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Illumina Inc hiseq4000 sequencing system
Hiseq4000 Sequencing System, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 91/100, 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 91 stars, based on 12 article reviews
Price from $9.99 to $1999.99
hiseq4000 sequencing system - by Bioz Stars, 2020-07
91/100 stars

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RNA Sequencing Assay:

Article Title: Phf15—a novel transcriptional repressor regulating inflammation in mouse microglia
Article Snippet: .. RNA sequencing (1 lane) was performed on a HiSeq4000 sequencing system (Illumina Inc., San Diego, CA; UC Berkeley Genomics Sequencing Laboratory). .. Sequencing reads were aligned to the Mus musculus reference genome assembly GRCm38 (mm10) using Spliced Transcripts Alignment to a Reference (STAR) aligner[ ] .

Isolation:

Article Title: Discovery and characterization of the tubercidin biosynthetic pathway from Streptomyces tubercidicus NBRC 13090
Article Snippet: .. Sequencing analysis of the genome of S. tubercidicus Genomic DNA of S. tubercidicus was isolated on the basis of the standard protocol [ ], and the genome sequencing was performed using the Illumina Hiseq4000 sequencing system, and the assembled sequence data was then annotated using the Glimmer 3.02 software. ..

Purification:

Article Title: Specific chromatin changes mark lateral organ founder cells in the Arabidopsis inflorescence meristem
Article Snippet: .. After purification and validation (2200 TapeStation; Agilent Technologies), libraries were quantified by using the KAPA Library Quantification kit (Peqlab) and the 7900HT Sequence Detection System (Applied Biosystems) and subsequently sequenced on an Illumina HiSeq4000 sequencing system with a paired-end 2×75-nt sequencing protocol. ..

Sequencing:

Article Title: Neoantigens Derived from Recurrently Mutated Genes as Potential Immunotherapy Targets for Gastric Cancer
Article Snippet: .. The whole exome sequencing was performed on Illumina Hiseq4000 sequencing system. .. An in-house developed integrated software “Tumor-Specific Neo-Antigen Detector” (TSNAD) [ ] was used to predict neoantigens.

Article Title: Specific chromatin changes mark lateral organ founder cells in the Arabidopsis inflorescence meristem
Article Snippet: .. After purification and validation (2200 TapeStation; Agilent Technologies), libraries were quantified by using the KAPA Library Quantification kit (Peqlab) and the 7900HT Sequence Detection System (Applied Biosystems) and subsequently sequenced on an Illumina HiSeq4000 sequencing system with a paired-end 2×75-nt sequencing protocol. ..

Article Title: Discovery and characterization of the tubercidin biosynthetic pathway from Streptomyces tubercidicus NBRC 13090
Article Snippet: .. Sequencing analysis of the genome of S. tubercidicus Genomic DNA of S. tubercidicus was isolated on the basis of the standard protocol [ ], and the genome sequencing was performed using the Illumina Hiseq4000 sequencing system, and the assembled sequence data was then annotated using the Glimmer 3.02 software. ..

Article Title: cAMP signaling regulates DNA hydroxymethylation by augmenting the intracellular labile ferrous iron pool
Article Snippet: .. DNA was then sequenced on a HiSeq4000 sequencing system (50 bp single-end reads, three samples per lane; Illumina, San Diego, CA). .. Reads were trimmed with trim_galore to remove low quality bases from reads (scores < 20 in Phred + 33 format), and Illumina adapters.

Article Title: Phf15—a novel transcriptional repressor regulating inflammation in mouse microglia
Article Snippet: .. RNA sequencing (1 lane) was performed on a HiSeq4000 sequencing system (Illumina Inc., San Diego, CA; UC Berkeley Genomics Sequencing Laboratory). .. Sequencing reads were aligned to the Mus musculus reference genome assembly GRCm38 (mm10) using Spliced Transcripts Alignment to a Reference (STAR) aligner[ ] .

Article Title: Identification of atrial fibrillation associated genes and functional non-coding variants
Article Snippet: .. Sequencing was performed on an Illumina Hiseq4000 sequencing system (50-bp single reads). .. Differential expression analysis Reads were mapped to hg19 build of the human transcriptome using STAR .

Article Title: A Single SNP Turns a Social Honey Bee (Apis mellifera) Worker into a Selfish Parasite
Article Snippet: .. Whole Genome Sequencing and Variant Calling The genomes of 71 A. m. capensis workers of the mapping population (42 with and 29 without confirmed phenotype) were sequenced on an Illumina HiSeq4000 Sequencing System (150 bp PE, TruSeq Nano DNA library preparation from 20 to 100 ng DNA, 350 bp insert size) to a coverage of ≥20× (raw reads are deposited in NCBI SRA, accession: PRJNA507348). ..

Article Title: A Single SNP Turns a Social Honey Bee (Apis mellifera) Worker into a Selfish Parasite
Article Snippet: .. For each time point and subspecies, three replicates were combined for full transcriptome sequencing (100 bp PE) on an Illumina HiSeq4000 Sequencing System (BGI, Hong Kong). ..

Variant Assay:

Article Title: A Single SNP Turns a Social Honey Bee (Apis mellifera) Worker into a Selfish Parasite
Article Snippet: .. Whole Genome Sequencing and Variant Calling The genomes of 71 A. m. capensis workers of the mapping population (42 with and 29 without confirmed phenotype) were sequenced on an Illumina HiSeq4000 Sequencing System (150 bp PE, TruSeq Nano DNA library preparation from 20 to 100 ng DNA, 350 bp insert size) to a coverage of ≥20× (raw reads are deposited in NCBI SRA, accession: PRJNA507348). ..

Software:

Article Title: Discovery and characterization of the tubercidin biosynthetic pathway from Streptomyces tubercidicus NBRC 13090
Article Snippet: .. Sequencing analysis of the genome of S. tubercidicus Genomic DNA of S. tubercidicus was isolated on the basis of the standard protocol [ ], and the genome sequencing was performed using the Illumina Hiseq4000 sequencing system, and the assembled sequence data was then annotated using the Glimmer 3.02 software. ..

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  • 94
    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: 94/100, based on 599 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/illumina hiseq2000/product/Illumina Inc
    Average 94 stars, based on 599 article reviews
    Price from $9.99 to $1999.99
    illumina hiseq2000 - by Bioz Stars, 2020-07
    94/100 stars
      Buy from Supplier

    94
    Illumina Inc illumina hiseq2000 sequencing
    The circulating miRNAs signatures identified by <t>Illumina</t> <t>Hiseq2000</t> 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 ).
    Illumina Hiseq2000 Sequencing, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 94/100, based on 205 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/illumina hiseq2000 sequencing/product/Illumina Inc
    Average 94 stars, based on 205 article reviews
    Price from $9.99 to $1999.99
    illumina hiseq2000 sequencing - by Bioz Stars, 2020-07
    94/100 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, 2020-07
    85/100 stars
      Buy from Supplier

    Image Search Results


    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

    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

    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

    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