Tag: heatmaps

Integrative cross-species analysis of GABAergic neuron cell types and their functions in Alzheimer’s disease

The heterogeneity of GABAergic neurons in human, macaque, mouse, and pig To perform a cross-species comparative study of the GABAergic neurons, we collected the snRNA-seq datasets of the cerebral cortex for human10,11, macaque12,13, mouse14,15, and pig16. After cell-type annotation and filtering out the excitatory neurons and non-neurons, the GABAergic neurons…

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Multiplexed base editing through Cas12a variant-mediated cytosine and adenine base editors

Robust C-to-T conversion by Cas12a variant-mediated CBEs for non-canonical PAMs We initially attempted to screen for optimal cytosine deaminases that confer powerful C-to-T editing for Cas12a-mediated CBEs. Seven dCas12a-CBEs fused with individual cytosine deaminases1,2,16,20,21,22,24,25,26 were compared in HEK293T cells and porcine embryos at sites with TTTV PAM sequences. The dCas12a-A3A…

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Insights on the bacterial composition of Parmigiano Reggiano Pure Whey Starter by a culture-dependent and 16S rRNA metabarcoding portrait

Smid, E. J. et al. Practical implications of the microbial group construction of undefined mesophilic starter cultures. Microb. Cell Factories 13, S2. doi.org/10.1186/1475-2859-13-S1-S2 (2014). Article  Google Scholar  Stadhouders, J. & Leenders, G. J. M. Spontaneously developed mixed-strain cheese starters. Their behaviour in direction of phages and their use within the…

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Identification of unique DNA methylation sites in Kabuki syndrome using whole genome bisulfite sequencing and targeted hybridization capture followed by enzymatic methylation sequencing

Niikawa N, Matsuura N, Fukushima Y, Ohsawa T, Kajii T. Kabuki make-up syndrome: a syndrome of mentalretardation, unusual facies, large and protruding ears, and postnatal growth deficiency. J Pediatrics. 1981;99:565–9. CAS  Article  Google Scholar  Kuroki Y, Suzuki Y, Chyo H, Hata A, Matsui I. A new malformation syndrome of long…

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Comparative chloroplast genome and phylogenetic analyses of Chinese Polyspora

Choo, L. M., Niissalo, M. A., Leong, P. K. F. & Khew, G. S. The complete plastome sequence of Gordonia penangensis Ridl. supports the transfer of Asian Gordonia into Polyspora (Theaceae). Phytotaxa 458, 159–166 (2020). Nguyet, H. N. L. et al. An updated checklist of Theaceae and a new species…

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Nanobody-based RFP-dependent Cre recombinase for selective anterograde tracing in RFP-expressing transgenic animals

Screening of efficient mCherry-binding protein (MBP) pairs to design Cre recombinase dependent on RFPs First, we aimed to construct Cre recombinase dependent on RFPs based on the reported tool named Cre-DOG30. In this system, N-terminal and C-terminal split Cre recombinase fragments are fused with specific nanobodies for target proteins, and…

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Dynamic mechanisms of CRISPR interference by Escherichia coli CRISPR-Cas3

In vitro reconstitution of Escherichia coli CRISPR-Cas3 interference E. coli CRISPR-Cas3 is generally well-characterized type I CRISPR complexes in vitro and in vivo32,33,37,38. However, recombinant EcoCas3 protein is difficult to purify because of poor solubility and propensity to aggregate at 37 °C25,26,30,39. Co-expression of HtpG chaperon40 and/or low temperature growth at…

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NODULIN HOMEOBOX is required for heterochromatin homeostasis in Arabidopsis

NDX is a heterochromatin-associated factor To understand the genome-wide regulatory roles of NDX, we first analyzed its genomic distribution. For this, we performed chromatin immunoprecipitation sequencing (ChIP-seq) in 10-day old Arabidopsis seedlings expressing N-terminally and C-terminally tagged NDX fusion proteins (flag-NDX/ndx1-1(FRI)/flc-2 and NDX-GFP/ndx1-1(FRI)/flc-2, respectively) expressed from their endogenous promoter21,32. The…

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Targeted inhibition of ubiquitin signaling reverses metabolic reprogramming and suppresses glioblastoma growth

Cell culture Human glioblastoma cells (U87MG and U87MG-Luc) and human embryonic kidney cells (HEK293) were obtained from the American Type Culture Collection (Manassas, Va.). Cells were cultured in Dulbecco’s Modified Eagle Medium supplemented with 10% fetal bovine serum (Gibco™ Fetal Bovine Serum South America, Thermo Scientific Fisher-US), 2 mM l-glutamine, 50 U/ml…

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bioconductor – Generating graphical results within from bioinformatics/nature genomics papers

I am a computational scientist with background in computer science and engineering however very new to the field of bioinformatics and computational genomics. Looking at papers in nature, PLOS, Cell, PNAS etc. within the topic of computational genomics, I see a very similar set of very sophisticated graphical results, ranging…

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Single-cell and bulk transcriptome sequencing identifies two epithelial tumor cell states and refines the consensus molecular classification of colorectal cancer

Cell-type annotation scRNA-seq data were filtered to discard low-quality cells and doublets (Supplementary Fig. 1, Extended Data Fig. 1 and Methods). Supervised clustering (Reference Component Analysis v2 (RCA2)) at low resolution grouped cells into 11 major cell types (Extended Data Fig. 1). To identify epithelial cell subtypes, we initially analyzed…

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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…

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Transcriptomic and proteomic profiling of peptidase expression in Fasciola hepatica eggs developing at host’s body temperature

From the bovine liver, we isolated 97 live F. hepatica adults. After overnight cultivation, we recovered approx. 228,000 laid eggs, which we divided in three groups. The first group (T0) was immediately frozen at − 80 °C, while the other two groups (T5 and T10) were incubated for 5 and 10 days at…

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Bioconductor – ComplexHeatmap

DOI: 10.18129/B9.bioc.ComplexHeatmap     This package is for version 3.14 of Bioconductor; for the stable, up-to-date release version, see ComplexHeatmap. Make Complex Heatmaps Bioconductor version: 3.14 Complex heatmaps are efficient to visualize associations between different sources of data sets and reveal potential patterns. Here the ComplexHeatmap package provides a highly…

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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…

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Bioinformatics analysis identifies widely expressed genes

1Department of Orthopedics, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, People’s Republic of China; 2Department of Pediatrics, The Shanxi Medical University, Taiyuan, Shanxi, People’s Republic of China Correspondence: Jun Qian, Department of Orthopedics, The First Affiliated Hospital of Anhui Medical University, 218 Jixi Road, Hefei, 230022, Anhui,…

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A Comprehensive Guide on ggplot2 in R

                                                                  Image source: Author       Introduction Visualization plays an important role in the decision-making process after analyzing relevant data. Graphical representation highlighting the interdependence of key elements affecting performance is important in the above process. There are many libraries in Python and R which provide different options showing…

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Secondary succession of bacterial communities and co-occurrence of phylotypes in oil-polluted Populus rhizosphere

doi.org/10.1016/j.soilbio.2012.11.018Get rights and content Abstract Oil pollution can be considered as a driver for bacterial secondary succession. A greenhouse study was conducted using forest mineral soil contaminated by heavy fuel oil and planted with hybrid aspen. The aim was to compare the bacterial succession in oil- and plant-amended ecosystems. Samples…

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Validation of hub genes in acute pancreatitis

Introduction Acute pancreatitis (AP) is a common disease found in clinics, and requires urgent Hospital admission. The incidence of AP is increasing in recent years worldwide.1 The patients with AP increased from 1,727,789.3 to 2,814,972.3 between 1990 and 2019 in 204 countries and territories.2 Meanwhile, nearly 20% of AP patients…

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Introduction to ggplot2 with R – LibCal

Overview This is a hands-on workshop that covers how to use ggplot2 for common visualizations using the R programming language. It is not an introductory R programming workshop. See prerequisities below. Objectives In this workshop you will see how to use ggplot2 for: describing single variables and plotting simple…

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nf-core/circrna

circRNA quantification, differential expression analysis and miRNA target prediction of RNA-Seq data Introduction nf-core/circrna is a best-practice analysis pipeline for the quantification, miRNA target prediction and differential expression analysis of circular RNAs in paired-end RNA sequencing data. The pipeline is built using Nextflow, a workflow tool to run tasks across…

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Bioinformatics Research Scientist (Blue Sky Initiative), Memphis, Tennessee

M. Madan Babus Group and the Center for Data-Driven Discovery in the Department of Structural Biology is seeking a highly driven, Full time Machine Learning Research Scientist support the Kalodimos and Babu Groups on the Blue Sky Initiative “Seeing the Invisible in Protein Kinases.” This project is supported by $35…

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Bioconductor – DaMiRseq (development version)

DOI: 10.18129/B9.bioc.DaMiRseq     This is the development version of DaMiRseq; for the stable release version, see DaMiRseq. Data Mining for RNA-seq data: normalization, feature selection and classification Bioconductor version: Development (3.15) The DaMiRseq package offers a tidy pipeline of data mining procedures to identify transcriptional biomarkers and exploit them…

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Time-course RNASeq of Camponotus floridanus forager and nurse ant brains indicate links between plasticity in the biological clock and behavioral division of labor | BMC Genomics

1. Sharma VK. Adaptive significance of circadian clocks. Chronobiol Int. 2003;20(6):901–19. PubMed  Google Scholar  2. Paranjpe DA, Sharma VK. Evolution of temporal order in living organisms. J Circadian Rhythms. 2005;3(1):7. PubMed  PubMed Central  Google Scholar  3. Yerushalmi S, Green RM. Evidence for the adaptive significance of circadian rhythms. Ecol Lett….

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an R package for interactive visualization of multi-omics data and annotation of chromosomes

Additional file 1. Example of chromoMap interactive plot constructed using various features of chromoMap including polyploidy (used as multi-track), feature-associated data visualization (scatter and bar plots), chromosome heatmaps, data filters (color-coded scatter and bars). Differential gene expression in a cohort of patients positive for COVID19 and healthy individuals (NCBI Gene…

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Immune-related Prognostic Genes of ccRCC

Introduction Kidney cancer is one of the most commonly diagnosed tumors around the globe.1 According to the statistics from the World Health Organization, annually, there are more than 140,000 RCC-related deaths.2 ccRCC is the most typical subtype of kidney cancer and contributes to the majority of kidney cancer-related deaths.3,4 Until…

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Identification of differentially expressed genes in AF

Defeng Pan,1,* Yufei Zhou,2,* Shengjue Xiao,1,* Yue Hu,3,* Chunyan Huan,1 Qi Wu,1 Xiaotong Wang,1 Qinyuan Pan,1 Jie Liu,1 Hong Zhu1 1Department of Cardiology, The Affiliated Hospital of Xuzhou Medical University, Xuzhou, Jiangsu, 221004, People’s Republic of China; 2Department of Cardiology, Shanghai Institute of Cardiovascular Diseases, Zhongshan Hospital and Institutes of…

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Circos plot of dominant OTU with phylogenetic tree

Circos plot of dominant OTU with phylogenetic tree 0 I am trying to create a circos plot of dominant OTUs (from metagenomic data) with a phylogenetic tree inside the circle and the heatmaps around (like the attached image). Kindly suggest how can I achieve this using circos. Thank you. analysis…

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miRNAs and mRNAs in intestinal ischemia-reperfusion injury

Introduction Intestinal ischemia-reperfusion (II/R) injury is a severe clinical complication common in the Intensive Care Unit (ICU). It is associated with high morbidity and mortality.1 Usually, this problem is followed by various causes, including sepsis, shock, trauma, and so on.2 Intestinal ischemia-reperfusion injury destroys intestinal tissue and impairs the function…

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Creating Heatmaps Of Diffrentially Expressed Genes In Angilent Single-Color Array Analysis

Creating Heatmaps Of Diffrentially Expressed Genes In Angilent Single-Color Array Analysis 0 I am using limma to analyze Agilent’s single color arrays to find differentially expressed genes, using the following procedure. targets <- limma::readTargets(“targets.txt”) project <- limma::read.maimages(targets,source=”agilent”, green.only=TRUE) project.bgc <- backgroundCorrect(project, method=”normexp”, offset=50) project.NormData <-normalizeBetweenArrays(project.bgc,method=”quantile”) design <- paste(targets$Target, sep=””) design…

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GitHub – MD-Anderson-Bioinformatics/EGFR-Structure-Function-Nature-Manuscript

These files contain the source data and code used for the analyses included in the publication Robichaux et al 2021, “Structure-based classification predicts drug response in EGFR mutant NSCLC” These files will be made public at the time of acceptance.The files include but are not limited to: Summary of EGFR…

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How do I determine p-value and fold change for TMM normalized data?

How do I determine p-value and fold change for TMM normalized data? 0 Hi, I have a TMM normalized data for cancer vs no cancer treatment. This data, however, does not contain p-value or fold change. I want to generate plots such as heatmaps and volcano plots, but I cann’t…

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Kaggle Mini Courses

Listing Results Kaggle mini courses Learn Python, Data Viz, Pandas & More Tutorials Kaggle Data Kaggle.com All Courses 8 hours agoPython Learn the most important language for data science. Intro to Machine Learning Learn the core ideas in machine learning, and build your first models. Intermediate Machine Learning Handle missing…

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kaggle datasets for tableau

The homepage is full of small visualizations telling stories about each data set. This is the default Tableau location (if you’ve not changed) so far. Transformation processes can also be referred to as data wrangling, or data munging, transforming and mapping data from one raw data form into another format…

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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…

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Advice on organizing large GSVA heatmap

Advice on organizing large GSVA heatmap 1 Hi there, I wanted to get some advice on how you might make your heatmap easier to read. In my case, I generated a heatmap from GSVA data which I filtered to only include significant pathways, here. I wanted to see how each…

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R Programming – how to make a simple heat map

R Programming – how to make a simple heat map 5 Hi can anyone guide me how to make a simple heat map in R? Heatmap R • 264 views There is github.com/XiaoLuo-boy/ggheatmap which is fully ggplot in case you feel more comfortable with it rather than the suggested pheatmap/ComplexHeatmap…

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R Programming

R Programming 4 Hi can anyone guide me how to make a simple heat map in R? in Heatmap R • 201 views There is github.com/XiaoLuo-boy/ggheatmap which is fully ggplot in case you feel more comfortable with it rather than the suggested pheatmap/ComplexHeatmap packages and want to have a consistent…

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