Tag: orf

A cell-based phenotypic library selection and screening approach for the de novo discovery of novel functional chimeric antigen receptors

Cell lines and culture Unless stated otherwise, all tumor target cell lines were sourced from the ATCC via LGC Standards. Human endogenous mesothelin (MSLN)-positive target cell lines H-226 (lung carcinoma, MSLN+, ATCC® CRL-5826™) and AsPC-1 (ATCC CRL-1682), and MSLN-negative Raji control cells (ATCC CCL-86) were cultured in RPMI-1640 Glutamax (Life Technologies,…

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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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AAV ShRNA Cloning Service – CD Biospeeds

AAV ShRNA Cloning Service AAV ShRNA Cloning Service Adeno-associated virus (AAV) is a type of parvovirus. Its genome is single-stranded DNA and has the ability to infect both dividing and non-dividing cells. Adenovirus or herpes virus is usually needed to help it replicate and expand in the…

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Chitosan Nanoparticles for Antiviral Drug Delivery

Introduction According to research conducted in many labs in the field of nanotechnology, particularly in nanomedicine, it appears that nanotechnology and nanomedicine should play an active role in treating and preventing the spread of Coronavirus Infectious Disease-19 (COVID-19).1–6 Polymeric nanoparticles, such as chitosan NPs,7 are one of the possibilities available…

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Human microRNA inhibits expression of pathogenic gene underlying facioscapulohumeral muscular dystrophy

Fig. 1: miR-675 targets the DUX4 ORF and 3′UTR. a RenLuc-DUX4-FL dual-luciferase reporter and CMV.H19 constructs, and U6.MIR675, H1.MIR675, U6.MIR675-3p, and U6.MIR675-5p miRNAs. RenLuc-DUX4-FL contains DUX4 ORF and 3′UTR sequences fused to Renilla luciferase after the stop codon. Exons 1–3 are indicated (Ex1,2,3). *SD5 indicates silent mutation of a cryptic…

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ncRNA | Free Full-Text | Common Features in lncRNA Annotation and Classification: A Survey

CONC 2006 SVM Eukaryotes (both protein-coding and non-coding genes) peptide length, amino acid composition, predicted secondary structure content, mean hydrophobicity, percentage of residues exposed to solvent, sequence compositional entropy, number of homologues, alignment entropy 10-fold CV on protein-coding: F1-score: 97.4% ☼ Precision: 97.1% ☼ Recall: 97.8% ◙ On non-coding: F1-score:…

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How to find the longest orf from a transcriptome

How to find the longest orf from a transcriptome 0 Hello, good day, sorry for the simplicity but, I have a super basic question. I have been trying to identify the longest ORF of a transcriptome for a long time, but from the previous failed attempts it seems that it…

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How to get the nucleotide sequence through ORF information?

How to get the nucleotide sequence through ORF information? 0 I have a file with ORF information, including the start position and end position on the chromosome. At first I wanted to create a bed file, and then use the getFastaFromBed of bedtools to get the sequence. But I found…

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EMBOSS transeq lines with “(REVERSE SENSE)” in not reverse sence translations(?)

EMBOSS transeq lines with “(REVERSE SENSE)” in not reverse sence translations(?) 0 Hi good day. Sorry, I have a silly doubt, if someone could help me I would really appreciate it. You see, I’m using EMBOSS’s transeq tool (something new for me) to translate an ORF file. When translating the…

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Emergence and expansion of highly infectious spike protein D614G mutant SARS-CoV-2 in central India

COVID-19 laboratory screening Nasopharyngeal/Nasal/Oropharyngeal swabs in viral transport medium (VTM) received from acute phase patients with defined symptoms, asymptomatic cases with contact history with positive patients/ travel history were processed for laboratory confirmation of SARS-CoV-2 at Defence Research and Development Establishment, (DRDE) Gwalior, M.P., India. These samples were referred for…

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High-purity production and precise editing of DNA base editing ribonucleoproteins

Abstract Ribonucleoprotein (RNP) complex–mediated base editing is expected to be greatly beneficial because of its reduced off-target effects compared to plasmid- or viral vector–mediated gene editing, especially in therapeutic applications. However, production of recombinant cytosine base editors (CBEs) or adenine base editors (ABEs) with ample yield and high purity in…

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DESeq2 with a small number of genes

DESeq2 with a small number of genes 1 Dear all, I am writing a program in order to study the coverage of only one sequence. To sum up the pipeline: Detect ORFs in the input sequence Align all reads on the sequence (bowtie), reads come from RNA-seq Count the number…

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New Mac program for molecular biologists

Tool:New Mac program for molecular biologists 12 I would like to present here a program – BioLabDonkey – for molecular biologists who are Mac users. This program is written from scratch in a language native for Mac – Swift. The program can be downloaded from mac App Store – apps.apple.com/us/app/biolabdonkey/id1470827582?ls=1&mt=12…

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