illumina hiseq3000 instrument Search Results


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  • 90
    Illumina Inc illumina hiseq3000 instrument
    After remixing hamPCR amplicons for efficient sequencing, original abundances can be reconstructed A) Scheme of remixing process. i: Products of individual PCRs (each containing both host and microbial amplicons) are pooled at equimolar ratios into a single tube. ii : An aliquot of DNA from the pool in i is re-amplified with 8 cycles of PCR to replace all barcodes in the pool with a new barcode, creating a reference sample. iii: A large aliquot of the pool from i is run on an agarose gel to physically separate and then purify the host and microbial fractions. iv: The host and microbial fractions and the reference sample are pooled in the ratio desired for sequencing. v: All sequences are quality filtered, demultiplexed, and taxonomically classified using the same parameters. vi: Host and microbial amplicon counts are summed from the samples comprising the pooled library ( h and m respectively), and from the reference sample ( H and M ). vi : H, h, M, and m are used to calculate the scaling constant f for the dataset. All host sequence counts are multiplied by f to reconstruct the original microbe-to-host ratios. vii: Reconstructed original abundances. B) Relative abundance (RA) of actual sequence counts from our original <t>HiSeq3000</t> run. C) Relative abundance of actual sequence counts from our adjusted library showing reduced host and 4 reference samples. D) The data from C after reconstructing original host abundance using the reference samples. E) The total fraction of host vs. other ASVs in the original library, reduced host library, and reconstruction. RA, relative abundance F) Relative abundances in the original and reconstructed library for all ASVs with a 0.05% minimum abundance, shown on 4 th -root transformed axes. R 2 , coefficient of determination. p -value from Kolmogorov–Smirnov test.
    Illumina Hiseq3000 Instrument, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 90/100, based on 111 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/illumina hiseq3000 instrument/product/Illumina Inc
    Average 90 stars, based on 111 article reviews
    Price from $9.99 to $1999.99
    illumina hiseq3000 instrument - by Bioz Stars, 2020-08
    90/100 stars
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    94
    Illumina Inc illumina hiseq2000 instrument
    Infrastructure, main tasks, and architecture . A) Infrastructure: Sequencing is performed on an <t>Illumina</t> <t>HiSeq2000</t> instrument. Data are stored on an Isilon mass storage device. Data are elaborated on a Sun Grid Engine High Performance Computing cluster (SGE-HPC). Application servers run web applications for Genome browsing, data listings, the SMITH LIMS, and host the MySQL information tier. The user data directories are organized by group leader name, user login name, file-type, and run date. B) Sample tracking in SMITH. A sample passes through four states (
    Illumina Hiseq2000 Instrument, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 94/100, based on 2611 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/illumina hiseq2000 instrument/product/Illumina Inc
    Average 94 stars, based on 2611 article reviews
    Price from $9.99 to $1999.99
    illumina hiseq2000 instrument - by Bioz Stars, 2020-08
    94/100 stars
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    90
    Illumina Inc illumina hiseq4000 instrument
    Infrastructure, main tasks, and architecture . A) Infrastructure: Sequencing is performed on an <t>Illumina</t> <t>HiSeq2000</t> instrument. Data are stored on an Isilon mass storage device. Data are elaborated on a Sun Grid Engine High Performance Computing cluster (SGE-HPC). Application servers run web applications for Genome browsing, data listings, the SMITH LIMS, and host the MySQL information tier. The user data directories are organized by group leader name, user login name, file-type, and run date. B) Sample tracking in SMITH. A sample passes through four states (
    Illumina Hiseq4000 Instrument, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 90/100, based on 230 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/illumina hiseq4000 instrument/product/Illumina Inc
    Average 90 stars, based on 230 article reviews
    Price from $9.99 to $1999.99
    illumina hiseq4000 instrument - by Bioz Stars, 2020-08
    90/100 stars
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    88
    BGI Shenzhen illumina hiseq2000 2500 instruments
    Infrastructure, main tasks, and architecture . A) Infrastructure: Sequencing is performed on an <t>Illumina</t> <t>HiSeq2000</t> instrument. Data are stored on an Isilon mass storage device. Data are elaborated on a Sun Grid Engine High Performance Computing cluster (SGE-HPC). Application servers run web applications for Genome browsing, data listings, the SMITH LIMS, and host the MySQL information tier. The user data directories are organized by group leader name, user login name, file-type, and run date. B) Sample tracking in SMITH. A sample passes through four states (
    Illumina Hiseq2000 2500 Instruments, supplied by BGI Shenzhen, used in various techniques. Bioz Stars score: 88/100, based on 9 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/illumina hiseq2000 2500 instruments/product/BGI Shenzhen
    Average 88 stars, based on 9 article reviews
    Price from $9.99 to $1999.99
    illumina hiseq2000 2500 instruments - by Bioz Stars, 2020-08
    88/100 stars
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    88
    Illumina Inc illumina hiseq1000 instrument
    Infrastructure, main tasks, and architecture . A) Infrastructure: Sequencing is performed on an <t>Illumina</t> <t>HiSeq2000</t> instrument. Data are stored on an Isilon mass storage device. Data are elaborated on a Sun Grid Engine High Performance Computing cluster (SGE-HPC). Application servers run web applications for Genome browsing, data listings, the SMITH LIMS, and host the MySQL information tier. The user data directories are organized by group leader name, user login name, file-type, and run date. B) Sample tracking in SMITH. A sample passes through four states (
    Illumina Hiseq1000 Instrument, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 88/100, based on 57 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/illumina hiseq1000 instrument/product/Illumina Inc
    Average 88 stars, based on 57 article reviews
    Price from $9.99 to $1999.99
    illumina hiseq1000 instrument - by Bioz Stars, 2020-08
    88/100 stars
      Buy from Supplier

    91
    Illumina Inc illumina hiseq2000 instrumentation
    Infrastructure, main tasks, and architecture . A) Infrastructure: Sequencing is performed on an <t>Illumina</t> <t>HiSeq2000</t> instrument. Data are stored on an Isilon mass storage device. Data are elaborated on a Sun Grid Engine High Performance Computing cluster (SGE-HPC). Application servers run web applications for Genome browsing, data listings, the SMITH LIMS, and host the MySQL information tier. The user data directories are organized by group leader name, user login name, file-type, and run date. B) Sample tracking in SMITH. A sample passes through four states (
    Illumina Hiseq2000 Instrumentation, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 91/100, based on 23 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/illumina hiseq2000 instrumentation/product/Illumina Inc
    Average 91 stars, based on 23 article reviews
    Price from $9.99 to $1999.99
    illumina hiseq2000 instrumentation - by Bioz Stars, 2020-08
    91/100 stars
      Buy from Supplier

    93
    Macrogen illumina hiseq2000 instrument
    Infrastructure, main tasks, and architecture . A) Infrastructure: Sequencing is performed on an <t>Illumina</t> <t>HiSeq2000</t> instrument. Data are stored on an Isilon mass storage device. Data are elaborated on a Sun Grid Engine High Performance Computing cluster (SGE-HPC). Application servers run web applications for Genome browsing, data listings, the SMITH LIMS, and host the MySQL information tier. The user data directories are organized by group leader name, user login name, file-type, and run date. B) Sample tracking in SMITH. A sample passes through four states (
    Illumina Hiseq2000 Instrument, supplied by Macrogen, used in various techniques. Bioz Stars score: 93/100, based on 2 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/illumina hiseq2000 instrument/product/Macrogen
    Average 93 stars, based on 2 article reviews
    Price from $9.99 to $1999.99
    illumina hiseq2000 instrument - by Bioz Stars, 2020-08
    93/100 stars
      Buy from Supplier

    93
    Denovo Biotechnology illumina hiseq2000 instrument
    Infrastructure, main tasks, and architecture . A) Infrastructure: Sequencing is performed on an <t>Illumina</t> <t>HiSeq2000</t> instrument. Data are stored on an Isilon mass storage device. Data are elaborated on a Sun Grid Engine High Performance Computing cluster (SGE-HPC). Application servers run web applications for Genome browsing, data listings, the SMITH LIMS, and host the MySQL information tier. The user data directories are organized by group leader name, user login name, file-type, and run date. B) Sample tracking in SMITH. A sample passes through four states (
    Illumina Hiseq2000 Instrument, supplied by Denovo Biotechnology, used in various techniques. Bioz Stars score: 93/100, based on 5 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/illumina hiseq2000 instrument/product/Denovo Biotechnology
    Average 93 stars, based on 5 article reviews
    Price from $9.99 to $1999.99
    illumina hiseq2000 instrument - by Bioz Stars, 2020-08
    93/100 stars
      Buy from Supplier

    89
    Illumina Inc illumina gaii hiseq2000 instruments
    Infrastructure, main tasks, and architecture . A) Infrastructure: Sequencing is performed on an <t>Illumina</t> <t>HiSeq2000</t> instrument. Data are stored on an Isilon mass storage device. Data are elaborated on a Sun Grid Engine High Performance Computing cluster (SGE-HPC). Application servers run web applications for Genome browsing, data listings, the SMITH LIMS, and host the MySQL information tier. The user data directories are organized by group leader name, user login name, file-type, and run date. B) Sample tracking in SMITH. A sample passes through four states (
    Illumina Gaii Hiseq2000 Instruments, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 89/100, based on 32 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/illumina gaii hiseq2000 instruments/product/Illumina Inc
    Average 89 stars, based on 32 article reviews
    Price from $9.99 to $1999.99
    illumina gaii hiseq2000 instruments - by Bioz Stars, 2020-08
    89/100 stars
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    90
    Illumina Inc hiseq2000 2500 illumina instruments
    Infrastructure, main tasks, and architecture . A) Infrastructure: Sequencing is performed on an <t>Illumina</t> <t>HiSeq2000</t> instrument. Data are stored on an Isilon mass storage device. Data are elaborated on a Sun Grid Engine High Performance Computing cluster (SGE-HPC). Application servers run web applications for Genome browsing, data listings, the SMITH LIMS, and host the MySQL information tier. The user data directories are organized by group leader name, user login name, file-type, and run date. B) Sample tracking in SMITH. A sample passes through four states (
    Hiseq2000 2500 Illumina Instruments, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 90/100, based on 4 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/hiseq2000 2500 illumina instruments/product/Illumina Inc
    Average 90 stars, based on 4 article reviews
    Price from $9.99 to $1999.99
    hiseq2000 2500 illumina instruments - by Bioz Stars, 2020-08
    90/100 stars
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    93
    Illumina Inc hiseq3000 device
    Infrastructure, main tasks, and architecture . A) Infrastructure: Sequencing is performed on an <t>Illumina</t> <t>HiSeq2000</t> instrument. Data are stored on an Isilon mass storage device. Data are elaborated on a Sun Grid Engine High Performance Computing cluster (SGE-HPC). Application servers run web applications for Genome browsing, data listings, the SMITH LIMS, and host the MySQL information tier. The user data directories are organized by group leader name, user login name, file-type, and run date. B) Sample tracking in SMITH. A sample passes through four states (
    Hiseq3000 Device, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 93/100, based on 25 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/hiseq3000 device/product/Illumina Inc
    Average 93 stars, based on 25 article reviews
    Price from $9.99 to $1999.99
    hiseq3000 device - by Bioz Stars, 2020-08
    93/100 stars
      Buy from Supplier

    92
    Illumina Inc hiseq 3000 4000 instrument
    Infrastructure, main tasks, and architecture . A) Infrastructure: Sequencing is performed on an <t>Illumina</t> <t>HiSeq2000</t> instrument. Data are stored on an Isilon mass storage device. Data are elaborated on a Sun Grid Engine High Performance Computing cluster (SGE-HPC). Application servers run web applications for Genome browsing, data listings, the SMITH LIMS, and host the MySQL information tier. The user data directories are organized by group leader name, user login name, file-type, and run date. B) Sample tracking in SMITH. A sample passes through four states (
    Hiseq 3000 4000 Instrument, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 92/100, based on 38 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/hiseq 3000 4000 instrument/product/Illumina Inc
    Average 92 stars, based on 38 article reviews
    Price from $9.99 to $1999.99
    hiseq 3000 4000 instrument - by Bioz Stars, 2020-08
    92/100 stars
      Buy from Supplier

    99
    Illumina Inc hiseq 3000 system instrument
    Infrastructure, main tasks, and architecture . A) Infrastructure: Sequencing is performed on an <t>Illumina</t> <t>HiSeq2000</t> instrument. Data are stored on an Isilon mass storage device. Data are elaborated on a Sun Grid Engine High Performance Computing cluster (SGE-HPC). Application servers run web applications for Genome browsing, data listings, the SMITH LIMS, and host the MySQL information tier. The user data directories are organized by group leader name, user login name, file-type, and run date. B) Sample tracking in SMITH. A sample passes through four states (
    Hiseq 3000 System Instrument, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 99/100, based on 14 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/hiseq 3000 system instrument/product/Illumina Inc
    Average 99 stars, based on 14 article reviews
    Price from $9.99 to $1999.99
    hiseq 3000 system instrument - by Bioz Stars, 2020-08
    99/100 stars
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    Image Search Results


    After remixing hamPCR amplicons for efficient sequencing, original abundances can be reconstructed A) Scheme of remixing process. i: Products of individual PCRs (each containing both host and microbial amplicons) are pooled at equimolar ratios into a single tube. ii : An aliquot of DNA from the pool in i is re-amplified with 8 cycles of PCR to replace all barcodes in the pool with a new barcode, creating a reference sample. iii: A large aliquot of the pool from i is run on an agarose gel to physically separate and then purify the host and microbial fractions. iv: The host and microbial fractions and the reference sample are pooled in the ratio desired for sequencing. v: All sequences are quality filtered, demultiplexed, and taxonomically classified using the same parameters. vi: Host and microbial amplicon counts are summed from the samples comprising the pooled library ( h and m respectively), and from the reference sample ( H and M ). vi : H, h, M, and m are used to calculate the scaling constant f for the dataset. All host sequence counts are multiplied by f to reconstruct the original microbe-to-host ratios. vii: Reconstructed original abundances. B) Relative abundance (RA) of actual sequence counts from our original HiSeq3000 run. C) Relative abundance of actual sequence counts from our adjusted library showing reduced host and 4 reference samples. D) The data from C after reconstructing original host abundance using the reference samples. E) The total fraction of host vs. other ASVs in the original library, reduced host library, and reconstruction. RA, relative abundance F) Relative abundances in the original and reconstructed library for all ASVs with a 0.05% minimum abundance, shown on 4 th -root transformed axes. R 2 , coefficient of determination. p -value from Kolmogorov–Smirnov test.

    Journal: bioRxiv

    Article Title: Measuring both microbial load and diversity with a single amplicon sequencing library

    doi: 10.1101/2020.05.19.103937

    Figure Lengend Snippet: After remixing hamPCR amplicons for efficient sequencing, original abundances can be reconstructed A) Scheme of remixing process. i: Products of individual PCRs (each containing both host and microbial amplicons) are pooled at equimolar ratios into a single tube. ii : An aliquot of DNA from the pool in i is re-amplified with 8 cycles of PCR to replace all barcodes in the pool with a new barcode, creating a reference sample. iii: A large aliquot of the pool from i is run on an agarose gel to physically separate and then purify the host and microbial fractions. iv: The host and microbial fractions and the reference sample are pooled in the ratio desired for sequencing. v: All sequences are quality filtered, demultiplexed, and taxonomically classified using the same parameters. vi: Host and microbial amplicon counts are summed from the samples comprising the pooled library ( h and m respectively), and from the reference sample ( H and M ). vi : H, h, M, and m are used to calculate the scaling constant f for the dataset. All host sequence counts are multiplied by f to reconstruct the original microbe-to-host ratios. vii: Reconstructed original abundances. B) Relative abundance (RA) of actual sequence counts from our original HiSeq3000 run. C) Relative abundance of actual sequence counts from our adjusted library showing reduced host and 4 reference samples. D) The data from C after reconstructing original host abundance using the reference samples. E) The total fraction of host vs. other ASVs in the original library, reduced host library, and reconstruction. RA, relative abundance F) Relative abundances in the original and reconstructed library for all ASVs with a 0.05% minimum abundance, shown on 4 th -root transformed axes. R 2 , coefficient of determination. p -value from Kolmogorov–Smirnov test.

    Article Snippet: Libraries were first diluted to 2.5 – 2.8 nM in elution buffer (EB, 10 mM Tris pH 8.0) and spiked into a compatible lane of the HiSeq3000 instrument (2 × 150 bp paired end reads) to occupy 2-3% of the lane.

    Techniques: Sequencing, Amplification, Polymerase Chain Reaction, Agarose Gel Electrophoresis, Transformation Assay

    Infrastructure, main tasks, and architecture . A) Infrastructure: Sequencing is performed on an Illumina HiSeq2000 instrument. Data are stored on an Isilon mass storage device. Data are elaborated on a Sun Grid Engine High Performance Computing cluster (SGE-HPC). Application servers run web applications for Genome browsing, data listings, the SMITH LIMS, and host the MySQL information tier. The user data directories are organized by group leader name, user login name, file-type, and run date. B) Sample tracking in SMITH. A sample passes through four states (

    Journal: BMC Bioinformatics

    Article Title: SMITH: a LIMS for handling next-generation sequencing workflows

    doi: 10.1186/1471-2105-15-S14-S3

    Figure Lengend Snippet: Infrastructure, main tasks, and architecture . A) Infrastructure: Sequencing is performed on an Illumina HiSeq2000 instrument. Data are stored on an Isilon mass storage device. Data are elaborated on a Sun Grid Engine High Performance Computing cluster (SGE-HPC). Application servers run web applications for Genome browsing, data listings, the SMITH LIMS, and host the MySQL information tier. The user data directories are organized by group leader name, user login name, file-type, and run date. B) Sample tracking in SMITH. A sample passes through four states ("requested", "queued", "confirmed", "analysed"). Submitted samples have status "requested". When a sample is added to the virtual flow cell, its status changes to "queued". Upon the group leader confirmation the status changes to "confirmed". The sample is then run and analysed by the workflow engine and assumes the final status "analysed". HPC refers to a high performance computing cluster. C) Architecture of the workflow unit. Generated commands invoke Galaxy workflows that subsequently call the un-pluggable core. A part of the instruments can be on the Galaxy side (proprietary tools and scripts) and the other part (open-source tools) is moved to the core.

    Article Snippet: The IIT Genomic unit sequences about 2000 samples per year on an Illumina HiSeq2000 instrument submitted by 150 users belonging to 20 different research groups.

    Techniques: Sequencing, Flow Cytometry, Generated