Tag: GC
Single-cell analyses define a continuum of cell state and composition changes in the malignant transformation of polyps to colorectal cancer
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…
Joint analysis of functionally related genes yields further candidates associated with Tetralogy of Fallot
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 …
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…
Reporting results from fastp Read GC content
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…
Capturing Actively Produced Microbial Volatile Organic Compounds from Human-Associated Samples with Vacuum-Assisted Sorbent Extraction
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…
LintonPharm to Release Data on Catumaxomab for Advanced Gastric Cancer with Peritoneal Metastasis at 2022 ASCO Annual Meeting
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….
LncRNA Sequencing Helps to Find Deep Links to Disease
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?
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…
Solved Need some help In C++, thanks!! /*Class
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…
Mitogenome-wise codon usage pattern from comparative analysis of the first mitogenome of Blepharipa sp. (Muga uzifly) with other Oestroid flies
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…
Engineering and validation of a dual luciferase reporter system for quantitative and systematic assessment of regulatory sequences in Chinese hamster ovary cells
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…
Enable MBEDTLS debugging Nordic provided security backend (for CoAP Secure via OpenThread on nRF5340) – Nordic Q&A – Nordic DevZone
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…
Extensively drug resistant E. coli LZ00114
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…
QUAST – BioGrids Consortium – Supported Software
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…
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…
Design and implementation of a novel pharmacogenetic assay for the identification of the CYP2D6*10 genetic variant | BMC Research Notes
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…
Gene Set – TFDP2
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…
Fatty infiltration after rotator cuff tear
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…
Genetic variants of XRCC1 and risk of hepatocellular carcinoma in chronic hepatitis C patients: British Journal of Biomedical Science: Vol 76, No 2
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…
Comprehensive circRNA Analyses in Human Vertebrae of GIOP and Its Molecular Mechanism
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…
Rapid, Efficient, and Cost-Effective Gene Editing of Enterococcus faecium with CRISPR-Cas12a
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,…
Comparing Compiled and Interpreted Programming Languages
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…
Petabase-scale sequence alignment catalyses viral discovery
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…
CIBERSORTxFractions ERROR: Could not read /src/outdir//temp.Fractions.simfracs.tsv
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…
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,…
Secret BBMAP helper page – HRGV/Marmics_Metagenomics Wiki
#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…
shRNA Adeno-associated Virus Serotype 2, p7SK-(OR8D1-shRNA-Seq5) (AAV-SI3323WQ)
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…
Index of /readarchive/Miseq/2014_05_21_run_miseq/Adapter_trimmed_nextera_samples/QC_after_trimming/Geo33_S19.R1.trimmed.paired_fastqc/Images
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 QUAST
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
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…
Dryad Data — Lichen fungi do not depend on the alga for ATP production
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…
AttCRISPR: a spacetime interpretable model for prediction of sgRNA on-target activity | BMC Bioinformatics
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….
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:…
laboratory jobs in germany
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…
Improving IR, UV/vis and NMR calculations by CRE sampling : comp_chem
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…
[moiexpositoalonsolab/grenepipe] freebayes causes early error about number of threads
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…
Complete mitochondrial genome sequencing of Oxycarenus laetus (Hemiptera: Lygaeidae) from two geographically distinct regions of India
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…
Identification of Hub Genes in Patients with Alzheimer Disease and Obs
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…
Bioconductor – flagme
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…
Biopython Contact Map | Contact Information Finder
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….
Genome-wide analysis reveals associations between climate and regional patterns of adaptive divergence and dispersal in American pikas
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…
Remains Found In Canada Identified As Missing Oaklyn Man
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…
Mutational Analysis of Mitochondrial tRNA Genes
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,…
Identification of immunodominant Bartonella bacilliformis proteins: a combined in-silico and serology approach
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)….
Interpreting TFBS enrichment from random genomic regions
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…
CRISPR Biotech Co. Mammoth Hires Sangamo Atty As GC
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
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)….
PacBio sequencing output increased through uniform and directional fivefold concatenation
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…
Bacterial endosymbionts protect beneficial soil fungus from nematode attack
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
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?
“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 ########…
P. aeruginosa isolated from patients with aural infections
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…
Bioconductor – geecc
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…
which normalization before differential expression analysis (legacy=TRUE vs. legacy=FALSE)
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…
Emergence of the Coexistence of mcr-1, blaNDM-5, and blaCTX-M-55 in Kl
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…
REditools2 (HPC-reditools) de-novo editing prediction from RNAseq?
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
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…
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…
How to interpret bimodal distribution of GC-content for RNAseq and can it be remedied ?
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…