Tag: qPCR

rprimer: an R/bioconductor package for design of degenerate oligos for sequence variable viruses | BMC Bioinformatics

Case study To illustrate and evaluate the functionality of rprimer, two assays targeted at norovirus GI were designed. Assay A: RT-qPCR for quantitative detection of norovirus GI The first task was to design a broadly reactive RT-qPCR assay for quantitative detection. For this, we decided to use the ‘ambiguous’ primer…

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Ultrasensitive, Specific, and Rapid Detection of Mycoplasma pneumoniae Using the ERA/CRISPR-Cas12a Dual System

Mycoplasma pneumoniae can cause severe respiratory tract infections and extrapulmonary diseases, which pose a significant threat to the health of children. Diagnostic methods for M. pneumoniae include isolation and culture, antibody detection, fluorescence quantitative PCR, and so on, but there are various shortcomings in time, cost, convenience, and sensitivity. In…

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

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

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Specific High-Sensitivity Enzymatic Molecular Detection System Termed RPA-Based CRISPR-Cas13a for Duck Tembusu Virus Diagnostics

journal contribution posted on 19.05.2022, 07:04 by Dalin He, Gang Liu, Jing Yang, Xiaoning Jiang, Hongzhi Wang, Yaru Fan, Shangyu Gong, Feng Wei, Youxiang Diao, Yi Tang In China, drastic losses in the economy have been caused by the Tembusu virus (TMUV), the causative agent of the egg-drop syndrome, to…

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Researchers identify cellular serpins as host factors that restrict SARS-CoV-2 infection

The mass vaccination programs against coronavirus disease 2019 (COVID-19) received massive media attention and were widely credited for reducing the threat of the disease. However, many countries struggle to obtain enough doses to immunize their population, and some immunocompromised individuals are less protected by the vaccines. There is still a…

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Biogenesis, biology and characterization of circular RNAs

Biogenesis, biology and characterization of circular RNAs Kristensen LS et al. The biogenesis, biology and characterization of circular RNAs. Nat Rev Genet. (2019) Summary text Biogenesis and properties of circRNAs Biogenesis of cirRNA Characteristics of circRNAs Discover and analyze circRNAs circRNA genome-wide analysis CircRNA site-specific analysis circRNA visualization Biological functions…

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Figure 3 | Bone Marrow-Derived Cells Contribute to the Maintenance of Thymic Stroma including TECs

Single sorted bone marrow-derived CD45+ EpCAM+ cells express both the CD45 and EpCAM genes and surface proteins. CD45+ EpCAM+ cells were sorted to high purity and analyzed for CD45 and EpCAM expression using immunofluorescence microscopy, as well as qRT-PCR. CD45+ EpCAM- cells were also sorted as a control. (a) FACS…

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Frontiers | COMMD2 Upregulation Mediated by an ncRNA Axis Correlates With an Unfavorable Prognosis and Tumor Immune Infiltration in Liver Hepatocellular Carcinoma

Introduction Liver hepatocellular carcinoma (LIHC) is the most common type of primary cancer in the liver and third leading cause of cancer-related mortality worldwide (1). Although substantial improvements have been made in LIHC therapy, particularly in molecular targeted therapy and immunotherapy (2, 3), the 5-year survival rate of LIHC is…

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Bioinformatics Jobs in White Waltham, England

3.3 Principal Scientist – R&D Omics and Bioinformatics Slough, Berkshire, South East England, England £35,587 – £45,000 (Glassdoor Est.) Providing oversight and executing scientific activities with elements of study design and implementation, laboratory work, scientific review, coaching of junior…… 3.6 3.3 Director, High Throughput Biologics R&D Slough, Berkshire, South East…

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CircRNA and miRNA expression profiles during remote ischemic postconditioning attenuate brain ischemia/reperfusion injury

. 2022 Apr 19;S0361-9230(22)00098-3. doi: 10.1016/j.brainresbull.2022.04.006. Online ahead of print. Chun-Yan Li  1 , Wei Ma  2 , Kuang-Pin Liu  2 , Jin-Wei Yang  3 , Xian-Bin Wang  2 , Zhen Wu  3 , Tong Zhang  3 , Jia-Wei Wang  3 , Wei Liu  2 , Jie Liu  2 , Yu Liang  2 , Xing-Kui Zhang  2 , Jun-Jun Li  2 , Jian-Hui…

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Transcriptional profiling of macrophages reveals distinct parasite stage-driven signatures during early infection by Leishmania donovani

Infection with L. donovani amastigotes or promastigotes promotes early changes in the mRNA pool of the host cell To compare the early effects of the two life stages L. donovani in the mature mRNA pool of the host cell, total cytosolic mRNA extracts from bone marrow-derived macrophage (BMDM) cultures infected…

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CRISPRi for specific inhibition of miRNA clusters and miRNAs with high sequence homology

Bartel, D. P. MicroRNAs: Target recognition and regulatory functions. Cell 136, 215–233 (2009). CAS  Article  Google Scholar  Bassett, A. R. et al. Understanding functional miRNA–target interactions in vivo by site-specific genome engineering. Nat. Commun. 5, 4640 (2014). ADS  CAS  Article  Google Scholar  Moore, M. J. et al. miRNA–target chimeras reveal…

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N6-methyladenosine modification of CENPK mRNA by ZC3H13 promotes cervical cancer stemness and chemoresistance | Military Medical Research

Bioinformatics analyses revealed the involvement of m6A modification in cervical cancer progression To better understand whether and how m6A regulators contribute to cervical cancer progression, we first identified 9 m6A writers (WTAP, ZC3H13, METTL3, METTL14, METTL16, VIRMA, RBM15B, RBM15, and CBLL1), 15 m6A readers (FMR1, hnRNPA2B1, hnRNPC, YTHDF1/2/3, YTHDC1/2, LRPPRC,…

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aCGH – Allie: Result by abbreviation

1  array comparative genomic hybridization(1473 times) Neoplasms(306 times) FISH (238 times)CNVs (135 times)MLPA (72 times) 2003 1-Mb resolution array-based comparative genomic hybridization using a BAC clone set optimized for cancer gene analysis. 2  array CGH(43 times) Neoplasms(12 times) CNVs (7 times)FISH (3 times)ID (3 times) 2003 Combined array comparative genomic hybridization and…

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Engineering and validation of a dual luciferase reporter system for quantitative and systematic assessment of regulatory sequences in Chinese hamster ovary cells

Experimental workflow and vector designs One way to validate the all-in-one reporter system is through transient or stable transfection of mammalian cells. Within this framework, the schematics in Fig. 1 illustrate the overall workflow of this study and feature the characteristics of promoters. To summarize, the study involves the engineering and…

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Genetic characteristics involving the PD-1/PD-L1/L2 and CD73/A2aR axes and the immunosuppressive microenvironment in DLBCL

Key messages What is already known on this topic Targeting immunosuppressive pathways have emerged as promising strategies for cancer treatment. The genetic characteristics of PD-1/PD-L1/L2 (programmed cell death protein 1/programmed cell death ligand 1/ligand 2) and CD73/A2aR (A2a adenosine receptor) and the effect of these two signalings on dysfunctional CD8+…

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Postdoc – Human Genome Engineering, Cell Therapies, iPSCs, Synthetic Biology

The Truong lab is hiring for multiple Postdoctoral Fellow positions at NYU. We use large scale human genome engineering to develop off-the-shelf cell therapies using iPSCs.   The lab uses Synthetic Biology to build allogeneic Dendritic Cells from iPSCs as a platform for cell immunotherapies. We are interested in all…

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qPCR Data Analysis & BioInformatics

qPCR Data Analysis & BioInformatics qPCR Data Analysis & BioInformatics – Bioinformatics derives knowledge from computer analysis of biological data, herein kinetic PCR. The expression results derived from real-time RT-PCR experiments must be analysed, normalised, compared with other genes and finally statistically processed. The software tools listed below are able…

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Type I Interferon Response Is Mediated by NLRX1-cGAS-STING Signaling in Brain Injury

doi: 10.3389/fnmol.2022.852243. eCollection 2022. Lauren E Fritsch  1 , Jing Ju  2 , Erwin Kristobal Gudenschwager Basso  3 , Eman Soliman  3 , Swagatika Paul  4 , Jiang Chen  2 , Alexandra M Kaloss  3 , Elizabeth A Kowalski  3 , Taylor C Tuhy  5 , Rachana Deven Somaiya  1 , Xia Wang  3 , Irving Coy Allen  3 , Michelle H…

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CRISPR/Cas12a-Enhanced Loop-Mediated Isothermal Amplification for the Visual Detection of Shigella flexneri

doi: 10.3389/fbioe.2022.845688. eCollection 2022. Affiliations Expand Affiliations 1 Provincial Key Laboratory for Transfusion-Transmitted Infectious Diseases, Institute of Blood Transfusion, Chinese Academy of Medical Sciences and Peking Union Medical College, Chengdu, China. 2 Clinical Laboratory Department, Yan’an Hospital Affiliated to Kunming Medical University, Kunming, China. 3 Department of Emergency, The Traditional…

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CircRNA circFADS2 is under-expressed in sepsis and protects lung cells from LPS-induced apoptosis by downregulating miR-133a | Journal of Inflammation

Sepsis patients and healthy controls A total of 62 sepsis patients (male/female: 32/30; mean age, 52.3±4.9 years) who were admitted to Minhang Hospital, Fudan University between March 2018 and March 2020 were enrolled in the study. In addition, 62 healthy controls (male/female: 32/30; mean age, 52.4±4.8 years) who were at…

Continue Reading CircRNA circFADS2 is under-expressed in sepsis and protects lung cells from LPS-induced apoptosis by downregulating miR-133a | Journal of Inflammation

Exploring m6A and m5C Epitranscriptomes upon Viral Infection: an Example with HIV

Hi, in this video we’ll show you how to explore the m6A and m5C epitranscriptomes upon viral infection. To start the experiment, you’ll need 50 million cells for the noninfected and 50 million for the infected condition. In order to obtain a high quality dataset upon analysis, you’ll need to…

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Convenient and High-Throughput PCR Primer Design for Circular RNA Quantification

Please use this url to cite or link to this publication: hdl.handle.net/1854/LU-8743723 MLA Vromman, Marieke, et al. “CIRCprimerXL: Convenient and High-Throughput PCR Primer Design for Circular RNA Quantification.” Frontiers in Bioinformatics, 2022, doi:10.3389/fbinf.2022.834655. APA Vromman, M., Anckaert, J., Vandesompele, J., & Volders, P.-J. (2022). CIRCprimerXL: Convenient and High-Throughput PCR Primer…

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Integrated Analysis of the CircRNA-Based ceRNA Network in Renal Fibrosis Induced by Ischemia Reperfusion Injury

This article was originally published here Front Genet. 2022 Feb 10;12:793182. doi: 10.3389/fgene.2021.793182. eCollection 2021. ABSTRACT Background: Circular RNAs (circRNAs), which have broad posttranscriptional regulatory potencies, are involved in the pathogenesis of fibrotic diseases and are promising diagnostic biomarkers and therapeutic targets. However, their specific roles in renal fibrosis remain…

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Optimization of cerebrospinal fluid microbial DNA metagenomic sequencing diagnostics

We implemented a metagenomic DNA sequencing methodology to unbiasedly detect microbial species in CSF samples from patients with CNS symptoms in which a pathogen or EBV had been detected (Additional 3: Table 1). Samples positively identified with pathogen-specific quantitative PCR (qPCR), 16S rRNA gene sequencing or bacterial/mycotic culture in CSF…

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Bioinformatics/Scientific Algorithms Developer (R and/or Julia)

Job Description Chai brings biotechnology into the real world, allowing anyone to perform molecular diagnostics, anywhere. Our solution is accurate as a lab test, costs 10x less, is easy enough for anyone to use, and provides on-site results in as little as 20 minutes. We’re looking for a bioinformatics developer…

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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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Exosomal microRNA-618 derived from mesenchymal stem cells attenuate the progression of hepatic fibrosis by targeting Smad4

Introduction Hepatic fibrosis (HF) is a pathological phenomenon produced in the process of long-term damage and repair in the liver [1,2]. During the formation of HF, hepatocytes are damaged by various factors, such as chronic liver disease, and excessive intake of alcohol, and secrete a variety of cytokines [3]. Subsequently,…

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Nuprobe USA Inc. Quality Assurance Manager

Quality Assurance Manager- Molecular NGS, PCR, IVD Quality Assurance ManagerHouston TX NuProbe USA Inc. is looking for a Quality Assurance Manager to lead the Quality program to establish and maintain compliance to ISO: 9001, ISO: 13485, and FDA 21 CFR Part 820 Quality System Regulations. NuProbe USA is a rapidly…

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A Simple and Highly Sensitive Naked-Eye Analysis of EGFR 19del via CRISPR/Cas12a Triggered No-Nonspecific Nucleic Acid Amplification

The mutation status of epidermal growth factor receptor (EGFR) exon 19 is of great importance for predicting sensitivity to tyrosine kinase inhibitors (TKIs) in the treatment of non-small-cell lung cancer (NSCLC). However, the development of simple, sensitive, and no-nonspecific amplification platforms for EGFR 19del detection in NSCLC remains a challenge….

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

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

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dCas9-VPR-mediated transcriptional activation of functionally equivalent genes for gene therapy

1. Dunbar, C. E. et al. Gene therapy comes of age. Science 359, eaan4672 (2018). PubMed Google Scholar  2. Wang, D., Tai, P. W. L. & Gao, G. Adeno-associated virus vector as a platform for gene therapy delivery. Nat. Rev. Drug Discov. 18, 358–378 (2019). CAS PubMed PubMed Central Google Scholar  3. Eid, A.,…

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Manufacturing Associate Job Opening in Houston, TX at Nuprobe USA Inc.

MANUFACTURING ASSOCIATE (T1 or T2) NuProbe USA is hiring one Manufacturing Associate (T1 or T2) for its Houston (TX) location. The successful candidate will have the opportunity to join the NuProbe family in the Manufacturing Department reporting directly to the Manufacturing Manager. PRIMARY PURPOSE OF POSITION The new hire will…

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16S rRNA gene sequence diversity in Faecalibacterium prausnitzii-complex taxa has marked impacts on quantitative analysis

doi: 10.1093/femsec/fiac004. Online ahead of print. Affiliations Expand Affiliations 1 Department of Food, Aroma and Cosmetic Chemistry, Faculty of Bioindustry, Tokyo University of Agriculture, 099-2493 Hokkaido, Japan. 2 Functional Food Forum, University of Turku, 20014 Turku, Finland. 3 Department of Microbiology and Biochemistry of Dairy Products, IPLA-CSIC, 33300 Villaviciosa, Spain….

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Post-doctoral Fellow – Analyst Bioinformatics in Oklahoma City, OK for Oklahoma Medical Research Foundation

Details Posted: 20-Jan-22 Location: Oklahoma City, Oklahoma Type: Full Time Required Education: Doctorate Categories: Biomedical Engineering Years of Experience: Less than 2 Post-doctoral Fellow – Analyst Bioinformatics OverviewOMRF is an independent, not-for-profit biomedical research institute adjacent to the University of Oklahoma Health Sciences Center (OUHSC) campus in Oklahoma City. Oklahoma…

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NuProbe Technology Showcases Quantitative PCR for

Houston, January 18, 2022 (GLOBE NEWSWIRE) – NuProbe, a genomics and molecular diagnostics company that develops ultra-sensitive tests for precision cancer research, today released research demonstrating new technology to qualitatively and quantitatively detect multiple low-grade variants frequency in a quantitative PCR (qPCR reaction). The new allele-specific BDA technology (As-BDA) uses…

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An intronic transposon insertion associates with a trans-species color polymorphism in Midas cichlid fishes

Conflicting results suggest a missing variant In order to narrow down candidates for the causal genetic variant, we performed genome-wide association mapping separately in individual lake populations (previously, association mapping was only performed across the whole species flock5). Interestingly, despite clear association peaks in the crater lakes (Fig. 1a, b), the…

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Rapid and sensitive point-of-care detection of Leptospira by RPA-CRISPR/Cas12a targeting lipL32.,PLOS Neglected Tropical Diseases

Rapid and sensitive point-of-care detection of Leptospira by RPA-CRISPR/Cas12a targeting lipL32. PLOS Neglected Tropical Diseases ( IF 4.411 ) Pub Date : 2022-01-06 , DOI: 10.1371/journal.pntd.0010112 Sirawit Jirawannaporn,Umaporn…

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Investigating changes in the proteostasis capabilities of iPSC-neurons during development and in FTD using iPSC-neurons with MAPT mutations

This article was originally published here Alzheimers Dement. 2021 Dec;17 Suppl 2:e058308. doi: 10.1002/alz.058308. ABSTRACT BACKGROUND: Mutations in microtubule-associated protein tau (MAPT) gene are causative of Frontotemporal Dementia (FTD). Many of the features associated with the development of tau pathology, e.g high levels of tau phosphorylation, are also present in…

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Sr. Manager of Manufacturing – Resumetojobs.com

NuProbe USA is seeking an experienced Sr. Manager, In-Vitro Diagnostics Operations who will be responsible for all aspects of manufacturing, including design transfer of newly developed products from research & development. The successful candidate will control production planning, scheduling and forecasting. The candidate will lead continuous improvements in manufacturing as…

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China Paper Sharing | SEU/TJU: circRNA is a gene therapy target for RCC Manufacturer and Supplier

  Basic information Title: ciRS-7 is a prognostic biomarker and potential gene therapy target for renal cell carcinoma   Journal: Molecular Cancer     Impact factor: 27.401   Vazyme products:   HiScript® III 1st Strand cDNA Synthesis Kit (+gDNA wiper)(number: Vazyme #R312, for 1st Strand cDNA Synthesis) AceQ® qPCR SYBR Green Master Mix (High ROX Premixed)(number: Vazyme…

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New bioinformatics method to analyze viral sgRNA

Single guide ribonucleic acid (sgRNA) molecules are produced by discontinuous transcription, in which viral RNA-dependant RNA polymerase pauses early negative-sense RNA synthesis and then jumps to the other end of the genome. The specifics of this process are still not fully understood. Since sgRNAs can play an important role in…

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Bioinformatician – qPCR and annotation directions Jobs at Nalagenetics, Jakarta

We are hiring a bioinformatics specialist interested in developing a clinical decision support for implementation of genetics in clinical settings. The person will be responsible of building analytical pipelines forpatients’ genomic, demographic, and individual data, as well as working with our senior software engineer tointegrate our knowledge base with existing…

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Adrenal aldosterone-producing adenoma | IJGM

Background Primary hyperaldosteronism (PA) is characterized by spontaneous secretion of excessive aldosterone and inhibition of plasma renin activity.1 The pathogenesis of adrenal aldosterone-producing adenoma (APA) involves the abnormal proliferation of adrenal cortex cells and the excessive secretion of aldosterone, accounting for nearly 30% of PA. Excessive secretion of aldosterone can…

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Sr Scientist – IVD Development – Houston

NuProbe USA Inc . is looking for a Staff/Senior Scientist to lead the IVD project development program at NuProbe to support both research and in vitro diagnostic (IVD) assays for use in medical research, clinical trials, regulatory submissions, and clinical diagnostic use.  NuProbe USA is a rapidly growing company and…

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bioinformatics vacancy

On the one hand, I really liked the diversity of the bioinformatics program, and, with a degree in bioinformatics, there are many possible career paths. Updated on 2 December 2021. Exact wages will depend on experience and the industry an individual works in. Working experience with structural antigen analyses and…

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Large-scale genome-wide study reveals climate adaptive variability in a cosmopolitan pest

Genomic data The foundational resource for this study was a dataset of 40,107,925 nuclear SNPs sequenced from a worldwide sample of 532 DBM individuals collected in 114 different sites based on our previous project15. DNA was extracted from each of the 532 individuals using DNeasy Blood and Tissue Kit (Qiagen,…

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Metagenomics combined with comprehensive validation as a public health risk assessment tool for urban and agricultural run-off

Early detection of emerging and life-threatening pathogens circulating in complex environments is urgently required to combat infectious diseases. This study proposed a public health risk assessment workflow with three stages, pathogen screening, pathogen genotyping, and risk assessment. In stage one, pathogens were screened with metagenomic sequencing, microfluidic chip, and qPCR….

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eli5 RNA Spike-ins : explainlikeimfive

I’m a data scientist trying to branch out into more bioinformatics/genetics. My tutorial is counting spike-ins, but his explanation was over my head: 1 – AnnData and Preprocessing spike-ins | Kaggle ” Because this is smartseq2 data, we may have spike-ins. An RNA spike-in is an RNA transcript of known…

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Research Fellow, Precision Medicine job with NATIONAL UNIVERSITY OF SINGAPORE

Job Description The NUS Resilience & Growth Research Fellow (NUS R&G-RF) will be responsible to work closely with the Principal Investigator and study team members to ensure the successful completion of industry-linked non-coding RNA (ncRNA) biomarker discovery research projects and subsequent functional validation of the identified ncRNA biomarkers in a…

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Integrated DNA Technologies hiring Bioinformatics Staff Scientist in Boston, Massachusetts, United States

IDT is the leading manufacturer of custom oligonucleotides and proprietary technologies for genomics applications. Our work is complex and cutting-edge, and our team members are curious, creative thinkers who understand that good data drives smart decisions. At IDT, we realize that although science may be uniform, people are unique. We…

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Bioinformatics Scientist – Houston | Mendeley Careers

NuProbe USA is hiring two NGS Bioinformatics Scientists for its Houston (TX) location. NuProbe is the US-based R&D subsidiary of NuProbe Global, a company devoted to the development of novel non-invasive DNA and RNA diagnostic assays. Currently, NuProbe has several products based on NGS, qPCR, and sanger technologies. The Innovation…

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dbCAN-PUL

dbCAN-PUL PULID Characterization Method(s) Substrate Organism Publication Publish Date Type Num Genes Num CAZymes CazyFamily PUL0046 NMR, sequence homology analysis O-antigen Escherichia coli 29738687 O-Antigens of Escherichia coli Strains O81 and HS3-104 Are Structurally and Genetically Related, Except O-Antigen Glucosylation in E. coli HS3-104. Biochemistry (Mosc). 2018 May;83(5):534-541. doi: 10.1134/S0006297918050061….

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Bioconductor – HTqPCR

Automated analysis of qPCR data Bioconductor version: 2.5 Analysis of Ct values from quantitative real-time PCR (qPCR) assays. Data can be analyzed in high throughput across multiple conditions or replicates, and in spatially-defined formats such ABI TaqMan Low Density Arrays and conventional 96- or 384-well plates. HTqPCR handles data loading,…

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New bioinformatics method for viral sgRNA analysis

Single guide ribonucleic acid (sgRNA) molecules are produced by discontinuous transcription, in which viral RNA-dependant RNA polymerase pauses early negative-sense RNA synthesis and then jumps to the other end of the genome. The specifics of this process are still not fully understood. Since sgRNAs can play an important role in…

Continue Reading New bioinformatics method for viral sgRNA analysis

26S rRNA gene is not useful for identifying Saccharomycodes ludwigii by qPCR

Through intensive research and development, quantitative polymerase chain reaction (qPCR) has emerged as a dominant tool for precision clinical detection of many pathogenic microbial species in difficult-to-analyse sample matrixes. The method requires precise and specific targeting of unique species-identifying regions of particular gene in a microbe. To do this, species-specific…

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Single-cell expression quantitative trait loci (eQTL) analysis of SLE-risk loci in lupus patient monocytes

This article was originally published here Arthritis Res Ther. 2021 Nov 30;23(1):290. doi: 10.1186/s13075-021-02660-2. ABSTRACT BACKGROUND: We performed expression quantitative trait locus (eQTL) analysis in single classical (CL) and non-classical (NCL) monocytes from patients with systemic lupus erythematosus (SLE) to quantify the impact of well-established genetic risk alleles on transcription…

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DNA Script Receives CE Mark for Syntax Enzymatic DNA Synthesis Platform

NEW YORK – DNA Script said on Tuesday that it has received CE marking for its Syntax enzymatic DNA synthesis platform, clearing the way for the benchtop DNA printer’s commercial sales in Europe. The CE marking covers the benchtop instrument, reagents, and consumables, the firm said. The Syntax platform can…

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Single-cell expression quantitative trait loci (eQTL) analysis of SLE-risk loci in lupus patient monocytes | Arthritis Research & Therapy

Patients and samples Whole blood samples from 15 Female SLE patients fulfilling the American College of Rheumatology criteria for the diagnosis of SLE [11, 12] and five age-sex matched healthy controls were procured from the Mayo Clinic, Rochester, MN. Exclusion criteria included pregnancy, active acute infection, chronic infection (e.g., hepatitis…

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A CRISPR/Cas12a-based DNAzyme visualization system for rapid, non-electrically dependent detection of Bacillus anthracis

Introduction Anthrax, a serious zoonotic disease, is caused by Bacillus anthracis. Because B. anthracis spores can be used as biological warfare and terrorism agents, the development of sensitive, efficient detection methods for this pathogen is important and urgently needed. Currently, B. anthracis is detected by identifying its vegetative cells and…

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Will Kallisto show a decrease in the TPM value if I have knocked out 2 of the 8 exons from a gene?

Will Kallisto show a decrease in the TPM value if I have knocked out 2 of the 8 exons from a gene? 0 Hello, I was wondering if Kallisto will show a decrease in the TPM value if I have knocked out 2 of the 8 exons from a gene?…

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Construction of a circRNA-miRNA-mRNA Regulated Pathway Involved in EGFR-TKI Lung Adenocarcinoma Resistance

1 Introduction Lung cancer is the leading cause of cancer-related deaths worldwide, with adenocarcinoma as the most common histological subtype.1 In recent years, epidermal growth factor receptor-tyrosine kinase inhibitors (EGFR-TKIs), such as gefitinib (first generation) and osimertinib (third generation), have been widely used for lung adenocarcinoma patients harboring activated EGFR…

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Pulmonary Infection Revealed by Metagenomic NGS

1Department of Biomedical Engineering, College of Life Science and Bioengineering, Beijing University of Technology, Beijing, People’s Republic of China; 2Department of Clinical Laboratory, Beijing Capitalbio Medlab, Beijing, People’s Republic of China Background: Treatment of pulmonary infections in the intensive care unit (ICU) represents a great challenge, especially infections caused by…

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TANK prevents IFN-dependent fatal diffuse alveolar hemorrhage by suppressing DNA-cGAS aggregation

Abstract Diffuse alveolar hemorrhage (DAH) is one of the serious complications associated with systemic lupus erythematosus, an autoimmune disease whose pathogenesis involves type I IFNs and cytokines. Here, we show that TANK, a negative regulator of the NF-κB signaling via suppression of TRAF6 ubiquitination, is critical for the amelioration of…

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Serial dilutions on qPCR should be compulsory ? What if I do have data without serial dilution? Objectively compute CT values.

Dear community, Let me put in context my question: I am working with qPCR to detect the absence/presence of a certain mutation in a given gene. However, the laboratorians that give me the data do not make serial dilutions on the input DNA samples, nor on the internal control. So…

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Data scientist bioinformatics, Singapore – Job Dispatch

Data Scientist (Bioinformatics) Our client is an emerging Biotech company that specialises in oncology diagnostics products. Responsibilities: In-depth data analysis with machine learning and statistical methods Identify novel DNA/RNA/ncRNA biomarkers Develop models for multi-marker diagnostic test Facilitate the design and execution of the experiment, the process set up and quality…

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Zhang Jin’s group reported that rRNA biogenesis regulates the fate transition of mouse ES-2C-like cells

On November 9, 2021, the Stem Cell and Regenerative Medicine Center of the Department of Basic Medicine, Zhejiang University School of Medicine/The First Affiliated Hospital of Zhejiang University School of Medicine/Zhejiang Liangzhu Laboratory Zhang Jin’s research group published a titled ” rRNA Biogenesis ” in Nature Communications . Regulates Mouse…

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Dura cells in the etiopathogenesis of Crouzon syndrome: the effects of FGFR2 mutations in the dura cells on the proliferation of osteoblasts through the hippo/YAP mediated transcriptional regulation pathway

Background: FGFR2 (fibroblast growth factor receptor 2) mutations are implicated in the etiopathogenesis of syndromic craniosynostosis, and C278F- or C342Y-FGFR2 mutations can lead to Crouzon syndrome. The dura mater exerts crucial effects in the regulation of cranial suture development. However, the underlying mechanisms of these biological processes are rarely studied….

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Quantitative assessment reveals the dominance of duplicated sequences in germline-derived extrachromosomal circular DNA

Significance Extrachromosomal circular DNA (eccDNA) plays a role in human diseases such as cancer, but little is known about the impact of eccDNA in healthy human biology. Since eccDNA is a tiny fraction of nuclear DNA, artificial amplification has been employed to increase eccDNA amounts, resulting in the loss of…

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Transcriptome Sequencing Explores the Mechanism of Baicalin on Bone Ca

Introduction With the continuous improvement of cancer treatment technology, the 3-year and 5-year survival rates of cancer patients have been greatly improved. However, cancer still cause pain to the patients, which seriously affects their quality of life. This is because in many common cancers, tumors can easily metastase to the…

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Bioinformatics NGS Data Analyst position in Andover, Massachusetts

Job Description: Position Summary: The qualified candidate will join the Analytical Research and Development Microbiology and Strategy Testing organization in Andover, MA, a QC (GMP) laboratory that supports biotherapeutic clinical manufacturing. Candidate will report directly to Microbiology Group Leader (Principal Scientist, Ph.D.). We are recruiting an expert…

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RNA-Seq and qPCR

RNA-Seq and qPCR 0 Greetings! For a rice gene LOC_Os06g51060 Relative (to control group) Log2FC values obtained by qPCR and RNA-Seq are as follows: See here: There is a difference in values as well a TREND. I have quite a few other such genes and this problem has effected them…

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Blackhawk Genomics Announces Launch of HerediSeq and PanSeq Genomic Analysis Kits

SAN FRANCISCO (PRWEB) November 16, 2021 Blackhawk Genomics LLC, a molecular diagnostics technology company, today announced the launch of the HerediSeq and PanSeq genomic analysis kits designed to detect structural variants and elucidate difficult-to-characterize genomic regions using long-read sequencing. HerediSeq chemistry resolves deletions and duplications, repetitive regions and pseudogenes,…

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Canine Somatic Cell Reprogramming and Its Facilitation through Inhibition of Endogenous p53

Numerous efforts have been made to establish bona fide iPSCs from companion animals such dogs and cats. Generation of iPSCs from companion animals would provide useful unrestricted cell resources with a vast scientific potential. To name a few applications, they can be exploited as new models for regenerative medicine and as therapeutic…

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Research Associate, Cell Engineering – Philadelphia

Position Title: Research Associate, Cell Engineering Position Level: Research Associate/Sr. Research Associate Reports to: Shelby Keating, Scientific Associate Company Background: Century Therapeutics is developing novel allogeneic living cell products for oncology that overcome the limitations of current cell therapies. Century’s genetically-engineered, universal iPSC-derived immune effector cell products are designed to…

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Multiple stages of evolutionary change in anthrax toxin receptor expression in humans

Human research participants We have complied with all relevant ethical regulations and informed consent was obtained from all participants. This work was approved by the Cornell University IRB under protocol 1506005662. Animal research This work was approved by the Cornell University IACUC under protocol 2009-0044. Welfare and handling of all…

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Hairpin structure facilitates high-fidelity DNA amplification reactions in both qPCR and high-throughput sequencing

Abstract Effective polymerase chain reactions (PCR) are important in bio-laboratories. It is essential to detect rare DNA-sequence variants for early cancer diagnosis or for drug-resistance mutations identification. Some of the common detection quantitative PCR (qPCR) methods are restricted in the limit of detection (LoD) because of the high polymerase misincorporation…

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In Brief This Week: Caris Life Sciences, Psomagen, Tempus, CareDx, HTG Molecular, Epigenomics, More

NEW YORK – Caris Life Sciences said this week that the Georgia Cancer Center at Augusta University has joined its Precision Oncology Alliance, a collaborative network of 55 leading cancer centers and academic institutions seeking to advance comprehensive cancer profiling and establish standards of care for molecular testing in oncology….

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Assessment of CircRNA Expression Profiles and Potential Functions in Brown Adipogenesis

doi: 10.3389/fgene.2021.769690. eCollection 2021. Affiliations Expand Affiliations 1 Department of Biotechnology, College of Life Sciences, Xinyang Normal University, Xinyang, China. 2 Institute of Animal Science and Veterinary Medicine, Hainan Academy of Agricultural Sciences, Haikou, China. 3 Institute for Conservation and Utilization of Agro-Bioresources in Dabie Mountains, Xinyang Normal University, Xinyang,…

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CRISPR-Cas9 Mediated Exonic Disruption for HIV-1 Elimination

Abstract Background A barrier to HIV-1 cure rests in the persistence of proviral DNA in infected CD4+ leukocytes. The high HIV-1 mutation rate leads to viral diversity, immune evasion, and consequent antiretroviral drug resistance. While CRISPR-spCas9 can eliminate latent proviral DNA, its efficacy is limited by HIV strain diversity and…

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MBE presentaties transformation/electroporation, PCR, AKTA, IC/50 –

Presentaties in het engels voor de onderwerpen transformation/electroporation, PCR/qPCR, A…Bekijk meer Geüpload doorBob Wildema Academisch jaar 2021/2022 Nuttig?10 Delen Reacties Log in of registreer om reacties te kunnen plaatsen. Studenten bekeken ook LABJOURNAAL MBE MBE PT1B – Dit zijn de voorbereidende PT’s Pt 3 mbe – Dit zijn de voorbereidende…

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DNA Script on Track for Release of Enzymatic DNA Synthesis Platform in 2022

NEW YORK – DNA Script is expanding its operations and is on track to commercially launch its Syntax enzymatic DNA synthesis platform early next year after gathering feedback from early-access users at the Broad Institute and elsewhere. Last month, the French company, which has locations in Paris and South San…

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The Shh/Gli3 gene regulatory network precedes the origin of paired fins and reveals the deep homology between distal fins and digits

Significance In this study, we show that the inactivation of the gli3 gene in medaka fish results in the formation of larger dorsal and paired fins. These mutant fins display multiple radial bones and fin rays which resemble polydactyly in Gli3-deficient mice. Our molecular and genetic analyses indicate that the…

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Laniakea@ReCaS: exploring the potential of customisable Galaxy on-demand instances as a cloud-based service | BMC Bioinformatics

Since the opening of the open-ended Call in February 2020 [30], Laniakea@ReCaS has accepted ten project proposals for a total of 18 Galaxy instances operating on the ReCaS infrastructure that altogether launched almost 30 k jobs, as of March 2021 (Fig. 3). Fig. 3 Cumulative number of jobs launched by all the…

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Transcription factor binding sites and variants around cis-regulaory elements

Hello, I need your help regarding transcription factors and their gene targets (association with protein coding genes). What do I have? List of several protein coding genes and experimentally confirmed variants located in their cis-regulatory elements (CREs), up to 3kbp from TSS in cancer cell lines. What do I want…

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Technical officer in Bioinformatics (m/f) at LNS

TECHNICAL OFFICER IN BIOINFORMATICS (M/F) Type of contract: Full-time and determined duration contract (CDD) The Laboratoire national de santé (Luxembourg public institution) is recruiting a Technical officer in Bioinformatics (m/f) for the Department of Microbiology in a full time position (40h/week) with a fixed-term contract of 12 months (ending 30 september 2022). About the Laboratoire…

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Researchers Develop CRISPR-based Rapid Diagnostic Tool for SARS-CoV-2

Study lead author Dan Brogan (left) and coauthor Calvin Lin review results from a SENSR reaction using a light cycler qPCR machine. Photo by Michelle Fredricks, UC San Diego Physical Sciences Blending experts from molecular genetics, chemistry and health sciences, researchers at the University of California San Diego have created a…

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ARGs as potential biomarkers & therapeutic targets in AF

Introduction Atrial fibrillation (AF) is the most common clinically sustained cardiac rhythm disorder. There is a high prevalence of AF all over the world, the highest in North America, Europe, China, and Southeast Asia, with approximately 270–360 cases per 100,000 people.1 Due to the lack of understanding of the pathogenesis…

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Phosphorus hiring DNA Sequencing Laboratory Technician in Secaucus, New Jersey, United States

Company OverviewAt Phosphorus, our mission is to extend and improve lives by making genomics a foundational part of everyone’s health and wellness journey. We have built a verticalized genetic testing platform, from wet lab chemistry to software and bioinformatics, allowing us to provide the most comprehensive, medical-grade genetic tests at…

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Recruitment of Research Associate/Senior Research Associate at IDEAYA Biosciences, San Francisco

About IDEAYA Biosciences: Biotechnology company IDEAYA Biosciences (NASDAQ: IDYA) develops synthetic lethality-focused precision medicine for cancer patients using DNA sequencing and other molecular diagnostics. The company is publicly traded. Small molecule drug discovery is integrated with biomarker identification and validation to identify patient populations most likely to benefit from the…

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New Products Posted to GenomeWeb: Roche, Jumpcode Genetics, Mikrogen, More

Roche Avenio Tumor Tissue Comprehensive Genomic Profiling Kit Roche has launched its Avenio Tumor Tissue Comprehensive Genomic Profiling (CGP) Kit for research use. The jointly developed project from Roche and Foundation Medicine delivers information about complex genomic signatures, including tumor mutational burden, microsatellite instability, and loss of heterozygosity, in addition…

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normalization – What statistics can I use on qPCR data composed of several runs if all normality tests fail on the dataset?

I have >100 qPCR experiments that I’d like to analyze together, each containing the same set of genes (10 genes of interest and 2 reference genes). I have four different samples (untreated & 3 treatments) from the same cell culture. Our setup allows two of them to be run at…

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Intergenerational Effects of Maternal Obesity on Offspring Mitochondrial Reactive Oxygen Species Production and DNA Damage

Abstract: Epidemiological studies have shown that offspring from pregnancies complicated by maternal obesity have a 4-fold greater risk for developing childhood obesity and symptoms of metabolic syndrome. The developmental origins of health and disease (DOHaD) hypothesis states that certain environmental exposures during critical windows of development may have consequences for…

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HTqPCR – Multiple plates for multiple samples: How made a correct pData?

I have a set of seven files from runs on 48 low-throughput qpcr system. So, our runs have 48 max samples. In fact, we have 30 reactions per run. Our file is like this: File1.csv 1 10-A1-C C9 1 IDH Endogenous Control 12.6929092407226 2 10-A1-C C10 1 IDH Endogenous Control…

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Single-cell Analysis of Genome Engineering | Learning Center

ENGINEERED CELLS & SINGLE-CELL ANALYSIS Many of today’s cutting-edge research methods and therapies rely on the engineering of cells. By precisely altering DNA, genome engineering makes it possible to probe the relationship between a gene and its function, repair dysfunctional genes, or add functionality to cells. Changing the genome often involves…

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LncRNA MIAT services as a noninvasive biomarker

Introduction BC is the most common cancer among women that is responsible for the most of the cancer-related death in worldwide.1 The occurrence of BC accounts for 7–8% of the entire number of malignant tumors.2 Accumulating evidence have shown that immunoreaction plays an important role in oncogenesis and progression.3,4 However,…

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Severe trauma and burns accompanied by sepsis

Introduction Trauma accounts for approximately 10% of deaths and 16% of disabilities worldwide.1 Billions of dollars have been spent on research into new biological therapeutics for severe injuries, as well as post-traumatic sepsis and septic shock.2 Burn injuries cause unpredictable trauma and sepsis is a complication associated with high morbidity…

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qPCR primer design for multiple transcript variants

qPCR primer design for multiple transcript variants 0 Hello, I am a little new to NCBI tools and can’t quite wrap my head around primer design on the website. I am trying to design primers to run single-step qPCR for one gene’s expression. There are 3 transcript variants, all of…

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Danaher Jobs – Bioinformatics Specialist in Shanghai, China

Three years of prior sales experience required; preferably in life science reagents/consumables. Proven track record of meeting or exceeding sales targets for at least 2 years required. Residing in the assigned region and extensive familiarity with existing academic, corporate, and government accounts in the region required. Applications experience within NGS,…

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very different outputs from rMATS vs altanalyze

alternative splicing: very different outputs from rMATS vs altanalyze 0 We are comparing two RNA-seq datasets (read length = 150nt, depth = 50M reads, 2 conditions, n = 4 per condition) for alternative splicing. I used rMATS and altanalyze to find alternative splicing events. However, there is very little overlap…

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