Tag: Nextseq

Broad Institute Study Evaluates Ultima Genomics Sequencer for Single-Cell RNA-Seq

NEW YORK – Results from single-cell RNA sequencing libraries run on the new Ultima Genomics UG100 are “very similar” to those produced on Illumina’s NovaSeq, a new study says. However, the platform shows bias against 3′ gene expression libraries. Led by researchers from the Broad Institute as part of a…

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Bronchoalveolar Lavage Fluid for Metagenomic Sequencing

Introduction Severe pneumonia is one of the most common causes of infectious diseases among patients in the intensive care unit (ICU), and this can lead to various complications and high mortality.1–3 Timely and accurate pathogen diagnoses are crucial for appropriate antimicrobial therapy and improved clinical outcomes. However, the low detection…

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Targeted inhibition of ubiquitin signaling reverses metabolic reprogramming and suppresses glioblastoma growth

Cell culture Human glioblastoma cells (U87MG and U87MG-Luc) and human embryonic kidney cells (HEK293) were obtained from the American Type Culture Collection (Manassas, Va.). Cells were cultured in Dulbecco’s Modified Eagle Medium supplemented with 10% fetal bovine serum (Gibco™ Fetal Bovine Serum South America, Thermo Scientific Fisher-US), 2 mM l-glutamine, 50 U/ml…

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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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Trimming adaptors and primers for RNAseq reads

Trimming adaptors and primers for RNAseq reads 2 Hi all, I have RNA sequencing (sequenced on NextSeq 2000) reads that I know I need to cut the adaptor sequences off of and was planning to use cutadapt to do so. I have identified the adaptor sequence in my reads, but…

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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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Pollinator sharing, copollination, and speciation by host shifting among six closely related dioecious fig species

Sampling Six dioecious fig species (F. erecta, F. formosana, F. vaccinioides, F. abelii, F. pyriformis, and F. variolosa) and their pollinator wasp species were examined in this study. As mentioned in the Introduction, these fig species were considered to be well suited for this study because they are distributed in…

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Low transcript quantification with Salmon using GRCm39 annotations

Hi everyone, first time working with mouse samples and unfortunately, there are fewer resources available for the latest mouse Ensembl genome than I was expecting. What I’ve done: I performed rRNA depletion on total RNA extracted from mouse tissue and created Illumina libraries using a cDNA synthesis kit with random…

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Transcriptional kinetics and molecular functions of long noncoding RNAs

Ethical compliance The research carried out in this study has been approved by the Swedish Board of Agriculture, Jordbruksverket: N343/12. Cell culture Mouse primary fibroblasts were derived from adult (>10 weeks old) CAST/EiJ × C57BL/6J or C57BL/6J × CAST/EiJ mice by skinning, mincing and culturing tail explants (for at least 10 d) in DMEM high…

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Extracellular circulating miRNAs as stress-related signature to search and rescue dogs

Study approval was provided by the Research Ethics Committee of the University of Perugia (report n.2018-21 of 11/12/2018) according to Italian Ministry of Health legislation18. All methods were carried out following relevant guidelines and regulations and the study was carried out in compliance with the ARRIVE guidelines. Informed consent is…

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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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Phylogenomic analysis of CTX-M-15-producing Enterobacter hormaechei belonging to the high-risk ST78 from animal infection: Another successful One Health clone?

Available online 18 February 2022 doi.org/10.1016/j.jgar.2022.02.010Get rights and content Highlights • ESBL-positive Enterobacter cloacae complex members are critical priority pathogens. • E. hormaechei belonging to sequence type (ST) ST78 is an emergent high-risk clone. • Phylogenomic data of an E. hormaechei ST78/CTX-M-15 infecting a calf is presented. • E. hormaechei…

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Single-cell delineation of lineage and genetic identity in the mouse brain

STICR lentiviral library preparation and validation We synthesized a high-complexity lentivirus barcode library that encodes approximately 60–70 million distinct oligonucleotide RNA sequences (STICR barcodes). STICR barcodes comprised three distinct oligonucleotide fragments cloned sequentially into a multicloning site within the 3′ UTR of an enhanced green fluorescent protein (eGFP) transgene under…

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Bacterial endosymbionts protect beneficial soil fungus from nematode attack

A healthy soil nourishes plants and animals, purifies water and air, and promotes sustainable agriculture. Characteristic for highly complex and competitive soil ecosystems are the frequent and direct interactions between all soil-dwelling microorganisms, animals, and plants (1, 2), all of which need to be provided with minerals and carbon sources….

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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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Gene mutation analysis in papillary thyroid carcinoma

Introduction Thyroid tumors are the most common malignant tumors of the endocrine system, and their incidence has been increasing in the recent decades. Currently, there are some target drugs that can effectively treat PTC, and next-generation sequencing (NGS) can be used for targeted therapy. In order to make better informed…

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