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Illumina Inc sequencing platform
Sequencing Platform, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 99/100, based on 4 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
https://www.bioz.com/result/sequencing platform/product/Illumina Inc
Average 99 stars, based on 4 article reviews
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sequencing platform - by Bioz Stars, 2020-04
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Amplification:

Article Title: Molecular Diagnosis of Vaginitis: Comparing Quantitative PCR and Microbiome Profiling Approaches to Current Microscopy Scoring
Article Snippet: The V3 variable region was amplified using modified 341F and 518R primers developed previously ( ). .. The amplicons were pooled and then quantified with the Bioanalyzer high-sensitivity DNA chip (Agilent, Mississauga, ON) before sequencing on the MiSeq using a reagent kit v3 according to the manufacturer’s instructions (Illumina).

Article Title: Cross-clade simultaneous HIV drug resistance genotyping for reverse transcriptase, protease, and integrase inhibitor mutations by Illumina MiSeq
Article Snippet: In addition, our method is technically simpler, requiring a single fragmented PCR amplicon over the three required for the Gibson et al. method. .. Lastly, Illumina MiSeq is the first and only next-generation sequencing platform to receive FDA approval for assays developed on that device, making it the optimal deep sequencing platform to develop a HIV drug resistance assay for possible clinical use in the future [ ].

Article Title: MiFish, a set of universal PCR primers for metabarcoding environmental DNA from fishes: detection of more than 230 subtropical marine species
Article Snippet: Massively parallel paired-end sequencing on the MiSeq platform (Illumina, San Diego, CA, USA) requires PCR amplicons to be flanked by: (i) primer-binding sites for sequencing; (ii) dual-index (i.e. barcode) sequences; and (iii) adapter sequences for binding to the flowcells of the MiSeq. .. The first-round PCR (first PCR; ) amplified the target region using primers 5′-ACACTCTTTCCCTACACGACGCTCTTCCGATCTNNNNNN + MiFish gene-specific sequences-3′ (forward) and 5′-GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCTNNNNNN + MiFish gene-specific sequences-3′ (reverse).

Polymerase Chain Reaction:

Article Title: Molecular Diagnosis of Vaginitis: Comparing Quantitative PCR and Microbiome Profiling Approaches to Current Microscopy Scoring
Article Snippet: PCR was completed in the S1000 thermocycler (Bio-Rad, Mississauga, ON) with an initial 2-min denaturation at 94°C followed by 30 cycles of 94°C for 30 s, 50°C for 30 s, and 72°C for 30 s before a final extension step at 72°C for 10 min. .. The amplicons were pooled and then quantified with the Bioanalyzer high-sensitivity DNA chip (Agilent, Mississauga, ON) before sequencing on the MiSeq using a reagent kit v3 according to the manufacturer’s instructions (Illumina).

Article Title: Cross-clade simultaneous HIV drug resistance genotyping for reverse transcriptase, protease, and integrase inhibitor mutations by Illumina MiSeq
Article Snippet: In addition, our method is technically simpler, requiring a single fragmented PCR amplicon over the three required for the Gibson et al. method. .. Lastly, Illumina MiSeq is the first and only next-generation sequencing platform to receive FDA approval for assays developed on that device, making it the optimal deep sequencing platform to develop a HIV drug resistance assay for possible clinical use in the future [ ].

Article Title: MiFish, a set of universal PCR primers for metabarcoding environmental DNA from fishes: detection of more than 230 subtropical marine species
Article Snippet: .. Massively parallel paired-end sequencing on the MiSeq platform (Illumina, San Diego, CA, USA) requires PCR amplicons to be flanked by: (i) primer-binding sites for sequencing; (ii) dual-index (i.e. barcode) sequences; and (iii) adapter sequences for binding to the flowcells of the MiSeq. .. We employed a two-step tailed PCR approach to construct the paired-end libraries ( ).

Article Title: Analysis of the genetic diversity of influenza A viruses using next-generation DNA sequencing
Article Snippet: Nearly 70% of the unprocessed reads obtained on the Illumina MiSeq (2x250 bp sequencing) have a length of 250 bp, and the mean read length is 233.70 bp ± 1.65 bp (Figure A). .. As analyzed on a High Sensitivity DNA Chip on the Agilent Bioanalyzer, the peak fragment size before emulsion PCR (emPCR) was situated around 450 bp (data not shown), indicating that Covaris shearing and subsequent size selection did not account for this relatively short average sequence length.

Construct:

Article Title: MiFish, a set of universal PCR primers for metabarcoding environmental DNA from fishes: detection of more than 230 subtropical marine species
Article Snippet: Massively parallel paired-end sequencing on the MiSeq platform (Illumina, San Diego, CA, USA) requires PCR amplicons to be flanked by: (i) primer-binding sites for sequencing; (ii) dual-index (i.e. barcode) sequences; and (iii) adapter sequences for binding to the flowcells of the MiSeq. .. We employed a two-step tailed PCR approach to construct the paired-end libraries ( ).

In Silico:

Article Title: Analysis of the genetic diversity of influenza A viruses using next-generation DNA sequencing
Article Snippet: The output data of both sequencing platforms were processed in silico as described above and used to count the number of reads with C/T at position 354 and A/T at position 645 in the M segment. .. Illumina MiSeq slightly overestimated and Ion Torrent PGM slightly underestimated the expected percentage of tracer mutations in the PR8:PR8mut mix (Table ).

Modification:

Article Title: Molecular Diagnosis of Vaginitis: Comparing Quantitative PCR and Microbiome Profiling Approaches to Current Microscopy Scoring
Article Snippet: The V3 variable region was amplified using modified 341F and 518R primers developed previously ( ). .. The amplicons were pooled and then quantified with the Bioanalyzer high-sensitivity DNA chip (Agilent, Mississauga, ON) before sequencing on the MiSeq using a reagent kit v3 according to the manufacturer’s instructions (Illumina).

Article Title: Analysis of the genetic diversity of influenza A viruses using next-generation DNA sequencing
Article Snippet: Next, the sequencing reads were trimmed from both sides using the modified Mott trimming algorithm to reach a Q20 score, which means that the chance that a particular base in the sequence is called incorrectly by the sequencer is 1 in 100. .. For the Illumina MiSeq, the broken pairs resulting from trimming and filtering were also removed.

Derivative Assay:

Article Title: Analysis of the genetic diversity of influenza A viruses using next-generation DNA sequencing
Article Snippet: Paragraph title: De novo assembly of sequencing reads derived from viral RNA ... The viral RT-PCR products were purified and subjected to NGS on the Illumina MiSeq and the Ion Torrent PGM platforms.

Ligation:

Article Title: Analysis of the genetic diversity of influenza A viruses using next-generation DNA sequencing
Article Snippet: Mechanical fragmentation followed by adaptor ligation enables comparable coverage of all bases of the influenza virus genome, and is therefore the preferred method for library preparation (Figures and ). .. For clinical samples, the shorter turnaround time of the Ion Torrent PGM (sample preparation, sequencing and analysis in about 2 days) is clearly advantageous to the Illumina MiSeq (about 3 days).

Article Title: Analysis of the genetic diversity of influenza A viruses using next-generation DNA sequencing
Article Snippet: Plasmid samples were fragmented with Nextera XT transposase for Illumina MiSeq and mechanically sheared by Covaris, followed by adaptor ligation before Ion Torrent PGM sequencing. .. Nearly 70% of the unprocessed reads obtained on the Illumina MiSeq (2x250 bp sequencing) have a length of 250 bp, and the mean read length is 233.70 bp ± 1.65 bp (Figure A).

Reverse Transcription Polymerase Chain Reaction:

Article Title: Analysis of the genetic diversity of influenza A viruses using next-generation DNA sequencing
Article Snippet: .. The viral RT-PCR products were purified and subjected to NGS on the Illumina MiSeq and the Ion Torrent PGM platforms. ..

Article Title: Analysis of the genetic diversity of influenza A viruses using next-generation DNA sequencing
Article Snippet: The proposed RT-PCR protocol and subsequent analysis pipeline for influenza viruses is widely applicable, e.g. to study vaccine composition, analyze virus evolution under selection pressure, monitor mutations associated with antiviral resistance, and assemble the reference genome of new viral isolates. .. For clinical samples, the shorter turnaround time of the Ion Torrent PGM (sample preparation, sequencing and analysis in about 2 days) is clearly advantageous to the Illumina MiSeq (about 3 days).

Article Title: Analysis of the genetic diversity of influenza A viruses using next-generation DNA sequencing
Article Snippet: PR8, PR8mut and a mixture of PR8 and PR8mut (99% PR8:1% PR8mut, v:v, virus samples mixed before RNA isolation), were used to prepare RT-PCR products that were subsequently sequenced on both platforms (in duplicate, except for the mixed sample) (Figure A). .. Illumina MiSeq slightly overestimated and Ion Torrent PGM slightly underestimated the expected percentage of tracer mutations in the PR8:PR8mut mix (Table ).

Article Title: Analysis of the genetic diversity of influenza A viruses using next-generation DNA sequencing
Article Snippet: For the Illumina MiSeq, the broken pairs resulting from trimming and filtering were also removed. .. In addition, the processed reads were also aligned with the pHW197-M plasmid reference sequence or the influenza PR8 reference genome (based on the sequences encoding the eight segments in the pHW vectors, determined by Sanger sequencing, with addition of the extra 20 nucleotides present at the 5′ site in the RT-PCR primers) using local alignment.

Binding Assay:

Article Title: MiFish, a set of universal PCR primers for metabarcoding environmental DNA from fishes: detection of more than 230 subtropical marine species
Article Snippet: .. Massively parallel paired-end sequencing on the MiSeq platform (Illumina, San Diego, CA, USA) requires PCR amplicons to be flanked by: (i) primer-binding sites for sequencing; (ii) dual-index (i.e. barcode) sequences; and (iii) adapter sequences for binding to the flowcells of the MiSeq. .. We employed a two-step tailed PCR approach to construct the paired-end libraries ( ).

Mutagenesis:

Article Title: Analysis of the genetic diversity of influenza A viruses using next-generation DNA sequencing
Article Snippet: Variant detection We considered the frequency of a given nucleotide significant (a real mutation) when it was higher than twice the sequencing error background, i.e. above 0.16% for the Illumina MiSeq and above 0.24% for the Ion Torrent PGM. .. In contrast, the variant calls on the Illumina MiSeq were mainly SNPs (Table ).

Isolation:

Article Title: Analysis of the genetic diversity of influenza A viruses using next-generation DNA sequencing
Article Snippet: PR8, PR8mut and a mixture of PR8 and PR8mut (99% PR8:1% PR8mut, v:v, virus samples mixed before RNA isolation), were used to prepare RT-PCR products that were subsequently sequenced on both platforms (in duplicate, except for the mixed sample) (Figure A). .. Illumina MiSeq slightly overestimated and Ion Torrent PGM slightly underestimated the expected percentage of tracer mutations in the PR8:PR8mut mix (Table ).

Purification:

Article Title: Molecular Diagnosis of Vaginitis: Comparing Quantitative PCR and Microbiome Profiling Approaches to Current Microscopy Scoring
Article Snippet: Purified DNA from the vaginal swabs was also tested by next-generation sequencing (NGS) using high-throughput 16S rRNA gene amplicon profiling on the MiSeq instrument (Illumina, San Diego, CA) at the Nicole Perkins Microbial Community Laboratory sequencing facility at the University of Calgary. .. The amplicons were pooled and then quantified with the Bioanalyzer high-sensitivity DNA chip (Agilent, Mississauga, ON) before sequencing on the MiSeq using a reagent kit v3 according to the manufacturer’s instructions (Illumina).

Article Title: Analysis of the genetic diversity of influenza A viruses using next-generation DNA sequencing
Article Snippet: .. The viral RT-PCR products were purified and subjected to NGS on the Illumina MiSeq and the Ion Torrent PGM platforms. ..

Sequencing:

Article Title: Analysis of the genetic diversity of influenza A viruses using next-generation DNA sequencing
Article Snippet: Despite this stringent cut-off, false positive errors were still detected, mostly as a consequence of the sequence specific error profiles of both sequencers (Table , [ , , ]). .. In contrast, the variant calls on the Illumina MiSeq were mainly SNPs (Table ).

Article Title: Molecular Diagnosis of Vaginitis: Comparing Quantitative PCR and Microbiome Profiling Approaches to Current Microscopy Scoring
Article Snippet: .. The amplicons were pooled and then quantified with the Bioanalyzer high-sensitivity DNA chip (Agilent, Mississauga, ON) before sequencing on the MiSeq using a reagent kit v3 according to the manufacturer’s instructions (Illumina). .. The sequencing run included a no-template negative sample as an internal control for contamination.

Article Title: Analysis of the genetic diversity of influenza A viruses using next-generation DNA sequencing
Article Snippet: .. Therefore, we conclude that the overall sequencing quality of the reads obtained on the Illumina MiSeq is higher than that obtained on the Ion Torrent PGM. ..

Article Title: Analysis of the genetic diversity of influenza A viruses using next-generation DNA sequencing
Article Snippet: Paragraph title: De novo assembly of sequencing reads derived from viral RNA ... The viral RT-PCR products were purified and subjected to NGS on the Illumina MiSeq and the Ion Torrent PGM platforms.

Article Title: Cross-clade simultaneous HIV drug resistance genotyping for reverse transcriptase, protease, and integrase inhibitor mutations by Illumina MiSeq
Article Snippet: .. Lastly, Illumina MiSeq is the first and only next-generation sequencing platform to receive FDA approval for assays developed on that device, making it the optimal deep sequencing platform to develop a HIV drug resistance assay for possible clinical use in the future [ ]. .. Data analysis considerations Data analysis of next-generation sequencing techniques can be exceptionally difficult and requires many considerations.

Article Title: Analysis of the genetic diversity of influenza A viruses using next-generation DNA sequencing
Article Snippet: .. For clinical samples, the shorter turnaround time of the Ion Torrent PGM (sample preparation, sequencing and analysis in about 2 days) is clearly advantageous to the Illumina MiSeq (about 3 days). .. In contrast, when analyzing many viral samples at high coverage, the greater output of the Illumina MiSeq is an important advantage.

Article Title: Analysis of the genetic diversity of influenza A viruses using next-generation DNA sequencing
Article Snippet: .. In addition, the Nextera transposon-based fragmentation that we used for the samples sequenced on the Illumina MiSeq has some sequence preference, which can lead to a fragmentation bias, particularly in small genomes [ ]. .. Since the plasmid reference sequence is known, we were confident that any mismatching nucleotide variant could be reported as a sequencing error.

Article Title: MiFish, a set of universal PCR primers for metabarcoding environmental DNA from fishes: detection of more than 230 subtropical marine species
Article Snippet: .. Massively parallel paired-end sequencing on the MiSeq platform (Illumina, San Diego, CA, USA) requires PCR amplicons to be flanked by: (i) primer-binding sites for sequencing; (ii) dual-index (i.e. barcode) sequences; and (iii) adapter sequences for binding to the flowcells of the MiSeq. .. We employed a two-step tailed PCR approach to construct the paired-end libraries ( ).

Article Title: Analysis of the genetic diversity of influenza A viruses using next-generation DNA sequencing
Article Snippet: .. Nearly 70% of the unprocessed reads obtained on the Illumina MiSeq (2x250 bp sequencing) have a length of 250 bp, and the mean read length is 233.70 bp ± 1.65 bp (Figure A). .. The length of the unprocessed reads generated by the Ion Torrent PGM (400-bp sequencing on Ion 318 chip v2) follows a Gaussian distribution with a peak around 280 bp and a mean read length of 261.06 bp ± 2.51 bp (Figure B).

Article Title: Analysis of the genetic diversity of influenza A viruses using next-generation DNA sequencing
Article Snippet: The output data of both sequencing platforms were processed in silico as described above and used to count the number of reads with C/T at position 354 and A/T at position 645 in the M segment. .. Illumina MiSeq slightly overestimated and Ion Torrent PGM slightly underestimated the expected percentage of tracer mutations in the PR8:PR8mut mix (Table ).

Chromatin Immunoprecipitation:

Article Title: Molecular Diagnosis of Vaginitis: Comparing Quantitative PCR and Microbiome Profiling Approaches to Current Microscopy Scoring
Article Snippet: .. The amplicons were pooled and then quantified with the Bioanalyzer high-sensitivity DNA chip (Agilent, Mississauga, ON) before sequencing on the MiSeq using a reagent kit v3 according to the manufacturer’s instructions (Illumina). .. The sequencing run included a no-template negative sample as an internal control for contamination.

Article Title: Analysis of the genetic diversity of influenza A viruses using next-generation DNA sequencing
Article Snippet: Nearly 70% of the unprocessed reads obtained on the Illumina MiSeq (2x250 bp sequencing) have a length of 250 bp, and the mean read length is 233.70 bp ± 1.65 bp (Figure A). .. The length of the unprocessed reads generated by the Ion Torrent PGM (400-bp sequencing on Ion 318 chip v2) follows a Gaussian distribution with a peak around 280 bp and a mean read length of 261.06 bp ± 2.51 bp (Figure B).

Plasmid Preparation:

Article Title: Analysis of the genetic diversity of influenza A viruses using next-generation DNA sequencing
Article Snippet: In addition, the Nextera transposon-based fragmentation that we used for the samples sequenced on the Illumina MiSeq has some sequence preference, which can lead to a fragmentation bias, particularly in small genomes [ ]. .. Since the plasmid reference sequence is known, we were confident that any mismatching nucleotide variant could be reported as a sequencing error.

Article Title: Analysis of the genetic diversity of influenza A viruses using next-generation DNA sequencing
Article Snippet: Plasmid samples were fragmented with Nextera XT transposase for Illumina MiSeq and mechanically sheared by Covaris, followed by adaptor ligation before Ion Torrent PGM sequencing. .. Nearly 70% of the unprocessed reads obtained on the Illumina MiSeq (2x250 bp sequencing) have a length of 250 bp, and the mean read length is 233.70 bp ± 1.65 bp (Figure A).

Article Title: Analysis of the genetic diversity of influenza A viruses using next-generation DNA sequencing
Article Snippet: .. Overall, the Illumina MiSeq is more accurate than the Ion Torrent PGM sequencer but they have similar sensitivities for detection of SNPs in plasmid DNA. .. Sequencing of influenza virus samples To compare the efficacy of the sequencers for detecting mutations in an influenza A virus sample, we generated influenza virus starting from eight plasmids, including pHW197-M or pHW197-Mmut.

Article Title: Analysis of the genetic diversity of influenza A viruses using next-generation DNA sequencing
Article Snippet: For the Illumina MiSeq, the broken pairs resulting from trimming and filtering were also removed. .. In addition, the processed reads were also aligned with the pHW197-M plasmid reference sequence or the influenza PR8 reference genome (based on the sequences encoding the eight segments in the pHW vectors, determined by Sanger sequencing, with addition of the extra 20 nucleotides present at the 5′ site in the RT-PCR primers) using local alignment.

Multiplex Assay:

Article Title: MiFish, a set of universal PCR primers for metabarcoding environmental DNA from fishes: detection of more than 230 subtropical marine species
Article Snippet: Of these 18 eDNA samples, five samples from the Kuroshio tank were additionally used for multiplex PCR using two universal plus one genus-specific primer pairs (MiFish-U/E/tuna) for correct assignments of Thunnus species. .. Massively parallel paired-end sequencing on the MiSeq platform (Illumina, San Diego, CA, USA) requires PCR amplicons to be flanked by: (i) primer-binding sites for sequencing; (ii) dual-index (i.e. barcode) sequences; and (iii) adapter sequences for binding to the flowcells of the MiSeq.

Selection:

Article Title: Analysis of the genetic diversity of influenza A viruses using next-generation DNA sequencing
Article Snippet: The proposed RT-PCR protocol and subsequent analysis pipeline for influenza viruses is widely applicable, e.g. to study vaccine composition, analyze virus evolution under selection pressure, monitor mutations associated with antiviral resistance, and assemble the reference genome of new viral isolates. .. For clinical samples, the shorter turnaround time of the Ion Torrent PGM (sample preparation, sequencing and analysis in about 2 days) is clearly advantageous to the Illumina MiSeq (about 3 days).

Article Title: Analysis of the genetic diversity of influenza A viruses using next-generation DNA sequencing
Article Snippet: Nearly 70% of the unprocessed reads obtained on the Illumina MiSeq (2x250 bp sequencing) have a length of 250 bp, and the mean read length is 233.70 bp ± 1.65 bp (Figure A). .. As analyzed on a High Sensitivity DNA Chip on the Agilent Bioanalyzer, the peak fragment size before emulsion PCR (emPCR) was situated around 450 bp (data not shown), indicating that Covaris shearing and subsequent size selection did not account for this relatively short average sequence length.

Sample Prep:

Article Title: Analysis of the genetic diversity of influenza A viruses using next-generation DNA sequencing
Article Snippet: .. For clinical samples, the shorter turnaround time of the Ion Torrent PGM (sample preparation, sequencing and analysis in about 2 days) is clearly advantageous to the Illumina MiSeq (about 3 days). .. In contrast, when analyzing many viral samples at high coverage, the greater output of the Illumina MiSeq is an important advantage.

In Vitro:

Article Title: Analysis of the genetic diversity of influenza A viruses using next-generation DNA sequencing
Article Snippet: Illumina MiSeq slightly overestimated and Ion Torrent PGM slightly underestimated the expected percentage of tracer mutations in the PR8:PR8mut mix (Table ). .. Next, we determined the number of variants at each nucleotide position in the virus-derived sequences, which would reflect the quasispecies diversity of in vitro grown PR8 and PR8mut virus.

Next-Generation Sequencing:

Article Title: Molecular Diagnosis of Vaginitis: Comparing Quantitative PCR and Microbiome Profiling Approaches to Current Microscopy Scoring
Article Snippet: Purified DNA from the vaginal swabs was also tested by next-generation sequencing (NGS) using high-throughput 16S rRNA gene amplicon profiling on the MiSeq instrument (Illumina, San Diego, CA) at the Nicole Perkins Microbial Community Laboratory sequencing facility at the University of Calgary. .. The amplicons were pooled and then quantified with the Bioanalyzer high-sensitivity DNA chip (Agilent, Mississauga, ON) before sequencing on the MiSeq using a reagent kit v3 according to the manufacturer’s instructions (Illumina).

Article Title: Analysis of the genetic diversity of influenza A viruses using next-generation DNA sequencing
Article Snippet: .. The viral RT-PCR products were purified and subjected to NGS on the Illumina MiSeq and the Ion Torrent PGM platforms. ..

Article Title: Cross-clade simultaneous HIV drug resistance genotyping for reverse transcriptase, protease, and integrase inhibitor mutations by Illumina MiSeq
Article Snippet: .. Lastly, Illumina MiSeq is the first and only next-generation sequencing platform to receive FDA approval for assays developed on that device, making it the optimal deep sequencing platform to develop a HIV drug resistance assay for possible clinical use in the future [ ]. .. Data analysis considerations Data analysis of next-generation sequencing techniques can be exceptionally difficult and requires many considerations.

High Throughput Screening Assay:

Article Title: Molecular Diagnosis of Vaginitis: Comparing Quantitative PCR and Microbiome Profiling Approaches to Current Microscopy Scoring
Article Snippet: Purified DNA from the vaginal swabs was also tested by next-generation sequencing (NGS) using high-throughput 16S rRNA gene amplicon profiling on the MiSeq instrument (Illumina, San Diego, CA) at the Nicole Perkins Microbial Community Laboratory sequencing facility at the University of Calgary. .. The amplicons were pooled and then quantified with the Bioanalyzer high-sensitivity DNA chip (Agilent, Mississauga, ON) before sequencing on the MiSeq using a reagent kit v3 according to the manufacturer’s instructions (Illumina).

Variant Assay:

Article Title: Analysis of the genetic diversity of influenza A viruses using next-generation DNA sequencing
Article Snippet: .. In contrast, the variant calls on the Illumina MiSeq were mainly SNPs (Table ). ..

Article Title: Analysis of the genetic diversity of influenza A viruses using next-generation DNA sequencing
Article Snippet: In addition, the Nextera transposon-based fragmentation that we used for the samples sequenced on the Illumina MiSeq has some sequence preference, which can lead to a fragmentation bias, particularly in small genomes [ ]. .. Since the plasmid reference sequence is known, we were confident that any mismatching nucleotide variant could be reported as a sequencing error.

Article Title: Analysis of the genetic diversity of influenza A viruses using next-generation DNA sequencing
Article Snippet: Since we started with viral RNA, we increased the background threshold for variant calling to 0.5%, what we believe is the biologically relevant frequency threshold. .. Illumina MiSeq slightly overestimated and Ion Torrent PGM slightly underestimated the expected percentage of tracer mutations in the PR8:PR8mut mix (Table ).

Article Title: Analysis of the genetic diversity of influenza A viruses using next-generation DNA sequencing
Article Snippet: Paragraph title: Variant detection ... Overall, the Illumina MiSeq is more accurate than the Ion Torrent PGM sequencer but they have similar sensitivities for detection of SNPs in plasmid DNA.

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  • 85
    Illumina Inc platform transcriptome sequencing strategy
    Phylogenetic reconstruction of metazoans using the gene methionine adenosyl transferase. Only bootstrap support values above 50% shown. Sequences derived from our <t>transcriptomes</t> are shown in red. GenBank accession numbers for all sequences used can be found in Additional file 9 .
    Platform Transcriptome Sequencing Strategy, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 85/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/platform transcriptome sequencing strategy/product/Illumina Inc
    Average 85 stars, based on 1 article reviews
    Price from $9.99 to $1999.99
    platform transcriptome sequencing strategy - by Bioz Stars, 2020-04
    85/100 stars
      Buy from Supplier

    99
    Illumina Inc illumina hiseq platform
    Identification of direct and regulated targets of UNC-62 in adults by ChIP–seq and RNA–seq. (A) An example of UNC-62 ChIP-seq read density at a significantly enriched binding site is shown. Top tracks show read density in ChIP-seq experiments for UNC-62 in young adults (green) and L3 larvae (blue) as well as non-immunoprecipitated input control (grey). Boxes underneath the read density tracks indicate significant binding sites ( q -value≤10 −5 ). Bottom tracks indicate genes (with coding exons in thick blue boxes). (B) Examples of unc-62 RNAi 3′-end enriched RNA-seq data is shown. We performed three independent experiments in which we fed worms either unc-62 RNAi or control bacteria, isolated mRNA and generated RNA-seq libraries, and sequenced these libraries on the <t>Illumina</t> <t>HiSeq</t> platform. For the ilys-5 (left) and vit-2 (right) genomic regions, reads map to annotated exon regions on the proper strand, and are enriched at the 3′ end of the transcript. Read densities are displayed for control (black) and unc-62 RNAi (blue), scaled as reads per million uniquely mapping reads. (C) Rank Products-based analysis (based on [27] ; see Methods and Figure S5 ) to identify genes reproducibly altered across all three biological replicates identified 67 genes significantly increased and 115 genes significantly decreased upon unc-62 RNAi at a 10% false positive rate.
    Illumina Hiseq Platform, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 99/100, based on 155 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/illumina hiseq platform/product/Illumina Inc
    Average 99 stars, based on 155 article reviews
    Price from $9.99 to $1999.99
    illumina hiseq platform - by Bioz Stars, 2020-04
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    85
    Illumina Inc illumina 660w quad platform
    The 1q21.1 region (adaptation from the UCSC hg18 Genome Browser) and the summary of findings in TOF and non-TOF mixed CHD cohort. ( A ) The region of 1q21.1 is complex (143.5–147.5 Mb is shown) due to the presence of extensive segmental duplication blocks and the existing gaps in the reference human genome sequence (NCBI Build 36.1). The largest pair of segmental duplications with > 99% homology that mediates most of the rearrangements in this locus is indicated by large orange arrows. ( B ) RefSeq genes in the region. The critical region is indicated by translucent gray block. ( C ) The coverage of the <t>Illumina</t> <t>660W-Quad</t> (the main platform used in this study) and the location of the custom-designed MLPA probes used in this study are shown. ( D ) Overview of 1q21.1 duplications (blue bars) and deletions (red bars) identified in our study. The cardiac phenotype is shown after the patient identifier. TGA, transposition of the great arteries; MV, mitral valve dysplasia with ventricular septal defect; ASD, atrial septal defect.
    Illumina 660w Quad Platform, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 85/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/illumina 660w quad platform/product/Illumina Inc
    Average 85 stars, based on 1 article reviews
    Price from $9.99 to $1999.99
    illumina 660w quad platform - by Bioz Stars, 2020-04
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    86
    Illumina Inc infinium humanmethylation beadchip platforms
    Schematic representation of colorectal cancer marker discovery and verification pipeline. We used DNA methylation data from the <t>Infinium</t> HumanMethylation27 <t>Beadchip</t> (HM27) and HumanMethylation450 Beadchip (HM450) Infinium platforms to screen 27,578 (HM27) and 482,421 (HM450) CpG loci for their methylation status in CRC samples, PBL samples from healthy subjects, paired normal colorectal tissue samples (NC) and 15 other types of cancer (OC). We used a stepwise approach eliminating probes that failed in any of the samples, probes that contained SNPs or repeat sequences, probes with a highest PBL β-value (β-PBL H ) or a mean normal colon tissue β-value (β-NC M ) higher than the associated 10th percentile of CRC tumor β-values (β-CRC 10 ) or higher than 0.2 in any of the PBL or NC samples (Infinium panel). The remaining probes were ranked based on the difference between β-CRC 10 and β-PBL H and the top 25 were selected from both datasets (HM27 and HM450) for filtering against OC samples. Probes with a mean OC β-value higher than the associated mean CRC β-value (β-CRC M ) were eliminated. A total of 15 MethyLight reactions (markers) were designed for 10 probes and tested in a sequence of verification steps (MethyLight panel). Markers were eliminated if their performance was suboptimal in controls such as in vitro methylated Sss 1 DNA, PBL and plasma samples from healthy controls and CRC tumor tissues. Markers were also eliminated if they failed to detect CRC methylated DNA in pooled plasma and serum from CRC patients. Two markers met all the selection criteria and were advanced in the pipeline for further verification on individual patient samples. (*Probes that failed in any of the samples, as well as those that included SNPs and repeat sequences; **Other cancer types used in this study are summarized in Table 1 , ***M. Sss I treated DNA).
    Infinium Humanmethylation Beadchip Platforms, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 86/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/infinium humanmethylation beadchip platforms/product/Illumina Inc
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    Image Search Results


    Phylogenetic reconstruction of metazoans using the gene methionine adenosyl transferase. Only bootstrap support values above 50% shown. Sequences derived from our transcriptomes are shown in red. GenBank accession numbers for all sequences used can be found in Additional file 9 .

    Journal: Frontiers in Zoology

    Article Title: Comparative description of ten transcriptomes of newly sequenced invertebrates and efficiency estimation of genomic sampling in non-model taxa

    doi: 10.1186/1742-9994-9-33

    Figure Lengend Snippet: Phylogenetic reconstruction of metazoans using the gene methionine adenosyl transferase. Only bootstrap support values above 50% shown. Sequences derived from our transcriptomes are shown in red. GenBank accession numbers for all sequences used can be found in Additional file 9 .

    Article Snippet: In this article we characterized the effectiveness of the Illumina platform transcriptome sequencing strategy across these selected species with respect to data yield and quality.

    Techniques: Derivative Assay

    Assembly of the transcriptome datasets through sequential addition of 5 million reads. a : N50; and b : total number of contigs, were plotted against the different assemblies obtained for each species. Note that the final values in this figure are different from those in Table 2 because we used a newer version of CLC Genomics Workbench (v. 5.1).

    Journal: Frontiers in Zoology

    Article Title: Comparative description of ten transcriptomes of newly sequenced invertebrates and efficiency estimation of genomic sampling in non-model taxa

    doi: 10.1186/1742-9994-9-33

    Figure Lengend Snippet: Assembly of the transcriptome datasets through sequential addition of 5 million reads. a : N50; and b : total number of contigs, were plotted against the different assemblies obtained for each species. Note that the final values in this figure are different from those in Table 2 because we used a newer version of CLC Genomics Workbench (v. 5.1).

    Article Snippet: In this article we characterized the effectiveness of the Illumina platform transcriptome sequencing strategy across these selected species with respect to data yield and quality.

    Techniques:

    Workflow followed for the transcriptome analysis.

    Journal: Frontiers in Zoology

    Article Title: Comparative description of ten transcriptomes of newly sequenced invertebrates and efficiency estimation of genomic sampling in non-model taxa

    doi: 10.1186/1742-9994-9-33

    Figure Lengend Snippet: Workflow followed for the transcriptome analysis.

    Article Snippet: In this article we characterized the effectiveness of the Illumina platform transcriptome sequencing strategy across these selected species with respect to data yield and quality.

    Techniques:

    Identification of direct and regulated targets of UNC-62 in adults by ChIP–seq and RNA–seq. (A) An example of UNC-62 ChIP-seq read density at a significantly enriched binding site is shown. Top tracks show read density in ChIP-seq experiments for UNC-62 in young adults (green) and L3 larvae (blue) as well as non-immunoprecipitated input control (grey). Boxes underneath the read density tracks indicate significant binding sites ( q -value≤10 −5 ). Bottom tracks indicate genes (with coding exons in thick blue boxes). (B) Examples of unc-62 RNAi 3′-end enriched RNA-seq data is shown. We performed three independent experiments in which we fed worms either unc-62 RNAi or control bacteria, isolated mRNA and generated RNA-seq libraries, and sequenced these libraries on the Illumina HiSeq platform. For the ilys-5 (left) and vit-2 (right) genomic regions, reads map to annotated exon regions on the proper strand, and are enriched at the 3′ end of the transcript. Read densities are displayed for control (black) and unc-62 RNAi (blue), scaled as reads per million uniquely mapping reads. (C) Rank Products-based analysis (based on [27] ; see Methods and Figure S5 ) to identify genes reproducibly altered across all three biological replicates identified 67 genes significantly increased and 115 genes significantly decreased upon unc-62 RNAi at a 10% false positive rate.

    Journal: PLoS Genetics

    Article Title: Roles of the Developmental Regulator unc-62/Homothorax in Limiting Longevity in Caenorhabditis elegans

    doi: 10.1371/journal.pgen.1003325

    Figure Lengend Snippet: Identification of direct and regulated targets of UNC-62 in adults by ChIP–seq and RNA–seq. (A) An example of UNC-62 ChIP-seq read density at a significantly enriched binding site is shown. Top tracks show read density in ChIP-seq experiments for UNC-62 in young adults (green) and L3 larvae (blue) as well as non-immunoprecipitated input control (grey). Boxes underneath the read density tracks indicate significant binding sites ( q -value≤10 −5 ). Bottom tracks indicate genes (with coding exons in thick blue boxes). (B) Examples of unc-62 RNAi 3′-end enriched RNA-seq data is shown. We performed three independent experiments in which we fed worms either unc-62 RNAi or control bacteria, isolated mRNA and generated RNA-seq libraries, and sequenced these libraries on the Illumina HiSeq platform. For the ilys-5 (left) and vit-2 (right) genomic regions, reads map to annotated exon regions on the proper strand, and are enriched at the 3′ end of the transcript. Read densities are displayed for control (black) and unc-62 RNAi (blue), scaled as reads per million uniquely mapping reads. (C) Rank Products-based analysis (based on [27] ; see Methods and Figure S5 ) to identify genes reproducibly altered across all three biological replicates identified 67 genes significantly increased and 115 genes significantly decreased upon unc-62 RNAi at a 10% false positive rate.

    Article Snippet: In order to identify genes that were consistently increased or decreased in expression upon unc-62 RNAi, we developed an analysis method based on the Rank Products method previously described for microarray analysis . (A) We performed three independent experiments in which we fed worms either unc-62 RNAi or control bacteria, isolated mRNA and generated RNA-seq libraries, and sequenced these libraries on the Illumina HiSeq platform.

    Techniques: Chromatin Immunoprecipitation, RNA Sequencing Assay, Binding Assay, Immunoprecipitation, Isolation, Generated

    The 1q21.1 region (adaptation from the UCSC hg18 Genome Browser) and the summary of findings in TOF and non-TOF mixed CHD cohort. ( A ) The region of 1q21.1 is complex (143.5–147.5 Mb is shown) due to the presence of extensive segmental duplication blocks and the existing gaps in the reference human genome sequence (NCBI Build 36.1). The largest pair of segmental duplications with > 99% homology that mediates most of the rearrangements in this locus is indicated by large orange arrows. ( B ) RefSeq genes in the region. The critical region is indicated by translucent gray block. ( C ) The coverage of the Illumina 660W-Quad (the main platform used in this study) and the location of the custom-designed MLPA probes used in this study are shown. ( D ) Overview of 1q21.1 duplications (blue bars) and deletions (red bars) identified in our study. The cardiac phenotype is shown after the patient identifier. TGA, transposition of the great arteries; MV, mitral valve dysplasia with ventricular septal defect; ASD, atrial septal defect.

    Journal: Human Molecular Genetics

    Article Title: Phenotype-specific effect of chromosome 1q21.1 rearrangements and GJA5 duplications in 2436 congenital heart disease patients and 6760 controls

    doi: 10.1093/hmg/ddr589

    Figure Lengend Snippet: The 1q21.1 region (adaptation from the UCSC hg18 Genome Browser) and the summary of findings in TOF and non-TOF mixed CHD cohort. ( A ) The region of 1q21.1 is complex (143.5–147.5 Mb is shown) due to the presence of extensive segmental duplication blocks and the existing gaps in the reference human genome sequence (NCBI Build 36.1). The largest pair of segmental duplications with > 99% homology that mediates most of the rearrangements in this locus is indicated by large orange arrows. ( B ) RefSeq genes in the region. The critical region is indicated by translucent gray block. ( C ) The coverage of the Illumina 660W-Quad (the main platform used in this study) and the location of the custom-designed MLPA probes used in this study are shown. ( D ) Overview of 1q21.1 duplications (blue bars) and deletions (red bars) identified in our study. The cardiac phenotype is shown after the patient identifier. TGA, transposition of the great arteries; MV, mitral valve dysplasia with ventricular septal defect; ASD, atrial septal defect.

    Article Snippet: TOF patients and family members (907 affected offspring and 747 unaffected parents), 1987 non-TOF CHD patients and 856 unrelated individuals from a French control cohort were genotyped on the Illumina 660W-Quad platform.

    Techniques: Sequencing, Blocking Assay, Multiplex Ligation-dependent Probe Amplification

    Schematic representation of colorectal cancer marker discovery and verification pipeline. We used DNA methylation data from the Infinium HumanMethylation27 Beadchip (HM27) and HumanMethylation450 Beadchip (HM450) Infinium platforms to screen 27,578 (HM27) and 482,421 (HM450) CpG loci for their methylation status in CRC samples, PBL samples from healthy subjects, paired normal colorectal tissue samples (NC) and 15 other types of cancer (OC). We used a stepwise approach eliminating probes that failed in any of the samples, probes that contained SNPs or repeat sequences, probes with a highest PBL β-value (β-PBL H ) or a mean normal colon tissue β-value (β-NC M ) higher than the associated 10th percentile of CRC tumor β-values (β-CRC 10 ) or higher than 0.2 in any of the PBL or NC samples (Infinium panel). The remaining probes were ranked based on the difference between β-CRC 10 and β-PBL H and the top 25 were selected from both datasets (HM27 and HM450) for filtering against OC samples. Probes with a mean OC β-value higher than the associated mean CRC β-value (β-CRC M ) were eliminated. A total of 15 MethyLight reactions (markers) were designed for 10 probes and tested in a sequence of verification steps (MethyLight panel). Markers were eliminated if their performance was suboptimal in controls such as in vitro methylated Sss 1 DNA, PBL and plasma samples from healthy controls and CRC tumor tissues. Markers were also eliminated if they failed to detect CRC methylated DNA in pooled plasma and serum from CRC patients. Two markers met all the selection criteria and were advanced in the pipeline for further verification on individual patient samples. (*Probes that failed in any of the samples, as well as those that included SNPs and repeat sequences; **Other cancer types used in this study are summarized in Table 1 , ***M. Sss I treated DNA).

    Journal: PLoS ONE

    Article Title: Genome-Scale Discovery of DNA-Methylation Biomarkers for Blood-Based Detection of Colorectal Cancer

    doi: 10.1371/journal.pone.0050266

    Figure Lengend Snippet: Schematic representation of colorectal cancer marker discovery and verification pipeline. We used DNA methylation data from the Infinium HumanMethylation27 Beadchip (HM27) and HumanMethylation450 Beadchip (HM450) Infinium platforms to screen 27,578 (HM27) and 482,421 (HM450) CpG loci for their methylation status in CRC samples, PBL samples from healthy subjects, paired normal colorectal tissue samples (NC) and 15 other types of cancer (OC). We used a stepwise approach eliminating probes that failed in any of the samples, probes that contained SNPs or repeat sequences, probes with a highest PBL β-value (β-PBL H ) or a mean normal colon tissue β-value (β-NC M ) higher than the associated 10th percentile of CRC tumor β-values (β-CRC 10 ) or higher than 0.2 in any of the PBL or NC samples (Infinium panel). The remaining probes were ranked based on the difference between β-CRC 10 and β-PBL H and the top 25 were selected from both datasets (HM27 and HM450) for filtering against OC samples. Probes with a mean OC β-value higher than the associated mean CRC β-value (β-CRC M ) were eliminated. A total of 15 MethyLight reactions (markers) were designed for 10 probes and tested in a sequence of verification steps (MethyLight panel). Markers were eliminated if their performance was suboptimal in controls such as in vitro methylated Sss 1 DNA, PBL and plasma samples from healthy controls and CRC tumor tissues. Markers were also eliminated if they failed to detect CRC methylated DNA in pooled plasma and serum from CRC patients. Two markers met all the selection criteria and were advanced in the pipeline for further verification on individual patient samples. (*Probes that failed in any of the samples, as well as those that included SNPs and repeat sequences; **Other cancer types used in this study are summarized in Table 1 , ***M. Sss I treated DNA).

    Article Snippet: We used data generated using two different Illumina Infinium HumanMethylation BeadChip platforms, HM27 and HM450 (see section).

    Techniques: Marker, DNA Methylation Assay, Methylation, Sequencing, In Vitro, Selection