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simulated next-generation sequencing data  (Illumina Inc)


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    Illumina Inc simulated next-generation sequencing data
    Simulated Next Generation Sequencing Data, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/product/simulated+next-generation+sequencing+data/next+generation+sequencing+data/pm40533801-89-6-19
    Average 90 stars, based on 1 article reviews
    simulated next-generation sequencing data - by Bioz Stars, 2026-10
    90/100 stars

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    Related Articles

    other:

    Article Title: KPop: accurate and scalable comparative analysis of microbial genomes by sequence embeddings.
    Article Snippet: In order to do so, simulated next-generation sequencing (NGS) data was generated for each genome using ART [43], emulating Illumina HiSeq 2500 paired-end reads of length 150 bp with an average coverage of 20-fold.

    Article Title: Rare twin cysteine residues in the HIV-1 envelope variable region 1 link to neutralization escape and breadth development
    Article Snippet: Consensus V1 sequences (N=6424) were derived from near full-length HIV-1 genome next generation sequence (NGS) data sets of plasma virus from the SHCS and ZPHI cohorts that were generated by long overlapping amplicon sequencing on Illumina MiSeq , followed by assembly with an in-house sequence alignment tool (available at https://github.com/medvir/SmaltAlign ).

    Next-Generation Sequencing:

    Article Title: Measurements of soil protist richness and community composition are influenced by primer pair, annealing temperature, and bioinformatics choices.
    Article Snippet: Protists are a diverse and understudied group of microbial eukaryotic organisms especially in terrestrial environments.. Advances in molecular methods are increasing our understanding of the distribution and functions of these creatures; however, there is a vast array of choices researchers make including barcoding genes, primer pairs, PCR settings, and bioinformatic options that can impact the outcome of protist community surveys.. Here, we tested four commonly used primer pairs targeting the V4 and V9 regions of the 18S rRNA gene using different PCR annealing temperatures and processed the sequences with different bioinformatic parameters in 10 diverse soils to evaluate how primer pair, amplification parameters, and bioinformatic choices influence the composition and richness of protist and non-protist taxa using Illumina sequencing.


    Article Title: Single-nucleus transcriptomic profiling of human orbitofrontal cortex reveals convergent effects of aging and psychiatric disease.
    Article Snippet: .. Software and code Policy information about availability of computer code Data collection Next-generation sequencing data were all generated on Illumina platforms, and demultiplexed at the sequencing facility. ..

    Article Title: Identifying Molecular Modulators of the Vascular Invasion in Rectal Carcinoma: Role of ADAMTS8 and Its Co-Dependent Genes.
    Article Snippet: .. The mRNA expression levels were available from the Illumina next-generation sequencing data and presented as the RNASeq V2 RSEM dataset, while DNA methylation data was derived from the HumanMethylation450 (HM450) Infinium array. ..

    Article Title: Pan-inhibition of super-enhancer-driven oncogenic transcription by next-generation synthetic ecteinascidins yields potent anti-cancer activity
    Article Snippet: .. Data Policy information about availability of data All manuscripts must include a data availability statement This statement should provide the following information, where applicable: - Accession codes, unique identifiers, or web links for publicly available datasets - A description of any restrictions on data availability - For clinical datasets or third party data, please ensure that the statement adheres to our policy Coin Frédéric Dec 9, 2024 Next-generation sequencing data were collected by Illumina HiSeq 4000 system. images of Western blot were coolected by Amersham Imager 600 system RTA version 2.7.7, bcl2fastq version 2.20.0.422, cutadapt version 1.10, STAR version 2.5.3a, htseq-count version 0.6.1p1, Ensembl version 75, DESeq2 version 1.16.1,Prism9 statistical software (GraphPad), Morpheus DeepVenn, ShinyGO, ENCODE blacklist V2, Macs2 2.2.7.1 ,BEDtools, Homer, deepTools 3.5.4, DESeq2, DiffBind seqMINER, ROSE algorithm version 0.1, RTA version 2.7.7, BCL Convert version 3.8.4, ENCODE ATACseq pipeline release v2.0.2 The publicly available data used in this study are available in the GEO database under the following accession codes: the RNA-seq, ChIP-seq and ATAC-seq data from 2 n atu re p o rtfo lio | rep o rtin g su m m ary A pril2023 Research involving human participants, their data, or biological material Policy information about studies with human participants or human data. ..

    Article Title: Morphological Structure Identification, Comparative Mitochondrial Genomics and Population Genetic Analysis toward Exploring Interspecific Variations and Phylogenetic Implications of Malus baccata 'ZA' and Other Species.
    Article Snippet: .. At the same time, Illumina data of next-generation sequencing related to the mitogenome assembly of M. baccata ‘ZA’ have been submitted to China National Center for Bioinformation (BIG Submission), and the corresponding accession numbers are BioProject: PRJCA025477 and Genome Sequence Archive (GSA): CRA016093, CRR1120135. ..

    Sequencing:

    Article Title: Measurements of soil protist richness and community composition are influenced by primer pair, annealing temperature, and bioinformatics choices.
    Article Snippet: Protists are a diverse and understudied group of microbial eukaryotic organisms especially in terrestrial environments.. Advances in molecular methods are increasing our understanding of the distribution and functions of these creatures; however, there is a vast array of choices researchers make including barcoding genes, primer pairs, PCR settings, and bioinformatic options that can impact the outcome of protist community surveys.. Here, we tested four commonly used primer pairs targeting the V4 and V9 regions of the 18S rRNA gene using different PCR annealing temperatures and processed the sequences with different bioinformatic parameters in 10 diverse soils to evaluate how primer pair, amplification parameters, and bioinformatic choices influence the composition and richness of protist and non-protist taxa using Illumina sequencing.

    Article Title: Single-nucleus transcriptomic profiling of human orbitofrontal cortex reveals convergent effects of aging and psychiatric disease.
    Article Snippet: .. Software and code Policy information about availability of computer code Data collection Next-generation sequencing data were all generated on Illumina platforms, and demultiplexed at the sequencing facility. ..

    Article Title: Morphological Structure Identification, Comparative Mitochondrial Genomics and Population Genetic Analysis toward Exploring Interspecific Variations and Phylogenetic Implications of Malus baccata 'ZA' and Other Species.
    Article Snippet: .. At the same time, Illumina data of next-generation sequencing related to the mitogenome assembly of M. baccata ‘ZA’ have been submitted to China National Center for Bioinformation (BIG Submission), and the corresponding accession numbers are BioProject: PRJCA025477 and Genome Sequence Archive (GSA): CRA016093, CRR1120135. ..

    Software:

    Article Title: Single-nucleus transcriptomic profiling of human orbitofrontal cortex reveals convergent effects of aging and psychiatric disease.
    Article Snippet: .. Software and code Policy information about availability of computer code Data collection Next-generation sequencing data were all generated on Illumina platforms, and demultiplexed at the sequencing facility. ..

    Article Title: Pan-inhibition of super-enhancer-driven oncogenic transcription by next-generation synthetic ecteinascidins yields potent anti-cancer activity
    Article Snippet: .. Data Policy information about availability of data All manuscripts must include a data availability statement This statement should provide the following information, where applicable: - Accession codes, unique identifiers, or web links for publicly available datasets - A description of any restrictions on data availability - For clinical datasets or third party data, please ensure that the statement adheres to our policy Coin Frédéric Dec 9, 2024 Next-generation sequencing data were collected by Illumina HiSeq 4000 system. images of Western blot were coolected by Amersham Imager 600 system RTA version 2.7.7, bcl2fastq version 2.20.0.422, cutadapt version 1.10, STAR version 2.5.3a, htseq-count version 0.6.1p1, Ensembl version 75, DESeq2 version 1.16.1,Prism9 statistical software (GraphPad), Morpheus DeepVenn, ShinyGO, ENCODE blacklist V2, Macs2 2.2.7.1 ,BEDtools, Homer, deepTools 3.5.4, DESeq2, DiffBind seqMINER, ROSE algorithm version 0.1, RTA version 2.7.7, BCL Convert version 3.8.4, ENCODE ATACseq pipeline release v2.0.2 The publicly available data used in this study are available in the GEO database under the following accession codes: the RNA-seq, ChIP-seq and ATAC-seq data from 2 n atu re p o rtfo lio | rep o rtin g su m m ary A pril2023 Research involving human participants, their data, or biological material Policy information about studies with human participants or human data. ..

    Generated:

    Article Title: Single-nucleus transcriptomic profiling of human orbitofrontal cortex reveals convergent effects of aging and psychiatric disease.
    Article Snippet: .. Software and code Policy information about availability of computer code Data collection Next-generation sequencing data were all generated on Illumina platforms, and demultiplexed at the sequencing facility. ..

    Expressing:

    Article Title: Identifying Molecular Modulators of the Vascular Invasion in Rectal Carcinoma: Role of ADAMTS8 and Its Co-Dependent Genes.
    Article Snippet: .. The mRNA expression levels were available from the Illumina next-generation sequencing data and presented as the RNASeq V2 RSEM dataset, while DNA methylation data was derived from the HumanMethylation450 (HM450) Infinium array. ..

    DNA Methylation Assay:

    Article Title: Identifying Molecular Modulators of the Vascular Invasion in Rectal Carcinoma: Role of ADAMTS8 and Its Co-Dependent Genes.
    Article Snippet: .. The mRNA expression levels were available from the Illumina next-generation sequencing data and presented as the RNASeq V2 RSEM dataset, while DNA methylation data was derived from the HumanMethylation450 (HM450) Infinium array. ..

    Derivative Assay:

    Article Title: Identifying Molecular Modulators of the Vascular Invasion in Rectal Carcinoma: Role of ADAMTS8 and Its Co-Dependent Genes.
    Article Snippet: .. The mRNA expression levels were available from the Illumina next-generation sequencing data and presented as the RNASeq V2 RSEM dataset, while DNA methylation data was derived from the HumanMethylation450 (HM450) Infinium array. ..

    Western Blot:

    Article Title: Pan-inhibition of super-enhancer-driven oncogenic transcription by next-generation synthetic ecteinascidins yields potent anti-cancer activity
    Article Snippet: .. Data Policy information about availability of data All manuscripts must include a data availability statement This statement should provide the following information, where applicable: - Accession codes, unique identifiers, or web links for publicly available datasets - A description of any restrictions on data availability - For clinical datasets or third party data, please ensure that the statement adheres to our policy Coin Frédéric Dec 9, 2024 Next-generation sequencing data were collected by Illumina HiSeq 4000 system. images of Western blot were coolected by Amersham Imager 600 system RTA version 2.7.7, bcl2fastq version 2.20.0.422, cutadapt version 1.10, STAR version 2.5.3a, htseq-count version 0.6.1p1, Ensembl version 75, DESeq2 version 1.16.1,Prism9 statistical software (GraphPad), Morpheus DeepVenn, ShinyGO, ENCODE blacklist V2, Macs2 2.2.7.1 ,BEDtools, Homer, deepTools 3.5.4, DESeq2, DiffBind seqMINER, ROSE algorithm version 0.1, RTA version 2.7.7, BCL Convert version 3.8.4, ENCODE ATACseq pipeline release v2.0.2 The publicly available data used in this study are available in the GEO database under the following accession codes: the RNA-seq, ChIP-seq and ATAC-seq data from 2 n atu re p o rtfo lio | rep o rtin g su m m ary A pril2023 Research involving human participants, their data, or biological material Policy information about studies with human participants or human data. ..

    RNA Sequencing:

    Article Title: Pan-inhibition of super-enhancer-driven oncogenic transcription by next-generation synthetic ecteinascidins yields potent anti-cancer activity
    Article Snippet: .. Data Policy information about availability of data All manuscripts must include a data availability statement This statement should provide the following information, where applicable: - Accession codes, unique identifiers, or web links for publicly available datasets - A description of any restrictions on data availability - For clinical datasets or third party data, please ensure that the statement adheres to our policy Coin Frédéric Dec 9, 2024 Next-generation sequencing data were collected by Illumina HiSeq 4000 system. images of Western blot were coolected by Amersham Imager 600 system RTA version 2.7.7, bcl2fastq version 2.20.0.422, cutadapt version 1.10, STAR version 2.5.3a, htseq-count version 0.6.1p1, Ensembl version 75, DESeq2 version 1.16.1,Prism9 statistical software (GraphPad), Morpheus DeepVenn, ShinyGO, ENCODE blacklist V2, Macs2 2.2.7.1 ,BEDtools, Homer, deepTools 3.5.4, DESeq2, DiffBind seqMINER, ROSE algorithm version 0.1, RTA version 2.7.7, BCL Convert version 3.8.4, ENCODE ATACseq pipeline release v2.0.2 The publicly available data used in this study are available in the GEO database under the following accession codes: the RNA-seq, ChIP-seq and ATAC-seq data from 2 n atu re p o rtfo lio | rep o rtin g su m m ary A pril2023 Research involving human participants, their data, or biological material Policy information about studies with human participants or human data. ..

    Chromatin Immunoprecipitation:

    Article Title: Pan-inhibition of super-enhancer-driven oncogenic transcription by next-generation synthetic ecteinascidins yields potent anti-cancer activity
    Article Snippet: .. Data Policy information about availability of data All manuscripts must include a data availability statement This statement should provide the following information, where applicable: - Accession codes, unique identifiers, or web links for publicly available datasets - A description of any restrictions on data availability - For clinical datasets or third party data, please ensure that the statement adheres to our policy Coin Frédéric Dec 9, 2024 Next-generation sequencing data were collected by Illumina HiSeq 4000 system. images of Western blot were coolected by Amersham Imager 600 system RTA version 2.7.7, bcl2fastq version 2.20.0.422, cutadapt version 1.10, STAR version 2.5.3a, htseq-count version 0.6.1p1, Ensembl version 75, DESeq2 version 1.16.1,Prism9 statistical software (GraphPad), Morpheus DeepVenn, ShinyGO, ENCODE blacklist V2, Macs2 2.2.7.1 ,BEDtools, Homer, deepTools 3.5.4, DESeq2, DiffBind seqMINER, ROSE algorithm version 0.1, RTA version 2.7.7, BCL Convert version 3.8.4, ENCODE ATACseq pipeline release v2.0.2 The publicly available data used in this study are available in the GEO database under the following accession codes: the RNA-seq, ChIP-seq and ATAC-seq data from 2 n atu re p o rtfo lio | rep o rtin g su m m ary A pril2023 Research involving human participants, their data, or biological material Policy information about studies with human participants or human data. ..



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    Data preprocessing workflow. When analyzing <t>NGS</t> datasets with KPop, one can optionally pre-process <t>sequencing</t> reads in order to eliminate biases and/or have the method focus on specific parts of the genome. For instance, one might align reads to a (pan-)genome and separate them into reads that align (likely to originate from the organism being studied) and reads that do not (likely to come from contaminations). Furthermore, reads that do map to the pan-genome might be separated into groups specific to different genomic features; for instance, one might align them to a set of MLST genes or AMR genes. Full k -mer spectra would then be separately obtained from each group of reads (contaminations, pan-genomic, MLST genes, AMR genes) and given as input to downstream/classification methods. The choice of the group of reads from which spectra are computed determines the set of sequences seen by the method, and hence the scope of the classification
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    Data preprocessing workflow. When analyzing NGS datasets with KPop, one can optionally pre-process sequencing reads in order to eliminate biases and/or have the method focus on specific parts of the genome. For instance, one might align reads to a (pan-)genome and separate them into reads that align (likely to originate from the organism being studied) and reads that do not (likely to come from contaminations). Furthermore, reads that do map to the pan-genome might be separated into groups specific to different genomic features; for instance, one might align them to a set of MLST genes or AMR genes. Full k -mer spectra would then be separately obtained from each group of reads (contaminations, pan-genomic, MLST genes, AMR genes) and given as input to downstream/classification methods. The choice of the group of reads from which spectra are computed determines the set of sequences seen by the method, and hence the scope of the classification

    Journal: Genome Biology

    Article Title: KPop: accurate and scalable comparative analysis of microbial genomes by sequence embeddings

    doi: 10.1186/s13059-025-03585-8

    Figure Lengend Snippet: Data preprocessing workflow. When analyzing NGS datasets with KPop, one can optionally pre-process sequencing reads in order to eliminate biases and/or have the method focus on specific parts of the genome. For instance, one might align reads to a (pan-)genome and separate them into reads that align (likely to originate from the organism being studied) and reads that do not (likely to come from contaminations). Furthermore, reads that do map to the pan-genome might be separated into groups specific to different genomic features; for instance, one might align them to a set of MLST genes or AMR genes. Full k -mer spectra would then be separately obtained from each group of reads (contaminations, pan-genomic, MLST genes, AMR genes) and given as input to downstream/classification methods. The choice of the group of reads from which spectra are computed determines the set of sequences seen by the method, and hence the scope of the classification

    Article Snippet: In order to do so, simulated next-generation sequencing (NGS) data was generated for each genome using ART [ ], emulating Illumina HiSeq 2500 paired-end reads of length 150 bp with an average coverage of 20-fold.

    Techniques: Sequencing