Results 41 to 50 of about 238,366 (195)

Highly Variable Genomic Landscape of Endogenous Retroviruses in the C57BL/6J Inbred Strain, Depending on Individual Mouse, Gender, Organ Type, and Organ Location. [PDF]

, 2017
Transposable repetitive elements, named the "TREome," represent ~40% of the mouse genome. We postulate that the germ line genome undergoes temporal and spatial diversification into somatic genomes in conjunction with the TREome activity.
Cho, Kiho, Greenhalgh, David, Lee, Kang-Hoon, Lim, Debora   +3 more
core   +2 more sources

Hormaphis cornu amplicon sequencing script

, 2020
Code used in analysis of the PCR amplicon sequencing data of the significant GWAS SNPs in dgc gene, associated with the publication "A novel family of secreted insect proteins linked to plant gall development" by Korgaonkar et al. (2021). amplicon_seq_haplotypes.R uses Hcor_ampliconSeq_plates1-12_shortRef_gatk_v2+bcftools_genotypes_manualEdited_AK.tsv ...
Aishwarya Korgaonkar, Han, Clair, Stern, David   +2 more
openaire   +1 more source

Grinder: a versatile amplicon and shotgun sequence simulator [PDF]

Nucleic Acids Research, 2012
We introduce Grinder (http://sourceforge.net/projects/biogrinder/), an open-source bioinformatic tool to simulate amplicon and shotgun (genomic, metagenomic, transcriptomic and metatranscriptomic) datasets from reference sequences. This is the first tool to simulate amplicon datasets (e.g. 16S rRNA) widely used by microbial ecologists.
Angly, Florent E., Willner, Dana, Rohwer, Forest, Hugenholtz, Philip, Tyson, Gene W.   +4 more
openaire   +3 more sources

A simple novel device for air sampling by electrokinetic capture. [PDF]

, 2015
BackgroundA variety of different sampling devices are currently available to acquire air samples for the study of the microbiome of the air. All have a degree of technical complexity that limits deployment.
Frazier, Angel, Gandhi, Prasanthi, Gilbert, Jack A, Gordon, Julian, Hampton-Marcell, Jarrad, Shekhawat, Gajendra   +5 more
core   +3 more sources

Nanopore amplicon sequencing v2

, 2022
This protocol describes the step-by-step procedures for performing nanopore amplicon sequencing using the latest Kit 14 chemistry. The method is versatile and can be applied to a wide range of sequence-based analyses, including human microbiome profiling and biodiversity assessment using environmental DNA (eDNA metabarcoding).
openaire   +1 more source

Reproducibility and quantitation of amplicon sequencing-based detection [PDF]

The ISME Journal, 2011
Abstract To determine the reproducibility and quantitation of the amplicon sequencing-based detection approach for analyzing microbial community structure, a total of 24 microbial communities from a long-term global change experimental site were examined.
Jizhong, Zhou, Liyou, Wu, Ye, Deng, Xiaoyang, Zhi, Yi-Huei, Jiang, Qichao, Tu, Jianping, Xie, Joy D, Van Nostrand, Zhili, He, Yunfeng, Yang   +9 more
openaire   +2 more sources

Microbial community dynamics and coexistence in a sulfide-driven phototrophic bloom [PDF]

, 2020
© The Author(s), 2020. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Bhatnagar, S., Cowley, E. S., Kopf, S. H., Pérez Castro, S., Kearney, S., Dawson, S. C., Hanselmann, K.
Bhatnagar, Srijak, Castro, Sherlynette Pérez, Cowley, Elise S, Dawson, Scott C, Hanselmann, Kurt, Kearney, Sean, Kearney, Sean Michael, Kopf, Sebastian H, Pérez Castro, Sherlynette, Ruff, S. E   +9 more
core   +1 more source

PCR amplicon next generation sequencing v3

, 2022
Preparation of Amplicons for deep sequencing is based on two PCR steps. The genomic loci of interest is enriched in a first PCR including a stubber sequence to both ends of the molecule. For the subsequent barcoding PCR the stubber sequence is targeted and the full NGS sequencing adapter including dual barcodes are introduced to the molecule ends ...
Susanne Kreutzer, Lilly van de Venn, Charles Yeh, Mark DeWitt   +3 more
openaire   +1 more source

Strategy for Modular Tagged High-Throughput Amplicon Sequencing [PDF]

Applied and Environmental Microbiology, 2011
ABSTRACT The use and validation of a strategy that allows a universal set of bar-coded sequencing primers to be appended to an amplified PCR product is described. The strategy allows a modular approach, in that the same bar code can be used with two or more target-specific primer sets, even simultaneously.
de Carcer, Daniel Aguirre, Denman, Stuart E., McSweeney, Chris, Morrison, Mark   +3 more
openaire   +4 more sources

PVAmpliconFinder: a workflow for the identification of human papillomaviruses from high-throughput amplicon sequencing

BMC Bioinformatics, 2020
Background The detection of known human papillomaviruses (PVs) from targeted wet-lab approaches has traditionally used PCR-based methods coupled with Sanger sequencing.
Alexis Robitaille, Rosario N. Brancaccio, Sankhadeep Dutta, Dana E. Rollison, Marcis Leja, Nicole Fischer, Adam Grundhoff, Tarik Gheit, Massimo Tommasino, Magali Olivier   +9 more
doaj   +1 more source