Categories
Tag: NovaSeq
Detection of DNA methylation signatures through the lens of genomic imprinting
Animals and samples The study included 10 pigs, 8 pigs were bred at the INRAE experimental farm (doi.org/doi.org/10.15454/1.5572415481185847E12) and 2 pigs come from breeding organizations in accordance with the French and European legislation on animal welfare. The animals belong to the same family, except for one LW animal. Animals were…
Seroprevalence and Molecular Characterization of B. abortus
Introduction Brucellosis is a zoonotic disease caused by Brucella spp., a gram-negative facultative intracellular coccobacillus.1 These microorganisms can infect livestock, wildlife, and humans, causing significant public concern and substantial agricultural economic loss. Currently, at least six novel Brucella species have been identified: Brucella pinnipedialis, Brucella ceti,2 Brucella papionis,3 Brucella microti,4…
The Biostar Herald for Tuesday, December 19, 2023
The Biostar Herald publishes user submitted links of bioinformatics relevance. It aims to provide a summary of interesting and relevant information you may have missed. You too can submit links here. This edition of the Herald was brought to you by contribution from Mensur Dlakic, Istvan Albert, and was edited…
Blazing the trail to empower agrigenomics research and conservation
Sequencing data for a single human genome, at 30× coverage, takes up to 70 gigabytes of storage. Illumina instruments produced 280 million gigabytes of data in 2021 alone, and by 2025, we’ll need storage capacity for 40 billion gigabytes—and that’s just for human genomes. The Genomics & Bioinformatics Service of…
Randomized phase II study of preoperative afatinib in untreated head and neck cancers: predictive and pharmacodynamic biomarkers of activity
Study objectives and endpoints The main objective consisted in identifying predictive biomarkers of efficacy by exploring correlation between baseline potential biomarkers and radiological and metabolic responses to afatinib. Secondary objectives were to identify potential pharmacodynamic biomarkers, to evaluate the efficacy and safety of afatinib and to assess the metabolic and…
bcl2fastq problems with the yield
bcl2fastq problems with the yield 1 Dear people, I am currently trying to demultiplex the raw data files I got from NovaSeq with bcl2fastq tool. Well, the code seems to work right as I am getting the output, the problem is that the index mismatch rate is 99 to 100,…
A transcriptomic taxonomy of mouse brain-wide spinal projecting neurons
Animals All experimental procedures were performed in compliance with animal protocols approved by the Institutional Animal Care and Use Committee at Boston Children’s Hospital (Protocol no. 20-05-4165 R). Mice were provided with food and water ad libitum, housed on a 12-hour light/dark schedule (7 a.m.–7 p.m. light period) with no more than five mice…
Single-cell analysis of chromatin accessibility in the adult mouse brain
Tissue preparation and nucleus isolation All experimental procedures using live animals were approved by the SALK Institute Animal Care and Use Committee under protocol number 18-00006. Adult C57BL/6J male mice were purchased from Jackson Laboratories. Brains were extracted from 56–63-day-old mice and sectioned into 600 µm coronal sections along the anterior–posterior…
QIAseq miRNA 96 Index Kit IL UDI-B (96)
Gel-free miRNA Sample to Insight solution for differential expression analysis and novel discovery using next-generation sequencing Features Gel-free miRNA sequencing library prep from as little as 1 ng of total RNA Elimination of adapter dimers and unwanted RNA species resulting in the highest fidelity and most efficient data Integrated Unique…
Single-cell DNA methylome and 3D multi-omic atlas of the adult mouse brain
Mouse brain tissues All experimental procedures using live animals were approved by the Salk Institute Animal Care and Use Committee under protocol number 18-00006. Adult (P56) C57BL/6J male mice were purchased from the Jackson Laboratory at 7 weeks of age and maintained in the Salk animal barrier facility on 12-h dark–light…
Bioactive glycans in a microbiome-directed food for children with malnutrition
Collection and handling of biospecimens obtained from participants in the randomized controlled clinical study of the efficacy of MDCF-2 The human study entitled ‘Community-based clinical trial with microbiota-directed complementary foods (MDCFs) made of locally available food ingredients for the management of children with primary moderate acute malnutrition (MAM)’ was approved…
Benchmarking DNA isolation methods for marine metagenomics
Scheme of the study The overall pipeline of our study is presented in Fig. 1 and is described in detail in the methods section. We processed three types of samples: fresh water, sea sediment, and digestive system of a marine invertebrate M. gigas (“gut flora”). These samples were treated in triplicates…
Illumina: Grail’s Divestment Could Unlock Significant Shareholder Value (NASDAQ:ILMN)
anamejia18/iStock via Getty Images Illumina (NASDAQ:ILMN) has been one of the worst performers in the S&P Health Care Select Fund (XLV), falling 40% in 2023 alone. Illumina’s market cap has fallen from over $75 billion to just $18 billion at the time of this writing, representing an 80% decline from…
Refurbished DNA Sequencing Platforms Market Insights, Market Players and Forecast Till 2030
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Introduction Leprosy is a disabling infectious disease that predominantly occurs in the skin and peripheral nerves and is transmitted by contact with pathogenic bacteria through the respiratory tract and broken skin. Leprosy is attributed to infection with Mycobacterium leprae (M. leprae)1 and the more recently discovered Mycobacterium lepromatosis.2 In addition,…
UK Biobank unveils world’s largest genetic data set
In a momentous landmark for medical research, UK Biobank has today [Thursday 30 November] unveiled incredible new data from whole genome sequencing of its half a million participants. This is set to drive the discovery of new diagnostics, treatments and cures and, uniquely, is available to approved researchers worldwide, via a protected…
Next-Generation Sequencing (NGS) kits Market projected to
Richmond, Dec. 04, 2023 (GLOBE NEWSWIRE) — According to a research report “NGS Kits Market”, By Workflow (Library Preparation, Cluster Generation, Sequencing Reagents/Kits), Sequencing Type (WES and WGS, Targeted Sequencing, Long-Read Sequencing, Others), Usage (Clinical, Research), Application (Oncology, Rare Diseases, Genetic Disorders, Reproductive Health, Others), End-User (Academic and Research Institutions,…
DNA Sequencing In Drug Discovery Market: Exploring Market Share, Market Trends, and Future Growth | by Orinsmitham | Dec, 2023
Market Overview and Report Coverage DNA sequencing plays a crucial role in drug discovery by enabling the identification and understanding of genetic variations that are associated with diseases. It involves the determination of the precise order of nucleotides within a DNA molecule, which provides valuable information about the function and…
Ribo-Zero Plus Microbiome rRNA Depletion Kit
Description Depletion of abundant transcripts from host and bacterial rRNA for metatranscriptomics research. Single-tube depletion of abundant transcripts from multiple species or transcripts Input Quantity Minimum 25 ng of total RNA, 50 ng recommended for optimal performance 1-1000 ng total RNA for standard-quality RNA samples….
Third Generation Sequencing Market Report on Size, Share, Scope and Forecast 2023-2031
PRESS RELEASE Published November 30, 2023 Third Generation Sequencing Market to reach over USD 27.59 billion by the year 2031 – Exclusive Report by InsightAce Analytic InsightAce Analytic Pvt. Ltd. announces the release of a market assessment report on the “Global Third Generation Sequencing Market Size, Share & Trends Analysis…
UK Biobank Releases Whole Genome Data from Half a Million People
After five years, more than 350,000 hours of genome sequencing, and over £200 million of investment, UK Biobank is releasing the world’s largest-by-far single set of human sequencing data—completing the most ambitious project of its kind ever undertaken. The new data, whole genome sequences of its half a million participants,…
UK Biobank reveals new data from world’s largest genetic project
UK Biobank has shared new data from its world’s largest whole genome sequencing project with researchers worldwide for the discovery of new diagnostics, treatments and cures. The set of sequencing data is the biggest ever seen globally and was curated across five years, with more than 350,000 hours of genome…
Identification of constrained sequence elements across 239 primate genomes
De novo assembly and repeat-masking To maximize the species diversity of primates in our analyses, we newly sequenced and assembled the genomes of 187 different primate species, initially presented in refs. 11,23, for which no other reference genome assembly was available. In brief, each individual was sequenced with 150 bp paired…
How to deeply sequence long inserts
How to deeply sequence long inserts 1 I have a DNA library encoding scFv antibody genes that consist of VH gene (~380 bp) + linker peptide (54 bp) + VL gene (~380 bp), and the library contains about 1M unique antibodies. We’ve performed some iterative selections on the library such…
Is It Finally Time To Dump Illumina Stock?
Vive la révolution! It’s not just desperate peasants who embrace radical change of the status quo. Innovations by technology companies are often hailed as revolutionary, disrupting the way we live and work. It’s worth remembering that many revolutionaries later became brutal dictators who ruled over their subjects with an iron…
Novaseq read coverage needed for demultiplexing
Novaseq read coverage needed for demultiplexing 0 Hi, I am a new graduate student in biology and am relatively new to sequencing in general. I am planning on doing a genome-wide CRISPR screen over many days. I plan to extract genomic DNA from each condition and amplify the sg region…
GDF11 slows excitatory neuronal senescence and brain ageing by repressing p21
Experimental model and subject details Mice Male ICR mice (Laboratory Animal Center of Zhejiang Academy of Medical Sciences) at age of 3 months (M), 9 M and 36 M, male C57BL/B6 wild‐type (WT) mice (Shanghai Slac Laboratory) at age of 3 M and 10 M, male GDF11-flox mice (GDF11f/f, mice carrying the “floxed” GDF11…
Genome sequence and characterization of Streptomyces phages Vanseggelen and Verabelle, representing two new species within the genus Camvirus
Bacteriophage isolation Streptomyces phages Vanseggelen and Verabelle were isolated from a soil sample obtained from the National Park Zuid-Kennemerland in the Netherlands (N52° 23′ 31″, E4° 34′ 49″) using Streptomyces coelicolor as the host. Details on isolation procedures are reported previously in detail12. The collected phage stock solutions were stored…
As Illumina stock bounces off a 10-year low, analysts see no quick fix
As shares of Illumina Inc. ILMN, +5.68% trade near 10-year lows, analysts are reining in expectations for the DNA-sequencing company. Illumina shares fell sharply late last week, after the company cut its full-year sales and profit outlook, and continued their tumble on Monday, falling 5.7% and closing at their lowest…
A Cre-dependent massively parallel reporter assay allows for cell-type specific assessment of the functional effects of non-coding elements in vivo
Animal models All procedures involving animals were approved by the Institutional Animal Care and Use Committee (IACUC) at Washington University in St. Louis, MO. Veterinary care and housing was provided by the veterinarians and veterinary technicians of Washington University School of Medicine under Dougherty lab’s approved IACUC protocol. All protocols…
How Much Does Personalized Genome Sequencing Cost? Start Now!
Introduction The field of genome sequencing has revolutionized healthcare by offering personalized insights into our genetic code. With advancements in technology and decreasing costs, personalized genome sequencing has become more accessible to individuals, families, and healthcare professionals. In fact, according to the latest statistical data, the global market for personalized…
Myeloid/Lymphoid Neoplasms with ETV6::PDGFRB Fusion Gene
Introduction The ETV6::PDGFRB fusion gene is commonly associated with myeloid neoplasms with monocytosis (such as CMML), and with eosinophilia.1 The PDGFRB gene, located on 5q33, encodes PDGFRβ, a type III tyrosine kinase comprising an extracellular domain consisting of five immunoglobulin (Ig)-like domains, a single-transmembrane helix domain, a juxtamembrance domain, and…
Illumina explores options for Grail, hires advisers
Listen to the article 4 min This audio is auto-generated. Please let us know if you have feedback. By the numbers Q3 Revenue: $1.12 billion Flat year-over-year Q3 Net loss: $754 million Compared with a net loss of $3.82 billion in the year-ago period Illumina said Thursday it…
NGS Updates from ASHG: What’s New in Sequencing?
As expected, the NGS companies were sharing their news, out in full force, at the annual American Society for Human Genetics (ASHG) meeting last week in Washington, DC. Whether the updates came from the expo booths showcasing instruments, or users sharing data in the lecture halls, each company had progress…
Next Generation Sequencing Market To Reach USD 45.9 Billion By 2032, Says DataHorizzon Research
DataHorizzon Research A Detailed Analysis Report of the Next Generation Sequencing Market. Fort Collins, Colorado, Nov. 09, 2023 (GLOBE NEWSWIRE) — According to DataHorizzon Research, the Next Generation Sequencing (NGS) Market size was valued at USD 7.2 Billion in 2022 and is expected to have USD 45.9 Billion by 2032 at…
Clonal Hematopoiesis and Cardiovascular Disease in Patients With Multiple Myeloma Undergoing Hematopoietic Cell Transplant | Cardiology | JAMA Cardiology
Key Points Question Is clonal hematopoiesis of indeterminate potential (CHIP) detected at the time of hematopoietic stem transplant (HCT) associated with increased rates of cardiovascular disease (CVD) among patients with multiple myeloma (MM) following HCT? Finding In this cohort study of patients with MM undergoing HCT, CHIP was highly prevalent…
Characteristics of Klebsiella pneumoniae co-infections
Introduction Tuberculosis (TB), caused by Mycobacterium tuberculosis (M. tuberculosis), is a prominent issue in the field of global public health, particularly in lower-middle-income-countries. Nearly two-thirds of global TB cases come from eight countries, including China.There are 780,000 new TB cases in China every year.1 TB is characterized by increased risk…
Exploring the cell-free total RNA transcriptome in diffuse large B-cell lymphoma and primary mediastinal B-cell lymphoma patients as biomarker source in blood plasma liquid biopsies
@article{01HEHWZT4PEWXFE7HXNHQ5885F, abstract = {{<jats:sec><jats:title>Introduction</jats:title><jats:p>Diffuse large B-cell lymphoma (DLBCL) and primary mediastinal B-cell lymphoma (PMBCL) are aggressive histological subtypes of non-Hodgkin’s lymphoma. Improved understanding of the underlying molecular pathogenesis has led to new classification and risk stratification tools, including the development of cell-free biomarkers through liquid biopsies. The goal of this…
SP500 useable read lengths
SP500 useable read lengths 1 Hi all, Can someone share what the usable read lengths are for the ‘NovaSeq 6000 SP Reagent Kit v1.5 (500 cycles)’? For example, the SP100 kit is advertised as 2x50bp but in reality is 2x61bp using a 8bp dual index (61|8|8|61) …what is the ’61’…
Comparative analysis of shotgun metagenomics and 16S rDNA sequencing of gut microbiota in migratory seagulls [PeerJ]
Introduction The microbiomes of different host organisms are currently described by using culture-independent sequencing methods (Harvey & Holmes, 2022). Shotgun metagenomic and 16S rDNA sequencing methods are commonly used to identify the taxonomic composition of microbial communities in several studies (de Melo et al., 2020; Mackelprang et al., 2011; Monaco…
Aegis Writes a New Chapter on Pathogen Surveillance
A US lab broadens its surveillance efforts to be able to respond to emerging pathogens and envision a future of improved public health NORTHAMPTON, MA / ACCESSWIRE / November 2, 2023 / Illumina Originally published on Illumina News Center Before SARS-CoV-2, Aegis Sciences Corporation was a small, well-established lab with…
Single-nucleus DNA sequencing reveals hidden somatic loss-of-heterozygosity in Cerebral Cavernous Malformations
Ethical statement Our research complies with all relevant ethical regulations, including the Declaration of Helsinki and has been approved by the Institutional Review Boards of University of Chicago, Duke University and the Alliance to Cure Cavernous Malformations. Cerebral cavernous malformation lesions All human CCM tissue specimens have been previously reported18,19…
Illumina launches advanced liquid biopsy assay to enable comprehensive genomic profiling of solid tumors
TSO 500 ctDNA Version 2 delivers faster turnaround time, greater analytical sensitivity, more streamlined workflow, further enabling precision medicine. SAN DIEGO, Nov. 1, 2023 /PRNewswire/ — Illumina, Inc. (NASDAQ: ILMN), a global leader in DNA sequencing and array-based technologies, today announced a new generation…
The future of cancer is very personal
On this planet of more than 7.8 billion people, there’s no one quite like you. Genetically speaking, that is. That’s why the future of cancer care is personal – tailored to fit the distinct variations in your genetic blueprint. Until now, cancer treatments have been largely reliant on surgery, or…
Future of cancer is very personal
On this planet of more than 7.8 billion people, there’s no one quite like you. Genetically speaking, that is. That’s why the future of cancer care is personal – tailored to fit the distinct variations in your genetic blueprint. Until now, cancer treatments have been largely reliant on surgery, or…
Inferring bacterial transmission dynamics using deep sequencing genomic surveillance data
Study design Experiments were performed in accordance with the New Zealand Animal Welfare Act (1999) and institutional guidelines provided by the University of Auckland Animal Ethics Committee, which reviewed and approved these experiments under application R1003. We did not use any specific randomisation process to allocate animals to a particular…
Complete Genomics demonstrates technical and commercial momentum in the sequencing market through new customers, partnerships and collaborations less than one year after launching in the U.S.
WASHINGTON, Oct. 31, 2023 /PRNewswire/ — Complete Genomics, a pioneering genomic sequencing company, announced today at the American Society of Human Genetics (ASHG) Annual Meeting, Nov. 1-5, in Washington details on the commercial and technical momentum it has demonstrated in the last 10 months since launching in the United States…
Mycobacterium tuberculosis Sub Lineage 4.2.2/SIT149 as DR
Introduction Antimicrobial resistance is a hidden global pandemic that shattered over 4.9 million people in 2019 alone, and the burden is highest, mainly in low-resource settings.1 Drug-resistant tuberculosis (DR-TB) caused by Mycobacterium tuberculosis (Mtb) complex (MTBC), which is resistant to one or more anti-TB drugs, is a leading global public…
Identification of CCZ1 as an essential lysosomal trafficking regulator in Marburg and Ebola virus infections
Cells and viruses Haploid mSCs AN3–12 are a feeder independent clonal derivative of HMSc2 isolated from mice oocyte and maintained at IMBA52. The AN3–12 library and knocked out cells used for the haploid screening was obtained from IMBA (Austria)14,52. AN3–12 cells were validated by STR analysis. Haploid mES cells were…
how to deal with Gs?
Small RNA sequencing using Illumina 2 channel SBS: how to deal with Gs? 1 I’m working on a small RNA sequencing experiment (150 PE on NovaSeq 6000), and many reads look like this when the fragment size is smaller than 150 bp, with Gs completing the sequence up to 150:…
NadPrep rRNA Blocking Reagent (Human) – Library Preparation
Feature Simple and Convenient Mix the rRNA Blocking Reagent directly with the reaction system in a single pipetting step Fast and Efficient Efficiently block rRNA in just 8 min Effectively enrich low-abundance RNA Enhance informative content and reduce sequencing costs Flexible Compatibility Compatible with samples of different RNA quality Support…
Neuron Navigator 1 (Nav1) regulates the response to cocaine in mice
Mouse strains All mouse procedures were approved by the Institutional Animal Care and Use Committees at Binghamton or Stanford University; and were conducted in accordance with the National Institute of Health Guide for Care and Use of Laboratory Animals, Eighth Edition. All mice were originally obtained from Jackson Laboratories, and…
Microbiome Sequencing Market Update 2023 : to Reach USD 3.4 Billion Revenue by 2031, Claims Report
The microbiome sequencing market size was valued for $859.42 million in 2021 and is estimated to reach $3,417.09 million by 2031, exhibiting a CAGR of 14.8% from 2022 to 2031. Understanding the Microbiome Before delving into the technological advancements, it’s essential to understand what the microbiome is. The microbiome refers…
Genotyping, sequencing and analysis of 140,000 adults from Mexico City
Recruitment of study participants The MCPS was established in the late 1990s following discussions between Mexican scientists at the National Autonomous University of Mexico (UNAM) and British scientists at the University of Oxford about how best to measure the changing health effects of tobacco in Mexico. These discussions evolved into…
Target Sequencing and Resequencing Market Will Grow at CAGR of 23.06% By 2032
The global target sequencing and resequencing market size is anticipated to reach around USD 45.72 billion by 2032 up from USD 5.74 billion in 2022 with a CAGR of 23.06% between 2023 and 2032. Targeted sequencing, often known as resequencing, is a technique for sequencing a sample’s partial genome or…
Query regarding genome coverage in de-novo assembly
Query regarding genome coverage in de-novo assembly 1 we did some genome sequencing of bacteria from a biotech company, They used de-novo assembly for sequencing with Shovill assembly method using Illumina NovaSeq I need to submission those genome data in NCBI but the problem I am facing with their provided…
I have a pair of read files where each is a mixed pool of reads from the Linked-read technology and Illumina short-read technology. Any suggestion on appropriate assembler that can handle this?
A genome assembly was under process. Earlier we had performed an assembly using the TELL-Seq linked-read technology. The assembly was unsatisfactory due to insufficient coverage. The assembler was Universal Sequencing Technology’s Turing assembler, accessed through the TELL-Link pipeline. Recently, we re-sequenced the stored sample, using NovaSeq X plus. These reads…
Seeking help with a hybrid assembly. I have a batch of linked-reads from NovaSeq 6000, and short-reads (not linked-reads) from NovaSeq X plus. Assembly using CLC genomics finished abnormally.
A genome assembly was under process. Earlier we had performed an assembly using the TELL-Seq linked-read technology. The assembly was unsatisfactory due to insufficient coverage. The assembler was Universal Sequencing Technology’s Turing assembler, accessed through the TELL-Link pipeline. Recently, we re-sequenced the stored sample, using NovaSeq X plus. These reads…
Differentially expressed circRNAs in peripheral blood samples as potential biomarkers and therapeutic targets for acute angle-closure glaucoma
Study approval and patient consent The study protocol was approved by the Ethics Committee of Qinghai Provincial People’s Hospital (approval number: 2023-141) and conducted in accordance with the ethical principles for medical research involving human subjects described in the Declaration of Helsinki in addition to relevant Chinese laws and institutional…
Impact of humid climate on rheumatoid arthritis faecal microbiome and metabolites
Animals and husbandry details Six-week-old healthy male SD rats were used in accordance with the Guidelines for the Care and Use of Laboratory Animals of the Institute of Laboratory Animal Resources, Institutional Animal Care and Use Committee of Beijing University of Chinese Medicine. The study is reported in accordance with…
Phylogenomics reveals the history of host use in mosquitoes
Taxon sampling and specimen collection All samples were collected legally following local requirements and our research complies with all relevant ethical regulations. Insect specimens were received at NC State University’s Insect Museum, pursuant to CITES permit 08US827653 (GRSCICOLL URI: grbio.org/cool/ij62-iybb). Our dataset contains representatives of 268 species from nine tribes,…
GENZEVA and RYLTI Partner to Develop a Groundbreaking Application to More Clearly Understand the Molecular Mechanisms of Disease
A joint study applying Genzeva’s new breakthrough genomic research process reveals remarkable discovery by uncovering hidden “dark” data. ROCKVILLE, MD / ACCESSWIRE / October 6, 2023 / Genzeva, a leading molecular genetic laboratory that performs whole genome and clinical exome sequencing for clinical diagnostics and research, has partnered with tech…
Basepaws Launches the Most Extensive DNA Test for Dogs, Focused on Health and Early Detection of Disease Risk
LOS ANGELES, October 6, 2023 (Newswire.com) – Basepaws, the leader in feline DNA testing and genetics, enters the canine market with the most extensive DNA test for dogs, accelerating the health genetic testing landscape. Basepaws Breed + Health Dog DNA Test helps pet owners shift from reactive to proactive care,…
Broken String Biosciences strengthens senior leadership team to accelerate product development and commercialization
Broken String Biosciences (“Broken String”), a genomics company building a technology platform to drive the development of cell and gene therapies that are safer by design, today announced the expansion of its senior leadership team with the appointments of Vincent Smith, Ph.D., as Chief Technology Officer and Jessica Rich as…
Do you wonder what 10X data looks like on the newest Illumina sequencer?
in Industry News, Information 18 hours ago 626 Views Single-cell analysis can help tease apart heterogeneity in complex cell populations, distinguishing cell types and revealing dynamic cell states. The 10x Genomics Chromium Single Cell Multiome ATAC + Gene Expression prepares sequencing-ready libraries to simultaneously profile gene expression and chromatin accessibility from the…
GenotypeGVCF too many genotypes from pooled samples
Hello, I am trying to create a VCF file using GentypeGVCFs in GATK4. I have 60 samples and each sample is pooled data. The ploidy per sample is 60. This is due to the biological system I work in. This data has been processed in Haplotypecaller, below is an example…
Purpose, Types, Applications, Bioinformatics and more
Next-Generation Sequencing (NGS), also known as high-throughput sequencing, is a revolutionary technology used for determining the sequence of DNA or RNA molecules. It has significantly advanced the field of genomics and has numerous applications in various biological and medical fields. Key Points of Next-Generation Sequencing (NGS): Revolutionary Technology: NGS represents…
Cost-effective DNA methylation profiling by FML-seq
The FML-seq method The protocol for FML-seq comprises only three steps (Fig 1A). First, genomic DNA (gDNA) is digested by a methylation-dependent restriction endonuclease that cuts at a certain distance from the 5-methylcytosine or 5-hydroxymethylcytosine in its motif and leaves a short overhang (10). Second, a master mix is added…
Genomic Analysis of CR-hvKP in a Chinese Tertiary Hospital
Introduction Klebsiella pneumoniae (KP) is a common opportunistic pathogen in clinical practice, capable of causing infectious diseases in the urinary tract, respiratory tract, blood, and soft tissues.1 Hypervirulent Klebsiella pneumoniae (hvKp) has a higher virulence than KP2 and can cause severe infectious diseases, including pyogenic liver abscess, endophthalmitis, and meningitis.3,4…
DNA Sequencing Instruments Market Size, Share and Forecast 2031
The GlobalDNA Sequencing Instruments Market is poised to value USD 26 billion in 2027 end at a CAGR of 20% during the forecast period 2023 to 2031. DNA Sequencing Instruments Market DNA sequencing has revolutionized the field of genomics, enabling scientists to decode the genetic information present in an organism’s…
ATAC-seq troubleshoot – Just Noise
ATAC-seq troubleshoot – Just Noise 0 Hi everyone, I have been processing paired end 150bp ATAC-seq data, but failing to get peaks at known promoters, the data just looks like noise through out. Started with QC, where reads had poly(G) towards their ends, this is known to happen in NovaSeq…
IJNS | Free Full-Text | Whole-Genome Sequencing Can Identify Clinically Relevant Variants from a Single Sub-Punch of a Dried Blood Spot Specimen
1. Introduction Newborn screening (NBS) plays a vital role in healthcare systems for the prompt identification of individuals who may develop one of a set of rare, but severe health conditions [1]. In the UK, for example, dried blood spot (DBS) specimens are routinely collected at 4–5 days of age…
Genome-wide probing of eukaryotic nascent RNA structure elucidates cotranscriptional folding and its antimutagenic effect
Yeast strain and growth conditions S. cerevisiae strain BY4741 was grown in YPD media at 30 °C. Saturated cultures were diluted into 300 ml YPD medium with an optical density at 660 nm (OD660) of approximately 0.1 and then grown at 30°C with shaking at 250 rpm until mid-log phase with an OD660 of…
Post-Doctoral Associate in the Division of Science (Biology), Dr. Shady Amin job with NEW YORK UNIVERSITY ABU DHABI
Description The Marine Microbiomics Lab at New York University Abu Dhabi seeks to appoint a Postdoctoral Associate starting January 15, 2024 to work on diatom ecophysiology under the supervision of Professor Shady Amin. We are looking for applicants with strong culturing or field work experience, and with bioinformatics and/or computational biology familiarity…
Genome-wide promoter responses to CRISPR perturbations of regulators reveal regulatory networks in Escherichia coli
PPTP-seq development and validation PPTP-seq uses plasmid to integrate each CRISPRi-based TF perturbation and each promoter activity reporter into one construct. Each plasmid contains a CRISPRi cassette that constitutively expresses a single guide RNA (sgRNA) to repress a specific TF in the genome19 and a promoter-reporter cassette to measure the…
DNA Sequencing Market – Extensive Number of Applications
Covina, Sept. 14, 2023 (GLOBE NEWSWIRE) — DNA sequencing is a procedure in which DNA is extracted, fragmented, and linked to primers and adapters for the amplification reaction (PCR) for library construction. It is a general lab technique used for determining the sequence of nucleotides in DNA molecule. Growing advancement…
Phage-microbe dynamics after sterile faecal filtrate transplantation in individuals with metabolic syndrome: a double-blind, randomised, placebo-controlled clinical trial assessing efficacy and safety
Study design We set up a prospective, double-blinded, randomised, placebo-controlled intervention study that was performed in our academic hospital, the Amsterdam University Medical Centres location AMC in the Netherlands. After passing screening, 24 subjects with MetSyn were randomised to receive a sterile FFT from a lean healthy donor or a…
Demultiplexing based on dual indices in headers while allowing 1 mismatch to each index
Demultiplexing based on dual indices in headers while allowing 1 mismatch to each index 1 Hey all, I am looking for a tool that will help me demultiplexe my Novaseq samples by two dual indices in the headers. Since I have designed my indices such that the minimum hamming distance…
DNA Sequencing Equipment market research report provides critical insights that can help shape business development by providing a CAGR of 7.3% from 2023 to 2030
This “DNA Sequencing Equipment Market” highlights key external drivers that affect the industry and assesses the current performance and revenue growth of the industry. This report helps to collect industry information for target audiences before commencing any advertising campaign. The DNA Sequencing Equipment market is expected to grow annually by…
Gut Microbiome of Children with Airway Allergic Disease
Introduction Allergic airway diseases affect many people worldwide, and incidences are still increasing gradually. Allergic rhinitis and allergic asthma, are typical chronic nasopharyngitis respiratory diseases in pediatric, causing an enormous burden of illness and high economic costs to the community.1 Allergic rhinitis and allergic asthma are immunoglobulin E (IgE)-mediated inflammatory…
Investors, Analysts Debate Background of New Illumina CEO
Jacob Thaysen, PhD will become Illumina’s new CEO effective September 25 In announcing Jacob Thaysen, PhD, as its new CEO on Tuesday, Illumina (ILMN) trumpeted his “extensive background and experience” in genomics, life sciences, and technology after more than a decade at Agilent Technologies and five years before that at…
Exosomal circEZH2_005, an intestinal injury biomarker, alleviates intestinal ischemia/reperfusion injury by mediating Gprc5a signaling
Human plasma collection Fifty patients who were assigned for CPB surgery between May 2021 and February 2022 at the Department of Cardiac Surgery, Southern Medical University Nanfang Hospital (Guangzhou, China) were recruited given their increased risk of intestinal I/R injury. In patients undergoing cardiac surgery, CPB is potentially responsible for…
Genome sequence and annotation of Periconia digitata a hopeful biocontrol agent of phytopathogenic oomycetes
Strain identification The strain Phoma sp. CNCM I-4278 was previously isolated from the rhizosphere of Nicotiana tabacum (cv Xanthi, Solanaceae) grown under controlled conditions17. The fungus was identified according to the closest similarity of its 18 S rRNA sequence (HM16174323) with those present in GenBank by that time and it was…
With 2024 Launch of Multi-Cancer Test, EDGC Plans Entry Into Early Cancer Screening Market
NEW YORK – Eone-Diagnomics Genome Center (EDGC) is on the verge of launching a blood-based multi-cancer early detection test that the firm hopes to ramp up in coming years to detect dozens of cancer types and potentially non-cancer applications such as Alzheimer’s progression. The South Korea-based joint venture between bioinformatics…
Inter-bacterial mutualism promoted by public goods in a system characterized by deterministic temperature variation
Location and sample collection Samples were taken from 10 composting piles (between May and August 2020) at a food waste (FW) composting facility (Zhejiang, China; 30°52′51.50″N; 119°46′12.87″E). A consistent pre-treatment method was used for each pile. Specifically, about 8 tons of FW was collected every 3 days and subsequently crushed into…
Symmetric inheritance of parental histones governs epigenome maintenance and embryonic stem cell identity
The research in this study was conducted under the ethical approval of the Danish Regulatory Authority under project license 2018-15-0201-01520. Cell culture and differentiation assays WT, MCM2-2A, MCM2-R and POLE4-KO mouse ESCs used in this study were derived from the male, E14JU cell line with a 129/Ola background81. Genome editing…
Generation of inactivated IL2RG and RAG1 monkeys with severe combined immunodeficiency using base editing
Animals The gene targeting experiment was conducted on cynomolgus monkeys, which served as the experimental subjects. These monkeys were housed at Guangdong LANDAU Biotechnology Co. Ltd and TOPGENE Biotechnology Co. Ltd, where they received unrestricted access to water and were provided with a standard diet in accordance with standard care…
Global Metagenomic Sequencing Market Size to Reach USD 9.07
Vancouver, Aug. 31, 2023 (GLOBE NEWSWIRE) — The anticipated value of the worldwide metagenomic sequencing market is projected to attain USD 9.07 Billion by the year 2032. As per the most recent assessment conducted by Emergen Research, there is a foreseen consistent Compound Annual Growth Rate (CAGR) of 17.5% in…
Global Metagenomic Sequencing Market Size to Reach USD 9.07 Billion in 2032
Emergen Research Continuous technological innovations in Next Generation Sequencing (NGS) platforms is a key factor driving market revenue growth Vancouver, Aug. 31, 2023 (GLOBE NEWSWIRE) — The anticipated value of the worldwide metagenomic sequencing market is projected to attain USD 9.07 Billion by the year 2032. As per the most…
Single-cell massively-parallel multiplexed microbial sequencing (M3-seq) identifies rare bacterial populations and profiles phage infection
Bacterial strains and growth conditions for eBW1 B. subtilis 168 and E. coli (MG1655) were streaked out from a frozen glycerol stock onto an LB plate and grown overnight at 37 °C. Following a night of growth, a single colony was picked and inoculated into 5 ml of LB broth and grown…
Despite 3-Week Decline, PacBio Stock Doubles in a Year
Pacific Biosciences of California (PacBio; PACB) investors could be forgiven for having questions about the company’s stock after it sank 26% between August 1–25, from $13.34 to $9.92 despite a flurry of developments that included the raising of its revenue forecast for this year and a growing challenge to longtime…