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Tag: pseudotime
Single-cell RNA-seq workflow
In this tutorial we walk through a typical single-cell RNA-seq analysis using Bioconductor packages. We will try to cover data from different protocols, but some of the EDA/QC steps will be focused on the 10X Genomics Chromium protocol. We start from the output of the Cell Ranger preprocessing software. This…
slingshot analysis on PCA but visualization on UMAP
slingshot analysis on PCA but visualization on UMAP 1 Hi Bio-community, I am using slingshot for TI. I am wondering If I can use PCA as reducedDim argument in the slingshot function and for visualization the UMAP in embedCurves? Since I am getting biologically more reasonable results, if working in…
Ultra-fast deep-learned CNS tumour classification during surgery
Data simulation Short nanopore sequencing runs yield sparse and random coverage of the genome. To enable model training, we generate simulated sparse nanopore runs based on microarray data. To this end, N simulated reads are randomly sampled from the read length distribution (D) and assigned a start mapping position in…
The effect of vitrification on blastocyst mitochondrial DNA dynamics and gene expression profiles
Bosch E, De Vos M, Humaidan P. The future of cryopreservation in assisted reproductive technologies. Front Endocrinol (Lausanne). 2020;11:1–15. Article Google Scholar De Geyter C, Calhaz-Jorge C, Kupka MS, Wyns C, Mocanu E, Motrenko T, et al. ART in Europe, 2015: results generated from European registries by ESHRE†. Hum Reprod…
Abnormal developmental trajectory and vulnerability to cardiac arrhythmias in tetralogy of Fallot with DiGeorge syndrome
Generation and characterisation of patient-specific hiPSCs and hiPSC-CMs hiPSC lines were established from two TOF-DG patients, two TOF-ND patients, and two healthy controls with pluripotency markers and germ layer markers verified (Supplementary Figs. 1 and 2). Whole genome sequencing confirmed, respectively, the presence and the absence of 22q11.2 deletion in the…
TimeTalk uses single-cell RNA-seq datasets to decipher cell-cell communication during early embryo development
Curation of early-embryo development single-cell RNA-seq data sets for studying cell-cell communication To identify and study eLRs, we collected public early embryo development scRNA-seq datasets from the mouse MII-oocyte stage to the late blastocyst stage to ensure that scRNA-seq datasets represented every stage of early embryo development. In addition, to…
Director, Bioinformatics – Immunology Center of Georgia job with Augusta University
Director, Bioinformatics – Immunology Center of Georgia Job ID: 253563Location: Augusta UniversityFull/Part Time: Full TimeRegular/Temporary: * About UsAugusta University is Georgia’s innovation center for education and health care, training the next generation of innovators, leaders, and healthcare providers in classrooms and clinics on four campuses in Augusta and locations across…
Image_1_Pseudotemporal ordering of spatial lymphoid tissue microenvironment profiles trails Unclassified DLBCL at the periphery of the follicle.pdf
We have established a pseudotemporal ordering for the transcriptional signatures of distinct microregions within reactive lymphoid tissues, namely germinal center dark zones (DZ), germinal center light zones (LZ), and peri-follicular areas (Peri). By utilizing this pseudotime trajectory derived from the functional microenvironments of DZ, LZ, and Peri, we have ordered…
Error in h(simpleError(msg, call)) in monocle2
Error in h(simpleError(msg, call)) in monocle2 0 Want to run monocle2 for a single cell RNAseq data processed using Seurat, but encountering following problem. library(monocle) Seurat An object of class Seurat 41445 features across 55683 samples within 1 assay Active assay: RNA (41445 features, 1850 variable features) 4 dimensional reductions…
Multiparametric senescent cell phenotyping reveals targets of senolytic therapy in the aged murine skeleton
Development and validation of a senescence CyTOF antibody panel We constructed and validated a comprehensive CyTOF antibody panel to include markers for both cell identity and senescent phenotype (Table 1). A defining characteristic of senescent cells is expression of cell cycle inhibitors, in particular p16 or p2129, so we carefully validated…
PhyloVelo enhances transcriptomic velocity field mapping using monotonically expressed genes
Salipante, S. J. & Horwitz, M. S. Phylogenetic fate mapping. Proc. Natl Acad. Sci. USA 103, 5448–5453 (2006). Article CAS PubMed PubMed Central Google Scholar Sulston, J. E., Schierenberg, E., White, J. G. & Thomson, J. N. The embryonic cell lineage of the nematode Caenorhabditis elegans. Dev. Biol. 100, 64–119…
A universal tool for predicting differentially active features in single-cell and spatial genomics data
singleCellHaystack methodology For a detailed description of the original singleCellHaystack implementation (version 0.3.2) we refer to Vandenbon and Diez19. In brief, singleCellHaystack uses the distribution of cells inside an input space to predict DAFs. First, it infers a reference distribution \(Q\) of all cells in the space by estimating the…
Organization of the human intestine at single-cell resolution
Tissue collection and processing This study complies with all relevant ethical regulations and was approved by the Washington University Institutional Review Board and the Stanford University Institutional Review Board. Human bowel tissues were procured from deceased organ donors. Written informed consent was obtained from the next-of-kin for all donor participants….
Augusta University hiring Director, Bioinformatics – Immunology Center of Georgia in Augusta, Georgia, United States
About UsAugusta University is Georgia’s innovation center for education and health care, training the next generation of innovators, leaders, and healthcare providers in classrooms and clinics on four campuses in Augusta and locations across the state. More than 9,000 students choose Augusta for educational opportunities at the center of Georgia’s…
Noncoding variants alter GATA2 expression in rhombomere 4 motor neurons and cause dominant hereditary congenital facial paresis
Tandem duplications and noncoding SNVs at the HCFP1 locus We enrolled families and simplex cases with nonsyndromic congenital facial paresis (CFP, cohort 1 US-based study) and performed genome-wide single-nucleotide polymorphism (SNP) analysis and whole-exome sequencing (WES) in two large dominant pedigrees, family 1 (Fam1) and family 9 (Fam9; Fig. 1a)….
Adipogenic and SWAT cells separate from a common progenitor in human brown and white adipose depots
Human samples Human adipogenic progenitor cells were isolated from the stromal vascular fraction of adipose tissue samples on the day they were obtained (surgery or biopsy) from four regions: (1) visceral adipose tissue (obtained during gallbladder surgery); (2) perirenal adipose tissue (obtained during nephrectomy surgery); (3) abdominal subcutaneous adipose tissue…
bioconductor – What trajectory analysis method allows to set the form of the trajectory?
I have single cell data from two samples : normal and pathological and I would like to track the progression of the cells (and find the genes that drive it) from normal to pathological. Upon first glance, it seems most reasonable to define the trajectory in advance in such a…
Mapping interindividual dynamics of innate immune response at single-cell resolution
Ethical compliance This project was approved by the Wellcome Sanger Institute Animal Welfare and Ethical Review Body and complied with all relevant ethical regulations regarding animal research and human studies. Human cells were obtained from HipSci24, where they were collected from volunteers recruited from the National Institute for Health and…
Tox4 regulates transcriptional elongation and reinitiation during murine T cell development
Pan-hematopoietic Tox4 deletion reduces number of multipotential progenitors and impairs T cell development To understand the role of TOX4 in development, we generated Tox4 conditional knockout mice by the CRISPR-Cas9 methodology, and two loxP sites in the same orientation were inserted upstream and downstream of exons 4–6, respectively (Supplementary Fig. 1a). Considering…
Transfer learning enables predictions in network biology
Vaswani, A. et al. Attention is all you need. Preprint at doi.org/10.48550/arXiv.1706.03762 (2017). Devlin, J., Chang, M. W., Lee, K. & Toutanova, K. BERT: pre-training of deep bidirectional transformers for language understanding. In Proc. 2019 Conference North American Chapter of the Association for Computational Linguistics: Human Language Technologies Vol. 1…
Single-cell RNA sequencing reveals the fragility of male spermatogenic cells to Zika virus-induced complement activation
Cell clusters in ZIKV-infected mouse testis defined by scRNA-Seq To investigate the influence of ZIKV infection on testes, testicular cells from ZIKV-infected (14 dpi.) and uninfected A6 male mice (Ifnar−/− mice) were analyzed by single-cell RNA sequencing (scRNA-Seq). After filtering out poor-quality cells, 11014 cells in control testes and 11974…
Identification of genetic variants that impact gene co-expression relationships using large-scale single-cell data | Genome Biology
Overview of the study To uncover the contexts and biological processes that affect gene expression regulation, this study took advantage of both the resolution of single-cell data and the directionality captured by co-eQTLs. First, we constructed cell-type-specific co-expression networks using five scRNA-seq PBMC datasets from three recently generated PBMC scRNA-seq…
Motixafortide and G-CSF to mobilize hematopoietic stem cells for autologous transplantation in multiple myeloma: a randomized phase 3 trial
Patient demographics were comparable across study cohorts From 22 January 2018 to 30 October 2020, a total of 122 patients from 18 sites in five countries were enrolled and randomized 2:1 to receive either motixafortide + G-CSF (80 patients) or placebo + G-CSF (42 patients) for HSPC mobilization (Fig. 1 and Extended Data Fig. 1a). Demographics between the two treatment…
Pseudotemporal ordering of spatial lymphoid tissue microenvironment profiles trails Unclassified DLBCL at the periphery of the follicle
Abstract We have established a pseudotemporal ordering for the transcriptional signatures of distinct microregions within reactive lymphoid tissues, namely germinal center dark zones (DZ), germinal center light zones (LZ), and peri-follicular areas (Peri). By utilizing this pseudotime trajectory derived from the functional microenvironments of DZ, LZ, and Peri, we have…
New technology maps where and how cells read their genome
Design and evaluation of spatial epigenome–transcriptome cosequencing with E13 mouse embryo. a, Schematic workflow. b, Comparison of number of unique fragments and fraction of reads in peaks (FRiP) in spatial ATAC–RNA-seq and spatial CUT&Tag–RNA-seq. c, Gene and UMI count distribution in spatial ATAC–RNA-seq and spatial CUT&Tag–RNA-seq. Number of pixels in…
The gut microbiome modulates the transformation of microglial subtypes
Single-cell nucleus RNA-seq profiling of Hip and PFC A schematic of nuclei isolation and the snRNA-seq workflow from the Hip and PFC is shown in Fig. 1a. Using the droplet-based single-nucleus method, we captured 72,226, and 67,698 nuclei from the Hip and PFC, respectively, in the 9 mice (3 per group)….
single-cell pseudotime analysis with monocle3
single-cell pseudotime analysis with monocle3 0 I have a question regarding pseudotime analysis. It seems, this analysis is done over only a certain cell type. However, I am wondering if we can apply it on all the cells we got from UMAP out of single-cell analysis. Can we? Also, If…
Automating iPSC generation to enable autologous photoreceptor cell replacement therapy | Journal of Translational Medicine
Starzl TE. The early days of transplantation. JAMA. 1994;272(21):1705. Article CAS PubMed PubMed Central Google Scholar Vanholder R, Dominguez-Gil B, Busic M, Cortez-Pinto H, Craig JC, Jager KJ, et al. Organ donation and transplantation: a multi-stakeholder call to action. Nat Rev Nephrol. 2021;17(8):554–68. Article PubMed PubMed Central Google Scholar Aubert…
A molecular atlas reveals the tri-sectional spinning mechanism of spider dragline silk
Chromosomal-scale genome assembly and full spidroin gene set of T. clavata To explore dragline silk production in T. clavata, we sought to assemble a high-quality genome of this species. Thus, we first performed a cytogenetic analysis of T. clavata captured from the wild in Dali City, Yunnan Province, China, and…
Seurat SmartSeq A.10-12
seurat v3 object ASSAYS: RNA: mRNA expression data DIMENSIONALITY REDUCTION projected: Data was projected on the main AML dataset from Cohorts A and B. scanorama: Data was integrated with Scanorama, using the patient as Batch key umap: umap computed from Scanorama components METADATA patient: Patient ct: Projected cell type (Triana…
Human fetal cerebellar cell atlas informs medulloblastoma origin and oncogenesis
Wang, J., Garancher, A., Ramaswamy, V. & Wechsler-Reya, R. J. Medulloblastoma: from molecular subgroups to molecular targeted therapies. Annu. Rev. Neurosci. 41, 207–232 (2018). Article CAS PubMed Google Scholar Cavalli, F. M. G. et al. Intertumoral heterogeneity within medulloblastoma subgroups. Cancer Cell 31, 737–754.e736 (2017). Article CAS PubMed PubMed Central …
Long-range phasing of dynamic, tissue-specific and allele-specific regulatory elements
Baylin, S. B. & Jones, P. A. A decade of exploring the cancer epigenome – biological and translational implications. Nat. Rev. Cancer 11, 726–734 (2011). CAS PubMed PubMed Central Article Google Scholar Greenberg, M. V. C. & Bourc’his, D. The diverse roles of DNA methylation in mammalian development and disease….
Polygenic enrichment distinguishes disease associations of individual cells in single-cell RNA-seq data
Visscher, P. M. et al. 10 years of GWAS discovery: biology, function, and translation. Am. J. Hum. Genet. 101, 5–22 (2017). CAS PubMed PubMed Central Article Google Scholar Hekselman, I. & Yeger-Lotem, E. Mechanisms of tissue and cell-type specificity in heritable traits and diseases. Nat. Rev. Genet. 21, 137–150 (2020)….
Human distal lung maps and lineage hierarchies reveal a bipotent progenitor
Verleden, S. E. et al. Small airways pathology in idiopathic pulmonary fibrosis: a retrospective cohort study. Lancet Respir. Med. 8, 573–584 (2020). CAS PubMed PubMed Central Google Scholar Hogg, J. C., Macklem, P. T. & Thurlbeck, W. M. The resistance of small airways in normal and diseased human lungs. Aspen…
DESeq2 pseudotime series design?
DESeq2 pseudotime series design? 1 @jordiplanells-19865 Last seen 22 hours ago Sweden Hi all. First things first, sorry for posting one more question about experimental design and time series in DESeq2.We have performed RNA-seq with two different treatments (control and protein over-expression) in two different time points (t=0 and t=8h)….
Single-cell delineation of lineage and genetic identity in the mouse brain
STICR lentiviral library preparation and validation We synthesized a high-complexity lentivirus barcode library that encodes approximately 60–70 million distinct oligonucleotide RNA sequences (STICR barcodes). STICR barcodes comprised three distinct oligonucleotide fragments cloned sequentially into a multicloning site within the 3′ UTR of an enhanced green fluorescent protein (eGFP) transgene under…
Which trajectory method is better !?
Which trajectory method is better !? 2 Hello I was engaged with a basic problem. I have dataset consist ~2000 cells and composed 8-9 clusters using Seurat package, then I transfer Seurat object to the Monocle. I tried monocle2 and monocle3. The problem is, how to make the trajectory ?…
Extract root(start) and leaf(end) states programmatically in monocle2
Extract root(start) and leaf(end) states programmatically in monocle2 0 Dear bioinformaticians, do you know how to extract starting state and end states from the CDS in monocle2 ? I know I can detect them visually inspecting the States plot after I compute the pseudotime. I am asking if there is…
Trouble running Cyclum for my scRNA-seq analysis
I have been analyzing some mouse T cell scRNA-seq data for a few months now using mostly the Seurat pipeline run with default parameters, and I have noticed that regressing out the ‘S.Score’ and ‘G2M.Score’ obtained from default Seurat::CellCycleScoring seems to be insufficient to remove (seemingly large) variation originating from…
Bioconductor – traviz (development version)
DOI: 10.18129/B9.bioc.traviz This is the development version of traviz; to use it, please install the devel version of Bioconductor. Trajectory functions for visualization and interpretation. Bioconductor version: Development (3.14) traviz provides a suite of functions to plot trajectory related objects from Bioconductor packages. It allows plotting trajectories in…
heatmap of genes pseudotime in monoclle3
heatmap of genes pseudotime in monoclle3 0 Login before adding your answer. Traffic: 1946 users visited in the last hour Source link