Tag: utr

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…

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

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…

Continue Reading circRNF13 Inhibits the Proliferation and Metastasis of Nasopharyngeal Carcinoma through SUMO2

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…

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

Home page

Home page The store will not work correctly in the case when cookies are disabled. JavaScript seems to be disabled in your browser. For the best experience on our site, be sure to turn on Javascript in your browser. Pioneer in Engineered Nucleases technologies from ZFNs and TALENs to CRISPRs…

Continue Reading Home page

Using whole exome data from different protocols

Using whole exome data from different protocols 1 We are doing whole exome sequencing for our samples to identify somatic mutation for a phenotype of our interest. We have used Agilent SureSelect Human All Exon V5+UTRs for some of our samples, and am planning to use Agilent SureSelect Human All…

Continue Reading Using whole exome data from different protocols

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,…

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

ncRNA | Free Full-Text | Current Status of Epitranscriptomic Marks Affecting lncRNA Structures and Functions

Non-Coding RNA 2022, 8(2), 23; doi.org/10.3390/ncrna8020023 (registering DOI) Non-Coding RNA 2022, 8(2), 23; doi.org/10.3390/ncrna8020023 (registering DOI) Received: 1 March 2022 / Revised: 21 March 2022 / Accepted: 25 March 2022 / Published: 28 March 2022 Round 1 Reviewer 1 Report In recent years, a great process has been made in the research…

Continue Reading ncRNA | Free Full-Text | Current Status of Epitranscriptomic Marks Affecting lncRNA Structures and Functions

AAV-delivered suppressor tRNA overcomes a nonsense mutation in mice

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  Li, C. & Samulski, R. J. Engineering adeno-associated virus vectors for gene therapy. Nat. Rev. Genet. 21, 255–272…

Continue Reading AAV-delivered suppressor tRNA overcomes a nonsense mutation in mice

High-throughput “dry and wet” experiments to explore the principles of optimal design of mRNA sequences

Today I share a preprint article Combinatorial optimization of mRNA structure, stability, and translation for RNA-based therapeutic uploaded by Rhiju Das on BioRxiv , to explore the universal rules for achieving mRNA stability and efficient expression. Barriers to mRNA therapeutics With rapid R&D capabilities and extensive R&D pipelines, especially in…

Continue Reading High-throughput “dry and wet” experiments to explore the principles of optimal design of mRNA sequences

Understanding signatures of positive natural selection in human zinc transporter genes

Datasets and populations We first compiled whole-genome sequencing data to analyze the patterns of variation in ZTGs on two geographical levels. Thus, we explored a worldwide dataset of 2,328 unrelated individuals representing 24 populations across Africa (AFR), Europe (EUR), East Asia (EAS), South Asia (SAS) and America (AMR), denoted as…

Continue Reading Understanding signatures of positive natural selection in human zinc transporter genes

Single-cell Iso-Sequencing enables rapid genome annotation for scRNAseq analysis

. 2022 Mar 3;220(3):iyac017. doi: 10.1093/genetics/iyac017. Affiliations Expand Affiliations 1 Institute of Ecology and Evolution, University of Oregon, Eugene, OR 97403, USA. 2 Presidential Initiative in Data Science, University of Oregon, Eugene, OR 97403, USA. Item in Clipboard Hope M Healey et al. Genetics. 2022. Show details Display options Display options…

Continue Reading Single-cell Iso-Sequencing enables rapid genome annotation for scRNAseq analysis

TargetScanHuman 7.1

TargetScanHuman 7.1 * broadly conserved = conserved across most vertebrates, usually to zebrafish  conserved = conserved across most mammals, but usually not beyond placental mammals TargetScan predicts biological targets of miRNAs by searching for the presence of conserved 8mer, 7mer, and 6mer sites that match the seed region of each…

Continue Reading TargetScanHuman 7.1

The Ribosomal Protein RpL22 Interacts In Vitro with 5′-UTR Sequences Found in Some Drosophila melanogaster Transposons

Mobility of eukaryotic transposable elements (TEs) are finely regulated to avoid an excessive mutational load caused by their movement. The transposition of retrotransposons is usually regulated through the interaction of host- and TE-encoded proteins, with non-coding regions (LTR and 5′-UTR) of the transposon. Examples of new potent cis-acting sequences, identified…

Continue Reading The Ribosomal Protein RpL22 Interacts In Vitro with 5′-UTR Sequences Found in Some Drosophila melanogaster Transposons

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,…

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

QuantSeq 3’ mRNA-Seq Library prep kits: Lexogen

QuantSeq 3’ mRNA-Seq Library Prep kits from Lexogen offers cost-efficient analysis of differential gene expression via 3’ mRNA-seq library preparation. Requiring fewer reads per samples and capable of multiplexing a high number of samples on a single sequencing lane, the 3’ mRNA-Seq technology simplifies your gene expression projects with no…

Continue Reading QuantSeq 3’ mRNA-Seq Library prep kits: Lexogen

Extract longest transcript or longest CDS transcript from GTF annotation file or gencode transcripts fasta file.

There are four types of methods to extract longest transcript or longest CDS regeion with longest transcript from transcripts fasta file or GTF file. 1.Extract longest transcript from gencode transcripts fasta file. 2.Extract longest transcript from gtf format annotation file based on gencode/ensembl/ucsc database. 3.Extract longest CDS regeion with longest…

Continue Reading Extract longest transcript or longest CDS transcript from GTF annotation file or gencode transcripts fasta file.

Floxed exon (Flexon): A flexibly positioned stop cassette for recombinase-mediated conditional gene expression

Significance Tools that afford spatiotemporal control of gene expression are crucial for studying genes and processes in multicellular organisms. Stop cassettes consist of exogenous sequences that interrupt gene expression and flanking site-specific recombinase sites to allow for tissue-specific excision and restoration of function by expression of the cognate recombinase. We…

Continue Reading Floxed exon (Flexon): A flexibly positioned stop cassette for recombinase-mediated conditional gene expression

Very important pharmacogene variants in the Blang population

Introduction The use of drugs should be different among diverse ethnic groups because of differences in ethnicity, age, sex, environmental factors and genetic factors. If these differences are ignored, then drug sensitivity, metabolic rate, and adverse reactions are affected, which influences the curative effect of drugs and aggravates the illness…

Continue Reading Very important pharmacogene variants in the Blang population

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…

Continue Reading Human microRNA inhibits expression of pathogenic gene underlying facioscapulohumeral muscular dystrophy

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:…

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

An assessment of pH-sensitive cationic lipid nanoparticles for drug delivery

A recent review in the Chemical and Pharmaceutical Bulletin looks at the molecular design of pH-sensitive cationic lipids and their applications for various tissues and cell types. The researchers also describe the application of lipid nanoparticles (LNPs) for delivering various macromolecules including small interfering ribonucleic acid (siRNA), antisense oligonucleotide, messenger…

Continue Reading An assessment of pH-sensitive cationic lipid nanoparticles for drug delivery

Easy Way To Get 3′ Utr Lengths Of A List Of Genes

Easy Way To Get 3′ Utr Lengths Of A List Of Genes 4 Hi, as the title says really, I’m wondering if there is any tool available that would allow me to drop in a list of say entrez gene ids and get their corresponding 3′ UTR lenghts? Thanks for…

Continue Reading Easy Way To Get 3′ Utr Lengths Of A List Of Genes

Doubts with Stacked barplot using R ggplot2

Doubts with Stacked barplot using R ggplot2 0 Hello! I am trying to plot some data using R but I am having some problems doing it. I have a data frame with two columns (genes and and type of mutation) and looks like: genes variant MLH1 Intronic ATR 5′ UTR…

Continue Reading Doubts with Stacked barplot using R ggplot2

Calculate the fraction of genome that is feature X

Calculate the fraction of genome that is feature X 2 I am trying to calculate enrichment of Structural variant breakpoints and SNV locations in genomic features (exon, intron, 5’UTR…) in a non-human genome. To know whether a feature is over/underrepresented in a SV/SNV dataset, I first need to know the…

Continue Reading Calculate the fraction of genome that is feature X

DAPARS2 generate region annotation output bed’s size is 0

DAPARS2 generate region annotation output bed’s size is 0 0 hello everyone, I want to generate region annotation using dapars2, but the output bed file’s size is zero, the bed file from the test data provided by dapars2 is also zero, the same as my data’s . Total extracted 3’…

Continue Reading DAPARS2 generate region annotation output bed’s size is 0

How to trim a GFF3 file based on specific coordinates?

How to trim a GFF3 file based on specific coordinates? 0 Hi, I would like to create a GFF3 file containing information only for specific coordinates from the chromosome level GFF3 file. I know how to extract gene and CDS info separately but don’t know how to do trimming based…

Continue Reading How to trim a GFF3 file based on specific coordinates?

How to create a BED12 file defining UTR sequences

Hello, I am doing an experiment and I need to build a BED12 file for some UTR sequences that I have. I have done a blast for those sequences and with that I was able to build a successful BED6 file, like this: 19 20752377 20758767 ENSDARG00000062634_Kat2b_Tscan 0 + 15…

Continue Reading How to create a BED12 file defining UTR sequences