scRNA-Seq of in vitro "induced sinoatrial bodies" and ex vivo sinoatrial node region
For scRNA-Seq, iSABs were dissociated using the Primary Cardiomyocyte Isolation Kit (Thermo Fisher Scientific) before library preparation was performed using the 10xGenomics system with subsequent sequencing on the HighSeq4000 (Illumina). The mouse-SAN scRNA-Seq protocol is described in Goodyer et al. Preprocessing of raw sequencing data from iSABs relied on tools of the Cell Ranger Software (v.6.1.0) as was the procedure in Goodyer et al. Downstream analyses were conducted similar for both datasets using Seurat (v.3.2.2). Plotting the %mtRNA we found that all pacemaker subpopulations in the iSABs dataset had values above the standard 5%-threshold. Automatically filtering with this quality control parameter causes a strong bias and loss of these data. The SAN cluster of Goodyer revealed similar %mtRNA values exposing them to the same bias.
SEEK ID: https://fairdomhub.org/assays/1438
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Projects: iRhythmics
Investigation: hidden item
Study: Quality control in scRNA‑Seq can discriminate pacemaker cells: the mtRNA bias
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Biological problem addressed: Gene Expression
Organisms: No organisms
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Created: 21st Apr 2021 at 08:24
Last updated: 3rd Sep 2021 at 07:46
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Projects: iRhythmics
Institutions: Leibniz Institute for Farm Animal Biology (FBN)
https://orcid.org/0000-0002-7968-3152
Projects: iRhythmics
Institutions: Rostock University Medical Centre
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Projects: Manchester Institute for Biotechnology, ICYSB 2015 - International Practical Course in Systems Biology, iRhythmics, INBioPharm, EmPowerPutida, Systo models, MycoSynVac - Engineering Mycoplasma pneumoniae as a broad-spectrum animal vaccine, Multiscale modelling of state transitions in the host-microbiome-brain network, Extremophiles metabolsim, NAD COMPARTMENTATION, Agro-ecological modelling, Bergen(Ziegler lab) project AF-NADase, NAMPT affinity, Stress granules, Modelling COVID-19 epidemics, Bio-crop, ORHIZON, Coastal Data, SASKit: Senescence-Associated Systems diagnostics Kit for cancer and stroke, hybrid sequencing, HOST-PAR, BioCreative VII, Boolean modeling of Parkinson disease map, Orphan cytochrome P450 20a1 CRISPR/Cas9 mutants and neurobehavioral phenotypes in zebrafish, Selective Destruction in Ageing, Viral Metagenomic, Synthetic biology in Synechococcus for bioeconomy applications (SynEco), testproject, SDBV ephemeral data exchanges, Test project, The BeeProject, PHENET, LiceVault, EbN1 Systems Biology, UMRPégase, DeCipher, Heat stress response of the red-tide dinoflagellate Prorocentrum cordatum, middle ear, datamgmt, Institut Pasteur's projects, The nucleus of Prorocentrum cordatum, qpcr, MRC-UNICORN, Test project for Sciender, qPCR, Artificial organelles_Pathogen digestion, Supplementary Information 2 associated with the manuscript entitled " Label free Mass spectrometry proteomics reveals different pathways modulated in THP-1 cells infected with therapeutic failure and drug resistance Leishmania infantum clinical isolates", FAIR Functional Enrichment, PTPN11 mutagenesis, Supplementary Information 2 associated with the manuscript entitled "Label free Mass spectrometry proteomics reveals different pathways modulated in THP-1 cells infected with therapeutic failure and drug resistance Leishmania infantum clinical isolates", iPlacenta- Placenta on a chip, Near Surface Wave-Coherent Measurements of Temperature and Humidity, A Meta-Analysis of Functional Recovery of Aphasia after Stroke by Acupuncture Combined with Language Rehabilitation Training, Phytoplankton phenology in the Bay of Biscay: using remote sensing to assess and raise awareness of climate change impacts on the sea, Master-BIDS, Endometriosis, Vitis Data Crop, MESI-STRAT Review, Establishing an innovative and transnational feed production approach for reduced climate impact of the aquaculture sector and future food supply, ARAX: a web-based computational reasoning system for translational biomedicine, Adaptation of Salmonella enterica, I AM FRONTIER, ., PhD Nicotinic Acetylcholine Receptors, SFB1361 playground, Amaizing, Conspicuous chloroplast with LHC‒PSI/II‒megacomplex and diverse PBPs in the marine dinoflagellate Prorocentrum cordatum, icpm-kth, SDBV/HITS, sample project, TestingSeek, Genomic Medicine, Remodeling of cIV, Virtual Human Platform for Safety Assessment, PROMISEANG, URGI, Matsutake, UNDESIRABLE EFFECTS OF POST COVID-19 VACCINATION: A DESCRIPTIVE STUDY, WINTER 2022, Semantic Table Interpretation in Chemistry, MS identification of L infantum proteins related to their drug resistance patterns for new drug targets identification and ecotoxicological evaluations of their environmental and interspecies impact, the Supplementary materials for paper, ToxiGen - Reproductive toxicity and transgenerational effects of petroleum mixtures in fish, PhotoBoost, Measurement of Fisheries Provisioning Services and its Pressure to Support Sustainability of Fisheries in The Jatigede Reservoir, Indonesia, FIsh data on 2022 in the Jatigede Reservoir, ImmPort - data sharing, MESI-Review 2024, REWIRED: comparative RNA-seq and ATAC-seq in six salmonids and six outgroup telest fishes, REWIRED, Data Repository, APPN Test Project, Enhanced Anticancer Effect of Thymidylate Synthase Dimer Disrupters Promoting Intracellular Accumulation, BIDS, BioRECIPE representation format, UMass Chan BioImage DMS Core_FAIR Metadata Templates, Function, control and engineering of microbial methylotrophy, Pectobacterium pangenome, New Optical Coherence Tomography Biomarkers Identified with Deep Learning for Risk Stratification of Patients with Age-related Macular Degeneration, Virulence-related genes expression in planktonic mixed cultures of Candida albicans and non-albicans Candida species, Screening of Secondary Plant Metabolites on Antihelmintic Activity in Ascaris scum, Munich Cluster for Systems Neurology, Test project May 2024, Biospecimen Collection Protocol, Winter Wheat (Triticum aestivum L.) 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Web page: Not specified
The project addresses the generation and establishment of programmed pacemaker cells for an in vitro drug testing possibility to perform predictive tests. This may lead to an improved treatment of cardiac arrhythmias or an accurate identification of potential drug molecules at a very early stage of development. Important benefits will arise in verifying the safety of a wide variety of medicines while reducing animal testing. For more information you may visit our project website at ...
Programme: Independent Projects
Public web page: https://irhythmics.med.uni-rostock.de/
Single-cell RNA-sequencing (scRNA-seq) provides high-resolution insights into complex tissues. Cardiac tissue, however, poses a major challenge due to the delicate isolation process and the large size of mature cardiomyocytes. Regardless of the experimental technique, captured cells are often impaired and some capture sites may contain multiple or no cells at all. All this refers to “low quality” potentially leading to data misinterpretation. Common standard quality control parameters involve the ...
Submitter: Markus Wolfien
Investigation: 1 hidden item
Assays: scRNA-Seq of in vitro "induced sinoatrial bodies" and ex vivo sinoatrial...
This file contains the script for the downstream scRNA-Seq analysis including quality control using the barcode ranking method together with the tool DropletUtils to exclude empty droplets and undetected genes as well as standard data processing (normalisation, variable feature identification, scaling, and dimensionality reduction) using tools of Seurat (v.3.2.2). After cluster annotation the %mtDNA was plotted for both datasets.
Creator: Anne-Marie Galow
Submitter: Anne-Marie Galow
This file contains the detailed experimental protocol for the cultivation of "induced sinoatrial bodies (iSABs), the scRNA-Seq procedure as well as the general computational workflow for data processing. The R-script is provided separately.
Creators: Anne-Marie Galow, Sophie Kussauer, Markus Wolfien
Submitter: Anne-Marie Galow
Abstract (Expand)
Authors: A. M. Galow, S. Kussauer, M. Wolfien, R. M. Brunner, T. Goldammer, R. David, A. Hoeflich
Date Published: 24th Aug 2021
Publication Type: Manual
This file contains Violin plots for mitochondrial gene transcripts (%mtRNA), cardiac marker (Tnnt2), and pace-maker marker (Hcn4) for identified cell clusters in iSABS and sinoatrial node region (results obtained from a data reanalysis of Goodyer et al.).
Creator: Anne-Marie Galow
Submitter: Anne-Marie Galow
This file contains several Scatter plots illustrating the correlation of %mtDNA and (a) Tnnt2 (b) Hcn4 (c) total number of gene transcripts per cell In Tnnt2 positive cells and (d) total number of gene transcripts per cell In Hcn4 positive cells.
Creator: Anne-Marie Galow
Submitter: Anne-Marie Galow
Graphical abstract for the manuscript "Quality control in scRNA-Seq can discriminate pacemaker cells – the mtDNA bias" by Anne-Marie Galow#, Sophie Kussauer, Markus Wolfien, Robert David*, and Andreas Hoeflich#*
Creator: Anne-Marie Galow
Submitter: Anne-Marie Galow
This file contains a UMAP plot generated for the Goodyer dataset illustrating the various cell populations and their proportions as well as the original t-SNE plot of the respective data published by Goodyer et al. in 2019 (doi: 10.1161/CIRCRESAHA.118.314578).
Creator: Anne-Marie Galow
Submitter: Anne-Marie Galow
This file contains a UMAP plot for the iSABs dataset illustrating the various cell populations and their proportions.
Creator: Anne-Marie Galow
Submitter: Anne-Marie Galow
