Category: qPCR

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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Precision modeling of mitochondrial disease in rats via DdCBE-mediated mtDNA editing

Author Correction: Generation of somatic mitochondrial DNA-replaced cells for mitochondrial dysfunction treatment “ρ(-)”. Consequently, Figure 2(g) legend has been modified accordingly,. “MirCs were generated from mitochondrial disease patient-derived (7S) fibroblasts. (a) mtDNA CN during the procedure of MirC generation. Fibroblasts that received gene transfer, designated as 7S_ρ(-) were cultivated with…

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Senior Director / VP of Bioinformatics

A successful candidate will manage a team of bioinformaticians and ultimately be responsible for providing technical guidance on data generation and analysis for gene expression, genotyping, microarray, sanger sequencing, Next-Generation Sequencing, and other genomic platform data. Additional activities include designing and developing new assays and protocols for genomic applications. These…

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randomreads.sh adding abundances for metagenomic like distribution

randomreads.sh adding abundances for metagenomic like distribution 0 Hi, I have 9 genomes, I would like to produce a metagenome like distribution using randomreads.sh. I concatenated genome fasta files in one reference file. Then, ran as below. ../bbmap/randomreads.sh ref=simplified_catgenome.fasta out1=20M.read1.fastq out2=20M.read2.fastq length=125 paired=t metagenome=t genome=9 reads=20000000 However, I would like…

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Labcorp Employment – Senior Bioinformatics Scientist

jobitlyem Saturday, 9th Oct 2021 Job Description: Labcorp is recruiting a Sr Bioinformatics Scientist for a dynamic team in either Westborough, MA, Raleigh, NC or Atlanta, GA. This position can also be Remote based. She/He will improve understanding of biological measurements and assay performance, to design, develop and extend algorithms…

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Research Bioinformatician I – Applied Genomics Job Opening in Los Angeles, CA at Cedars-Sinai

JOB SUMMARY:Under close supervision, the Research Bioinformatician I performs general bioinformatics analysis and software support for projects involving in omics. The RBI will manage omic data including loading and querying data from database system and public repositories, and transform and merge multilevel omic data into user-friendly formats, assist in development,…

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Integrated DNA Technologies hiring Bioinformatics Staff Scientist in Coralville, Iowa, 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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Tumor Biology Lab Research Associate Job at UC San Diego Health

– Advertisement – Tumour Biology Lab Research Associate Job at UC San Diego Health Filing Deadline: Mon 10/18/2021 For the safety and well-being of the entire university community, the University of California requires, with few exceptions, that all students, faculty and staff be vaccinated against the COVID-19 virus before they…

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Frontiers | Free DNA and Metagenomics Analyses: Evaluation of Free DNA Inactivation Protocols for Shotgun Metagenomics Analysis of Human Biological Matrices

Introduction The advent of modern culture-independent bacterial DNA sequencing technologies allows to achieve an in-depth characterization of the microbial communities inhabiting the human and animal bodies as well as the microbial consortia residing in other environments (Browne et al., 2016; Milani et al., 2017). These innovative metagenomics approaches, such as…

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Quantitative PCR assay for detection of Helicobacter pylori

Introduction Helicobacter pylori is a common pathogen that infects nearly 50% of the global population.1 Infection with this pathogen causes chronic gastritis, which can cause chronic gastroduodenal diseases such as gastritis, gastric ulcer, duodenal ulcer, gastric cancer, and gastric mucosa-associated lymphoid tissue (MALT) B-cell lymphoma.2 Although H. pylori is the…

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Cis-acting mutation affecting GJA5 transcription is underlying the Melanotic within-feather pigmentation pattern in chickens

Significance The molecular mechanisms underlying pigmentation patterns in animals is to a large extent an unresolved mystery in biology. For example, compared with mammals, birds show a stunning diversity in pigmentation patterns. This study advances the knowledge concerning the mechanisms creating periodic pigmentation patterns in individual feathers. We show that…

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Mitochondrial DNA Copy Number in Rett Syndrome Caused by MECP2 Variants

Available online 4 October 2021 doi.org/10.1016/j.jpeds.2021.09.052Get rights and content Abstract Objective To determine changes of mitochondrial DNA (mtDNA) copy number in peripheral blood in Rett syndrome caused by methyl-CpG-binding protein-2 (MECP2) variants and explore the mechanism of mitochondrial dysfunction in RTT. Study design Female patients who were diagnosed as RTT…

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40th Anniversary Recollections & Predictions

To help celebrate GEN’s 40th Anniversary with this special October issue, we asked scientists and business professionals in academia and industry to give us their reflections, impressions, and insights on the biotechnology industry and the life sciences. We also queried them on what they believe the future might look like…

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CRISPR Gene Therapies: Assessing the Success of Gene Edits Using ddPCR

β-thalassemia is one of the most common autosomal recessive diseases in the world and researchers are seeking to produce a gene therapy to treat the condition. Scientists are applying a variety of strategies and techniques to correct the underlying genetic imbalance that causes β-thalassemia, including using CRISPR to correct the…

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Director for the Experimental Bioinformatics Laboratory (ref. PD/21/21) – Institute for Research in Biomedicine Barcelona – job portal

A) RESEARCH LABORATORIES · Barcelona Created in 2005 by the Generalitat de Catalunya (Government of Catalonia) and the University of Barcelona, IRB Barcelona is a Severo Ochoa Centre of Excellence–a seal that was awarded in 2011. The institute is devoted to conducting research of excellence in biomedicine and to transferring…

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Network plot from expression data in R using igraph

[last update: January 27, 2020] igraph allows you to generate a graph object and search for communities (clusters or modules) of related nodes / vertices. igraph is utilised in the R implementation of the popular Phenograph cluster and community detection algorithm (used in scRNA-seq and mass cytometry), and also in…

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bioinformatics data scientist

A light-hearted and analogy-filled companion to the authors’ acclaimed online course (coursera.org/course/bioinformatics), this book presents students with a dynamic approach to learning bioinformatics. * Proposes own bioinformatics projects that can improve our business * Acts as a bioinformatics leader in the projects in charge and provides appropriate and effective supports….

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Plasmodium falciparum is evolving to escape malaria rapid diagnostic tests in Ethiopia

Study design and data collection We performed a cross-sectional, multisite study in 11 districts along Ethiopia’s borders with Eritrea, Sudan and South Sudan, located within three of its nine administrative regions. On average, ten health facilities were selected from each district, including four districts of Amhara Region (northwest Ethiopia), six…

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Quercetin inhibits the proliferation of multiple myeloma cells by upregulating PTPRR expression

This article was originally published here Acta Biochim Biophys Sin (Shanghai). 2021 Sep 24:gmab128. doi: 10.1093/abbs/gmab128. Online ahead of print. ABSTRACT Multiple myeloma (MM) is an incurable disease characterized by malignant plasma cell clonal expansion in the bone marrow; therefore, inhibiting the proliferation of plasma cells is an important approach…

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Epistasis shapes the fitness landscape of an allosteric specificity switch

Computational design Protein modeling and design was performed with Rosetta version 3.5 (2015.19.57819)35,37. Python and shell scripts for generating input from Rosetta and analyzing from Rosetta are available at: github.com/raman-lab/biosensor_design The high-resolution TtgR structure co-crystalized with tetracycline was selected as the starting point for computational design (PDB: 2UXH)28. The structure…

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Persistent Systems hiring Bioinformatics Data Scientist – South SFO, CA in Santa Clara, California, United States

About PersistentWe are a trusted Digital Engineering and Enterprise Modernization partner, combining deep technical expertise and industry experience to help our clients anticipate what’s next. Our offerings and proven solutions create unique competitive advantage for our clients by giving them the power to see beyond and rise above. We are…

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MYO10 drives genomic instability and inflammation in cancer

INTRODUCTION Genomic instability often refers to the existence of a variety of DNA alterations, ranging from single nucleotide changes (such as base substitution, deletion, and insertion) to chromosomal rearrangements (e.g., gain or loss of a segment or the whole chromosome) (1). Loss of genome stability can lead to early onset…

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Dr. J. Curtis Nickel Urinary Microbiome Study Using MicroGenDX NGS Indicates Microbial Diversity Varies by Age and Gender | News

ORLANDO, Fla., Sept. 14, 2021 /PRNewswire-PRWeb/ — A study to help understand the implications of Next-Generation DNA Sequencing (NGS) in the diagnosis and treatment of Urinary Tract Infections (UTIs) and other inflammatory urological conditions has been completed, and results were presented at the September, 2021 AUA Conference. The study, a collaboration…

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Dr. J. Curtis Nickel Urinary Microbiome Study Using MicroGenDX NGS Indicates Microbial Diversity Varies by Age and Gender

MicroGenDX Logo The study, a collaboration between Dr. J. Curtis Nickel and MicroGen Diagnostics, identified some 643 microbial species among 211 healthy subjects (106 female and 105 male) using NGS, with significant differences in microbial diversity based on gender, age, and previous antibiotic use. ORLANDO, Fla. (PRWEB) September 14,…

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Genetic basis and adaptation trajectory of soybean from its temperate origin to tropics

Resequencing of soybean accessions from low latitudes To investigate the genomic basis for the natural variation in soybean adaptation to low latitudes, we conducted whole-genome resequencing of a panel of 329 soybean accessions collected from 15 countries and covering all soybean subgroups in which 165 accessions are from in low-latitude…

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Disabling de novo DNA methylation in embryonic stem cells allows an illegitimate fate trajectory

The mammalian genome is characterized by widespread methylation of cytosine residues. After fertilization, however, both maternal and paternal genomes undergo extensive demethylation, reaching a low point in the blastocyst (1⇓⇓–4). The embryo genome is then remethylated by the activity of de novo DNA methylation enzymes (5). Mouse embryonic stem (ES)…

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Outliers on DESEq2 Results

I have an RNAseq dataset, where one of the genes I intend to analyze has hundreds of counts ranging from 10 to 12, with a few counts > 9000. I process this data in Deseq2 and get that the gene is differentially expressed across several samples of interest. What can…

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Gene expression profiling of contralateral dorsal root gangl

Introduction Mirror-image pain (MIP) is a mysterious pain phenomenon which is accompanied with many clinical pain conditions.1 MIP develops from the healthy body region which is contralateral to the actual injured site.1–3 MIP is typically characterized by increased mechanical hypersensitivity on the uninjured mirror-image body side.4 It can be triggered…

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Advanced Enzymes to facilitate SARS-CoV-2 Research

Research focused on SARS-CoV-2 has become a primary focus in genomic and molecular biology fields. The availability of accurate, efficient, and consistent analytical tools, including new methods for screening and studying virus-host interactions, is critical. In this webinar we will discuss the latest advancements in thermostable DNA polymerases enabling sensitive…

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Startup BugSeq Bioinformatics Achieves High SARS-CoV-2 Detection Rate With Nanopore Sequencing

CHICAGO – Canadian startup BugSeq Bioinformatics has devised a method of detecting pathogens via metagenomic nanopore sequencing that the company says is more accurate and sensitive than PCR and microbial cultures. Notably, the technology does not need to target specific pathogens like PCR and microbial culture tests must. The firm…

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An epigenetic basis of inbreeding depression in maize

INTRODUCTION Charles R. Darwin documented inbreeding depression as growth disadvantages from self-fertilization compared to outcrossing in many plants (1). Prevailing hypotheses suggest that inbreeding depression results from the exposure of deleterious recessive alleles and/or loss of overdominant alleles due to increased homozygosity (2, 3) or reduced recombination frequency in some…

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Multiform antimicrobial resistance from a metabolic mutation

Abstract A critical challenge for microbiology and medicine is how to cure infections by bacteria that survive antibiotic treatment by persistence or tolerance. Seeking mechanisms behind such high survival, we developed a forward-genetic method for efficient isolation of high-survival mutants in any culturable bacterial species. We found that perturbation of…

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qPCR data analysis

qPCR data analysis 1 Hi All, We are currently using the Applied biosciences StepOne qPCR system. The software does not give us the SD, SEM, P-value for the expression profile. Is there any package in R, which can do data analysis with all the statistics involved? Please do let me…

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RT-qPCR really high fold change

RT-qPCR really high fold change 0 Hello everyone, I am getting really high gene fold change values for one of the gene of interest i.e. ~70000 folds. I am using SYBR green as a polymerase. Is this normal ? If something is wrong, how can I improve my experiment and…

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Bioconductor – unifiedWMWqPCR

DOI: 10.18129/B9.bioc.unifiedWMWqPCR     This package is for version 3.11 of Bioconductor; for the stable, up-to-date release version, see unifiedWMWqPCR. Unified Wilcoxon-Mann Whitney Test for testing differential expression in qPCR data Bioconductor version: 3.11 This packages implements the unified Wilcoxon-Mann-Whitney Test for qPCR data. This modified test allows for testing…

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Pericentromeric noncoding RNA changes DNA binding of CTCF and inflammatory gene expression in senescence and cancer

Significance During the aging process, senescent cells secrete inflammatory factors, causing various age-related pathologies. Thus, controlling the senescence-associated secretory phenotype (SASP) can tremendously benefit human health. Although SASP seems to be induced by the alteration of chromosomal organization, its underlying mechanism remains unclear. Here, it has been revealed that noncoding…

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Biostar Systems

Comment: STAR vs Novoalign IGV Browser visualization by chasem ▴ 10 That is good to know that it isn’t just my set of reads…still concerning, though. Comment: STAR vs Novoalign IGV Browser visualization by chasem ▴ 10 I was not expecting this — not sure what to make of it…

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normalization to “housekeeping” genes of RNAseq data vs qPCR result

normalization to “housekeeping” genes of RNAseq data vs qPCR result 1 It is relatively common to use “housekeeping” genes when performing qPCR experiments. I would like to know how common (or uncommon) that a gene expression found in RNAseq can be replicated with qPCR. Indeed, I usually get fairly comparable…

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