Effect of Amplicon Sequencing Depth in Environmental Microbiome Research.
Sign Up to like & getrecommendations! Published in 2021 at "Current microbiology"
DOI: 10.1007/s00284-021-02345-8
Abstract: Amplicon sequencing approach is commonly employed in microbiome studies and sequencing depth is considered as a major factor influencing the outcome of data analyses. As of now, the effect of amplicon sequencing depth in environmental… read more here.
Keywords: effect amplicon; data analyses; environmental microbiome; microbiome ... See more keywords
Increased sequencing depth does not increase captured diversity of arbuscular mycorrhizal fungi
Sign Up to like & getrecommendations! Published in 2017 at "Mycorrhiza"
DOI: 10.1007/s00572-017-0791-y
Abstract: The arrival of 454 sequencing represented a major breakthrough by allowing deeper sequencing of environmental samples than was possible with existing Sanger approaches. Illumina MiSeq provides a further increase in sequencing depth but shorter read… read more here.
Keywords: fungal richness; illumina sequencing; 454 sequencing; arbuscular mycorrhizal ... See more keywords
Impact of sequencing depth and read length on single cell RNA sequencing data of T cells
Sign Up to like & getrecommendations! Published in 2017 at "Scientific Reports"
DOI: 10.1038/s41598-017-12989-x
Abstract: Single cell RNA sequencing (scRNA-seq) provides great potential in measuring the gene expression profiles of heterogeneous cell populations. In immunology, scRNA-seq allowed the characterisation of transcript sequence diversity of functionally relevant T cell subsets, and… read more here.
Keywords: single cell; scrna seq; length; sequencing depth ... See more keywords
The effects of sequencing depth on the assembly of coding and noncoding transcripts in the human genome
Sign Up to like & getrecommendations! Published in 2022 at "BMC Genomics"
DOI: 10.1101/2022.01.30.478357
Abstract: Investigating the functions and activities of genes requires proper annotation of the transcribed units. However, transcript assembly efforts have produced a surprisingly large variation in the number of transcripts, and especially so for noncoding transcripts.… read more here.
Keywords: effects sequencing; read data; noncoding transcripts; long read ... See more keywords
Optimal microRNA Sequencing Depth to Predict Cancer Patient Survival with Random Forest and Cox Models
Sign Up to like & getrecommendations! Published in 2022 at "Genes"
DOI: 10.1101/2022.10.21.513222
Abstract: (1) Background tumor profiling enables patient survival prediction. The two essential parameters to be calibrated when designing a study based on tumor profiles from a cohort are the sequencing depth of RNA-seq technology and the… read more here.
Keywords: seq; random; prediction; patient survival ... See more keywords
DNA Input, sequencing depth, and maximum somatic allele frequency may affect the concordance between blood TMB and tumor TMB.
Sign Up to like & getrecommendations! Published in 2019 at "Journal of Clinical Oncology"
DOI: 10.1200/jco.2019.37.15_suppl.e13163
Abstract: e13163 Background: Tumor mutation burden (TMB) is recognized as a promising biomarker for PD-1/PD-L1 blockade therapy. However, a tissue biopsy is often not available, and hence a liquid biopsy using blood can be used to… read more here.
Keywords: sequencing depth; concordance; btmb ttmb; tmb ... See more keywords
Phylogenetic microbiota profiling in fecal samples depends on combination of sequencing depth and choice of NGS analysis method
Sign Up to like & getrecommendations! Published in 2019 at "PLoS ONE"
DOI: 10.1371/journal.pone.0222171
Abstract: The human gut microbiota is well established as an important factor in health and disease. Fecal sample microbiota are often analyzed as a proxy for gut microbiota, and characterized with respect to their composition profiles.… read more here.
Keywords: microbiota; method; choice; sequencing depth ... See more keywords
Towards Strain-Level Complexity: Sequencing Depth Required for Comprehensive Single-Nucleotide Polymorphism Analysis of the Human Gut Microbiome
Sign Up to like & getrecommendations! Published in 2022 at "Frontiers in Microbiology"
DOI: 10.3389/fmicb.2022.828254
Abstract: Intestinal bacteria strains play crucial roles in maintaining host health. Researchers have increasingly recognized the importance of strain-level analysis in metagenomic studies. Many analysis tools and several cutting-edge sequencing techniques like single cell sequencing have… read more here.
Keywords: level complexity; ultra deep; analysis; strain level ... See more keywords
Sequencing Depth Has a Stronger Effect than DNA Extraction on Soil Bacterial Richness Discovery
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DOI: 10.3390/biom12030364
Abstract: Although Next-Generation Sequencing techniques have increased our access to the soil microbiome, each step of soil metagenomics presents inherent biases that prevent the accurate definition of the soil microbiome and its ecosystem function. In this… read more here.
Keywords: dna extraction; soil; sequencing depth; richness ... See more keywords