Tag: RNA

Peripheral Neuroblastic Tumor Transcriptomes Point to Transitional Cell State

NEW YORK – With the help of single-cell RNA sequencing, investigators in China and Australia have untangled diverse tumor and microenvironment features for peripheral neuroblastic tumors (PNT), including a transitional tumor cell state that appears to coincide with more aggressive and difficult-to-treat forms of the pediatric neural crest cancers. “Historically,…

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It is time to start the renaissance of aptamers

Who here has heard of an aptamer? Most people by now would have heard of RNA and are likely to have been the recipient of a strand or two thanks to COVID vaccines. Macugen was the first RNA biotherapeutic approved by the US Food and Drug Administration (FDA) in 2004,…

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Long-range phasing of dynamic, tissue-specific and allele-specific regulatory elements

Baylin, S. B. & Jones, P. A. A decade of exploring the cancer epigenome – biological and translational implications. Nat. Rev. Cancer 11, 726–734 (2011). CAS  PubMed  PubMed Central  Article  Google Scholar  Greenberg, M. V. C. & Bourc’his, D. The diverse roles of DNA methylation in mammalian development and disease….

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The comprehensive detection of miRNA and circRNA in the regulation of intramuscular and subcutaneous adipose tissue of Laiwu pig

Zhou, G. et al. Global comparison of gene expression profiles between intramuscular and subcutaneous adipocytes of neonatal landrace pig using microarray. Meat. Sci. 86(2), 440–450 (2010). CAS  PubMed  Article  Google Scholar  Alfaia, C. M. et al. Current feeding strategies to improve pork intramuscular fat content and its nutritional quality. Adv….

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Number of sequences in RefSeq.

Number of sequences in RefSeq. 2 Dear colleagues I can not understand. When I download all the genomic sequences from the refseq database, after counting, I see that there are much fewer records than presented in the release (123394 organisms ftp.ncbi.nlm.nih.gov/refseq/release/release-notes/RefSeq-release214.txt). What am I doing wrong? 1. wget ftp.ncbi.nlm.nih.gov/genomes/refseq/assembly_summary_refseq.txt 2….

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Research Scientist, Bioinformatician, Cancer Science Institute 1 job with NATIONAL UNIVERSITY OF SINGAPORE

JOB DESCRIPTION Analyze and integrate various NGS data Build and reproduce pipelines to process all types of DNA and RNA sequencing data Maintain all source code within Git and Dockerize all pipeline components Liaise with the Scaling Unit to convert pipelines into scalable workflows To…

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Deseq2 Output Explained With Code Examples

Deseq2 Output Explained With Code Examples In this session, we are going to try to solve the Deseq2 Output Explained puzzle by using the computer language. The code that follows serves as an illustration of this point. Column Description 1 Gene Identifiers 2 mean normalised counts, averaged over all samples…

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Bioinformatics Workflow Developer job with Barrington James

Global biotechnology company focusing on molecular biology and applications, informatics, engineering, electronics, manufacturing and commercialisation. Their sequencing platform allows for rapid insights, that analyse DNA and RNA data. The Customer Analysis Workflows are responsible for communicating bioinformatic analyses to end users through various media from software libraries, notebook tutorials,…

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Three Noteworthy Applications of CRISPR

Only 10 years ago, Nobel prize-winning work introduced CRISPR, or clustered regularly interspaced short palindromic repeats, as a new and powerful genome editing tool. Since then, many exciting applications of the CRISPR-Cas9 system have been developed and proposed, giving a taste of what is yet to come.   Progress has…

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Bioinformatics Analyst job in Lexington, Kentucky at University of Kentucky

Posting Details Posting Details Job Title Bioinformatics Analyst Requisition Number RE35885 Working Title Department Name 7H025:CANCER CENTER-CORE SUPPORT Work Location Lexington, KY Grade Level 46 Salary Range $50,981-84,115/year Type of Position Staff Position Time Status Full-Time Required Education MS Click here for more information about equivalencies: www.uky.edu/hr/employment/working-uk/equivalencies Required Related Experience…

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DESeq2. Multi-factor Interactions designs

DESeq2. Multi-factor Interactions designs 0 Dear all, I want to get your feedback, please !! I have gene expression data from two tissue(Tissue_1 and Tissue_2) in three conditions(A, B and C). I want to get genes upregulated in Tissue_2 in condition C vs A+B. I was trying this, but not…

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Order of reads in Long read FASTQ file

Order of reads in Long read FASTQ file 0 Hi all, FASTQ files contain sequencing reads ‘as they come off the sequencing instrument.’ Is there any particular order to them in long read fastq file for ONT and PacBio? E.g. based on the position of the flow cell? Quality? I…

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CRISPR Could Make Testing for SARS-COV-2 Fast and Easy

An engineered CRISPR-based method that finds RNA from SARS-CoV-2, the virus that causes COVID-19, promises to make testing for that and other diseases fast and easy, researchers report. The researchers further engineered the RNA-editing CRISPR-Cas13 system to boost their power for detecting minute amounts of the SARS-CoV-2 virus in biological…

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Rockefeller University Jobs – Bioinformatics Specialist in New York, New York, United States

Job: IRC28479 Description Job Title Bioinformatics Specialist Laboratory / Department Systems Cancer Biology Department Description Cancer remains a daunting problem despite decades of active research into its molecular causes. Such studies have predominantly focused on the earliest stages of cancer progression such as the formation of a cancer or genes…

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Batch effect correction with cell type enrichment analysis

Batch effect correction with cell type enrichment analysis 0 I have RNA-seq data samples regarding several types of cancer that came from the same source, and RNA-seq of control samples from a different source. For the cancer data and for the control data, I run cell type enrichment analysis separately…

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Technician I/II (NGS) Jobs in NuProbe USA Inc. Texas

The Technician I/II will execute most of the Research & Development protocol activity which is vital to the success of the company. This position handles sensitive data and comes with a high degree of trust. NGS library preparation and sequencing PCR and qPCR DNA and/or RNA extraction…

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Identification of unique DNA methylation sites in Kabuki syndrome using whole genome bisulfite sequencing and targeted hybridization capture followed by enzymatic methylation sequencing

Niikawa N, Matsuura N, Fukushima Y, Ohsawa T, Kajii T. Kabuki make-up syndrome: a syndrome of mentalretardation, unusual facies, large and protruding ears, and postnatal growth deficiency. J Pediatrics. 1981;99:565–9. CAS  Article  Google Scholar  Kuroki Y, Suzuki Y, Chyo H, Hata A, Matsui I. A new malformation syndrome of long…

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A global collaboration to map the whole human brain

Baylor College of Medicine researchers in the Tolias Lab and the Xiaolong Jiang Lab are part of a global collaborative led by the Allen Institute to map the whole human brain. In what is being called the brain equivalent of the Human Genome Project, this initiative will map 200 billion cells in the human brain by…

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Population-level variation in enhancer expression identifies disease mechanisms in the human brain

Schizophrenia Working Group of the Psychiatric Genomics Consortium. Biological insights from 108 schizophrenia-associated genetic loci. Nature 511, 421–427 (2014). PubMed Central  Article  CAS  Google Scholar  Visscher, P. M. et al. 10 years of GWAS discovery: biology, function, and translation. Am. J. Hum. Genet. 101, 5–22 (2017). CAS  PubMed  PubMed Central …

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Low number of nCount_RNA in single-cell RNAseq clusters?

Low number of nCount_RNA in single-cell RNAseq clusters? 0 Hello, after standard Seurat workflow, I checked the metrics of each cluster in the object. Please see the attached picture. How may I explain, in some of clusters, such as cluster 9 which has low nCount_RNA and nFeature_RNA but with an…

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Whole Transcriptome Data Analysis Course, EMBL Advanced Training Centre, Heidelberg, Baden-Wurttemberg, Germany

Overview Whole Transcriptome Data Analysis Course is organized by European Molecular Biology Laboratory (EMBL) and will be held from May 21 – 26, 2023 at EMBL Advanced Training Centre, Heidelberg, Baden-Wurttemberg, Germany. Description:This course will teach biological researchers how to analyze biological data sets using open-source software. Most of the…

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Special Issue : Recent Advances in Chemical Biology to Study and Target ncRNAs

Dear Colleagues, In recent decades, ncRNAs have been shown to play a critical role in a myriad of cellular processes, impacting normal gene expression as well as disease progression, making them an attractive target for drug discovery. Moreover, their complex impacts on molecular biology still require revealing and studying. Recent…

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Modelling urea cycle disorders using iPSCs

Gebhardt, R. & Matz-Soja, M. Liver zonation: Novel aspects of its regulation and its impact on homeostasis. World J. Gastroenterol. 20, 8491–8504 (2014). PubMed  PubMed Central  Article  Google Scholar  Summar, M. L. et al. The incidence of urea cycle disorders. Mol. Genet Metab. 110, 179–180 (2013). CAS  PubMed  PubMed Central …

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Project Scientist – Knott Lab – Bioinformatics & Functional Genomics

Are you passionate about applying genomics, computer science, and probability theory to study cancer progression? The Knott laboratory at Cedars-Sinai Medical Center is searching for a Project Scientist with a strong background in tumor biology and the immune microenvironment to lead single cell-based omics studies of immunotherapy clinical trials being…

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How do I get separate ADT / CITE-seq fastq’s from single SRA / BAM files? (originally generated from cellranger)

How do I get separate ADT / CITE-seq fastq’s from single SRA / BAM files? (originally generated from cellranger) 0 Hello all. I am trying to pre-process some single cell RNA and ADT (Totalseq-C) data from an GEO SRA, but having some issues getting separate fastq’s for the “CITE-seq” (ADT)…

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Engineered LwaCas13a with enhanced collateral activity for nucleic acid detection

doi: 10.1038/s41589-022-01135-y. Online ahead of print. Jie Yang #  1 , Yang Song #  2   3 , Xiangyu Deng  4 , Jeffrey A Vanegas  1 , Zheng You  1 , Yuxuan Zhang  2   3 , Zhengyan Weng  2   3 , Lori Avery  5 , Kevin D Dieckhaus  6 , Advaith Peddi  4 , Yang Gao  7 , Yi Zhang  8…

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Single-cell multi-omics of human clonal hematopoiesis reveals that DNMT3A R882 mutations perturb early progenitor states through selective hypomethylation

Martincorena, I. et al. Somatic mutant clones colonize the human esophagus with age. Science 362, 911–917 (2018). CAS  PubMed  PubMed Central  Google Scholar  Yizhak, K. et al. RNA sequence analysis reveals macroscopic somatic clonal expansion across normal tissues. Science 364, eaaw0726 (2019). CAS  PubMed  PubMed Central  Google Scholar  Yokoyama, A….

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Plastomes of limestone karst gesneriad genera Petrocodon and Primulina, and the comparative plastid phylogenomics of Gesneriaceae

Features of the newly sequenced Petrocodon and Primulina plastomes Sizes of the nine newly sequenced plastomes of Petrocodon and Primulina range from 152,323 bp in Pr. medica (D.Fang ex W.T.Wang) Yin Z.Wang to 153,786 bp in Pr. cordata Mich.Möller & A.Weber (Tables 1, S1). These nine plastomes display the typical quadripartite structure…

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Removal of rRNA from Deproteinized, Phenol-Extracted Total RNA by Hybrid Selection

Adapted from RNA: A Laboratory Manual by Donald C. Rio, Manuel Ares Jr, Gregory J. Hannon, and Timothy W. Nilsen. CSHL Press, Cold Spring Harbor, NY, USA, 2011. Abstract In this protocol, rRNAs are selectively removed from a total RNA sample by hybridizing the rRNAs to complementary biotinylated oligodeoxynucleotides that…

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HISAT2 and HTSEQ command

HISAT2 and HTSEQ command 0 @4fedfa78 Last seen 10 hours ago Japan Hello, For analysis of the data by rna-sequencing I selected HISAT2 and HTSeq-count for mapping and counting the genes levels, the libraryLayout is paired, I am using the below command for both but the results are not exact…

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Multiple conditions DESeq2

Multiple conditions DESeq2 1 Hi, I am working on differentially expressed genes analysis of RNA-seq data extracted from multiple but related experiments: experiment DESH21_E DESH40_S DESN21_E DESN21_S DESN40_E DESN40_S ES21_E ES21_S ES40_E ES40_S where, DES and ES are different in vitro cells; 21/40 are concentration (low/high), and H/N are additional…

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Postdoctoral Research Fellow in Molecular Biology job with QUEENS UNIVERSITY BELFAST

Job description The School of Medicine, Dentistry & Biomedical Sciences (MDBS) at Queen’s University Belfast, is currently seeking to appoint an exceptional candidate to the post of Postdoctoral Research Fellow. The Tiwari Lab (www.tiwarilab.com) is looking for a Postdoctoral Research Fellow in Molecular Biology. Our team works on employing functional genomics…

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Postdoctoral Scientist – Bioinformatics and Integrative Genomics Research Cluster at Cedars-Sinai

Responsibilities Requisition # 20002022A At Cedars-Sinai, postdoctoral scientists and other junior researchers fulfill a critical role in expanding the horizons of medical knowledge through biomedical research. By hosting more than 100 postdocs, who conduct vital research and receive advanced training with expert faculty mentors, Cedars-Sinai supports the ongoing medical education process that continues…

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Oligonucleotide Pool Library Market Incredible Possibilities, Growth Analysis and Forecast To 2028

The research literature of Oligonucleotide Pool Library market consists of vital information regarding the growth stimulants, challenges, and other prospects which are shaping the business trends over the period of 2022-2028. According to seasoned experts, the market is expected to exhibit a CAGR of XX% over the…

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How new COVID-19 vaccines work

; DAY New vaccines against COVID-19 begin to be authorized around the world. How do they work, who makes them? Update on these new serums.  Adaptation to the evolution of viruses The virus of the disease COVID-19, SARS-CoV-2 , has the ability to mutate, like other viruses. It is a…

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Senior/Junior Postdoctoral fellow in Bioinformatics

Highly motivated candidates are invited to apply for a 2-year postdoctoral position (with the possibility of an extension) in the laboratory of Assoc. Professor David Gomez-Cabrero in the Biological and Environmental Sciences and Engineering (BESE) Division at the King Abdullah University of Science and Technology (KAUST) (www.kaust.edu.sa/en/study/faculty/david-gomez-cabrero). The project investigates…

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GenScript, Avectas Partner on Cell Therapy Manufacturing

NEW YORK – GenScript and Ireland’s Avectas said on Tuesday that they’re partnering to develop a non-viral cell therapy manufacturing process. Under the terms of the agreement, their research teams will apply Avectas’ Solupore technology to permeabilize target cell membranes to deliver GenScript’s GenCRISPR single guide RNA, CRISPR-Cas9 protein, and GenExact…

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Scientist* Bioinformatics & Statistics | datacareer.de

Mainz Work experience Research, development, teaching Become a member of the BioNTech Family! As a part of our team of more than 2.500 pioneers, you will play a key role in developing solutions for some of the most crucial scientific challenges of our age. Within less than a year, we…

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Isolation of Preadipocytes from Broiler Chick Embryos

The present protocol describes a simple method for isolating preadipocytes from adipose tissue in broiler embryos. This method enables isolation with high yield, primary culture, and adipogenic differentiation of preadipocytes. Oil Red O staining and lipid/DNA stain measured the adipogenic ability of isolated cells induced with differentiation media. Primary preadipocytes…

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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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Intellia Therapeutics : In vivo CRISPR/Cas9 editing of KLKB1 in patients with HAE

In vivo CRISPR/Cas9 editing of KLKB1 in patients with HAE Hilary Longhurst1, Lauré M. Fijen2, Karen Lindsay1, Carri Boiselle3, James Butler3, Adele Golden3, David Maag3, Joseph Vogel3, Yuanxin Xu3, and Danny M. Cohn2 1Auckland District Health Board and University of Auckland, New…

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COVID-19 Antivirals & Diagnostics Toolbox for Research: Creative Biolabs Does Its Bit

After reviewing the existing detection and treatment modalities for SARS-CoV-2, including vaccines, diagnostics, and antivirals, Creative Biolabs actively participates in building the COVID-19 research toolbox to curb emerging viral variants. New York, USA – September 14, 2022 – Given existing vaccines and therapeutics may become inefficacious with the evolution of…

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Animals | Free Full-Text | LAMP Coupled CRISPR-Cas12a Module for Rapid, Sensitive and Visual Detection of Porcine Circovirus 2

Porcine circovirus 2 (PCV2) is the main pathogen of porcine circovirus-associated disease (PCVAD), which can cause considerable economic loss to the pig industry. The diagnosis of PCVAD is complicated and requires a series of clinical, pathological, and virological methods. Therefore, a rapid, highly sensitive, on-site, and visual diagnostic approach would…

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All transcript variants in gene MAD1L1 – BIPMed SNP Array

Legend Please note that a short description of a certain column can be displayed when you move your mouse cursor over the column’s header and hold it still. Below, a more detailed description is shown per column. Effect: The variant’s effect on the protein’s function, in the format ‘R/C’ where…

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Epidemiology, genetic diversity, and association of canine circovirus infection in dogs with respiratory disease

Animal and ethics A total of 190 dogs, comprising both healthy dogs (n = 76) and dogs with respiratory symptoms (n = 114), were included in this study. The research assessed nasal swab (NS) and oropharyngeal swab (OS) collected between January and November 2020. The samples from the healthy group were collected from clinically…

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Aptorum Group Ltd. (APM) Updates on the Clinical Validation of RPIDD Infectious Disease Liquid Biopsy Molecular Diagnostics

Get instant alerts when news breaks on your stocks. Claim your 1-week free trial to StreetInsider Premium here. Aptorum Group Limited (Nasdaq: APM, Euronext Paris: APM) a clinical stage biopharmaceutical company dedicated to tackling unmet medical needs in oncology, autoimmune diseases and infectious diseases, is pleased to announce further updates…

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Research Fellow, Bioinformatician – Cancer Science Institute job with NATIONAL UNIVERSITY OF SINGAPORE

Job Description A postdoctoral position is available immediately in Prof Chng Wee Joo’s groups for a highly motivated PhD graduate with experience in Bioinformatics (computational genomics). The focus of the lab is on deciphering transcriptional and genomic abnormalities in the context of blood cancer, including epigenetic and superenhancer deregulation, using single cell…

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Challenges of single-cell and single-nucleus RNA-sequencing from core needle biopsy specimens

Single-cell RNA sequencing (scRNA-seq) and single-nucleus RNA-seq (snRNA-seq) allow transcriptomic profiling of thousands of cells from a renal biopsy specimen at a single-cell resolution. Both methods are promising tools to unravel the underlying pathophysiology of glomerular diseases. KU Leuven researchers provide an overview of the technical challenges that should be…

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Celyad Oncology (NASDAQ:CYAD) Shares Cross Below Fifty Day Moving Average of $1.88

Celyad Oncology SA (NASDAQ:CYAD – Get Rating)’s stock price crossed below its 50 day moving average during trading on Friday . The stock has a 50 day moving average of $1.88 and traded as low as $1.84. Celyad Oncology shares last traded at $1.84, with a volume of 9,089 shares…

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The crisprVerse: a comprehensive Bioconductor ecosystem for the design of CRISPR guide RNAs across nucleases and technologies

Abstract The success of CRISPR-mediated gene perturbation studies is highly dependent on the quality of gRNAs, and several tools have been developed to enable optimal gRNA design. However, these tools are not all adaptable to the latest CRISPR modalities or nucleases, nor do they offer comprehensive annotation methods for advanced…

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SR. SCIENTIST, HUMAN GENETICS BIOINFORMATICS in San Francisco, CA for Genentech

Details Posted: 09-Sep-22 Location: San Francisco, California Type: Full Time Years of Experience: Less than 2 Join a Team that Lives to Improve Lives  People come to Genentech from across disciplines and across the world to solve our most challenging medical conditions. You’ll find inspiration in our passion for biotechnology,…

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05 Postdoctoral Fellowship at Lund University, Scania, Sweden

Lund University, Scania, Sweden invites online Application for various Postdoctoral Fellowship in their different Departments. We are providing a list of Postdoc Fellowship positions available at Lund University, Scania, Sweden. Eligible candidate may Apply as soon as possible.   (01) Postdoctoral Fellowship Position Postdoc Fellowship Position summary/title:  Postdoctoral researcher in…

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Lonza gains access to Touchlight’s enzymatic DNA technology

Under the terms of the agreement, Lonza can now provide its customers with seamless access to Touchlight’s enzymatic DNA technology. The Hampton, UK headquartered company said the synthetic DNA source enables GMP production at unprecedented speed, scale, and purity.   Both parties have agreed not to disclose financial or contractual terms…

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Understanding bam tracks

Understanding bam tracks 0 Sorry i am having trouble understanding this concept. For example, when I view a bam file after alignment in igv, I see that there are different tracks that form. How are these tracks formed/why do some aligned sequences belong together or are part of the same…

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Early Trading Has Applied Dna (APDN) Climbing for September 6

Last Price $ Last Trade Change $ Change Percent % Open $ Prev Close $ High $ low $ 52 Week High $ 52 Week Low $ Market Cap PE Ratio Volume Exchange APDN – Market Data & News Trade Applied Dna Sciences Inc (NASDAQ:APDN) is active in pre-market…

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Should reproductive technology be inevitable?

Alan Kadish, M.D., president of the Touro College and University System. Photograph by William Taufic. Recently, Alan Kadish, M.D., and John D. Loike, Ph.D., co-authored an article in The Scientist magazine about the medical and ethical limits of such reproductive technologies as cloning and parthenogenesis (the creation of an organism, almost…

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Human hg38 chr7:73,678,750-73,740,129 UCSC Genome Browser v435

Use drop-down controls below and press refresh to alter tracks displayed.Tracks with lots of items will automatically be displayed in more compact modes.    Custom Tracks H3K27ac Meta NeuN SCZhidedensesquishpackfull H3K27ac NeuN SCZ del_CRDhidedensesquishpackfull H3K27ac NeuN SCZ del_CRD_del_peakshidedensesquishpackfull H3K27ac Tissuehidedensesquishpackfull H3K27ac Tissue BDhidedensesquishpackfull H3K27ac Tissue BD del_CRDhidedensesquishpackfull H3K27ac Tissue BD…

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KGDCMI: A New Approach for Predicting circRNA-miRNA Interactions From Multi-Source Information Extraction and Deep Learning

doi: 10.3389/fgene.2022.958096. eCollection 2022. Affiliations Expand Affiliations 1 School of Information Engineering, Xijing University, Xi’an, China. 2 College of Grassland and Environment Sciences, Xinjiang Agricultural University, Urumqi, China. 3 School of Computer Science, Northwestern Polytechnical University, Xi’an, China. Item in Clipboard Xin-Fei Wang et al. Front Genet. 2022. Show details Display…

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Scientists uncover molecular mechanism of RNA-mediated organelle contact sites and regulation mechanism of cholesterol metabolism

As an important carrier of material and energy metabolism, the ordinated modulation of organelle-associated molecules are vital for proper cellular and systemic functions. For example, sterol-regulatory element binding proteins (SREBPs), located on the surface of the endoplasmic reticulum (ER), can rapidly sense changes in intracellular lipid levels, modulate the rate…

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Long non-coding RNA SNHG16 decreased SMAD4 to induce gemcitabine resistance in pancreatic cancer via EZH2-mediated epigenetic modification

doi: 10.1002/kjm2.12574. Online ahead of print. Affiliations Expand Affiliations 1 Department of Pediatrics, Ruijin Hospital, Shanghai Jiaotong University, School of Medicine, Shanghai, China. 2 Department of General Surgery, Shanghai Fifth People’s Hospital Affiliated to Fudan University, Shanghai, China. Item in Clipboard Yi Yu et al. Kaohsiung J Med Sci. 2022. Show…

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Analysis of allele-specific expression in mouse liver by RNA-seq: a comparison with cis-eQTL identified using genetic linkage

S. Lagarrigue, L. Martin, F. Hormozdiari, P.F. Roux, A. van Nas, O. Demeure, A. Ghazalpour, E. Eskin, A.J. Lusis Abstract We report an analysis of allele-specific expression (ASE) and parent-of-origin expression in adult mouse liver using next generation sequencing (RNA-Seq) of reciprocal crosses of heterozygous F1 mice from the parental…

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Which is a stop codon?

A stop codon is a sequence of three nucleotides (a trinucleotide) in DNA or messenger RNA (mRNA) that signals a halt to protein synthesis in the cell. There are 64 different trinucleotide codons: 61 specify amino acids and 3 are stop codons (i.e., UAA, UAG and UGA). What are the…

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Evolution of stickleback spines through independent cis-regulatory changes at HOXDB

Darwin, C. On the Origin of Species by Means of Natural Selection (John Murray, 1859). Owen, R. On the Archetype and Homologies of the Vertebrate Skeleton (Richard and John E. Taylor, 1848). Stern, D. L. & Orgogozo, V. Is genetic evolution predictable? Science 323, 746–751 (2009). CAS  PubMed  PubMed Central …

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Polygenic enrichment distinguishes disease associations of individual cells in single-cell RNA-seq data

Visscher, P. M. et al. 10 years of GWAS discovery: biology, function, and translation. Am. J. Hum. Genet. 101, 5–22 (2017). CAS  PubMed  PubMed Central  Article  Google Scholar  Hekselman, I. & Yeger-Lotem, E. Mechanisms of tissue and cell-type specificity in heritable traits and diseases. Nat. Rev. Genet. 21, 137–150 (2020)….

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Stock Market | FinancialContent Business Page

New York, USA – August 31, 2022 – BOC Sciences offers ready-to-use mRNA in vivo delivery kits for mRNA vaccine/drug research and CRISPR/Cas9 genome editing applications with high efficiency and low toxicity. In vivo transfection reagents are the most powerful alternative to viral vectors for nucleic acid delivery. They are…

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Lexogen Introduces RiboCop rRNA Depletion Kit for Yeast

VIENNA, Sept. 1, 2022 /PRNewswire/ — Lexogen, a transcriptomics and Next-Generation Sequencing company announced the release of the new RiboCop rRNA Depletion Kit for Yeast today. Total RNA is comprised of large amounts of undesired ribosomal RNA (rRNA), which accounts for up to 95 % of all transcripts in an…

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Caribou Biosciences to Participate in Upcoming Investor Conferences

Caribou Biosciences, Inc. BERKELEY, Calif., Aug. 31, 2022 (GLOBE NEWSWIRE) — Caribou Biosciences, Inc. (Nasdaq: CRBU), a leading clinical-stage CRISPR genome-editing biopharmaceutical company, today announced the company’s participation in the following investor conferences: Citi 17th Annual BioPharma Conference, BostonPanel participation on September 8, 2022, 11:20 am ETWebcast H.C. Wainwright 24th…

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Dynamic mechanisms of CRISPR interference by Escherichia coli CRISPR-Cas3

In vitro reconstitution of Escherichia coli CRISPR-Cas3 interference E. coli CRISPR-Cas3 is generally well-characterized type I CRISPR complexes in vitro and in vivo32,33,37,38. However, recombinant EcoCas3 protein is difficult to purify because of poor solubility and propensity to aggregate at 37 °C25,26,30,39. Co-expression of HtpG chaperon40 and/or low temperature growth at…

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Is low N in-vivo research a blind spot for RNA-seq?

Forum:Is low N in-vivo research a blind spot for RNA-seq? 1 My thoughts on this have very much not changed since you asked a similar question two years ago: Am I crazy, or are most published RNA-seq studies vastly underpowered? Both your proposed explanations are in play – but I…

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NFT of mRNA vaccine research to go on sale

LONDON: A new NFT digital asset from the University of Pennsylvania showcases pivotal mRNA research that could lead to life-changing vaccines for COVID-19 and beyond. Dr. Drew Weissman, a physician and immunologist known for his groundbreaking contributions to RNA biology, and the RNA biochemist Dr. Katalin Kariko developed the modified…

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TPM and RPKM normalization from counts dataframe

TPM and RPKM normalization from counts dataframe 2 Folks: I have two dataframes for counts information from two RNAseq data… is there a quick way to get from counts to TPM or RPKM or both efficiently? Thanks RNA-Seq • 3.5k views • link updated 5.8 years ago by Ron ★…

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NODULIN HOMEOBOX is required for heterochromatin homeostasis in Arabidopsis

NDX is a heterochromatin-associated factor To understand the genome-wide regulatory roles of NDX, we first analyzed its genomic distribution. For this, we performed chromatin immunoprecipitation sequencing (ChIP-seq) in 10-day old Arabidopsis seedlings expressing N-terminally and C-terminally tagged NDX fusion proteins (flag-NDX/ndx1-1(FRI)/flc-2 and NDX-GFP/ndx1-1(FRI)/flc-2, respectively) expressed from their endogenous promoter21,32. The…

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What Are The Functions Of MRNA TRNA And RRNA Quizlet?

What are the functions of mRNA tRNA and rRNA quizlet? Terms in this set (3) tRNA. transfer RNA; type of RNA that carries amino acids to the ribosome. mRNA. messenger RNA; type of RNA that carries instructions from DNA in the nucleus to the ribosome. ribosomal RNA. type of RNA…

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circRNF13 Inhibits the Proliferation and Metastasis of Nasopharyngeal Carcinoma through SUMO2

Circular RNAs (circRNAs) are widely expressed in human cells and are closely related to the development of cancer. However, they are rarely studied in the context of nasopharyngeal carcinoma (NPC). Here, the researchers found that a novel circRNF13 was stably expressed at low levels in clinical tissues and cells of…

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Simultaneously induced mutations in eIF4E genes by CRISPR/Cas9 enhance PVY resistance in tobacco

Pasin, F., Daròs, J.-A. & Tzanetakis, I. E. Proteome expansion in the Potyviridae evolutionary radiation. FEMS Microbiol. Rev. 46, 011. doi.org/10.1093/femsre/fuac011 (2022). Article  Google Scholar  Karasev, A. V. & Gray, S. M. Continuous and emerging challenges of Potato virus Y in potato. Annu. Rev. Phytopathol. 51, 571–586 (2013). CAS  PubMed …

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Differential enrichment of H3K9me3 in intrahepatic cholangiocarcinoma | BMC Medical Genomics

Sia D, Tovar V, Moeini A, Llovet JM. Intrahepatic cholangiocarcinoma: pathogenesis and rationale for molecular therapies. Oncogene. 2013;32(41):4861–70. CAS  Article  Google Scholar  Sungwan P, Lert-Itthiporn W, Silsirivanit A, Klinhom-On N, Okada S, Wongkham S, Seubwai W. Bioinformatics analysis identified CDC20 as a potential drug target for cholangiocarcinoma. PeerJ. 2021;9:e11067. Article …

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Research Fellow, Bioinformatician, Department of Medicine job with NATIONAL UNIVERSITY OF SINGAPORE

Job Description To provide specialist bioinformatics analyses of genomic, transcriptomic, proteomic and cellular phenotypic data to investigate genetic influences on gene expression and vascular cell behaviour in relation to cardiovascular diseases. To provide input into the design of experimental studies and the preparation of research grants and scientific…

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Global Genome Editing Market Report 2022: Developing Biotechnology Industry in Emerging Regions Presents Opportunities – ResearchAndMarkets.com

DUBLIN–(BUSINESS WIRE)–The “Genome Editing Market Forecast to 2028 – COVID-19 Impact and Global Analysis By Technology, Application, and End User” report has been added to ResearchAndMarkets.com‘s offering. The genome editing market is projected to reach US$ 16,986.69 million by 2028 from US$ 5,199.40 million in 2021; it is expected to…

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BBmap bbduk.sh for filtering reads

I’m looking to filter reads that contain a stretch of A’s, I found these posts looking for polyA tails, meaning this should work all the same (Identify RNA-seq reads containing polyA sequence, Identifying RNA-seq reads containing polyA stretch). However, I cannot get it to work. Given just these two reads,…

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Protocol for Human Blastoids Modeling Blastocyst Development and Implantation

A protocol outlining the formation of human blastoids that efficiently, timely, and sequentially generate blastocyst-like cells. Research on human embryos is limited by their low availability and ethical concerns, thus obtaining individual models that faithfully replicate early human development would support scientific and medical progress. The ability of this technique…

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How is rRNA synthesized in eukaryotes?

rRNA Processing in Eukaryotes: The precursor rRNA in eukaryotes contain one copy of 18S coding region, one copy of 5.8S and one copy of 28S coding region. This rRNA precursor is transcribed in the nucleolus by RNA polymerase I. The eukaryotic 5S rRNA is transcribed by RNA polymerase III from…

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Long non-coding RNA SNHG6 couples cholesterol sensing with mTORC1 activation in hepatocellular carcinoma

Chu, B. B. et al. Cholesterol transport through lysosome-peroxisome membrane contacts. Cell 161, 291–306 (2015). CAS  Article  Google Scholar  Luo, J., Yang, H. & Song, B. L. Mechanisms and regulation of cholesterol homeostasis. Nat. Rev. Mol. Cell Biol. 21, 225–245 (2020). CAS  Article  Google Scholar  Luo, J., Jiang, L., Yang,…

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New annotations in RefSeq – NCBI Insights

In June and July, the NCBI Eukaryotic Genome Annotation Pipeline released twenty-six new annotations in RefSeq for the following organisms: Anopheles coluzzii (mosquito) Anopheles funestus (African malaria mosquito) Astyanax mexicanus (Mexican tetra) Athalia rosae (coleseed sawfly) Bactrocera dorsalis (oriental fruit fly) Brassica napus (rape) Brienomyrus brachyistius (bony fish) Canis lupus dingo (dingo) (pictured) Caretta…

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Hands On Next Generation Sequencing Using Galaxy Servers | Free eBooks Download

Category: Tutorial Posted on 2022-08-20, by voska89. Description Published 08/2022MP4 | Video: h264, 1280×720 | Audio: AAC, 44.1 KHz, 2 ChGenre: eLearning | Language: English + srt | Duration: 28 lectures (2h 6m) | Size: 615.8 MBLearn about Next-generation sequencing and use of online platform and perform Data analysis of…

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Time course RNA seq with DESEq2

Hi all, Hope you are well. I am running time course experiment to examine differentially expressed genes from tumour tissues between two conditions, radiotherapy and sham-radiotherpapy groups at 4 time points post radiotherapy. Each time point had size matched untreated controls. I used the following code to run model with…

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Bioinformatics Software Engineer I – Genomics | Memorial Sloan Kettering Cancer Center

Nationwide, Company Overview At Memorial Sloan Kettering (MSK), we’re not only changing the way we treat cancer, but also the way the world thinks about it. By working together and pushing forward with innovation and discovery, we’re driving excellence and improving outcomes. We’re treating cancer, one patient at a time….

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Scientists discover a technique to restore some diseased cells to their proper state

Scientists developed a novel screening methodology for identifying genes that regulate specific microglial functions that may contribute to Alzheimer’s disease (AD) in a recent article published inNature Neuroscience. Characterizing regulatory genes that cause microglia to shift from a healthy state to a diseased state, such as in the brains of…

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Subtype and cell type specific expression of lncRNAs provide insight into breast cancer

lncRNA expression according to breast cancer clinicopathological subtypes To identify lncRNAs expressed by specific breast cancer subtypes or associated with clinicopathological features, we analyzed RNA-sequencing data from two large independent breast cancer cohorts: SCAN-B (n = 3455)17 and TCGA-BRCA (n = 1095). We focused on lncRNAs annotated in the Ensembl18 v93 non-coding reference transcriptome…

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The Unbreakable Attraction of Mosquitoes to Humans

A female Aedes aegypti  mosquito feeds from a researcher at The Rockefeller University. Credit: © Alex Wild More than a decade ago, Leslie Vosshall, then a relatively new Howard Hughes Medical Institute (HHMI) Investigator, decided to switch from studying innocuous fruit flies to a far deadlier creature—the mosquito. Perhaps her extensive knowledge of…

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how to use mirdeep2 without a small RNA library

how to use mirdeep2 without a small RNA library 1 Hello everyone, I’m currenly working on a project where collecting tissue samples would be almost imposible… so we have to work with public data (reference genome and the RNA seq data that is already avaliable) and from what I’ve seen…

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using gatk haplotypecaller for variants extraction

using gatk haplotypecaller for variants extraction 0 Hi, I have rna-sequenced data from covid patients. I am using hisat2 for aligning the reads to reference. So, the resulted bam files after indexing are now ready. I would like to use gatk happlotypecaller for extracting variants from my bam files. First,…

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Solved Which of the following statement best defines the

Transcribed image text: Which of the following statement best defines the RNA? Select ALL that apply. Hint: Read “Nucleic Acids” in experimental glossary. Hide answer choices a RNA is a double-stranded macromolecule with different types of RNA; Ribosomal (rRNA), transfer (tRNA) and messanger (mRNA) RNA is a single-stranded macromolecule composed…

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Orna goes into orbit on $3.65B Merck megadeal, $221M series B round

Orna Therapeutics Inc., which is pioneering a novel circular RNA protein expression technology in several therapeutic areas, has achieved lift-off. The Cambridge, Mass.-based company has closed a broadly based alliance in infectious disease and oncology with Merck & Co. Inc., under which it is getting $150 million up front and…

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mapping – STAR error in snakemake pipeline: “EXITING because of FATAL ERROR: could not open genome file”

I’m trying to use a 2 pass STAR mapping strategy (also explained here informatics.fas.harvard.edu/rsem-example-on-odyssey.html), but I’m getting an error. I’ve read through this page [https://github.com/alexdobin/STAR/issues/181] and I have a similar issue, but the discussed solutions don’t seem to help. Perhaps this is more a snakemake issue rather than a STAR…

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Proscillaridin A induces mitochondrial damage and autophagy in pancreatic cancer and reduces the stability of SMAD4 in Panc-1 cells – Hou

Introduction Pancreatic cancer (PC) is one of the most aggressive and lethal cancers (1). Previous studies have shown that aging, environmental and behavioral changes are more closely related to the dramatic increase in the incidence of PC worldwide than genetic factors (2–5). A position paper published by the European Federation…

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Circular RNA circ-BNC2 (hsa_circ_0008732) inhibits the progression of ovarian cancer through microRNA-223-3p/ FBXW7 axis | Journal of Ovarian Research

Ethics statement and patient samples 40 pairs of OC tissues and adjacent tissue samples were collected from patients who were diagnosed with OC and received surgical resection in the Affiliated Hospital of Zunyi Medical University. None of the patients received any anti-cancer treatment before surgery, and all samples were immediately…

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Patrick Murphy Bulk RNA-Seq – HackMD

Patrick Murphy Bulk RNA-Seq – HackMD        owned this note   Published Linked with GitHub — title: ‘Patrick Murphy Bulk RNA-Seq’ disqus: hackmd — Patrick Murphy bulk RNA-Seq Analysis === ## Table of Contents [TOC] ## 1. Introduction This is a bulk RNA-Seq project, which includes human data….

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Transcription-independent regulation of STING activation and innate immune responses by IRF8 in monocytes

Reagents, antibodies, viruses and cells LMW-Poly(I:C), LPS, 2′3′-cGAMP and DMXAA (InvivoGen); hydroxyurea, camptothecin and mitomycin C (MCE); GM-CSF, Flt3L (peproTech); lipofectamine 2000 (Invitrogen); polybrene (Millipore); RNAiso Plus (Takara); HT-DNA (Sigma); SYBR (BIO-RAD); dual-specific luciferase assay kit (Promega); ELISA kit for murine Ifn-β (PBL); ELISA kits for murine IP-10 (Biolegend) were…

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TPM normalization starting with read counts

Hello everyone I have multiple bulk RNA-seq datasets that I need to apply the same pipe line on. I want to normalize them from counts data to TPM. In all datasets, I have the genes as rows, and samples as columns. Unfortunately, I don’t have the fastq files, all I…

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Efficient genome editing in wild strains of mice using the i-GONAD method

Mice A laboratory strain B6 was purchased from CLEA Japan Inc. (Tokyo, Japan), while nine wild strains (BFM/2, BLG2, CHD, HMI, KJR, MSM, NJL, PGN2, and SWN) were bred at NIG (Shizuoka, Japan) (Table 1). All mice were maintained at the animal facility in NIG, under specific-pathogen-free conditions and controlled…

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