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second-generation dna sequencing data  (Illumina Inc)


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    Structured Review

    Illumina Inc second-generation dna sequencing data
    Second Generation Dna 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/second-generation+sequencing+data/dna+sequencing/pm38760710-47-4-18
    Average 90 stars, based on 1 article reviews
    second-generation dna sequencing data - by Bioz Stars, 2026-11
    90/100 stars

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    other:

    Article Title: The ability of SAMHD1-deficient monocytes to trigger the type I IFN response depends on cGAS and mitochondrial DNA.
    Article Snippet: Subsequently, DNA was extracted from the cytoplasmic fraction of each cell population and prepared for total DNA sequencing on the Illumina platform.

    Article Title: Comparative analysis of plastome structure in Sphagnum species from China.
    Article Snippet: Authors’ contributions X-LG and HC conceived the study and designed experiments; X-LG, KF, F-MX, C-JW collected the samples and extracted DNA for sequencing by using the Illumina platform; F-MX, W-CY, KF, and Y-HD assembled and annotated the plastomes; X-LG, F-MX, W-CY and C-JW carried out the comparative genome analysis; X-LG drafted the manuscript.

    Article Title: The Somatic Mosaicism across Human Tissues Network.
    Article Snippet: This allows assessing cell-type specificity for clonal expansion of certain Box 2 Experimental and analytical methods adopted by the SMaHT Network Core assays • Short-read DNA sequencing (Illumina) • Short-read RNA sequencing (Illumina) • Long-read DNA sequencing (PacBio and Oxford Nanopore Technologies) • Long-read full-length transcript sequencing (PacBio) Extended assays • Single-cell DNA sequencing with PTA • Duplex sequencing: concatenating original duplex for error correction, nanorate sequencing (NanoSeq), Tn5duplex-seq (CompDuplex-seq and VISTA-seq) or Ultima Genomics ppmSeq Scale-up approaches and technological developments Single-molecule sequencing • Hairpin duplex-enhanced fidelity sequencing (HiDEF-seq) Single-cell duplex sequencing • scNanoSeq and scUduplex-seq Structural variants detection • Single-cell full-length RNA sequencing for MEI detection • Single-cell, mini-bulk mobile element-targeted sequencing (PTA-HAT-seq) • Single-cell total RNA sequencing miniaturized sequencing (STORM-seq) • Strand-seq Spatial variant detection • Slide-tags Genotype-to-phenotype multi-omics For epigenome: • Single-cell 3C-seq protocols (for example, Dip-C) • Assay for transposase-accessible chromatin (ATAC-seq) • Genotyping of targeted loci with chromatin accessibility (GoT-ChA and GoT-EpiM) • Fiber-seq (single-molecule chromatin accessibility, nucleosome occupancy, transcription factor occupancy, RNA polymerase occupancy, CpG methylation and genetic variant identification) • Var-CUT&Tag (enrichment and epigenetic annotation of variants in regulatory elements) • Strand-seq (nucleosome occupancy and structural variants in the same cell) For transcriptome: • ResolveOme method • GoT-ChA-RNA • Duplex-seq-based large-scale single-cell dual omics profiling For proteome: • GoT-ChA-Pro Computational tools • Donor-specific reference genome assemblies (paired Fiber-seq, ultra-long Oxford Nanopore Technologies and Hi-C data) • Hybrid approach for single-cell WGA-RUFUS (a reference-free, kmer-based variant detection algorithm) Infrastructure • Centralized three germ layer tissue collection banking with donor metadata • Automated analysis pipelines for quality control • A variant catalogue containing a curated set of annotated somatic mutations • Computational pipelines with multi-omics platforms • Human pangenome visualization with somatic mutation detection pipelines • A cloud-based infrastructure and a web portal The SMaHT Network will apply a set of standard approaches as well as benchmark new methods to improve detection, analysis and functional annotation of somatic variants across tissues and individuals.

    Produced:

    Article Title: A transient mutational burst occurs during yeast colony development.
    Article Snippet: .. The datasets and computer code produced in this study are available in the following databases: Illumina DNA sequencing: fastq files from whole-genome sequencing of 35 DC strains (https://www.ebi.ac.uk/ ena/browser/view/PRJEB70654). .. Oxford Nanopore DNA sequencing: fastq files from whole-genome sequencing of 12 strains (https:// www.ebi.ac.uk/ena/browser/view/PRJEB70654).

    DNA Sequencing:

    Article Title: A transient mutational burst occurs during yeast colony development.
    Article Snippet: .. The datasets and computer code produced in this study are available in the following databases: Illumina DNA sequencing: fastq files from whole-genome sequencing of 35 DC strains (https://www.ebi.ac.uk/ ena/browser/view/PRJEB70654). .. Oxford Nanopore DNA sequencing: fastq files from whole-genome sequencing of 12 strains (https:// www.ebi.ac.uk/ena/browser/view/PRJEB70654).

    Article Title: RNA-guided DNA integration using Tn7-like transposons
    Article Snippet: The genetic payload may be a short adaptor, such as a sequence used for downstream primer binding during a PCR amplification step, as would be performed for NGS library preps for massively parallel DNA sequencing, such as with the Illumina®, Pacbio, Ion Torrent, or Nanopore, platforms. .. The genetic payload may be a short adaptor, such as a sequence used for downstream primer binding during a PCR amplification step, as would be performed for NGS library preps for massively parallel DNA sequencing, such as with the Illumina®, Pacbio, Ion Torrent, or Nanopore, platforms. ..

    Article Title: Identification of novel strain Acinetobacter baumannii H1 and its improvement capacity for nutrient removal after coimmobilized on activated carbon and CaCO 3 in real aquaculture wastewater.
    Article Snippet: A new strain H1, Acinetobacter baumannii, exhibited the 96 % nitrogen and 76 % phosphate removal efficiencies in suspension environment after 48 h, and the optimal conditions were obtained at pH of 7–8, temperature of 30 C, carbon source of succinate, carbon-nitrogen ratio of 10 and phosphorus-nitrogen ratio of 0.2, respectively.. The immobilization experiments with activated carbon and CaCO3 were carried out, the optimal formula was 30 g/L CaCO3, 15 g/L activated carbon-bacteria complex, 2 % CaCl2 and a 1:1 embedding agent ratio.. The removal efficiency of NH4-N, total nitrogen, total phosphorus and chemical oxygen demand in immobilized H1 was 288.89 %, 121.87 %, 135.69 % and 667.21 % higher than that by free strain in group With Indigenous Bacteria, respectively.

    Sequencing:

    Article Title: A transient mutational burst occurs during yeast colony development.
    Article Snippet: .. The datasets and computer code produced in this study are available in the following databases: Illumina DNA sequencing: fastq files from whole-genome sequencing of 35 DC strains (https://www.ebi.ac.uk/ ena/browser/view/PRJEB70654). .. Oxford Nanopore DNA sequencing: fastq files from whole-genome sequencing of 12 strains (https:// www.ebi.ac.uk/ena/browser/view/PRJEB70654).

    Article Title: RNA-guided DNA integration using Tn7-like transposons
    Article Snippet: The genetic payload may be a short adaptor, such as a sequence used for downstream primer binding during a PCR amplification step, as would be performed for NGS library preps for massively parallel DNA sequencing, such as with the Illumina®, Pacbio, Ion Torrent, or Nanopore, platforms. .. The genetic payload may be a short adaptor, such as a sequence used for downstream primer binding during a PCR amplification step, as would be performed for NGS library preps for massively parallel DNA sequencing, such as with the Illumina®, Pacbio, Ion Torrent, or Nanopore, platforms. ..

    Binding Assay:

    Article Title: RNA-guided DNA integration using Tn7-like transposons
    Article Snippet: The genetic payload may be a short adaptor, such as a sequence used for downstream primer binding during a PCR amplification step, as would be performed for NGS library preps for massively parallel DNA sequencing, such as with the Illumina®, Pacbio, Ion Torrent, or Nanopore, platforms. .. The genetic payload may be a short adaptor, such as a sequence used for downstream primer binding during a PCR amplification step, as would be performed for NGS library preps for massively parallel DNA sequencing, such as with the Illumina®, Pacbio, Ion Torrent, or Nanopore, platforms. ..

    Polymerase Chain Reaction:

    Article Title: RNA-guided DNA integration using Tn7-like transposons
    Article Snippet: The genetic payload may be a short adaptor, such as a sequence used for downstream primer binding during a PCR amplification step, as would be performed for NGS library preps for massively parallel DNA sequencing, such as with the Illumina®, Pacbio, Ion Torrent, or Nanopore, platforms. .. The genetic payload may be a short adaptor, such as a sequence used for downstream primer binding during a PCR amplification step, as would be performed for NGS library preps for massively parallel DNA sequencing, such as with the Illumina®, Pacbio, Ion Torrent, or Nanopore, platforms. ..

    Article Title: Identification of novel strain Acinetobacter baumannii H1 and its improvement capacity for nutrient removal after coimmobilized on activated carbon and CaCO 3 in real aquaculture wastewater.
    Article Snippet: A new strain H1, Acinetobacter baumannii, exhibited the 96 % nitrogen and 76 % phosphate removal efficiencies in suspension environment after 48 h, and the optimal conditions were obtained at pH of 7–8, temperature of 30 C, carbon source of succinate, carbon-nitrogen ratio of 10 and phosphorus-nitrogen ratio of 0.2, respectively.. The immobilization experiments with activated carbon and CaCO3 were carried out, the optimal formula was 30 g/L CaCO3, 15 g/L activated carbon-bacteria complex, 2 % CaCl2 and a 1:1 embedding agent ratio.. The removal efficiency of NH4-N, total nitrogen, total phosphorus and chemical oxygen demand in immobilized H1 was 288.89 %, 121.87 %, 135.69 % and 667.21 % higher than that by free strain in group With Indigenous Bacteria, respectively.

    Amplification:

    Article Title: RNA-guided DNA integration using Tn7-like transposons
    Article Snippet: The genetic payload may be a short adaptor, such as a sequence used for downstream primer binding during a PCR amplification step, as would be performed for NGS library preps for massively parallel DNA sequencing, such as with the Illumina®, Pacbio, Ion Torrent, or Nanopore, platforms. .. The genetic payload may be a short adaptor, such as a sequence used for downstream primer binding during a PCR amplification step, as would be performed for NGS library preps for massively parallel DNA sequencing, such as with the Illumina®, Pacbio, Ion Torrent, or Nanopore, platforms. ..

    Article Title: Identification of novel strain Acinetobacter baumannii H1 and its improvement capacity for nutrient removal after coimmobilized on activated carbon and CaCO 3 in real aquaculture wastewater.
    Article Snippet: A new strain H1, Acinetobacter baumannii, exhibited the 96 % nitrogen and 76 % phosphate removal efficiencies in suspension environment after 48 h, and the optimal conditions were obtained at pH of 7–8, temperature of 30 C, carbon source of succinate, carbon-nitrogen ratio of 10 and phosphorus-nitrogen ratio of 0.2, respectively.. The immobilization experiments with activated carbon and CaCO3 were carried out, the optimal formula was 30 g/L CaCO3, 15 g/L activated carbon-bacteria complex, 2 % CaCl2 and a 1:1 embedding agent ratio.. The removal efficiency of NH4-N, total nitrogen, total phosphorus and chemical oxygen demand in immobilized H1 was 288.89 %, 121.87 %, 135.69 % and 667.21 % higher than that by free strain in group With Indigenous Bacteria, respectively.

    Next-Generation Sequencing:

    Article Title: RNA-guided DNA integration using Tn7-like transposons
    Article Snippet: The genetic payload may be a short adaptor, such as a sequence used for downstream primer binding during a PCR amplification step, as would be performed for NGS library preps for massively parallel DNA sequencing, such as with the Illumina®, Pacbio, Ion Torrent, or Nanopore, platforms. .. The genetic payload may be a short adaptor, such as a sequence used for downstream primer binding during a PCR amplification step, as would be performed for NGS library preps for massively parallel DNA sequencing, such as with the Illumina®, Pacbio, Ion Torrent, or Nanopore, platforms. ..

    Article Title: Genetic profile of ASXL1 gene in risk assessment in acute myeloid leukemia
    Article Snippet: .. This study was conducted to determine and assess the impact of ASXL1 gene variants in 38 AML patients of a South Asian population (Pakistan) by using the Illumina next generation DNA sequencing technology. ..

    Article Title: Genetic profile of ASXL1 gene in risk assessment in acute myeloid leukemia.
    Article Snippet: .. ASXL1 mutational landscape in AML This study was conducted to determine and assess the impact of ASXL1 gene variants in 38 AML patients of a South Asian population (Pakistan) by using the Illumina next generation DNA sequencing technology. ..

    Extraction:

    Article Title: Identification of novel strain Acinetobacter baumannii H1 and its improvement capacity for nutrient removal after coimmobilized on activated carbon and CaCO 3 in real aquaculture wastewater.
    Article Snippet: A new strain H1, Acinetobacter baumannii, exhibited the 96 % nitrogen and 76 % phosphate removal efficiencies in suspension environment after 48 h, and the optimal conditions were obtained at pH of 7–8, temperature of 30 C, carbon source of succinate, carbon-nitrogen ratio of 10 and phosphorus-nitrogen ratio of 0.2, respectively.. The immobilization experiments with activated carbon and CaCO3 were carried out, the optimal formula was 30 g/L CaCO3, 15 g/L activated carbon-bacteria complex, 2 % CaCl2 and a 1:1 embedding agent ratio.. The removal efficiency of NH4-N, total nitrogen, total phosphorus and chemical oxygen demand in immobilized H1 was 288.89 %, 121.87 %, 135.69 % and 667.21 % higher than that by free strain in group With Indigenous Bacteria, respectively.

    Purification:

    Article Title: Identification of novel strain Acinetobacter baumannii H1 and its improvement capacity for nutrient removal after coimmobilized on activated carbon and CaCO 3 in real aquaculture wastewater.
    Article Snippet: A new strain H1, Acinetobacter baumannii, exhibited the 96 % nitrogen and 76 % phosphate removal efficiencies in suspension environment after 48 h, and the optimal conditions were obtained at pH of 7–8, temperature of 30 C, carbon source of succinate, carbon-nitrogen ratio of 10 and phosphorus-nitrogen ratio of 0.2, respectively.. The immobilization experiments with activated carbon and CaCO3 were carried out, the optimal formula was 30 g/L CaCO3, 15 g/L activated carbon-bacteria complex, 2 % CaCl2 and a 1:1 embedding agent ratio.. The removal efficiency of NH4-N, total nitrogen, total phosphorus and chemical oxygen demand in immobilized H1 was 288.89 %, 121.87 %, 135.69 % and 667.21 % higher than that by free strain in group With Indigenous Bacteria, respectively.

    Concentration Assay:

    Article Title: Identification of novel strain Acinetobacter baumannii H1 and its improvement capacity for nutrient removal after coimmobilized on activated carbon and CaCO 3 in real aquaculture wastewater.
    Article Snippet: A new strain H1, Acinetobacter baumannii, exhibited the 96 % nitrogen and 76 % phosphate removal efficiencies in suspension environment after 48 h, and the optimal conditions were obtained at pH of 7–8, temperature of 30 C, carbon source of succinate, carbon-nitrogen ratio of 10 and phosphorus-nitrogen ratio of 0.2, respectively.. The immobilization experiments with activated carbon and CaCO3 were carried out, the optimal formula was 30 g/L CaCO3, 15 g/L activated carbon-bacteria complex, 2 % CaCl2 and a 1:1 embedding agent ratio.. The removal efficiency of NH4-N, total nitrogen, total phosphorus and chemical oxygen demand in immobilized H1 was 288.89 %, 121.87 %, 135.69 % and 667.21 % higher than that by free strain in group With Indigenous Bacteria, respectively.



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