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Illumina Inc pcr free fragment libraries
'PER' genome-wide base composition bias curves . (a,b) Shown is the GC bias in <t>Illumina</t> reads from a 400-bp fragment library amplified using the standard <t>PCR</t> protocol (Phusion HF, short denaturation) on a fast-ramping thermocycler (red squares), Phusion HF with long denaturation and 2M betaine (black triangles), AccuPrime Taq HiFi with long denaturation and primer extension at 65°C (blue diamonds) or 60°C (purple diamonds). To calculate the observed to expected (unbiased) read coverage, the number of reads aligning to 50-bp windows at a given %GC was divided by the number of 50-bp windows that fall in this %GC category. This value was then normalized relative to the average value from 48% through 52% GC and plotted on a log 10 scale (a) or linear scale (b).
Pcr Free Fragment Libraries, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 85/100, based on 2 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
https://www.bioz.com/result/pcr free fragment libraries/product/Illumina Inc
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pcr free fragment libraries - by Bioz Stars, 2020-08
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Article Title: Analyzing and minimizing PCR amplification bias in Illumina sequencing libraries

Journal: Genome Biology

doi: 10.1186/gb-2011-12-2-r18

'PER' genome-wide base composition bias curves . (a,b) Shown is the GC bias in Illumina reads from a 400-bp fragment library amplified using the standard PCR protocol (Phusion HF, short denaturation) on a fast-ramping thermocycler (red squares), Phusion HF with long denaturation and 2M betaine (black triangles), AccuPrime Taq HiFi with long denaturation and primer extension at 65°C (blue diamonds) or 60°C (purple diamonds). To calculate the observed to expected (unbiased) read coverage, the number of reads aligning to 50-bp windows at a given %GC was divided by the number of 50-bp windows that fall in this %GC category. This value was then normalized relative to the average value from 48% through 52% GC and plotted on a log 10 scale (a) or linear scale (b).
Figure Legend Snippet: 'PER' genome-wide base composition bias curves . (a,b) Shown is the GC bias in Illumina reads from a 400-bp fragment library amplified using the standard PCR protocol (Phusion HF, short denaturation) on a fast-ramping thermocycler (red squares), Phusion HF with long denaturation and 2M betaine (black triangles), AccuPrime Taq HiFi with long denaturation and primer extension at 65°C (blue diamonds) or 60°C (purple diamonds). To calculate the observed to expected (unbiased) read coverage, the number of reads aligning to 50-bp windows at a given %GC was divided by the number of 50-bp windows that fall in this %GC category. This value was then normalized relative to the average value from 48% through 52% GC and plotted on a log 10 scale (a) or linear scale (b).

Techniques Used: Genome Wide, Amplification, Polymerase Chain Reaction

Sequencing bias with PCR-amplified and PCR-free libraries . (a,b) Shown is the mean normalized coverage of 50-bp windows in the human genome having the GC-content indicated on the x-axis for a PCR-free (orange dots) and a PCR-amplified (blue diamonds) Illumina sequencing library. Both fragment libraries had approximately 180-bp inserts. The PCR amplification was performed with AccuPrime Taq HiFi (long denat., primer extension at 65°C). The coverage was plotted on a log 10 (a) and a linear scale (b). The data points at extremely high GC, where the reads from the PCR-free library had a mean base quality of less than Q20 (open symbols), were omitted in the middle panel (b). (c) The ratios of the two curves in (a,b), that is, the fold-increase in mean coverage by sequencing a PCR-free library instead of a PCR-amplified library. The shaded histogram is the %GC distribution of 50-bp windows in the human genome. More than 99.9% of all 50-bp windows in the genome contain 8% to 88% GC and received a less than 1.25-fold increase in coverage. Less than 0.01% of all 50-bp windows contain 90% or more GC. The open circles at 96% and 98% GC denote data for which the mean base quality of the reads from the PCR-free library was below Q20.
Figure Legend Snippet: Sequencing bias with PCR-amplified and PCR-free libraries . (a,b) Shown is the mean normalized coverage of 50-bp windows in the human genome having the GC-content indicated on the x-axis for a PCR-free (orange dots) and a PCR-amplified (blue diamonds) Illumina sequencing library. Both fragment libraries had approximately 180-bp inserts. The PCR amplification was performed with AccuPrime Taq HiFi (long denat., primer extension at 65°C). The coverage was plotted on a log 10 (a) and a linear scale (b). The data points at extremely high GC, where the reads from the PCR-free library had a mean base quality of less than Q20 (open symbols), were omitted in the middle panel (b). (c) The ratios of the two curves in (a,b), that is, the fold-increase in mean coverage by sequencing a PCR-free library instead of a PCR-amplified library. The shaded histogram is the %GC distribution of 50-bp windows in the human genome. More than 99.9% of all 50-bp windows in the genome contain 8% to 88% GC and received a less than 1.25-fold increase in coverage. Less than 0.01% of all 50-bp windows contain 90% or more GC. The open circles at 96% and 98% GC denote data for which the mean base quality of the reads from the PCR-free library was below Q20.

Techniques Used: Sequencing, Polymerase Chain Reaction, Amplification

Related Articles

Sequencing:

Article Title: A Missense Variant in SCN8A in Alpine Dachsbracke Dogs Affected by Spinocerebellar Ataxia
Article Snippet: .. Whole-Genome Resequencing Whole-genome sequence (WGS) data at 23x coverage was obtained from a single affected Alpine Dachsbracke dog ( ) after preparation of a PCR-free fragment library with a 450 bp insert size and collection of 206,013,034 paired-end reads (2 × 150 bp) using NovaSeq6000 Sequencing System (Illumina). ..

Article Title: Analyzing and minimizing PCR amplification bias in Illumina sequencing libraries
Article Snippet: .. PCR-free fragment libraries for Illumina sequencing Shearing, end-repair, single-dA extension and adapter ligation were performed as described above for standard Illumina fragment libraries with the following exceptions: the genomic DNA (9 μg of NA12878 total human DNA) was sheared in three batches of 3 μg each; the ligation reaction contained 120 pmol pre-annealed full-length paired-end Illumina adapters [ ]; the product of the adapter-ligation was size-selected to an apparent size range of 320 to 350 bp relative to a double-stranded size marker. .. qPCR Primer pairs for 'PER' and human qPCR assays, their genome of origin, sequence, length and GC-content of amplicons are listed in Tables S1 and S2 in Additional file .

Polymerase Chain Reaction:

Article Title: A Missense Variant in SCN8A in Alpine Dachsbracke Dogs Affected by Spinocerebellar Ataxia
Article Snippet: .. Whole-Genome Resequencing Whole-genome sequence (WGS) data at 23x coverage was obtained from a single affected Alpine Dachsbracke dog ( ) after preparation of a PCR-free fragment library with a 450 bp insert size and collection of 206,013,034 paired-end reads (2 × 150 bp) using NovaSeq6000 Sequencing System (Illumina). ..

Article Title: Analyzing and minimizing PCR amplification bias in Illumina sequencing libraries
Article Snippet: .. PCR-free fragment libraries for Illumina sequencing Shearing, end-repair, single-dA extension and adapter ligation were performed as described above for standard Illumina fragment libraries with the following exceptions: the genomic DNA (9 μg of NA12878 total human DNA) was sheared in three batches of 3 μg each; the ligation reaction contained 120 pmol pre-annealed full-length paired-end Illumina adapters [ ]; the product of the adapter-ligation was size-selected to an apparent size range of 320 to 350 bp relative to a double-stranded size marker. .. qPCR Primer pairs for 'PER' and human qPCR assays, their genome of origin, sequence, length and GC-content of amplicons are listed in Tables S1 and S2 in Additional file .

Article Title: A transposable element insertion in APOB causes cholesterol deficiency in Holstein cattle
Article Snippet: .. We prepared PCR‐free fragment libraries with 400‐bp insert sizes from both animals, which were sequenced to 19.2× (affected calf) and 16.4× (non‐affected carrier) coverage on a single lane of an Illumina HiSeq3000 instrument using 2× 150‐bp paired‐end reads. .. The genome sequencing data were deposited in the European Nucleotide Archive (ENA) ( http://www.ebi.ac.uk/ena ) under accession no. PRJEB11963.

Marker:

Article Title: Analyzing and minimizing PCR amplification bias in Illumina sequencing libraries
Article Snippet: .. PCR-free fragment libraries for Illumina sequencing Shearing, end-repair, single-dA extension and adapter ligation were performed as described above for standard Illumina fragment libraries with the following exceptions: the genomic DNA (9 μg of NA12878 total human DNA) was sheared in three batches of 3 μg each; the ligation reaction contained 120 pmol pre-annealed full-length paired-end Illumina adapters [ ]; the product of the adapter-ligation was size-selected to an apparent size range of 320 to 350 bp relative to a double-stranded size marker. .. qPCR Primer pairs for 'PER' and human qPCR assays, their genome of origin, sequence, length and GC-content of amplicons are listed in Tables S1 and S2 in Additional file .

Ligation:

Article Title: Analyzing and minimizing PCR amplification bias in Illumina sequencing libraries
Article Snippet: .. PCR-free fragment libraries for Illumina sequencing Shearing, end-repair, single-dA extension and adapter ligation were performed as described above for standard Illumina fragment libraries with the following exceptions: the genomic DNA (9 μg of NA12878 total human DNA) was sheared in three batches of 3 μg each; the ligation reaction contained 120 pmol pre-annealed full-length paired-end Illumina adapters [ ]; the product of the adapter-ligation was size-selected to an apparent size range of 320 to 350 bp relative to a double-stranded size marker. .. qPCR Primer pairs for 'PER' and human qPCR assays, their genome of origin, sequence, length and GC-content of amplicons are listed in Tables S1 and S2 in Additional file .

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  • 99
    Illumina Inc truseq dna pcr free ht library preparation kit
    Experimental design. Samples consisting of 1, 3 or 5 cells were collected from the Loucy cell line using micromanipulation for each WGA method in triplicate. Cells were amplified with either Ampli-1, REPLI-g or DOPlify, followed by <t>PCR-free</t> Illumina library preparation and sequencing. A fourth method, Picoseq, performs WGA and library preparation simultaneously, without the need for a separate library preparation. A bulk <t>DNA</t> sample was extracted from 5 * 10 6 Loucy cells using a column-based extraction method from Qiagen, also followed by PCR-free Illumina library preparation and sequencing.
    Truseq Dna Pcr Free Ht Library Preparation Kit, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 99/100, based on 51 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/truseq dna pcr free ht library preparation kit/product/Illumina Inc
    Average 99 stars, based on 51 article reviews
    Price from $9.99 to $1999.99
    truseq dna pcr free ht library preparation kit - by Bioz Stars, 2020-08
    99/100 stars
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    85
    Illumina Inc pcr free fragment libraries
    'PER' genome-wide base composition bias curves . (a,b) Shown is the GC bias in <t>Illumina</t> reads from a 400-bp fragment library amplified using the standard <t>PCR</t> protocol (Phusion HF, short denaturation) on a fast-ramping thermocycler (red squares), Phusion HF with long denaturation and 2M betaine (black triangles), AccuPrime Taq HiFi with long denaturation and primer extension at 65°C (blue diamonds) or 60°C (purple diamonds). To calculate the observed to expected (unbiased) read coverage, the number of reads aligning to 50-bp windows at a given %GC was divided by the number of 50-bp windows that fall in this %GC category. This value was then normalized relative to the average value from 48% through 52% GC and plotted on a log 10 scale (a) or linear scale (b).
    Pcr Free Fragment Libraries, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 85/100, based on 2 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/pcr free fragment libraries/product/Illumina Inc
    Average 85 stars, based on 2 article reviews
    Price from $9.99 to $1999.99
    pcr free fragment libraries - by Bioz Stars, 2020-08
    85/100 stars
      Buy from Supplier

    88
    Illumina Inc polymerase chain reaction pcr free fragment library
    Electropherograms of the COL6A1:c.289G > T variant. A fragment harboring exon 3 and flanking sequences of the COL6A1 gene was amplified by polymerase chain reaction and sequenced with the Sanger method. Shown are representative traces from <t>Landseer</t> dogs with the three different genotypes. The position of the variant is indicated by an arrow.
    Polymerase Chain Reaction Pcr Free Fragment Library, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 88/100, based on 2 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/polymerase chain reaction pcr free fragment library/product/Illumina Inc
    Average 88 stars, based on 2 article reviews
    Price from $9.99 to $1999.99
    polymerase chain reaction pcr free fragment library - by Bioz Stars, 2020-08
    88/100 stars
      Buy from Supplier

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    Experimental design. Samples consisting of 1, 3 or 5 cells were collected from the Loucy cell line using micromanipulation for each WGA method in triplicate. Cells were amplified with either Ampli-1, REPLI-g or DOPlify, followed by PCR-free Illumina library preparation and sequencing. A fourth method, Picoseq, performs WGA and library preparation simultaneously, without the need for a separate library preparation. A bulk DNA sample was extracted from 5 * 10 6 Loucy cells using a column-based extraction method from Qiagen, also followed by PCR-free Illumina library preparation and sequencing.

    Journal: Scientific Reports

    Article Title: Performance of four modern whole genome amplification methods for copy number variant detection in single cells

    doi: 10.1038/s41598-017-03711-y

    Figure Lengend Snippet: Experimental design. Samples consisting of 1, 3 or 5 cells were collected from the Loucy cell line using micromanipulation for each WGA method in triplicate. Cells were amplified with either Ampli-1, REPLI-g or DOPlify, followed by PCR-free Illumina library preparation and sequencing. A fourth method, Picoseq, performs WGA and library preparation simultaneously, without the need for a separate library preparation. A bulk DNA sample was extracted from 5 * 10 6 Loucy cells using a column-based extraction method from Qiagen, also followed by PCR-free Illumina library preparation and sequencing.

    Article Snippet: Sequencing libraries of the fragmented samples were prepared with the TruSeq DNA PCR-free HT library preparation kit (Illumina) on the IP-Star Compact (Diagenode, Seraing, Belgium).

    Techniques: Micromanipulation, Whole Genome Amplification, Amplification, Polymerase Chain Reaction, Sequencing

    Figure 2. Gain of function of the endogenous Mp MYB14 gene in the #3483 line. (A) Schematic illustration of the T-DNA inserted region of the #3483 genome. (B) Up-regulated gene expression of Mp MYB14 in the #3483 line. RT-PCR experiments were performed for Mp MYB14 and ELONGATION FACTOR 1 ( EF1 ) from M. polymorpha as a control. The PCR amplifications with 25 cycles are shown (Supplementary Figure S1). Closed arrowhead and arrow indicate MYB14 and EF1 fragments, respectively. Open arrowhead indicates non-specific faint signal. (C) Hyper-accumulation of riccionidin A in the #3483 line. Gray line, wild type (WT); black line, #3483. Bars indicate standard deviation (three technical replicates).

    Journal: Plant Biotechnology

    Article Title: A gain-of-function T-DNA insertion mutant of Marchantia polymorpha hyper-accumulates flavonoid riccionidin A

    doi: 10.5511/plantbiotechnology.19.0722a

    Figure Lengend Snippet: Figure 2. Gain of function of the endogenous Mp MYB14 gene in the #3483 line. (A) Schematic illustration of the T-DNA inserted region of the #3483 genome. (B) Up-regulated gene expression of Mp MYB14 in the #3483 line. RT-PCR experiments were performed for Mp MYB14 and ELONGATION FACTOR 1 ( EF1 ) from M. polymorpha as a control. The PCR amplifications with 25 cycles are shown (Supplementary Figure S1). Closed arrowhead and arrow indicate MYB14 and EF1 fragments, respectively. Open arrowhead indicates non-specific faint signal. (C) Hyper-accumulation of riccionidin A in the #3483 line. Gray line, wild type (WT); black line, #3483. Bars indicate standard deviation (three technical replicates).

    Article Snippet: The fragmented DNA was used to prepare a library using the Illumina TruSeq® DNA PCR-Free Library Preparation Kit according to the manufacturer’s instructions.

    Techniques: Expressing, Reverse Transcription Polymerase Chain Reaction, Polymerase Chain Reaction, Standard Deviation

    'PER' genome-wide base composition bias curves . (a,b) Shown is the GC bias in Illumina reads from a 400-bp fragment library amplified using the standard PCR protocol (Phusion HF, short denaturation) on a fast-ramping thermocycler (red squares), Phusion HF with long denaturation and 2M betaine (black triangles), AccuPrime Taq HiFi with long denaturation and primer extension at 65°C (blue diamonds) or 60°C (purple diamonds). To calculate the observed to expected (unbiased) read coverage, the number of reads aligning to 50-bp windows at a given %GC was divided by the number of 50-bp windows that fall in this %GC category. This value was then normalized relative to the average value from 48% through 52% GC and plotted on a log 10 scale (a) or linear scale (b).

    Journal: Genome Biology

    Article Title: Analyzing and minimizing PCR amplification bias in Illumina sequencing libraries

    doi: 10.1186/gb-2011-12-2-r18

    Figure Lengend Snippet: 'PER' genome-wide base composition bias curves . (a,b) Shown is the GC bias in Illumina reads from a 400-bp fragment library amplified using the standard PCR protocol (Phusion HF, short denaturation) on a fast-ramping thermocycler (red squares), Phusion HF with long denaturation and 2M betaine (black triangles), AccuPrime Taq HiFi with long denaturation and primer extension at 65°C (blue diamonds) or 60°C (purple diamonds). To calculate the observed to expected (unbiased) read coverage, the number of reads aligning to 50-bp windows at a given %GC was divided by the number of 50-bp windows that fall in this %GC category. This value was then normalized relative to the average value from 48% through 52% GC and plotted on a log 10 scale (a) or linear scale (b).

    Article Snippet: PCR-free fragment libraries for Illumina sequencing Shearing, end-repair, single-dA extension and adapter ligation were performed as described above for standard Illumina fragment libraries with the following exceptions: the genomic DNA (9 μg of NA12878 total human DNA) was sheared in three batches of 3 μg each; the ligation reaction contained 120 pmol pre-annealed full-length paired-end Illumina adapters [ ]; the product of the adapter-ligation was size-selected to an apparent size range of 320 to 350 bp relative to a double-stranded size marker.

    Techniques: Genome Wide, Amplification, Polymerase Chain Reaction

    Sequencing bias with PCR-amplified and PCR-free libraries . (a,b) Shown is the mean normalized coverage of 50-bp windows in the human genome having the GC-content indicated on the x-axis for a PCR-free (orange dots) and a PCR-amplified (blue diamonds) Illumina sequencing library. Both fragment libraries had approximately 180-bp inserts. The PCR amplification was performed with AccuPrime Taq HiFi (long denat., primer extension at 65°C). The coverage was plotted on a log 10 (a) and a linear scale (b). The data points at extremely high GC, where the reads from the PCR-free library had a mean base quality of less than Q20 (open symbols), were omitted in the middle panel (b). (c) The ratios of the two curves in (a,b), that is, the fold-increase in mean coverage by sequencing a PCR-free library instead of a PCR-amplified library. The shaded histogram is the %GC distribution of 50-bp windows in the human genome. More than 99.9% of all 50-bp windows in the genome contain 8% to 88% GC and received a less than 1.25-fold increase in coverage. Less than 0.01% of all 50-bp windows contain 90% or more GC. The open circles at 96% and 98% GC denote data for which the mean base quality of the reads from the PCR-free library was below Q20.

    Journal: Genome Biology

    Article Title: Analyzing and minimizing PCR amplification bias in Illumina sequencing libraries

    doi: 10.1186/gb-2011-12-2-r18

    Figure Lengend Snippet: Sequencing bias with PCR-amplified and PCR-free libraries . (a,b) Shown is the mean normalized coverage of 50-bp windows in the human genome having the GC-content indicated on the x-axis for a PCR-free (orange dots) and a PCR-amplified (blue diamonds) Illumina sequencing library. Both fragment libraries had approximately 180-bp inserts. The PCR amplification was performed with AccuPrime Taq HiFi (long denat., primer extension at 65°C). The coverage was plotted on a log 10 (a) and a linear scale (b). The data points at extremely high GC, where the reads from the PCR-free library had a mean base quality of less than Q20 (open symbols), were omitted in the middle panel (b). (c) The ratios of the two curves in (a,b), that is, the fold-increase in mean coverage by sequencing a PCR-free library instead of a PCR-amplified library. The shaded histogram is the %GC distribution of 50-bp windows in the human genome. More than 99.9% of all 50-bp windows in the genome contain 8% to 88% GC and received a less than 1.25-fold increase in coverage. Less than 0.01% of all 50-bp windows contain 90% or more GC. The open circles at 96% and 98% GC denote data for which the mean base quality of the reads from the PCR-free library was below Q20.

    Article Snippet: PCR-free fragment libraries for Illumina sequencing Shearing, end-repair, single-dA extension and adapter ligation were performed as described above for standard Illumina fragment libraries with the following exceptions: the genomic DNA (9 μg of NA12878 total human DNA) was sheared in three batches of 3 μg each; the ligation reaction contained 120 pmol pre-annealed full-length paired-end Illumina adapters [ ]; the product of the adapter-ligation was size-selected to an apparent size range of 320 to 350 bp relative to a double-stranded size marker.

    Techniques: Sequencing, Polymerase Chain Reaction, Amplification

    Electropherograms of the COL6A1:c.289G > T variant. A fragment harboring exon 3 and flanking sequences of the COL6A1 gene was amplified by polymerase chain reaction and sequenced with the Sanger method. Shown are representative traces from Landseer dogs with the three different genotypes. The position of the variant is indicated by an arrow.

    Journal: G3: Genes|Genomes|Genetics

    Article Title: A Nonsense Variant in COL6A1 in Landseer Dogs with Muscular Dystrophy

    doi: 10.1534/g3.115.021923

    Figure Lengend Snippet: Electropherograms of the COL6A1:c.289G > T variant. A fragment harboring exon 3 and flanking sequences of the COL6A1 gene was amplified by polymerase chain reaction and sequenced with the Sanger method. Shown are representative traces from Landseer dogs with the three different genotypes. The position of the variant is indicated by an arrow.

    Article Snippet: Whole-genome sequencing of an affected Landseer dog We prepared a polymerase chain reaction (PCR)-free fragment library with 300-bp insert size and collected 330,331,465 Illumina HiSeq2500 paired-end reads (2 × 100 bp) or roughly 14.2× coverage.

    Techniques: Variant Assay, Amplification, Polymerase Chain Reaction