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Illumina Inc hiseq4000 sequencing system
Hiseq4000 Sequencing System, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 90/100, based on 12 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
https://www.bioz.com/result/hiseq4000 sequencing system/product/Illumina Inc
Average 90 stars, based on 12 article reviews
Price from $9.99 to $1999.99
hiseq4000 sequencing system - by Bioz Stars, 2021-01
90/100 stars

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Sequencing:

Article Title: Evolutionarily conserved regulation of immunity by the splicing factor RNP-6/PUF60
Article Snippet: .. The libraries were then sequenced on one lane of an Illumina HiSeq4000 sequencing system using a paired end 2 × 75 nt sequencing protocol. ..

Article Title: Characterization of the chloroplast genome of the Osmanthus didymopetalus
Article Snippet: .. The voucher specimen was deposited at the herbarium of Nanjing Forestry University (NF, accession number NF000096) and DNA compounds were stored at −20 °C, and was used to prepare the shotgun library following the manufacturer’s protocol for Hiseq4000 Sequencing System (Illumina, San Diego, CA). ..

Article Title: Identification of SNP Markers Associated with Iron and Zinc Concentrations in Cicer Seeds
Article Snippet: .. The sequencing of the amplicons was implemented using the Illumina HiSeq4000 sequencing system using a 100 bases reads protocol at the University of California Davis Genomics Facility. .. The raw sequencing data was analyzed by the GATK pipeline as described by Mc-Kenna et al. [ ] by mapping them according to the C. arietinum CDC Frontier reference by Varshney et al. [ ] in Haplotype Caller program.

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  • 92
    Illumina Inc illumina hiseq2000
    Overview of the reference transcriptome sequencing, and result of the Velvet/Oases assembly . A) RNA for the reference was pooled from all of the test samples. The <t>Illumina</t> <t>HiSeq2000</t> platform was used to generate data for de novo assembly including large transcripts (LT) equivalent to 15,493 potential protein coding sequences. B) The accuracy and integrity of the assembly was assessed by BLAST comparison (100 bp overlap and ≥ 98% sequence identity) with the publicly available collection of sugar beet ESTs at the Sugar Beet Gene Index (SBGI), hosted at the Dana Farber Cancer Institute (DFCI).
    Illumina Hiseq2000, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 92/100, based on 804 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/illumina hiseq2000/product/Illumina Inc
    Average 92 stars, based on 804 article reviews
    Price from $9.99 to $1999.99
    illumina hiseq2000 - by Bioz Stars, 2021-01
    92/100 stars
      Buy from Supplier

    85
    Illumina Inc hiseq2000 next generation sequencer
    Experimental workflow of the study. RNA samples were extracted from mouse palatal tissues of TGFβ3 knockout mice (homozygous, heterozygous, and wildtype) at three developmental stages (E14.5, E15.5, and E16.5); libraries were prepared, converted to cDNA, and sequenced by using the Illumina <t>HiSeq2000</t> next generation sequencer. Fastq files were uploaded to the server for quality control analysis of sequence reads using FastQC. There were no sequence manipulation processes performed for any fastq file, given that the quality score was high at both the 3 ′ and 5 ′ ends. All of the reads were mapped to the reference genome (mm9, built name NCBIM37) by using TopHat. Quantification of transcripts, statistics tests for differential expression, and detection of splice variants were performed using Cufflinks; quality assessments of biological and technical replicates were performed using CummeRbund; and pairwise comparisons of samples and differential expression of transcripts were analyzed using CuffDiff. Venn diagrams of all significantly altered (FC ≥ 2.0) transcripts were drawn using the R VennDiagram package [ 75 ]. CP related genes (n = 322) were extracted from human (OMIM) and mouse (MGI) genome databases. CP genes were classified based on their patterns of expression (n = 9) for each genotype and their heatmaps were generated using the R pheatmap package. Expression pattern groups of CP genes were uploaded to IPA software as datasets and core analyses were run to detect downstream effects: canonical pathways and biological functions relevant to sample datasets.
    Hiseq2000 Next Generation Sequencer, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 85/100, based on 2 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/hiseq2000 next generation sequencer/product/Illumina Inc
    Average 85 stars, based on 2 article reviews
    Price from $9.99 to $1999.99
    hiseq2000 next generation sequencer - by Bioz Stars, 2021-01
    85/100 stars
      Buy from Supplier

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    Overview of the reference transcriptome sequencing, and result of the Velvet/Oases assembly . A) RNA for the reference was pooled from all of the test samples. The Illumina HiSeq2000 platform was used to generate data for de novo assembly including large transcripts (LT) equivalent to 15,493 potential protein coding sequences. B) The accuracy and integrity of the assembly was assessed by BLAST comparison (100 bp overlap and ≥ 98% sequence identity) with the publicly available collection of sugar beet ESTs at the Sugar Beet Gene Index (SBGI), hosted at the Dana Farber Cancer Institute (DFCI).

    Journal: BMC Genomics

    Article Title: A new RNASeq-based reference transcriptome for sugar beet and its application in transcriptome-scale analysis of vernalization and gibberellin responses

    doi: 10.1186/1471-2164-13-99

    Figure Lengend Snippet: Overview of the reference transcriptome sequencing, and result of the Velvet/Oases assembly . A) RNA for the reference was pooled from all of the test samples. The Illumina HiSeq2000 platform was used to generate data for de novo assembly including large transcripts (LT) equivalent to 15,493 potential protein coding sequences. B) The accuracy and integrity of the assembly was assessed by BLAST comparison (100 bp overlap and ≥ 98% sequence identity) with the publicly available collection of sugar beet ESTs at the Sugar Beet Gene Index (SBGI), hosted at the Dana Farber Cancer Institute (DFCI).

    Article Snippet: Digital gene expression profiling and mapping to reference cDNA libraries generated from sub-samples of each test sample were sequenced (Illumina HiSeq2000, 50 bp single read module).

    Techniques: Sequencing

    The circulating miRNAs signatures identified by Illumina Hiseq2000 sequencing. The length distribution and frequency percentages of the sequences identified in LOH ( a ) and control samples ( b ) RNA species (unique tags aligning) in LOH ( c ) and control samples ( d ) and RNA read counts (total tags aligning) in LOH samples ( e ) and control samples ( f ).

    Journal: Scientific Reports

    Article Title: The plasma miR-125a, miR-361 and miR-133a are promising novel biomarkers for Late-Onset Hypogonadism

    doi: 10.1038/srep23531

    Figure Lengend Snippet: The circulating miRNAs signatures identified by Illumina Hiseq2000 sequencing. The length distribution and frequency percentages of the sequences identified in LOH ( a ) and control samples ( b ) RNA species (unique tags aligning) in LOH ( c ) and control samples ( d ) and RNA read counts (total tags aligning) in LOH samples ( e ) and control samples ( f ).

    Article Snippet: Using Illumina HiSeq2000 sequencing at discovery phase, and then two-step validated by reverse transcriptase polymerase chain reaction (RT-PCR) assays in verification phases.

    Techniques: Sequencing

    Schematic overview of the study. We collected one sample for each tissue type, including root, stem, leaf, flower bud, column, lip, petal, sepal and seeds from three developmental stages of P. equestris . Next, we sequenced cDNAs generated from the tissues on an Illumina HiSeq2000 in 90-bp paired-end (PE) reads, with 75-bp paired-end (PE) reads from the leaf tissue. The analysis started with assembling the short reads using the de novo assembly program Trinity and continued with functional analysis using BLASTX. Moreover, we performed quality control assessments at each step from the raw reads to the annotation datasets. Finally, we used YABBY and NBS-encoding gene families as examples of the usage of these datasets.

    Journal: Scientific Data

    Article Title: De novo transcriptome assembly databases for the butterfly orchid Phalaenopsis equestris

    doi: 10.1038/sdata.2016.83

    Figure Lengend Snippet: Schematic overview of the study. We collected one sample for each tissue type, including root, stem, leaf, flower bud, column, lip, petal, sepal and seeds from three developmental stages of P. equestris . Next, we sequenced cDNAs generated from the tissues on an Illumina HiSeq2000 in 90-bp paired-end (PE) reads, with 75-bp paired-end (PE) reads from the leaf tissue. The analysis started with assembling the short reads using the de novo assembly program Trinity and continued with functional analysis using BLASTX. Moreover, we performed quality control assessments at each step from the raw reads to the annotation datasets. Finally, we used YABBY and NBS-encoding gene families as examples of the usage of these datasets.

    Article Snippet: Sequencing using the Illumina HiSeq2000 system was performed to generate 90-bp paired-end (PE) reads, except in the leaf, for which 75-bp paired-end reads were generated.

    Techniques: Generated, Functional Assay

    Experimental workflow of the study. RNA samples were extracted from mouse palatal tissues of TGFβ3 knockout mice (homozygous, heterozygous, and wildtype) at three developmental stages (E14.5, E15.5, and E16.5); libraries were prepared, converted to cDNA, and sequenced by using the Illumina HiSeq2000 next generation sequencer. Fastq files were uploaded to the server for quality control analysis of sequence reads using FastQC. There were no sequence manipulation processes performed for any fastq file, given that the quality score was high at both the 3 ′ and 5 ′ ends. All of the reads were mapped to the reference genome (mm9, built name NCBIM37) by using TopHat. Quantification of transcripts, statistics tests for differential expression, and detection of splice variants were performed using Cufflinks; quality assessments of biological and technical replicates were performed using CummeRbund; and pairwise comparisons of samples and differential expression of transcripts were analyzed using CuffDiff. Venn diagrams of all significantly altered (FC ≥ 2.0) transcripts were drawn using the R VennDiagram package [ 75 ]. CP related genes (n = 322) were extracted from human (OMIM) and mouse (MGI) genome databases. CP genes were classified based on their patterns of expression (n = 9) for each genotype and their heatmaps were generated using the R pheatmap package. Expression pattern groups of CP genes were uploaded to IPA software as datasets and core analyses were run to detect downstream effects: canonical pathways and biological functions relevant to sample datasets.

    Journal: BMC Genomics

    Article Title: Systematic analysis of palatal transcriptome to identify cleft palate genes within TGF?3-knockout mice alleles: RNA-Seq analysis of TGF?3 Mice

    doi: 10.1186/1471-2164-14-113

    Figure Lengend Snippet: Experimental workflow of the study. RNA samples were extracted from mouse palatal tissues of TGFβ3 knockout mice (homozygous, heterozygous, and wildtype) at three developmental stages (E14.5, E15.5, and E16.5); libraries were prepared, converted to cDNA, and sequenced by using the Illumina HiSeq2000 next generation sequencer. Fastq files were uploaded to the server for quality control analysis of sequence reads using FastQC. There were no sequence manipulation processes performed for any fastq file, given that the quality score was high at both the 3 ′ and 5 ′ ends. All of the reads were mapped to the reference genome (mm9, built name NCBIM37) by using TopHat. Quantification of transcripts, statistics tests for differential expression, and detection of splice variants were performed using Cufflinks; quality assessments of biological and technical replicates were performed using CummeRbund; and pairwise comparisons of samples and differential expression of transcripts were analyzed using CuffDiff. Venn diagrams of all significantly altered (FC ≥ 2.0) transcripts were drawn using the R VennDiagram package [ 75 ]. CP related genes (n = 322) were extracted from human (OMIM) and mouse (MGI) genome databases. CP genes were classified based on their patterns of expression (n = 9) for each genotype and their heatmaps were generated using the R pheatmap package. Expression pattern groups of CP genes were uploaded to IPA software as datasets and core analyses were run to detect downstream effects: canonical pathways and biological functions relevant to sample datasets.

    Article Snippet: Analysis of RNA-seq data As outlined in the experimental workflow of our study (Figure ), RNA samples were extracted from mouse palatal tissues of TGFβ3 knockout mice (homozygous (−/−), heterozygous (+/−), and wildtype (+/+)) at three developmental stages (E14.5, E15.5, and E16.5); libraries were prepared, converted to cDNA, and sequenced by using the Illumina HiSeq2000 next generation sequencer.

    Techniques: Knock-Out, Mouse Assay, Sequencing, Expressing, Generated, Indirect Immunoperoxidase Assay, Software