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next generation sequencing data  (Biotechnology Information)

 
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    Biotechnology Information next generation sequencing data
    Next Generation Sequencing Data, supplied by Biotechnology Information, used in various techniques. Bioz Stars score: 86/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/product/next+generation+sequencing+data/data+genome+sequencing+whole/pm41095186-151-2-13
    Average 86 stars, based on 1 article reviews
    next generation sequencing data - by Bioz Stars, 2026-09
    86/100 stars

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    Related Articles

    Sequencing:

    Article Title: Fiber intake associates with increased treatment response in patients with multiple myeloma along with changes in gut microbiome
    Article Snippet: .. The raw shotgun metagenome sequencing data from stool samples have been registered with the National Center for Biotechnology Information Sequence Read Archive under the submission code SUB14621986. ..

    Article Title: Successful treatment of an NDM-5-producing, carbapenem-resistant Salmonella Kentucky ST198 infection with aztreonam and ceftazidime-avibactam in a patient with acute erythroid leukemia: a case report.
    Article Snippet: .. The whole-genome sequencing results have been deposited in National Center for Biotechnology Information (accession number: JBOEPZ000000000) that are publicly accessible at https://www.ncbi.nlm.nih.gov/nuccore/JBOEPZ000000000. ..

    Construct:

    Article Title: Integrative comparative genomics and transcriptomics reveal key roles of SAG17 and SAG23 in early-stage virulence divergence of Eimeria tenella.
    Article Snippet: .. These loci were then used to construct a functional gene set at the DNA level for subsequent analysis.The raw resequencing data were deposited in the National Center for Biotechnology Information (NCBI) database under the following accession numbers: SRR35396008 for the Beijing strain, and SRR35396007 for the Guizhou strain. .. Total RNA was extracted using the TRIzol reagent (Invitrogen Life Technologies), and RNA purity, concentration, and integrity (RIN ≥ 7) were assessed with a NanoDrop 2000 spectrophotometer.

    Functional Assay:

    Article Title: Integrative comparative genomics and transcriptomics reveal key roles of SAG17 and SAG23 in early-stage virulence divergence of Eimeria tenella.
    Article Snippet: .. These loci were then used to construct a functional gene set at the DNA level for subsequent analysis.The raw resequencing data were deposited in the National Center for Biotechnology Information (NCBI) database under the following accession numbers: SRR35396008 for the Beijing strain, and SRR35396007 for the Guizhou strain. .. Total RNA was extracted using the TRIzol reagent (Invitrogen Life Technologies), and RNA purity, concentration, and integrity (RIN ≥ 7) were assessed with a NanoDrop 2000 spectrophotometer.

    Next-Generation Sequencing:

    Article Title: Deciphering potential significances of biliary microbiome in cholelithiasis and cholangiocarcinoma.
    Article Snippet: communities and these biliary diseases.. Methods: We conducted a comprehensive bioinformatics analysis using high-throughput sequencing data obtained from the Sequence Read Archive (SRA) database to characterize the composition of microbial communities in patients with CCA and CHOL.. We performed operational taxonomic unit (OTU) clustering, statistical analyses and Mendelian randomization (MR) to elucidate the causal relationships between specific bacterial strains and disease outcomes.

    Derivative Assay:

    Article Title: Deciphering potential significances of biliary microbiome in cholelithiasis and cholangiocarcinoma.
    Article Snippet: communities and these biliary diseases.. Methods: We conducted a comprehensive bioinformatics analysis using high-throughput sequencing data obtained from the Sequence Read Archive (SRA) database to characterize the composition of microbial communities in patients with CCA and CHOL.. We performed operational taxonomic unit (OTU) clustering, statistical analyses and Mendelian randomization (MR) to elucidate the causal relationships between specific bacterial strains and disease outcomes.

    Gene Expression:

    Article Title: HDAC2 enhances the antimicrobial activity of neutrophils by promoting the formation of neutrophil extracellular traps (NETs) in sepsis
    Article Snippet: .. Sepsis high-throughput gene chips GSE95233 were screened from the Gene Expression Omnibus (GEO) database of the National Center for Biotechnology Information ( https://www.ncbi.nlm.nih.gov/geo ). ..

    other:

    Article Title: Insights into lentil diversity, domestication, and the genetic basis of important agronomic traits through resequencing of 238 Lens accessions
    Article Snippet: Whole‐genome resequencing raw data are available at the National Center for Biotechnology Information‐Sequence Read Archive (NCBI‐SRA) database ( https://www.ncbi.nlm.nih.gov/sra ) under accession number PRJNA1128027.

    Generated:

    Article Title: Genes Versus Environment: Body Size Variation Among Recruitment Cohorts of Dungeness Crab.
    Article Snippet: .. Data Availability Statement The whole- genome resequencing data generated for this study are deposited in the National Center for Biotechnology Information (NCBI) database under BioProject PRJNA1399483. ..



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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