Cell Reports · 2020 · 215 citations · 73 references
Life SciencesCardiologyCell BiologyGene ExpressionInflammationTranscriptomicsIschemic Heart DiseaseSingle-cell TranscriptomicsAcute-phase MediatorsCollagen Type I DepositionEpicardial Cell ActivationInterstitial Cell LossPerivascular Stromal CellsSingle-cell Rna Sequencing
Cardiac ischemia leads to the loss of myocardial tissue and the activation of a repair process that culminates in the formation of a scar whose structural characteristics dictate propensity to favorable healing or detrimental cardiac wall rupture. To elucidate the cellular processes underlying scar formation, here we perform unbiased single-cell mRNA sequencing of interstitial cells isolated from infarcted mouse hearts carrying a genetic tracer that labels epicardial-derived cells. Sixteen interstitial cell clusters are revealed, five of which were of epicardial origin. Focusing on stromal cells, we define 11 sub-clusters, including diverse cell states of epicardial- and endocardial-derived fibroblasts. Comparing transcript profiles from post-infarction hearts in C57BL/6J and 129S1/SvImJ inbred mice, which displays a marked divergence in the frequency of cardiac rupture, uncovers an early increase in activated myofibroblasts, enhanced collagen deposition, and persistent acute phase response in 129S1/SvImJ mouse hearts, defining a crucial time window of pathological remodeling that predicts disease outcome.
73
R: A Language and Environment for Statistical Computing
R Core Team · 2000 · 353K citations · Full text
Natural Sciences, Computer Science, Statistical Computing +10
Fiji: an open-source platform for biological-image analysis
Johannes Schindelin, Ignacio Arganda‐Carreras, Erwin Frise et al. · Nature Methods · 2012 · 70.9K citations
STAR: ultrafast universal RNA-seq aligner
Alexander Dobin, Carrie Davis, Felix Schlesinger et al. · Bioinformatics · 2012 · 56.2K citations · Full text
Fast, sensitive and accurate integration of single-cell data with Harmony
Ilya Korsunsky, Nghia Millard, Jean Fan et al. · Nature Methods · 2019 · 10.5K citations · Full text