Tag: GC

By Kiana Aran, PhD The adoption of CRISPR-Cas systems in therapeutics development has led to the rapid emergence of several clinical candidates for treating rare and challenging diseases, including sickle-cell anemia, β-thalassemia, Duchenne muscular dystrophy, and ocular diseases. Translation into the clinic has been facilitated by a robust preclinical framework…

Isolation, characterization and classification of BC-producing strain Isolation of single clones from CaCO3 halo zones in Glucose-Yeast Extract-Calcium carbonate agar and iterated subculturing in HS-Glu agar resulted in enrichment of an isolate with beige-coloured, smooth-edged and umbonate shaped colonies characteristics (Fig. S1A). The isolate is hereafter called ‘ENS15’. Under 100X magnification,…

Why do Illumina 850k/EPIC arrays ignore CpGs which are “GC” in the forward strand? 0 CpGs are symmetrical, in that a CG sequence on the forward strand is hybridized to a GC — and both dinucleotides on each opposing strand are CpGs dinucleotides which can be methylated. Conversely, CpGs can…

How to check gene properties (eg GC, repetitiveness, average expression level)? 0 Hello, I am trying to compare the data from 2 sequencing machines. I aligned my data with Kallisto and then I performed DESeq2 like I normally do. I was checking to see if I was getting similar results…

Forensic Technologies Market: Introduction According to the report, the global forensic technologies market was valued at US$ 51.6 Bn in 2020 and is projected to expand at a CAGR of 13.2% from 2021 to 2028. The forensic technology refers to the scientific system of searching, investigating, retrieving, and analyzing the evidence gathered…

Ethics statement All procedures involving laboratory mice were approved by the Duke University IACUC under the protocol numbers A189-18-08 and A142-21-07. Mice were housed with up to five mice per cage and the ambient room conditions ranged from 70–74 °F and 30–70% humidity with a 12-hour dark/light cycle. Animals were assessed…

Ai H, Fang X, Yang B, Huang Z, Chen H, Mao L et al. (2015) Adaptation and possible ancient interspecies introgression in pigs identified by whole-genome sequencing. Nat Genet 47:217–225 CAS  PubMed  Article  Google Scholar  Alexander DH, Lange K (2011) Enhancements to the ADMIXTURE algorithm for individual ancestry estimation. BMC…

Methylation is one of the most classical epigenetic modifications in eukaryotes. DNA methylation regulates gene expression and has important implications in both growth and disease-related research. DNA methylation affects the maturation of germ cells or embryonic cells subject to specific gene expression. It has also been widely studied and applied…

Who here has heard of an aptamer? Most people by now would have heard of RNA and are likely to have been the recipient of a strand or two thanks to COVID vaccines. Macugen was the first RNA biotherapeutic approved by the US Food and Drug Administration (FDA) in 2004,…

Features of the newly sequenced Petrocodon and Primulina plastomes Sizes of the nine newly sequenced plastomes of Petrocodon and Primulina range from 152,323 bp in Pr. medica (D.Fang ex W.T.Wang) Yin Z.Wang to 153,786 bp in Pr. cordata Mich.Möller & A.Weber (Tables 1, S1). These nine plastomes display the typical quadripartite structure…

NEW YORK – Results from single-cell RNA sequencing libraries run on the new Ultima Genomics UG100 are “very similar” to those produced on Illumina’s NovaSeq, a new study says. However, the platform shows bias against 3′ gene expression libraries. Led by researchers from the Broad Institute as part of a…

trimmomatic 0 Hello, Which parameter in trimmomatic is most suitable for rectify per sequence GC content, sequence duplication level, and over represented sequences. Your suggestions will be highly appreciated!! fastqc trimm trimmomatic • 166 views Login before adding your answer. Read more here: Source link

Merlino, C. P. Bartolomeo Bizio’s letter to the most eminent priest, Angelo Bellani, concerning the phenomenon of the red-colored polenta [translated from the Italian]. J. Bacteriol. 9, 527–543 (1924). Grimont, P. A. D. & Dulong de Rosnay, H. L. C. Numerical study of 60 strains of Serratia. J. Gen. Microbiol….

Use drop-down controls below and press refresh to alter tracks displayed.Tracks with lots of items will automatically be displayed in more compact modes.    Custom Tracks H3K27ac Meta NeuN SCZhidedensesquishpackfull H3K27ac NeuN SCZ del_CRDhidedensesquishpackfull H3K27ac NeuN SCZ del_CRD_del_peakshidedensesquishpackfull H3K27ac Tissuehidedensesquishpackfull H3K27ac Tissue BDhidedensesquishpackfull H3K27ac Tissue BD del_CRDhidedensesquishpackfull H3K27ac Tissue BD…

A stop codon is a sequence of three nucleotides (a trinucleotide) in DNA or messenger RNA (mRNA) that signals a halt to protein synthesis in the cell. There are 64 different trinucleotide codons: 61 specify amino acids and 3 are stop codons (i.e., UAA, UAG and UGA). What are the…

Patrick Murphy Bulk RNA-Seq – HackMD        owned this note   Published Linked with GitHub — title: ‘Patrick Murphy Bulk RNA-Seq’ disqus: hackmd — Patrick Murphy bulk RNA-Seq Analysis === ## Table of Contents [TOC] ## 1. Introduction This is a bulk RNA-Seq project, which includes human data….

Research Paper Advance Articles Changan Zhao1,2, *, , Jiyu Miao3, *, , Ruifang Sun1, *, , Rui Liang4, , Wenhu Chen5, , Yi Gao6, , Xiaofei Wang2, , Shuiping Han1, , Wenbao Zhao1, , Ting Lei1, , Chen Huang2,7, , 1 Department of Pathology, School of Basic Medical Sciences, Xi’an…

Increased GC content after trimming RNAseq data 0 Hi, I’ve trimmed rnaseq data (PE 100bp reads) thanks to trimgalore ro remove adapters. After trimmming I’ve noticed an increased on GC content (see below), specifically for reverse reads, and for high value of GC %. I’m having trouble to understand where…

Mapping molecular changes across malignant transformation We generated single-cell data for 81 samples collected from eight FAP and seven non-FAP donors (Fig. 1a and Supplementary Tables 1 and 2). For each tissue, we performed matched scATAC-seq and snRNA-seq (10x Genomics). We obtained high-quality single-cell chromatin accessibility profiles for 447,829 cells…

Bailliard F, Anderson RH. Tetralogy of Fallot. Orphanet J Rare Dis. 2009;4:2. Article  Google Scholar  Jin SC, Homsy J, Zaidi S, Lu Q, Morton S, DePalma SR, et al. Contribution of rare inherited and de novo variants in 2,871 congenital heart disease probands. Nat Genet. 2017;49:1593–601. CAS  Article  Google Scholar …

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…

Reporting results from fastp Read GC content 1 Hi, I have some QC results for a Paired end seq before and after filtering (Mouse samples). I am unable to interpret the plot Read GC content and I am not sure if the results are fine in this case. I am…

This protocol describes the extraction of volatile organic compounds from a biological sample with the vacuum-assisted sorbent extraction method, gas chromatography coupled with mass spectrometry using the Entech Sample Preparation Rail, and data analysis. It also describes culture of biological samples and stable isotope probing. This protocol allows us to…

GUANGZHOU, China–(BUSINESS WIRE)–LintonPharm Co., Ltd., a China-based biopharmaceutical company focusing on the development of T cell engaging bispecific antibodies for cancer immunotherapy, announces that preliminary results of Catumaxomab for advanced Gastric Cancer (GC) with peritoneal metastasis is published online at the 2022 American Society of Clinical Oncology (ASCO) Annual Meeting….

Long non-coding RNAs (lncRNAs) are a class of RNAs that do not code for proteins and are typically greater than 200 nucleotides in length. Studies have shown that lncRNAs are quite complex in function and play an important role in various biological processes such as development, differentiation, proliferation, metastasis, apoptosis,…

DMRs, how common are they and how long? 1 Hi! Does anyone know how common differentially methylated regions (DMRs) (or just methylated regions) are? Say, in a 10,000bp region how many DMRs can one expect? Also, does anyone know about the distribution of the size/length of DMRs, i.e. how many…

Need some help In C++, thanks!! /*Class Hierarchy Design a Class “Hierarchy” of 4 derived classes representing 4 generations of a family tree as follow:Grandparent -> Parent -> Child -> Grandchild Add a unique “trait” data member of type integer to EACH CLASS in the hierarchy: A, B, C, DNote…

Outcome of DNA sequencing, assembly, and validation In this study, initially total DNA was isolated from the finely chopped, full-grown pupa of Blepharipa sp. The NanoDrop spectrophotometer (1294 ng/μl) and the Qubit fluorometer (732.8 ng/μl) both found that the concentration of total DNA in the sample at an optimum level for mitochondrial DNA enrichment. The Tape Station profile showed…

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…

Goal Hi guys, is there an option to enable MBEDTLS debugging as with the CONFIG_MBEDTLS_DEBUG_LEVEL=4 for the MBEDTLS_BUILTIN? I am trying to setup a DTLS client based in order to establish a CoAP Secure Session via Openthread to a Borderrouter and I am struggling in the handshake process. It would…

Introduction Escherichia coli is a common Gram-negative opportunistic pathogen that causes invasive host infections through virulence factors such as flagella, toxin secretion, and adhesins. According to the source of the infection, pathogenic E. coli can be classified as intestinal (diarrheagenic) and extraintestinal (ExPEC). Uropathogenic E. coli (UPEC) is the most…

AllHigh-Throughput SequencingGenomicsProteomicsVisualizationOther QUAST Description (QUality ASsessment Tool) evaluates genome assemblies by computing various metrics, including N50, length for which the collection of all contigs of that length or longer covers at least 50% of assembly length; NG50, where length of the reference genome is being covered; NA50 and NGA50, where…

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…

Methods The study was conducted at the Human Genetics Unit, Faculty of Medicine, University of Colombo. It was an experimental study, where a novel assay was designed for the targeted variant, and a cohort of hormone receptor positive breast cancer patients were genotyped for the CYP2D6*10 variant using the optimized…

Symbol Name ACBD6 acyl-CoA binding domain containing 6 ACO2 aconitase 2, mitochondrial ADAMTS2 ADAM metallopeptidase with thrombospondin type 1 motif, 2 AK2 adenylate kinase 2 ALDH6A1 aldehyde dehydrogenase 6 family, member A1 AP1S1 adaptor-related protein complex 1, sigma 1 subunit AP4M1 adaptor-related protein complex 4, mu 1 subunit APH1A APH1A…

Introduction Rotator cuff tear (RCT) is a common shoulder disorder causing shoulder pain and disability. The prevalence of full-thickness RCT is 20.7% in the general population, and increased with age.1 Rotator cuff play essential roles in shoulder function and the treatment of proximal humeral fractures.2,3 It is important to repair…

ABSTRACT Background: Hepatitis C virus (HCV) related liver cirrhosis occurs in about 20% of chronically infected patients over a duration of 10–20 years, and within 5 years approximately 10–20% of these cirrhotic patients will develop hepatocellular carcinoma (HCC). Previous studies report that the X-ray repair cross-complementing group1 gene (XRCC1) is…

Circular RNAs (circRNAs) are a novel class of noncoding RNAs that play important roles in human diseases. However, the regulation of circRNAs in glucocorticoid-induced osteoporosis (GIOP) has not been reported. In this study, we performed high-throughput sequencing to identify altered circRNAs in the vertebrae from GIOP patients. A total of…

W. Hong et al. (12) previously demonstrated the utility of a CRISPR-Cas12a system in the low-GC Gram-positive organism C. difficile (12). As C. difficile and E. faecium have similar codon usage, we utilized Cas12a placed under the control of the tetracycline-inducible promoter (Ptet) from pRPF185 on the pMTL82151 backbone (pDL1,…

Only binary code can be understood and executed by computers. High–programmers use level programming languages like C, C++, Python, and Java. Because they mimic human languages and mathematical notation, such languages are easier to work with. On the other hand, Computers are unable to execute code written in a high–level…

Serratus alignment architecture Serratus (v0.3.0) (github.com/ababaian/serratus) is an open-source cloud-infrastructure designed for ultra-high-throughput sequence alignment against a query sequence or pangenome (Extended Data Fig. 1). Serratus compute costs are dependent on search parameters (expanded discussion available: github.com/ababaian/serratus/wiki/pangenome_design). The nucleotide vertebrate viral pangenome search (bowtie2, database size: 79.8 MB) reached processing rates…

Hello, can anyone offer any insight into the following problem? I am trying to run the following CIBERSORTx function locally: docker run -v /media/mark/seagate2/data/CIBERSORTx_GC:/src/data -v /media/mark/seagate2/data/CIBERSORTx_GC:/src/outdir cibersortx/fractions –username <my_user_name> –token <my_token> –single_cell TRUE –refsample reference.txt –mixture rsem_mixture_TPM.tsv –fraction 0 –rmbatchSmode TRUE I get the following output to the terminal: >Running…

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,…

#How to map to the assembled scaffolds.fasta bbmap is a powerful and highly flexible read mapper jgi.doe.gov/data-and-tools/bbtools/bb-tools-user-guide/bbmap-guide/. For the upcoming analysis you are not interested in the typical mapping output but in statistics on the coverage on every scaffold, you can get them with scaffstats. We want to be specific…

For Research Use Only. Do NOT use in humans or animals. This product is a OR8D1-shRNA encoding AAV, which is based on AAV-2 serotype. The OR8D1 gene encodes a olfactory receptor protein that interacts with odorant molecules in the nose, to initiate a neuronal response that triggers the perception of…

Name Last modified Size Description Parent Directory   –   duplication_levels.png 24-May-2014 17:58 17K   kmer_profiles.png 24-May-2014 17:58 433K   per_base_gc_content.png 24-May-2014 17:58 48K   per_base_n_content.png 24-May-2014 17:58 26K   per_base_quality.png 24-May-2014 17:58 32K   per_base_sequence_content.png 24-May-2014 17:58 96K   per_sequence_gc_content.png 24-May-2014 17:58 25K   per_sequence_quality.png 24-May-2014 17:58 19K  …

About Short intro Further reading How to cite Brief project history Authors Funding License and Terms of use Short intro QUAST evaluates genome assemblies by computing various metrics, including N50, length for which the collection of all contigs of that length or longer covers at least 50% of assembly length…

Average Read length 3 Hello Everyone! Is there a standard tool commonly used to calculate the average read length of fastq files? If yes please mention it here because I want to know the size of average reads of my fastq files so that I can decide the cutoff for…

Lichen fungi live in a symbiotic association with unicellular phototrophs and have no known aposymbiotic stage. A recent study postulated that some of them have lost mitochondrial oxidative phosphorylation and rely on their algal partners for ATP. This claim originated from an apparent lack of ATP9, a gene encoding one subunit…

Dataset The dataset we used for training, validation and testing is the DeepHF dataset [17]. We extracted 55604, 58617, 56888 sgRNAs with activity (represented by insertion/deletion (indel)) for WT-SpCas9, eSpCas9(1.1) and SpCas9-HF1, respectively, from its source data, and use the same partition method to divide train set and test set….

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:…

We wish you a good luck and have a prosperous career. Working at Labcorp | Jobs and Careers at Labcorp 15 GNeuS Postdoc Positions in Neutron Science of 24 Months Each (Full-time Job) FZJ – Forschungszentrum Jülich. What other similar jobs are there to Laboratory jobs in Germany? Clinical Laboratory…

TL;DR: I try to learn how to improve the prediction of spectra (mainly IR, UV/vis and NMR) and calculate Boltzmann weights from iMTD-GC calculations using CREST and I don’t really understand the software’s output. First question is for my comprehension, second one CREST specific, 3-5 general questions. CREST has been…

Hi Lucas, got a weird one for you. If I change the caller from hapotypecaller to freebayes, I get the error below. It’s doubly strange because it seems to occur well before freebayes would be used in the pipeline. [Sat Dec 11 11:13:02 2021] rule samtools_stats: input: dedup/111D03-1.bam output: qc/samtools-stats/111D03-1.txt…

Genome organization and structure of O. laetus The MiSeq data of BTI and CBE samples of O. laetus was submitted to the NCBI SRA database under the accession numbers SRR11024516 and SRR11024517, respectively. The study was done to understand whether there exists a different species of the genus Oxycarenus similar…

Introduction Alzheimer’s disease (AD) ranks first among the common dementia type of the world. According to epidemiological investigation from the International Alzheimer’s disease association, about 45 million people has been suffered from AD, and the number is expected to increase to 131 million in 2050.1 Despite the widespread prevalence of…

    This package is for version 2.9 of Bioconductor; for the stable, up-to-date release version, see flagme. Analysis of Metabolomics GC/MS Data Bioconductor version: 2.9 Fragment-level analysis of gas chromatography – mass spectrometry metabolomics data Author: Mark Robinson <mrobinson at wehi.edu.au> Maintainer: Mark Robinson <mrobinson at wehi.edu.au> Citation (from…

Listing Results Biopython Contact Map Protein Contact Maps using Biopython Warwick 9 hours ago Warwick.ac.uk View All Protein Contact Maps using Biopython. When working with protein 3D structures, a contact map is usually defined as a binary matrix with the rows and columns representing the residues of two different chains….

Alexander DH, Novembre J, Lange K (2009) Fast model-based estimation of ancestry in unrelated individuals. Genome Res 19:1655–1664 CAS  PubMed  PubMed Central  Article  Google Scholar  Alexander DH, Shringarpure SS, Novembre J, Lange K (2015) Admixture 1.3 software manual. UCLA Hum Genet Softw Distrib, Los Angeles Google Scholar  Angert AL, Bontrager…

HADDON TOWNSHIP, NJ — A man who was found deceased in Canada in 1983 has been identified as a missing Haddon Township man, authorities announced. The circumstances surrounding Theodore Frederick Kampf’s death remain suspicious, and the investigation into his death continues, according to the Royal Mounted Canadian Police. Kampf, of…

Introduction Diabetes is a very complex disease characterized by the presence of chronic hyperglycemia. Clinically, insulin-dependent type 1 and non-insulin-dependent type 2 are the main types of diabetes. Among them, type 2 diabetes mellitus (T2DM, [MIM125853]) is a common endocrine disorder affecting approximately 10% of adult population.1 In most cases,…

Introduction Carrión’s disease is a vector-borne biphasic illness restricted to the South American Andes, with Peru as the most affected country. 1 Gomes C Pons MJ Del Valle Mendoza J Ruiz J Carrion’s disease: an eradicable illness?. The causative agent, Bartonella bacilliformis, is transmitted to humans by sandflies (Lutzomyia spp)….

Hi all, To make a long story short, my lab has developed a computational method for analyzing WGBS data that results in genomic regions of interest. These are regions defined by sequencing reads with mixed methylation states (i.e. consecutive CpGs having non-matching methylation). My boss wants me to use some…

By Clarice Silber · September 9, 2021, 4:25 PM EDT CRISPR biotech startup Mammoth Biosciences has tapped the former top attorney for Sangamo Therapeutics Inc. to serve as its general counsel, an appointment that comes as the company earned so-called unicorn… Want to continue reading? Unlock these benefits today when…

Bacterial morphology details 1 hi, I have a list of bacteria (~ >2000), is there a data source or a way (other than manual literature study) i can get information like- its shape (cocci, rod or spiral), whether it is gram positive or negative and respiration detail (Anaerobic or Aerobic)….

Strategy and design of the method We sought to develop a simple method to increase the sequencing capability of PacBio CCS to sequence several diverse DNA libraries ~ 870 bp in length that encoded protein variants originating from a directed evolution campaign. To achieve an increase in the throughput of a PacBio sequencing…

A healthy soil nourishes plants and animals, purifies water and air, and promotes sustainable agriculture. Characteristic for highly complex and competitive soil ecosystems are the frequent and direct interactions between all soil-dwelling microorganisms, animals, and plants (1, 2), all of which need to be provided with minerals and carbon sources….

getting different value list from GATK gc content and CANOES 0 I was trying to run codes from this paper “A machine-learning approach for accurate detection of copy-number variants from exome sequencing” I need to get data from GATK GC content and CANOES and combined them, but I got a…

“Simplifing” a very fragmented genome for visualisation? 1 Hi there, I have a very fragmented reference genome that i want to visualize (with jbrowse or similar) this is the paper for the genome: link here the genome can be found: link2 here are the quast statistics: ######## QUAST Results ########…

Introduction Aural infections are one of the most common diseases of the head and neck and are predominantly caused by bacterial infections of the ear canal. Several studies from different countries have reported that Pseudomonas aeruginosa is the most common pathogen isolated from ear canal secretions, followed by Staphylococcus aureus.1…

DOI: 10.18129/B9.bioc.geecc     This package is for version 3.11 of Bioconductor. This package has been removed from Bioconductor. For the last stable, up-to-date release version, see geecc. Gene Set Enrichment Analysis Extended to Contingency Cubes Bioconductor version: 3.11 Use log-linear models to perform hypergeometric and chi-squared tests for gene…

TCGAbiolinks: which normalization before differential expression analysis (legacy=TRUE vs. legacy=FALSE) 1 Dear All, I am following the TCGAbiolinks tutorial for conducting differential expression analysis on TCGA data (“TCGAanalyze: Analyze data from TCGA” section). I have 2 questions about it. 1) I don’t understand the following: when dealing with legacy=TRUE data…

Introduction Klebsiella pneumoniae (K. pneumoniae) is an opportunistic pathogen and the leading cause of healthcare-associated infections.1 Multidrug-resistant (MDR) K. pneumoniae isolates are rapidly spreading, thus limiting the choice of antimicrobial agents for empiric treatment of infections caused by these microorganisms; hence, this is a public health challenge.2 Polymyxins are last-resort…

I am having some trouble with REditools2 (HPC-Reditools). In the original version of reditools there was a python script for de-novo prediction of editing sites from RNAseq data using a strategy outlined in Picardi et al 2012. I assumed reditools2 would have this same feature. However, after inputting the appropriate…

From amino acid sequence to DNA sequence using Reverse Translate software 3 Hi. I have Identified amino acid sequence motif using MEME. Now I want to know what is the DNA sequence corresponding to this amino acid sequence: KDEKIKEIFEDLAKEERNHY. It seems that the only software that does this conversion is…

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…

How to interpret bimodal distribution of GC-content for RNAseq and can it be remedied ? 0 A colleague of mine have got the following distribution of GC-content for RNAseq. How to interpret bimodal distribution of GC-content for RNAseq ? Does it mean some contamination ? Is there any method to…