Tag: RT-qPCR
A fast, highly sensitive, point-of-care RT-LAMP and CRISPR/Cas12a assay for the detection of SARS-CoV-2 & More Breaking News
In a latest research posted to the Research Square* preprint server, researchers used isothermal amplification with clustered often interspaced brief palindromic repeats (CRISPR)-Cas12a to detect extreme acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Study: Rapid, multiplex detection of SARS-CoV-2 utilizing isothermal amplification coupled with CRISPR-Cas12a. Image Credit: creativeneko/Shutterstock Background To…
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…
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…
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…
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…
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…
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…
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…
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…
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,…
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…
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,…
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…
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…
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…
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…