Structured Review

Illumina Inc illumina gaiix instrument
Illumina Gaiix Instrument, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 91/100, based on 13 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
https://www.bioz.com/result/illumina gaiix instrument/product/Illumina Inc
Average 91 stars, based on 13 article reviews
Price from $9.99 to $1999.99
illumina gaiix instrument - by Bioz Stars, 2020-07
91/100 stars

Images

Related Articles

Amplification:

Article Title: Single Round, Multiplexed Antibody Mimetic Design via mRNA Display
Article Snippet: .. Next, samples were amplified by PCR below saturation prior to performing sequencing on an Illumina GAIIx instrument. .. Following sequencing, we ranked each unique clone by copy number. demonstrates the clone frequency landscape for the input library (purified fusions prior to selection) and the two semi-enriched pools that had undergone one round of affinity selection versus IgG(Fc) ( ) or MBP ( ).

Article Title: Barcoding bias in high-throughput multiplex sequencing of miRNA
Article Snippet: .. A sample of total RNA from human brain tissue was subdivided into 12 equal independent aliquots before the ligation of the adapters, marked by 12 different barcodes during the PCR amplification step and sequenced on one lane of Illumina GAIIx instrument using a 75-bp single pass sequencing read (our design also allows independent sequencing of indexing read if desired). .. The same variance analysis revealed that the PCR-based barcodes almost completely suppressed the barcode bias , bringing the typical barcode-dependent error down to ±3%.

RNA Sequencing Assay:

Article Title: Construction of Pseudomolecule Sequences of the aus Rice Cultivar Kasalath for Comparative Genomics of Asian Cultivated Rice
Article Snippet: .. To facilitate annotation of the expressed sequences, we constructed cDNA libraries with insert sizes of 350–400 bp from total RNA samples prepared from the young leaves or young panicles of Kasalath, and used these libraries to generate short-read RNA-Seq data on the Illumina GAIIx instrument as described. .. Genome assembly Raw sequence read data generated on both platforms were preprocessed to trim low-quality or adapter sequences on both ends as described previously.

Ligation:

Article Title: Barcoding bias in high-throughput multiplex sequencing of miRNA
Article Snippet: .. A sample of total RNA from human brain tissue was subdivided into 12 equal independent aliquots before the ligation of the adapters, marked by 12 different barcodes during the PCR amplification step and sequenced on one lane of Illumina GAIIx instrument using a 75-bp single pass sequencing read (our design also allows independent sequencing of indexing read if desired). .. The same variance analysis revealed that the PCR-based barcodes almost completely suppressed the barcode bias , bringing the typical barcode-dependent error down to ±3%.

Construct:

Article Title: Construction of Pseudomolecule Sequences of the aus Rice Cultivar Kasalath for Comparative Genomics of Asian Cultivated Rice
Article Snippet: .. To facilitate annotation of the expressed sequences, we constructed cDNA libraries with insert sizes of 350–400 bp from total RNA samples prepared from the young leaves or young panicles of Kasalath, and used these libraries to generate short-read RNA-Seq data on the Illumina GAIIx instrument as described. .. Genome assembly Raw sequence read data generated on both platforms were preprocessed to trim low-quality or adapter sequences on both ends as described previously.

Purification:

Article Title: Genomic Analyses Reveal Broad Impact of miR-137 on Genes Associated with Malignant Transformation and Neuronal Differentiation in Glioblastoma Cells
Article Snippet: .. The samples were purified using Zymo DNA Clean kit and quantitated by using a bioanalyzer and Qubit methods, then sequenced on an Illumina GAIIx instrument for 36 cycles. .. After Ribo-Zero treating the RNA samples from the U343 cells, 50 ng were converted into double-stranded cDNA using the TotalScript cDNA kit (Epicentre, cat. #TSCD12924) as per the supplied protocol and purified using the Zymo DNA Clean and Concentrator kit.

Polymerase Chain Reaction:

Article Title: Single Round, Multiplexed Antibody Mimetic Design via mRNA Display
Article Snippet: .. Next, samples were amplified by PCR below saturation prior to performing sequencing on an Illumina GAIIx instrument. .. Following sequencing, we ranked each unique clone by copy number. demonstrates the clone frequency landscape for the input library (purified fusions prior to selection) and the two semi-enriched pools that had undergone one round of affinity selection versus IgG(Fc) ( ) or MBP ( ).

Article Title: Barcoding bias in high-throughput multiplex sequencing of miRNA
Article Snippet: .. A sample of total RNA from human brain tissue was subdivided into 12 equal independent aliquots before the ligation of the adapters, marked by 12 different barcodes during the PCR amplification step and sequenced on one lane of Illumina GAIIx instrument using a 75-bp single pass sequencing read (our design also allows independent sequencing of indexing read if desired). .. The same variance analysis revealed that the PCR-based barcodes almost completely suppressed the barcode bias , bringing the typical barcode-dependent error down to ±3%.

Sequencing:

Article Title: Single Round, Multiplexed Antibody Mimetic Design via mRNA Display
Article Snippet: .. Next, samples were amplified by PCR below saturation prior to performing sequencing on an Illumina GAIIx instrument. .. Following sequencing, we ranked each unique clone by copy number. demonstrates the clone frequency landscape for the input library (purified fusions prior to selection) and the two semi-enriched pools that had undergone one round of affinity selection versus IgG(Fc) ( ) or MBP ( ).

Article Title: Barcoding bias in high-throughput multiplex sequencing of miRNA
Article Snippet: .. A sample of total RNA from human brain tissue was subdivided into 12 equal independent aliquots before the ligation of the adapters, marked by 12 different barcodes during the PCR amplification step and sequenced on one lane of Illumina GAIIx instrument using a 75-bp single pass sequencing read (our design also allows independent sequencing of indexing read if desired). .. The same variance analysis revealed that the PCR-based barcodes almost completely suppressed the barcode bias , bringing the typical barcode-dependent error down to ±3%.

Article Title: A tale of three next generation sequencing platforms: comparison of Ion Torrent, Pacific Biosciences and Illumina MiSeq sequencers
Article Snippet: .. Illumina sequencing Each multiplexed library pool was sequenced on: i) an Illumina GAIIx instrument for 76 cycles from each end plus an 8 base-index sequence read, using version 2 chemistry, ii) an Illumina MiSeq for 151 cycles from each end plus an 8 base-index sequence read, iii) an Illumina HiSeq 2000 instrument for 75 cycles from each end plus an 8 base-index sequence read, using version 3 chemistry. ..

Similar Products

  • Logo
  • About
  • News
  • Press Release
  • Team
  • Advisors
  • Partners
  • Contact
  • Bioz Stars
  • Bioz vStars
  • 95
    Illumina Inc illumina gaiix
    Technology overview of NGS using the 1052-amplicon targeted sequencing panel. Sample qualification is performed using a real-time PCR assay to determine the percent “functional” DNA copies in FFPE samples using the Quantitative Functional Index (QFI). The library preparation is based on RainDance technologies picodroplet PCR to amplify target sequences with subsequent sequencing on an <t>Illumina</t> platform <t>(GAIIx</t> or HiSeq). The bioinformatics workflow trims adaptors and filters out low-quality reads, then includes genomic alignments, variant calling and result reporting (See Materials and Methods for more details and Additional file 1 : Figure S6 for the result visualization).
    Illumina Gaiix, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 95/100, based on 1624 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/illumina gaiix/product/Illumina Inc
    Average 95 stars, based on 1624 article reviews
    Price from $9.99 to $1999.99
    illumina gaiix - by Bioz Stars, 2020-07
    95/100 stars
      Buy from Supplier

    91
    Illumina Inc illumina gaii instrument
    Calling Card–seq. ( A ) A DNA-binding protein fused to Sir4 directs integration of Ty5 into the genome near to where it binds. (1) After Ty5 transposition, (2) cells that have undergone Ty5 transposition are selected. (3) Genomic DNA is isolated and cleaved with restriction enzymes that cut near the end of Ty5 and (4) ligated in a dilute solution to favor recircularization of the fragments. (5) This is followed by amplification of the circular DNA that contains the end of the transposon and flanking genomic DNA by an “inverse PCR” (the PCR primers contain the <t>Illumina</t> sequencing primers and adaptors). The DNA sequence of the inverse-PCR products is then determined on an Illumina Genome Analyzer II. ( B ) Analyzing multiple TFs in one experiment: (1) Each strain was cotransformed with a plasmid encoding a TF–Sir4 fusion and a plasmid carrying its matched barcoded Ty5 Calling Card. (2) After transposition, the Calling Cards are deposited across the genome and then (3) recovered by inverse PCR and (4) sequenced on the Illumina <t>GAII</t> with a paired-end module. (5) For each paired sequence, we identify the Calling Card insertion site and the TF that deposited it there.
    Illumina Gaii Instrument, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 91/100, based on 92 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/illumina gaii instrument/product/Illumina Inc
    Average 91 stars, based on 92 article reviews
    Price from $9.99 to $1999.99
    illumina gaii instrument - by Bioz Stars, 2020-07
    91/100 stars
      Buy from Supplier

    Image Search Results


    Technology overview of NGS using the 1052-amplicon targeted sequencing panel. Sample qualification is performed using a real-time PCR assay to determine the percent “functional” DNA copies in FFPE samples using the Quantitative Functional Index (QFI). The library preparation is based on RainDance technologies picodroplet PCR to amplify target sequences with subsequent sequencing on an Illumina platform (GAIIx or HiSeq). The bioinformatics workflow trims adaptors and filters out low-quality reads, then includes genomic alignments, variant calling and result reporting (See Materials and Methods for more details and Additional file 1 : Figure S6 for the result visualization).

    Journal: BMC Medical Genomics

    Article Title: Evaluation of an integrated clinical workflow for targeted next-generation sequencing of low-quality tumor DNA using a 51-gene enrichment panel

    doi: 10.1186/s12920-014-0062-0

    Figure Lengend Snippet: Technology overview of NGS using the 1052-amplicon targeted sequencing panel. Sample qualification is performed using a real-time PCR assay to determine the percent “functional” DNA copies in FFPE samples using the Quantitative Functional Index (QFI). The library preparation is based on RainDance technologies picodroplet PCR to amplify target sequences with subsequent sequencing on an Illumina platform (GAIIx or HiSeq). The bioinformatics workflow trims adaptors and filters out low-quality reads, then includes genomic alignments, variant calling and result reporting (See Materials and Methods for more details and Additional file 1 : Figure S6 for the result visualization).

    Article Snippet: Figure shows the sample analysis workflow including: 1) functional DNA sample quantification and quality control using real-time PCR; 2) target enrichment using massively parallel picodroplet PCR; 3) NGS using multiple instruments, including the Illumina GAIIx and HiSeq, and Personal Genome Machine (PGM) for confirmation studies; and 4) bioinformatics processing including read preprocessing, alignment, variant calling and result visualization (see also reference [ ]).

    Techniques: Next-Generation Sequencing, Amplification, Sequencing, Real-time Polymerase Chain Reaction, Formalin-fixed Paraffin-Embedded, Functional Assay, Polymerase Chain Reaction, Variant Assay

    Calling Card–seq. ( A ) A DNA-binding protein fused to Sir4 directs integration of Ty5 into the genome near to where it binds. (1) After Ty5 transposition, (2) cells that have undergone Ty5 transposition are selected. (3) Genomic DNA is isolated and cleaved with restriction enzymes that cut near the end of Ty5 and (4) ligated in a dilute solution to favor recircularization of the fragments. (5) This is followed by amplification of the circular DNA that contains the end of the transposon and flanking genomic DNA by an “inverse PCR” (the PCR primers contain the Illumina sequencing primers and adaptors). The DNA sequence of the inverse-PCR products is then determined on an Illumina Genome Analyzer II. ( B ) Analyzing multiple TFs in one experiment: (1) Each strain was cotransformed with a plasmid encoding a TF–Sir4 fusion and a plasmid carrying its matched barcoded Ty5 Calling Card. (2) After transposition, the Calling Cards are deposited across the genome and then (3) recovered by inverse PCR and (4) sequenced on the Illumina GAII with a paired-end module. (5) For each paired sequence, we identify the Calling Card insertion site and the TF that deposited it there.

    Journal: Genome Research

    Article Title: Calling Cards enable multiplexed identification of the genomic targets of DNA-binding proteins

    doi: 10.1101/gr.114850.110

    Figure Lengend Snippet: Calling Card–seq. ( A ) A DNA-binding protein fused to Sir4 directs integration of Ty5 into the genome near to where it binds. (1) After Ty5 transposition, (2) cells that have undergone Ty5 transposition are selected. (3) Genomic DNA is isolated and cleaved with restriction enzymes that cut near the end of Ty5 and (4) ligated in a dilute solution to favor recircularization of the fragments. (5) This is followed by amplification of the circular DNA that contains the end of the transposon and flanking genomic DNA by an “inverse PCR” (the PCR primers contain the Illumina sequencing primers and adaptors). The DNA sequence of the inverse-PCR products is then determined on an Illumina Genome Analyzer II. ( B ) Analyzing multiple TFs in one experiment: (1) Each strain was cotransformed with a plasmid encoding a TF–Sir4 fusion and a plasmid carrying its matched barcoded Ty5 Calling Card. (2) After transposition, the Calling Cards are deposited across the genome and then (3) recovered by inverse PCR and (4) sequenced on the Illumina GAII with a paired-end module. (5) For each paired sequence, we identify the Calling Card insertion site and the TF that deposited it there.

    Article Snippet: The DNA sequence of the genomic region immediately flanking the Calling Card (which reveals where in the genome the Calling Card landed) and the DNA sequence of the barcode (which reveals which TF was responsible for depositing the Calling Card there) are determined by paired-end DNA sequencing on an Illumina GAII instrument.

    Techniques: Binding Assay, Isolation, Amplification, Polymerase Chain Reaction, Sequencing, Inverse PCR, Plasmid Preparation

    Average spatial distribution of coverage depths for ROI of 1000 human 500-bp dbSNP loci obtained from mapping analysis after sequence enrichment from a human genomic DNA sample and Illumina GAII sequencing. The x -axis shows the nucleotide positions of

    Journal: Genome Research

    Article Title: Microarray-based multicycle-enrichment of genomic subsets for targeted next-generation sequencing

    doi: 10.1101/gr.091942.109

    Figure Lengend Snippet: Average spatial distribution of coverage depths for ROI of 1000 human 500-bp dbSNP loci obtained from mapping analysis after sequence enrichment from a human genomic DNA sample and Illumina GAII sequencing. The x -axis shows the nucleotide positions of

    Article Snippet: Processing of the enriched samples on an Illumina GAII instrument yielded 8,217,673 and 7,624,181 paired-end reads of 2 × 36 bp for the individual samples.

    Techniques: Sequencing

    Statistical analysis of average coverage depths and consensus coverages of 1000 human 500-bp loci obtained from mapping analysis after sequence enrichment from the two HapMap reference samples NA18558 and NA18561 and Illumina GAII sequencing. Shown is

    Journal: Genome Research

    Article Title: Microarray-based multicycle-enrichment of genomic subsets for targeted next-generation sequencing

    doi: 10.1101/gr.091942.109

    Figure Lengend Snippet: Statistical analysis of average coverage depths and consensus coverages of 1000 human 500-bp loci obtained from mapping analysis after sequence enrichment from the two HapMap reference samples NA18558 and NA18561 and Illumina GAII sequencing. Shown is

    Article Snippet: Processing of the enriched samples on an Illumina GAII instrument yielded 8,217,673 and 7,624,181 paired-end reads of 2 × 36 bp for the individual samples.

    Techniques: Sequencing