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Illumina Inc illumina hiseq2000 platform
Illumina Hiseq2000 Platform, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 92/100, based on 109 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
https://www.bioz.com/result/illumina hiseq2000 platform/product/Illumina Inc
Average 92 stars, based on 109 article reviews
Price from $9.99 to $1999.99
illumina hiseq2000 platform - by Bioz Stars, 2021-01
92/100 stars

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Sequencing:

Article Title: Folic Acid Induces Intake-Related Changes in the Mammary Tissue Transcriptome of C57BL/6 Mice
Article Snippet: .. Sequencing was performed on the Illumina HiSeq2000 platform using TruSeq v3 chemistry (Illumina, San Diego, CA, USA). ..

Article Title: Population variation in miRNAs and isomiRs and their impact on human immunity to infection
Article Snippet: .. Regarding the mRNA sequencing dataset, libraries from total RNA samples and transcriptome sequencing were performed using TruSeq RNA Sample Prep Kit v2 for mRNA library construction, TruSeq SR Cluster Kit v3-HS for cluster generation, and TruSeq SBS kit v3-HS for sequencing on an Illumina HiSeq2000 platform. ..

RNA Sequencing Assay:

Article Title: Reduced Brd1 expression leads to reversible depression-like behaviors and gene-expression changes in female mice
Article Snippet: .. For AMG samples, libraries were prepared using TruSeq library preparation kit and RNA-sequencing performed on the Illumina HiSeq2000 platform (Illumina, San Diego, USA). .. For CPU and aCC samples, libraries were prepared using Beijing Genomics Institute (BGI) library preparation kits and protocols and sequencing performed on the BGISEQ-500 platform.

Article Title: Dopamine 2 Receptor Signaling Controls the Daily Burst in Phagocytic Activity in the Mouse Retinal Pigment Epithelium
Article Snippet: .. RNA-Seq Runs, Mapping and Estimation of Reads Per Kilobase Per Million The 12 RNA-sequence (RNA-seq) libraries were then sequenced on the Illumina HiSeq2000 platform to produce approximately 65 million, 100 nucleotide paired-end reads per sample (reads 1 and 2). .. The reads were mapped to the University of California – Santa Cruz (UCSC; Santa Cruz, CA, USA) mouse genome assembly and transcript annotation (mm10).

Sample Prep:

Article Title: Population variation in miRNAs and isomiRs and their impact on human immunity to infection
Article Snippet: .. Regarding the mRNA sequencing dataset, libraries from total RNA samples and transcriptome sequencing were performed using TruSeq RNA Sample Prep Kit v2 for mRNA library construction, TruSeq SR Cluster Kit v3-HS for cluster generation, and TruSeq SBS kit v3-HS for sequencing on an Illumina HiSeq2000 platform. ..

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  • 92
    Illumina Inc illumina hiseq2000 platform
    (A) Schematic diagram of the experimental design. Patient derived envelope quasispecies amplicons (amplicon libraries) were cloned into replication competent NL4.3 Env-luc + reporter vector (plasmid libraries) and expressed in 293T cells as replication competent virions that were used to infect CCR5 and CXCR4 expressing cell lines. The functionally validated env quasispecies (functional libraries) were prepared by polymerase-chain reaction of the proviral DNA using env -specific primers from the genomic DNA of the infected cells. The three sets of libraries were sequenced by <t>Illumina</t> <t>HiSeq2000;</t> functional libraries were also sequenced by Pacific Biosciences RS II. (B) SNP based clustering analysis of 16 amplicon libraries based on Illumina sequencing of the full-length env gene. SNPs were called with HXB2 env as the reference sequence using GATK. A Euclidean-distance based clustering of 16 amplicon libraries was constructed using 843 SNPs present in all samples.
    Illumina Hiseq2000 Platform, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 92/100, based on 109 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/illumina hiseq2000 platform/product/Illumina Inc
    Average 92 stars, based on 109 article reviews
    Price from $9.99 to $1999.99
    illumina hiseq2000 platform - by Bioz Stars, 2021-01
    92/100 stars
      Buy from Supplier

    92
    Illumina Inc hiseq4000 sequencing platforms
    Comparison of sequencing quality among BGISEQ-500 PE75, BGISEQ-500 PE100 and <t>HiSeq4000</t> PE100. a Base quality representation for clean reads and Q20. b Reads quality evaluation and mapping percentage. c Reads distribution along the relative position of genes
    Hiseq4000 Sequencing Platforms, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 92/100, based on 5 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/hiseq4000 sequencing platforms/product/Illumina Inc
    Average 92 stars, based on 5 article reviews
    Price from $9.99 to $1999.99
    hiseq4000 sequencing platforms - by Bioz Stars, 2021-01
    92/100 stars
      Buy from Supplier

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    (A) Schematic diagram of the experimental design. Patient derived envelope quasispecies amplicons (amplicon libraries) were cloned into replication competent NL4.3 Env-luc + reporter vector (plasmid libraries) and expressed in 293T cells as replication competent virions that were used to infect CCR5 and CXCR4 expressing cell lines. The functionally validated env quasispecies (functional libraries) were prepared by polymerase-chain reaction of the proviral DNA using env -specific primers from the genomic DNA of the infected cells. The three sets of libraries were sequenced by Illumina HiSeq2000; functional libraries were also sequenced by Pacific Biosciences RS II. (B) SNP based clustering analysis of 16 amplicon libraries based on Illumina sequencing of the full-length env gene. SNPs were called with HXB2 env as the reference sequence using GATK. A Euclidean-distance based clustering of 16 amplicon libraries was constructed using 843 SNPs present in all samples.

    Journal: Virology

    Article Title: Evolution of coreceptor utilization to escape CCR5 antagonist therapy

    doi: 10.1016/j.virol.2016.04.010

    Figure Lengend Snippet: (A) Schematic diagram of the experimental design. Patient derived envelope quasispecies amplicons (amplicon libraries) were cloned into replication competent NL4.3 Env-luc + reporter vector (plasmid libraries) and expressed in 293T cells as replication competent virions that were used to infect CCR5 and CXCR4 expressing cell lines. The functionally validated env quasispecies (functional libraries) were prepared by polymerase-chain reaction of the proviral DNA using env -specific primers from the genomic DNA of the infected cells. The three sets of libraries were sequenced by Illumina HiSeq2000; functional libraries were also sequenced by Pacific Biosciences RS II. (B) SNP based clustering analysis of 16 amplicon libraries based on Illumina sequencing of the full-length env gene. SNPs were called with HXB2 env as the reference sequence using GATK. A Euclidean-distance based clustering of 16 amplicon libraries was constructed using 843 SNPs present in all samples.

    Article Snippet: The concentration of each library fraction was verified through qPCR according to the manufacturer's protocol (Kapa Biosystems) to produce cluster counts appropriate for the Illumina HiSeq2000 platform.

    Techniques: Derivative Assay, Amplification, Clone Assay, Plasmid Preparation, Expressing, Functional Assay, Polymerase Chain Reaction, Infection, Sequencing, Construct

    Illumina HiSeq2000 QC of one representative sample. A) Raw quality scores (FASTQ) of reads from one bisulfite treated library (G12; lane 6). B) Graph showing the representation of each base at each position in a 50 base read. Notice the very low level of Cytosine residues compared to the high content of Adenosine residues; non-bisulifte converted DNA shows approximately equal base composition at each site. One metric of C-T conversion rate is the ratio of C residues at bases 1–10 and 40–50. In the graph above, this ratio is about 1, as expected. In RRBS libraries, a large increase in Guanidine at positions 2 and 3 (~95% of reads have GG at these positions) should also be observed.

    Journal: BMC Genomics

    Article Title: BisQC: an operational pipeline for multiplexed bisulfite sequencing

    doi: 10.1186/1471-2164-15-290

    Figure Lengend Snippet: Illumina HiSeq2000 QC of one representative sample. A) Raw quality scores (FASTQ) of reads from one bisulfite treated library (G12; lane 6). B) Graph showing the representation of each base at each position in a 50 base read. Notice the very low level of Cytosine residues compared to the high content of Adenosine residues; non-bisulifte converted DNA shows approximately equal base composition at each site. One metric of C-T conversion rate is the ratio of C residues at bases 1–10 and 40–50. In the graph above, this ratio is about 1, as expected. In RRBS libraries, a large increase in Guanidine at positions 2 and 3 (~95% of reads have GG at these positions) should also be observed.

    Article Snippet: Massively parallel (next generation) sequencing We used the Illumina HiSeq2000 platform, with single-end 50 cycle sequencing.

    Techniques:

    NGS-based cancer genomic profiling test workflow. ( a ) DNA is extracted from routine FFPE biopsy or surgical specimens. ( b ) 50–200 ng of DNA undergoes whole-genome shotgun library construction and hybridization-based capture of 4,557 exons of 287 cancer-related genes and 47 introns of 19 genes frequently rearranged in solid tumors. Hybrid-capture libraries are sequenced to high depth using the Illumina HiSeq2000 platform. ( c ) Sequence data are processed using a customized analysis pipeline designed to accurately detect multiple classes of genomic alterations: base substitutions, short insertions/deletions, copy-number alterations and selected gene fusions. ( d ) Detected mutations are annotated according to clinical significance and reported.

    Journal: Nature biotechnology

    Article Title: Development and validation of a clinical cancer genomic profiling test based on massively parallel DNA sequencing

    doi: 10.1038/nbt.2696

    Figure Lengend Snippet: NGS-based cancer genomic profiling test workflow. ( a ) DNA is extracted from routine FFPE biopsy or surgical specimens. ( b ) 50–200 ng of DNA undergoes whole-genome shotgun library construction and hybridization-based capture of 4,557 exons of 287 cancer-related genes and 47 introns of 19 genes frequently rearranged in solid tumors. Hybrid-capture libraries are sequenced to high depth using the Illumina HiSeq2000 platform. ( c ) Sequence data are processed using a customized analysis pipeline designed to accurately detect multiple classes of genomic alterations: base substitutions, short insertions/deletions, copy-number alterations and selected gene fusions. ( d ) Detected mutations are annotated according to clinical significance and reported.

    Article Snippet: Using the Illumina HiSeq2000 platform, hybrid-capture–selected libraries were sequenced to high uniform depth (targeting > 500× coverage by non-PCR duplicate read pairs, with > 99% of exons at coverage > 100×).

    Techniques: Next-Generation Sequencing, Formalin-fixed Paraffin-Embedded, Hybridization, Sequencing

    Comparison of sequencing quality among BGISEQ-500 PE75, BGISEQ-500 PE100 and HiSeq4000 PE100. a Base quality representation for clean reads and Q20. b Reads quality evaluation and mapping percentage. c Reads distribution along the relative position of genes

    Journal: Plant Methods

    Article Title: Comparative performance of the BGISEQ-500 and Illumina HiSeq4000 sequencing platforms for transcriptome analysis in plants

    doi: 10.1186/s13007-018-0337-0

    Figure Lengend Snippet: Comparison of sequencing quality among BGISEQ-500 PE75, BGISEQ-500 PE100 and HiSeq4000 PE100. a Base quality representation for clean reads and Q20. b Reads quality evaluation and mapping percentage. c Reads distribution along the relative position of genes

    Article Snippet: The intra- and inter-platform correlations of gene quantification, DEG detection, AS identification, SNP and INDEL detection between BGISEQ-500 and Illumina HiSeq4000 sequencing platforms have been critically evaluated.

    Techniques: Sequencing