Tag: MISeq

Mobile resistome of microbial communities and antimicrobial residues from drinking water supply systems in Rio de Janeiro, Brazil

Ilyas, M. et al. Environmental and health impacts of industrial wastewater effluents in Pakistan: A review. Rev. Environ. Health 34, 171–186 (2019). MathSciNet  PubMed  CAS  Google Scholar  Roy, M. A. et al. A Metagenomic approach to evaluating surface water quality in Haiti. Int. J. Environ. Res. Public Health 15, 2211…

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Simulated global warming affects endophytic bacterial and fungal communities of Antarctic pearlwort leaves and some bacterial isolates support plant growth at low temperatures

Sample collection Colobanthus quitensis samples were collected at King George Island near the Henryk Arctowski Polish Antarctic Station, Maritime Antarctica (62°14’ S, 58°48’ W) during the summer season (February 2018). Samples were collected inside the Antarctic Specially Protected Area (ASPA) 128 using permits provided by The Chilean Antarctic Institute (INACH)…

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Cellular glycan modification by B3GAT1 broadly restricts influenza virus infection

Ethics statement All procedures involving laboratory mice were approved by the Duke University IACUC under the protocol numbers A189-18-08 and A142-21-07. Mice were housed with up to five mice per cage and the ambient room conditions ranged from 70–74 °F and 30–70% humidity with a 12-hour dark/light cycle. Animals were assessed…

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Next Generation Sequencing (NGS) Market, Outlook Size Share Industry Segmentation, Targeting, Positioning Exclusive Report by |Quince Market Insights

Next Generation Sequencing (NGS) Market Scope The Next Generation Sequencing (NGS)-market size was assessed at USD in 2023. Developing number of organizations tapping the nearness Next Generation Sequencing (NGS) market, alongside expanding interests in the Next Generation Sequencing (NGS) Market innovation, is supposed to move the business development. expected to…

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A New Kind of Liquid Biopsy

Canada’s STREAM project uses genomics to advance watershed health monitoring Northampton, MA –News Direct– Illumina Photo: Community members sample the Skeena sub-watershed in Smithers, British Columbia. Rivers and streams are vital to communities everywhere, for drinking water, transportation, and leisure. But pollution, drought, and climate change are taking their toll,…

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Careers in genomics – The Hindu

As scientists and other professionals use discoveries in genetics to revolutionise the world, careers in genetics and genomics are booming, given the advances in the field of personalised medicine, DNA sequencing technologies and commercial applications of genetics research. ‘Genomics’ stands for the study of whole genomes. While ‘genes’ are instructions…

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How many lanes does the Nextseq (illumina) flow cell have?

How many lanes does the Nextseq (illumina) flow cell have? 1 Hi all, How many lanes does the Nextseq (illumina) flow cell have? Thanks. sequencing • 12k views MiSeq – 1 lane cells HiSeg machines had 8 lanes in High Output Mode and 2 lane cells in Rapid Mode (only…

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CISA Warned About Critical Vulnerabilities in Illumina’s DNA Sequencing Devices

The U.S. Cybersecurity and Infrastructure Security Agency (CISA) and Food and Drug Administration (FDA) have issued an advisory about critical security vulnerabilities in Illumina’s next-generation sequencing (NGS) software. Three of the flaws are rated 10 out of 10 for severity on the Common Vulnerability Scoring System (CVSS), with two others…

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cfDNA-Based NGS IG Analysis in Lymphoma

Circulating cell-free DNA (cfDNA) is fragmented extracellular DNA, which is released from apoptotic and necrotic cells in small fragments of <200 bp [1]. cfDNA is typically isolated from the blood stream; however, it is also possible to detect cfDNA in other biological fluids such as urine or cerebrospinal fluid [2, 3,…

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MicrobioSeq Releases Nanopore-Based Microbial Epigenomics Solutions to Accelerate Your Research

MicrobioSeq is the microbial genomics division of CD Genomics, committed to delivering comprehensive microbial solutions to human health, agriculture, the environment, and industry by characterizing microbiomes and leveraging microorganisms. The company recently announced the launch of Nanopore-Based Microbial Epigenomics Solutions to detect more types of DNA modifications.   Epigenetic modifications…

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Index of /~psgendb/doc/pkg/cd-hit-v4.8.1-2019-0228/doc

Name Last modified Size Description Parent Directory   –   Figure1.png 2015-05-05 00:44 43K   Figure2.png 2015-05-05 00:44 42K   Figure3.png 2015-05-05 00:44 129K   Figure4.png 2015-05-05 00:44 30K   cd-hit-est.man 2020-06-16 12:13 5.6K   cd-hit-otu-miseq-Fig..> 2017-03-25 12:00 117K   cd-hit.man 2020-06-16 12:12 4.4K   cdhit-user-guide.pdf 2017-05-01 11:52 412K  …

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illumina miseq reagent Bids, RFP & Government Contracts

Reagent (Chemistry) Kits Quick View Type : Bid Notification Due : 04 Aug, 2017 (about 4 years ago) Posted : about 4 years ago Started : 28 Jul, 2017 (about 4 years ago) All of which require Reagent (Chemistry) Kits for data analysis as follows:• Sequencing by Synthesis (SBS) Kits•…

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Bioconductor – Rsubread

    This package is for version 2.13 of Bioconductor; for the stable, up-to-date release version, see Rsubread. Rsubread: high-performance read alignment, quantification and mutation discovery Bioconductor version: 2.13 This R package provides easy-to-use tools for analyzing next-gen sequencing read data. Functions of these tools include quality assessment, read alignment,…

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Using mothur toolsuite on Galaxy to analyze microbial datasets : bioinformatics

Hi all, I am using the mothur toolsuite on Galaxy to attempt to process duodenal microbiome samples in humans. The datasets I am using are paired reads generated by WGS. I am directly following this guide: training.galaxyproject.org/training-material/topics/metagenomics/tutorials/mothur-miseq-sop/tutorial.html I’m stuck on the OTU Clustering section for my data samples, specifically the…

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DNA and MiSeq Sample Submission Form

Required fields are marked with an asterisk (*). NameYour initials and amplicon e.g. KA_16S_Sequencing Number of samples DNA and sequencing project and quote number Service requested* DNA extraction Bacterial 16S 341F/805R Bacterial 16S 515F/806R Bacterial 16S 27F/519R Bacterial 16S 799F/1193R Fungal ITS2 fITS7/ITS4 Fungal ITS1 ITS1f/ITS2 Fungal ITS1&2 ITS1oo/ITS4 Fungal…

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CEFAS22-11 Next Generation Sequencing Services Framework: | Construction Tenders

Tender Details Reference ocds-h6vhtk-031eee Common Procurement Vocabulary Technical analysis or consultancy services Procurement Method Open procedure Value £500,000 Tender Details Reference ocds-h6vhtk-031eee Common Procurement Vocabulary Technical analysis or consultancy services Procurement Method Open procedure Value £500,000 Section I: Contracting authority I.1) Name and addresses CEFAS Pakefield Road Lowestoft NR33 0HT…

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UWI performs Next Generation Sequencing service for the first time in Jamaica

The UWI Mona Campus, Kingston, Jamaica. Friday, February 25, 2022 —The University of the West Indies (The UWI) Mona Campus – working in close collaboration with the University Hospital of the West Indies (UHWI) and the Ministry of Health and Wellness (MOHW) – has established a Next Generation Sequencing (NGS) Service…

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QuantSeq 3’ mRNA-Seq Library prep kits: Lexogen

QuantSeq 3’ mRNA-Seq Library Prep kits from Lexogen offers cost-efficient analysis of differential gene expression via 3’ mRNA-seq library preparation. Requiring fewer reads per samples and capable of multiplexing a high number of samples on a single sequencing lane, the 3’ mRNA-Seq technology simplifies your gene expression projects with no…

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Pathogenomix Developing Infectious Disease Testing Platform Enabled by Cloud-Based Analytics, NGS

NEW YORK — Pathogenomix is combining sequencer-agnostic, cloud-based analytics software with 16S rRNA gene sequencing to enable hospital laboratories to identify the pathogens behind life-threatening bacterial infections. Though no NGS-based tests have obtained full US Food and Drug Administration authorization to identify infectious disease pathogens, Pathogenomix said it is on…

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Requirement of Xk and Vps13a for the P2X7-mediated phospholipid scrambling and cell lysis in mouse T cells

Significance The extracellular concentration of adenosine triphosphate (ATP) reaches several hundred micromoles in the inflamed tissues or tumor environment. A high concentration of ATP activates P2X7, a purinergic receptor, and induces the formation of a nonselective cation channel, accompanied by reversible phosphatidylserine (PtdSer) exposure, leading to cell lysis. Here, we…

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Cell Strain-Derived Induced Pluripotent Stem Cells as an Isogenic Approach To Investigate Age-Related Host Response to Flaviviral Infection

INTRODUCTION Dengue is the most common mosquito-borne viral disease globally (1). This acute disease, which can be life-threatening, is caused by four different dengue viruses (DENVs) (DENV-1, DENV-2, DENV-3, and DENV-4). An estimated 390 million people are infected with these DENVs annually (2), and populations throughout the tropics face frequent…

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DNA Labs International Launches the Newest Technology for Forensic Genetic Genealogy

MiSeq FGx platform by Verogen DEERFIELD BEACH, Fla. (PRWEB) January 26, 2022 DNA Labs International, which specializes in forensic DNA analysis including forensic genetic genealogy (FGG) for law enforcement agencies, government forensic labs, and attorneys, is announcing the release of their newest technology, Single Nucleotide Polymorphism (SNP) testing with…

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Novel gene rearrangement in the mitochondrial genome of Anastatus fulloi (Hymenoptera Chalcidoidea) and phylogenetic implications for Chalcidoidea

1. Osellame, L. D., Blacker, T. S. & Duchen, M. R. Cellular and molecular mechanisms of mitochondrial function. Best Pract. Res. Clin. Endocrinol. Metab. 26, 711–723 (2012). CAS  PubMed  PubMed Central  Google Scholar  2. Bernt, M., Braband, A., Schierwater, B. & Stadler, P. F. Genetic aspects of mitochondrial genome evolution….

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Insight into the symbiotic lifestyle of DPANN archaea revealed by cultivation and genome analyses

Significance The DPANN superphylum is a grouping of symbiotic microorganisms categorized based on their genomic contents and a few examples of cultivation experiments. Although the genome information of DPANN archaea is increasing year by year, most of them have remained uncultivated, limiting our knowledge of these organisms. Herein, a thermoacidophilic…

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Estimating individual mtDNA haplotypes in mixed DNA samples by combining MinION and MiSeq

doi: 10.1007/s00414-021-02763-0. Online ahead of print. Affiliations Expand Affiliations 1 Department of Forensic Medicine, Juntendo University School of Medicine, 2-1-1, Hongo, Bunkyo-Ku, Tokyo, 113-8421, Japan. hnakani@juntendo.ac.jp. 2 Department of Forensic Medicine, Saitama Medical University, 38 Morohongo, Moroyama, Saitama, 350-0495, Japan. 3 Department of Forensic Medicine, Juntendo University School of Medicine,…

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[PDF] MISEQ%2BSYSTEM%2BILLUMINA%2BPDF | streetfoodunion.com

File Name: miseq%2Bsystem%2Billumina%2Bpdf.pdfSize: 4498 KBType: PDF, ePub, eBook Category: BookUploaded: 10 May 2019, 19:33 PMRating: 4.6/5 from 971 votes. Status: AVAILABLE Last checked: 2 Minutes ago! In order to read or download miseq%2Bsystem%2Billumina%2Bpdf ebook, you need to create a FREE account. eBook includes PDF, ePub and Kindle version In order…

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Illumina MiSeq Instruments Preventative Maintenance

From: Federal Government(Federal) Start Date 27 May, 2021 (7 months ago) Due Date 07 Jun, 2021 (6 months ago) Opportunity Type Bid Notification Opportunity Identifier FDA-CSS-1241810 Customer / Agency HEALTH AND HUMAN SERVICES, DEPARTMENT OF Location Jefferson , AR 72079 USA Illumina MiSeq Instruments Preventative Maintenance per the attached Combined…

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Index of /readarchive/Miseq/2014_05_21_run_miseq/Adapter_trimmed_nextera_samples/QC_after_trimming/Geo33_S19.R1.trimmed.paired_fastqc/Images

Name Last modified Size Description Parent Directory   –   duplication_levels.png 24-May-2014 17:58 17K   kmer_profiles.png 24-May-2014 17:58 433K   per_base_gc_content.png 24-May-2014 17:58 48K   per_base_n_content.png 24-May-2014 17:58 26K   per_base_quality.png 24-May-2014 17:58 32K   per_base_sequence_content.png 24-May-2014 17:58 96K   per_sequence_gc_content.png 24-May-2014 17:58 25K   per_sequence_quality.png 24-May-2014 17:58 19K  …

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Verogen MiSeq FGx Sequencing Reagents

The MiSeq FGx System achieves exceptional data quality by employing a proprietary, reversible terminator‑based method that detects single bases as they are incorporated into massively parallel DNA strands. Fluorescent terminator dyes are imaged as each deoxynucleotide triphosphate (dNTP) is added and then cleaved to allow incorporation of the next base….

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16S rRNA gene amplicon sequence data from sunflower endosphere bacterial community

doi.org/10.1016/j.dib.2021.107636Get rights and content Abstract Insights into plant endosphere bacterial diversity and exploration of their bioincentives in the formulation of biofertilizers promise to avert ecological disturbances. Here, we presented the sequence dataset of the endophytic bacterial community from the roots and stems of sunflower obtained from farmlands in Itsoseng and…

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LOCS files not found during MiSeq run?

Hi everyone! We experienced a problem that our team had not encountered for almost 10 years of working with the MiSeq platform. We ran a 24-sample VeriSeq PGS library on MiSeq. On the next day when the data was expected to be generated, we noticed that the run had stopped…

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16s rRNA Sequencing Meta-analysis Reconstruction Tool (using mothur).

16SMaRT is a bioinformatics analysis pipeline for 16s rRNA gene sequencing data. 16SMaRT is a “one-click” solution towards performing microbial community analysis of amplicon sequencing data. 16SMaRT aims to be your go-to solution for your next microbiome/metagenomics project. The primary objective of 16SMaRT analysis is to determine what genes are…

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Complete mitochondrial genome sequencing of Oxycarenus laetus (Hemiptera: Lygaeidae) from two geographically distinct regions of India

Genome organization and structure of O. laetus The MiSeq data of BTI and CBE samples of O. laetus was submitted to the NCBI SRA database under the accession numbers SRR11024516 and SRR11024517, respectively. The study was done to understand whether there exists a different species of the genus Oxycarenus similar…

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Galaxy Is a Suitable Bioinformatics Platform for the Molecular Diagnosis of Human Genetic Disorders Using High-Throughput Sequencing Data Analysis. Five Years of Experience in a Clinical Laboratory

Background: To date, the usage of Galaxy, an open-source bioinformatics platform, has been reported primarily in research. We report 5 years’ experience (2015 to 2020) with Galaxy in our hospital, as part of the “Assistance Publique-Hôpitaux de Paris” (AP-HP), to demonstrate its suitability for high-throughput sequencing (HTS) data analysis in…

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which tool can I use to detect CNVs?

which tool can I use to detect CNVs? 0 Hi everyone, I have performed target sequencing on tumour samples (with MiSeq, Illumina). I must perform CNV detection, which tool do you suggest me to use ? (I do not have the normal samples, only tumour samples). Thanks, Elisa calling CNV…

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Illumina Begins Climate Week by Highlighting How Sequencing Supports Resilient Responses to Climate Change

How Southern California scientists are working to stay ahead of dangerous outbreaks Northampton, MA –News Direct– Illumina The use of genomics is critical to help build strategies of resilience in our global response to climate change. In honor of Climate Week, we’re highlighting the important work of algae biologists at…

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Toxic Algae Blooms Are on the Rise. Sequencing Can Help Manage Them.

This was a summer of unprecedented heat and runaway algae. At hundreds of beaches, lakes, and rivers across the US, the public was greeted by signs like this one at Hensley Lake in northern California: “Harmful algae may be present in this water.” Although blue-green algae, known as cyanobacteria, occur…

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High frequency of an otherwise rare phenotype in a small and isolated tiger population

Significance Small and isolated populations have low genetic variation due to founding bottlenecks and genetic drift. Few empirical studies demonstrate visible phenotypic change associated with drift using genetic data in endangered species. We used genomic analyses of a captive tiger pedigree to identify the genetic basis for a rare trait,…

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ABRF Study Benchmarks NGS Platforms on Human, Microbial Samples, Provides Peek at Genapsys Data

NEW YORK – The results of a major, core facilities-driven benchmarking study for next-generation sequencing platforms are in, and just about every major player in the field can claim a victory of some sort. The data support longstanding advantages touted by market leader Illumina, while also providing a sneak peak…

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MiXCR error with the complied cat TCR library

MiXCR error with the complied cat TCR library 0 Dear great helpers, I compiled json library for cat’s TCR using ‘repseqio’ as attached file. The command lines were as followed: $MIXCR analyze amplicon –threads 20 –library imgt –species “cat” –starting-material rna –5-end v-primers –3-end j-primers –adapters adapters-present –receptor-type tcr –region-of-interest…

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Assistant Research Professor – Genomics and Bioinformatics job with City of Hope

About City of Hope City of Hope, an innovative biomedical research, treatment and educational institution with over 6000 employees, is dedicated to the prevention and cure of cancer and other life-threatening diseases and guided by a compassionate, patient-centered philosophy. Founded in 1913 and headquartered in Duarte, California, City of Hope…

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Mapping digested synthetic oligos back to original sequences.

Mapping digested synthetic oligos back to original sequences. 0 Hi, I have several synthetic dsDNA of 70bp and I digest them with some enzyme. I am interested to see the exact cut site of the enzyme so I had the products sequenced using MiSeq. They are single-end read. What is…

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NextSeq 2000 Sequencing | University of Minnesota Genomics Center

The NextSeq 2000 is Illumina’s newest platform that uses advancements in optics, instrument design, and 2-channel chemistry to increase output. This new sequencing technology makes it possible for researchers to sequence a range of conventional and emerging applications by increasing throughput while cutting down on costs per run when compared…

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The LpoA activator is required to stimulate the peptidoglycan polymerase activity of its cognate cell wall synthase PBP1a

Significance Class A penicillin-binding proteins (aPBPs) assemble the bacterial cell wall and are the targets of penicillin and related β-lactam antibiotics. In gram-negative bacteria, the aPBPs require outer membrane lipoproteins to function. However, little is known about how these proteins promote the activity of their cognate synthases in cells. Here,…

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Validation of somatic variant calling pipeline

Validation of somatic variant calling pipeline 0 Hi everyone, I’ve implemented a somatic variant calling pipeline in order to detect somatic variants in ovaric tumour samples (Targeted Sequencing done by MiSeq, Illumina). I now need to validate this pipeline; at this aim I’d like to know which are the best…

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