Nanopore Long Read Sequencing Rt Pcr Amplicons (Exons 13–17), supplied by Oxford Nanopore, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
https://www.bioz.com/product/pcr+amplicon+sequencing/oxford+nanopore+long+read+sequencing+rt+pcr+amplicons++exons+13+17+/pmc11339655-291-6-3
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oxford nanopore long-read sequencing rt-pcr amplicons (exons 13–17) - by Bioz Stars, 2026-10
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traditional amplicon sequencing (pcr-cdna sequencing, pcs)  (Oxford Nanopore)
90
Oxford Nanopore traditional amplicon sequencing (pcr-cdna sequencing, pcs)
Investigation of RNA variants in SMGs using transactivation of HDFs (A) Illustration of USH2A mRNA expression (red) in human adult tissues as reported by the Human Protein Atlas (HPA). (B) Diagram depicts the USH2A variant under investigation. Sashimi plots report USH2A mRNA splicing. Data derived from Oxford Nanopore long read <t>sequencing</t> of RT-PCR <t>amplicons</t> (exons 13–16) produced using RNA isolated following transactivation of USH2A in HDFs derived from healthy control and affected individuals in the presence and absence of cycloheximide (CHX). Arrows in the sashimi plots specify the reads coming from the alleles with pathogenic variant and allele with VUS as segregated by allelic phasing. (C) Illustration of SCN1A mRNA expression (red) in human adult tissues (HPA). (D) Diagram depicts the SCN1A variant under investigation. Sashimi plots report SCN1A mRNA splicing. Data derived from Oxford Nanopore long-read sequencing RT-PCR amplicons (exons 13–17) produced from RNA isolated following transactivation of SCN1A in HDFs derived from healthy control and affected individuals in the presence and absence of CHX. Arrows on the sashimi plot indicates the position of the pathogenic variant. (E) Illustration of DMD mRNA expression (red) in human adult tissues (HPA). (F) Diagram depicts the DMD variant under investigation. Graphs represent relative read depth of reported across DMD exons 2–5 as determined using long read sequencing of RT-PCR amplicons produced from RNA isolated following transactivation of DMD in HDFs derived from healthy control and affected individuals in the presence and absence of CHX. Note read depth is 1.8 times greater (∼double) in exons 3– and 4 only in samples from the affected individual and is not influenced by CHX.
Traditional Amplicon Sequencing (Pcr Cdna Sequencing, Pcs), supplied by Oxford Nanopore, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
https://www.bioz.com/product/pcr+amplicon+sequencing/traditional+amplicon+sequencing++pcr+cdna+sequencing++pcs+/pmc07600144-227-6-0
Average 90 stars, based on 1 article reviews
traditional amplicon sequencing (pcr-cdna sequencing, pcs) - by Bioz Stars, 2026-10
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pcr amplicons sequencing  (AGRF Ltd)
90
AGRF Ltd pcr amplicons sequencing
Investigation of RNA variants in SMGs using transactivation of HDFs (A) Illustration of USH2A mRNA expression (red) in human adult tissues as reported by the Human Protein Atlas (HPA). (B) Diagram depicts the USH2A variant under investigation. Sashimi plots report USH2A mRNA splicing. Data derived from Oxford Nanopore long read <t>sequencing</t> of RT-PCR <t>amplicons</t> (exons 13–16) produced using RNA isolated following transactivation of USH2A in HDFs derived from healthy control and affected individuals in the presence and absence of cycloheximide (CHX). Arrows in the sashimi plots specify the reads coming from the alleles with pathogenic variant and allele with VUS as segregated by allelic phasing. (C) Illustration of SCN1A mRNA expression (red) in human adult tissues (HPA). (D) Diagram depicts the SCN1A variant under investigation. Sashimi plots report SCN1A mRNA splicing. Data derived from Oxford Nanopore long-read sequencing RT-PCR amplicons (exons 13–17) produced from RNA isolated following transactivation of SCN1A in HDFs derived from healthy control and affected individuals in the presence and absence of CHX. Arrows on the sashimi plot indicates the position of the pathogenic variant. (E) Illustration of DMD mRNA expression (red) in human adult tissues (HPA). (F) Diagram depicts the DMD variant under investigation. Graphs represent relative read depth of reported across DMD exons 2–5 as determined using long read sequencing of RT-PCR amplicons produced from RNA isolated following transactivation of DMD in HDFs derived from healthy control and affected individuals in the presence and absence of CHX. Note read depth is 1.8 times greater (∼double) in exons 3– and 4 only in samples from the affected individual and is not influenced by CHX.
Pcr Amplicons Sequencing, supplied by AGRF Ltd, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
https://www.bioz.com/product/pcr+amplicon+sequencing/pcr+amplicons+sequencing/pm36481310-46-0-14
Average 90 stars, based on 1 article reviews
pcr amplicons sequencing - by Bioz Stars, 2026-10
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Image Search Results


A , Schematic of 3 methods reading out reporter expression (2 methods of library preparation and 2 sequencing methods) from an upstream MPRA assay used to identify confounders. “BC only prep” is the typical readout, uses a splice junction-spanning PCR primer to enrich for spliced transcripts, and only reads out the barcode sequence. “Full transcript prep” uses a template switch oligo to add a primer handle to the 5’-end of the cDNA allowing for amplification of the full-length transcript, which can then be sequenced at just the 5’-end or the whole transcript with long-read sequencing. B , Schematic of all potential intended and confounding RNA species produced from an upstream reporter design, along with which are both captured in the reporter transcript preparation method (“captured”) and distinguishable from the method of sequencing readout (“distinguish”) by the 3 methods of library preparation and sequencing. For example, the BC only prep “captures” properly spliced transcripts whether they initiate within the promoter or enhancer but cannot distinguish the two types of transcripts because only the BC is sequenced. Alternatively spliced (“alt-spliced”) or unspliced transcripts are rarer but undistinguishable even by full transcript prep with 5’-end sequencing. These species can cause even more unexpected, pathological confounding. C, Expression of each E-P pair of the 21E x 26P library in the upstream integrated design where each E-P pair is colored by whether the 5’-end mapping short reads predominantly (>90%) align to the intended promoter TSS (red if yes and black if no). Gray points indicate E-P pairs with too few 5’ TSO PCR reads were detected and/or alignment quality. E-P pairs with the “seq14780” enhancer are outlined in blue. D , Expression of E-P pairs in the 21E x 26P library by the BC only short read readout (y-axis) versus the 5’-end mapping short read readout (x-axis). Off-diagonal E-P pairs are due to additional, alternatively spliced reporter transcripts illustrated in B that confound expression from the reporter but are undetectable by typical BC only readouts. Examples of a few of the alternatively spliced (“alt-spliced”) transcripts that led to the discrepancy were identified through long read sequencing of the full-length transcripts rather than 5’-end short read sequencing only. E , Enhancer effects and enhancer activity computed from upstream integrated assay after filtering out enhancer-promoter pairs confounded by upstream enhancer transcripts. FTH1, MRPS23, JUNB, and LYL1 promoter sequences are genomic in origin, and the endogenous gene is highly expressed. Similar to and . F , Histogram the fraction of 5’-end mapping short reads aligning to the promoter for the larger 203E x 78P and 21E x 500P library promoters after first removing seq14780 from the set of enhancer-promoter pairs to analyze. A cutoff of 90% (red dashed line) was used for determining promoter suitable for enhancer activation quantification. G, Promoter activity versus apparent enhancer activity of the enhancer sequences in the 203E library. Promoter activity is quantified by the expression of each enhancer with negative control sequence (noTFBS) in the promoter position (BC only short reads). “Apparent” enhancer activity is the average log2FC relative to basal promoter activity of the enhancer over the set of promoters preliminarily kept after filtering in panel F , which could still be confounded by autonomous promoter activity of some enhancer sequences. Enhancer sequences “chr3:128134842-128135106-enhancer” and its reverse complement “chr3:128134842-128135106-enhancer_rc” are labeled only with genome coordinates for brevity. Generally, stronger enhancers had more promoter activity. Enhancers with promoter activity greater than -1 were filtered out before further E-P activation quantification.

Journal: bioRxiv

Article Title: Intrinsic promoter responsiveness dictates sensitivity to transcriptional activation by enhancers

doi: 10.64898/2026.06.25.734173

Figure Lengend Snippet: A , Schematic of 3 methods reading out reporter expression (2 methods of library preparation and 2 sequencing methods) from an upstream MPRA assay used to identify confounders. “BC only prep” is the typical readout, uses a splice junction-spanning PCR primer to enrich for spliced transcripts, and only reads out the barcode sequence. “Full transcript prep” uses a template switch oligo to add a primer handle to the 5’-end of the cDNA allowing for amplification of the full-length transcript, which can then be sequenced at just the 5’-end or the whole transcript with long-read sequencing. B , Schematic of all potential intended and confounding RNA species produced from an upstream reporter design, along with which are both captured in the reporter transcript preparation method (“captured”) and distinguishable from the method of sequencing readout (“distinguish”) by the 3 methods of library preparation and sequencing. For example, the BC only prep “captures” properly spliced transcripts whether they initiate within the promoter or enhancer but cannot distinguish the two types of transcripts because only the BC is sequenced. Alternatively spliced (“alt-spliced”) or unspliced transcripts are rarer but undistinguishable even by full transcript prep with 5’-end sequencing. These species can cause even more unexpected, pathological confounding. C, Expression of each E-P pair of the 21E x 26P library in the upstream integrated design where each E-P pair is colored by whether the 5’-end mapping short reads predominantly (>90%) align to the intended promoter TSS (red if yes and black if no). Gray points indicate E-P pairs with too few 5’ TSO PCR reads were detected and/or alignment quality. E-P pairs with the “seq14780” enhancer are outlined in blue. D , Expression of E-P pairs in the 21E x 26P library by the BC only short read readout (y-axis) versus the 5’-end mapping short read readout (x-axis). Off-diagonal E-P pairs are due to additional, alternatively spliced reporter transcripts illustrated in B that confound expression from the reporter but are undetectable by typical BC only readouts. Examples of a few of the alternatively spliced (“alt-spliced”) transcripts that led to the discrepancy were identified through long read sequencing of the full-length transcripts rather than 5’-end short read sequencing only. E , Enhancer effects and enhancer activity computed from upstream integrated assay after filtering out enhancer-promoter pairs confounded by upstream enhancer transcripts. FTH1, MRPS23, JUNB, and LYL1 promoter sequences are genomic in origin, and the endogenous gene is highly expressed. Similar to and . F , Histogram the fraction of 5’-end mapping short reads aligning to the promoter for the larger 203E x 78P and 21E x 500P library promoters after first removing seq14780 from the set of enhancer-promoter pairs to analyze. A cutoff of 90% (red dashed line) was used for determining promoter suitable for enhancer activation quantification. G, Promoter activity versus apparent enhancer activity of the enhancer sequences in the 203E library. Promoter activity is quantified by the expression of each enhancer with negative control sequence (noTFBS) in the promoter position (BC only short reads). “Apparent” enhancer activity is the average log2FC relative to basal promoter activity of the enhancer over the set of promoters preliminarily kept after filtering in panel F , which could still be confounded by autonomous promoter activity of some enhancer sequences. Enhancer sequences “chr3:128134842-128135106-enhancer” and its reverse complement “chr3:128134842-128135106-enhancer_rc” are labeled only with genome coordinates for brevity. Generally, stronger enhancers had more promoter activity. Enhancers with promoter activity greater than -1 were filtered out before further E-P activation quantification.

Article Snippet: For full transcript, long-read sequencing, libraries were sent to Plasmidsaurus for Premium PCR sequencing by their Oxford Nanopore Technologies platform.

Techniques: Expressing, Sequencing, Amplification, Produced, Activity Assay, Activation Assay, Negative Control, Labeling

Investigation of RNA variants in SMGs using transactivation of HDFs (A) Illustration of USH2A mRNA expression (red) in human adult tissues as reported by the Human Protein Atlas (HPA). (B) Diagram depicts the USH2A variant under investigation. Sashimi plots report USH2A mRNA splicing. Data derived from Oxford Nanopore long read sequencing of RT-PCR amplicons (exons 13–16) produced using RNA isolated following transactivation of USH2A in HDFs derived from healthy control and affected individuals in the presence and absence of cycloheximide (CHX). Arrows in the sashimi plots specify the reads coming from the alleles with pathogenic variant and allele with VUS as segregated by allelic phasing. (C) Illustration of SCN1A mRNA expression (red) in human adult tissues (HPA). (D) Diagram depicts the SCN1A variant under investigation. Sashimi plots report SCN1A mRNA splicing. Data derived from Oxford Nanopore long-read sequencing RT-PCR amplicons (exons 13–17) produced from RNA isolated following transactivation of SCN1A in HDFs derived from healthy control and affected individuals in the presence and absence of CHX. Arrows on the sashimi plot indicates the position of the pathogenic variant. (E) Illustration of DMD mRNA expression (red) in human adult tissues (HPA). (F) Diagram depicts the DMD variant under investigation. Graphs represent relative read depth of reported across DMD exons 2–5 as determined using long read sequencing of RT-PCR amplicons produced from RNA isolated following transactivation of DMD in HDFs derived from healthy control and affected individuals in the presence and absence of CHX. Note read depth is 1.8 times greater (∼double) in exons 3– and 4 only in samples from the affected individual and is not influenced by CHX.

Journal: American Journal of Human Genetics

Article Title: RNA variant assessment using transactivation and transdifferentiation

doi: 10.1016/j.ajhg.2024.06.018

Figure Lengend Snippet: Investigation of RNA variants in SMGs using transactivation of HDFs (A) Illustration of USH2A mRNA expression (red) in human adult tissues as reported by the Human Protein Atlas (HPA). (B) Diagram depicts the USH2A variant under investigation. Sashimi plots report USH2A mRNA splicing. Data derived from Oxford Nanopore long read sequencing of RT-PCR amplicons (exons 13–16) produced using RNA isolated following transactivation of USH2A in HDFs derived from healthy control and affected individuals in the presence and absence of cycloheximide (CHX). Arrows in the sashimi plots specify the reads coming from the alleles with pathogenic variant and allele with VUS as segregated by allelic phasing. (C) Illustration of SCN1A mRNA expression (red) in human adult tissues (HPA). (D) Diagram depicts the SCN1A variant under investigation. Sashimi plots report SCN1A mRNA splicing. Data derived from Oxford Nanopore long-read sequencing RT-PCR amplicons (exons 13–17) produced from RNA isolated following transactivation of SCN1A in HDFs derived from healthy control and affected individuals in the presence and absence of CHX. Arrows on the sashimi plot indicates the position of the pathogenic variant. (E) Illustration of DMD mRNA expression (red) in human adult tissues (HPA). (F) Diagram depicts the DMD variant under investigation. Graphs represent relative read depth of reported across DMD exons 2–5 as determined using long read sequencing of RT-PCR amplicons produced from RNA isolated following transactivation of DMD in HDFs derived from healthy control and affected individuals in the presence and absence of CHX. Note read depth is 1.8 times greater (∼double) in exons 3– and 4 only in samples from the affected individual and is not influenced by CHX.

Article Snippet: Data derived from Oxford Nanopore long-read sequencing RT-PCR amplicons (exons 13–17) produced from RNA isolated following transactivation of SCN1A in HDFs derived from healthy control and affected individuals in the presence and absence of CHX.

Techniques: Expressing, Variant Assay, Derivative Assay, Sequencing, Reverse Transcription Polymerase Chain Reaction, Produced, Isolation, Control