Scrublet: Computational Identification of Cell Doublets in Single-Cell Transcriptomic Data

Wolock, Samuel L.; Lopez, Romain; Klein, Allon M.

doi:10.1016/j.cels.2018.11.005

Cited by 1,659 publications

(973 citation statements)

References 30 publications

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“…We selected nuclei with at least 1,000 sequenced fragments that displayed high enrichment (>10) in the annotated transcriptional start sites (TSS; Extended Data Figure 2b). We also removed the snATAC-seq profiles likely resulting from potential barcode collision or doublets using a procedure modified from Scrublet 33 (Extended Data Figure. 2c, see Methods ).…”

Section: Resultsmentioning

confidence: 99%

An Atlas of Gene Regulatory Elements in Adult Mouse Cerebrum

Preissl

Hou

et al. 2020

Preprint

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25The mammalian cerebrum performs high level sensory, motor control and cognitive 26 functions through highly specialized cortical networks and subcortical nuclei. Recent 27 surveys of mouse and human brains with single cell transcriptomics 1-3 and high-28 throughput imaging technologies 4,5 have uncovered hundreds of neuronal cell types and 29 a variety of non-neuronal cell types distributed in different brain regions, but the cell-type-30 specific transcriptional regulatory programs responsible for the unique identity and 31 function of each brain cell type have yet to be elucidated. Here, we probe the accessible 32 chromatin in >800,000 individual nuclei from 45 regions spanning the adult mouse 33 isocortex, olfactory bulb, hippocampus and cerebral nuclei, and use the resulting data to 34 define 491,818 candidate cis regulatory DNA elements in 160 distinct sub-types. We link 35 a significant fraction of them to putative target genes expressed in diverse cerebral cell 36 types and uncover transcriptional regulators involved in a broad spectrum of molecular 37 and cellular pathways in different neuronal and glial cell populations. Our results provide 38 a foundation for comprehensive analysis of gene regulatory programs of the mammalian 39 brain and assist in the interpretation of non-coding risk variants associated with various 40 neurological disease and traits in humans. To facilitate the dissemination of information, 41 we have set up a web portal (http://catlas.org/mousebrain).42 45 functions such as sensory processing, motor control, emotion, and cognition 6 . It is divided 46 into two hemispheres, each consisting of the cerebral cortex and various cerebral nuclei. 47The cerebral cortex is further divided into isocortex and allocortex. Isocortex, 48 characterized by six cortical layers, is a phylogenetically more recent structure that has 49 further expanded greatly in primates. It is responsible for sensory motor integration, 50 decision making, volitional motor command and reasoning. The allocortex, by contrast, is 51 phylogenetically the older structure that features three or four cortical layers. It includes 52 the olfactory bulb responsible for processing the sense of smell and the hippocampus 53 involved in learning, memory and spatial navigation. 54 55 The cerebral cortex and basal ganglia are made up of a vast number of neurons and glial 56 cells. The neurons can be classified into different types of excitatory projection neurons 57 and inhibitory interneurons, defined by the neural transmitters they produce and their 58 connective patterns with other neurons 7-9 . Understanding how the identity and function of 59 each brain cell type is established during development and modified by experience is one 60 of the fundamental challenges in brain research. Recent single cell RNA-seq and high 61 throughput imaging experiments have produced detailed cell atlases for both mouse and 62human brains 3-5,10-15 , leading to a comprehensive view of gene expression patterns in 63 different brain regions, c...

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Section: Resultsmentioning

confidence: 99%

An Atlas of Gene Regulatory Elements in Adult Mouse Cerebrum

Preissl

Hou

et al. 2020

Preprint

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“…Briefly: total counts were normalized to the median total counts for each cell and highly variable genes selected using the SPRING gene filtering function ("filter_genes") using parameters (90, 3, 3). Putative doublet cells were removed using Scrublet (8% of cells removed) 75 . Prior to two-dimensional visualization, the dimensionality of the data was reduced to 40 using principal components analysis (PCA).…”

Section: Mouse Scseq Datasetsmentioning

confidence: 99%

“…Single-cell RNA-seq data from HBC-derived cells from Fletcher et al and Gadye et al 37,49 , labeled via Krt5-CreER driver mice, were downloaded from GEO at accession GSE99251 using the file "GSE95601_oeHBCdiff_Cufflinks_eSet_counts_table.txt.gz". Processing was performed as described above, including total counts normalization and filtering for highly variable genes using the SPRING gene filtering function "filter_genes" with parameters (75,20,10). The resulting data were visualized in SPRING and a subset of cells were removed for quality control, including a cluster of cells with low total counts and another with predominantly reads from ERCC spike-in controls.…”

Section: Mouse Scseq Datasetsmentioning

confidence: 99%

Non-neuronal expression of SARS-CoV-2 entry genes in the olfactory system suggests mechanisms underlying COVID-19-associated anosmia

Brann

Tsukahara

Weinreb

et al. 2020

Preprint

294

346

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Recent reports suggest an association between COVID-19 and altered olfactory function. Here we analyze bulk and single cell RNA-Seq datasets to identify cell types in the olfactory epithelium that express molecules that mediate infection by SARS-CoV-2 (CoV-2), the causal agent in COVID-19. We find in both mouse and human datasets that olfactory sensory neurons do not express two key genes involved in CoV-2 entry, ACE2 and TMPRSS2. In contrast, olfactory epithelial support cells and stem cells express both of these genes, as do cells in the nasal respiratory epithelium. Taken together, these findings suggest possible mechanisms through which CoV-2 infection could lead to anosmia or other forms of olfactory dysfunction.

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“…(6) We removed the cells that had total RNA counts lower than 2% quantile or higher than 98% quantile. (7) We removed potential doublets using Scrublet 70 . Briefly, principal component analysis (PCA) was used to train a k-nearest neighbor (kNN) classifier to predict a doublet score for each cell.…”

Section: Cell Clustering Analysis Of Merfish Datamentioning

confidence: 99%

Molecular, spatial and projection diversity of neurons in primary motor cortex revealed by in situ single-cell transcriptomics

Zhang

Eichhorn

Zingg

et al. 2020

Preprint

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A mammalian brain is comprised of numerous cell types organized in an intricate manner to form functional neural circuits. Single-cell RNA sequencing provides a powerful approach to identify cell types based on their gene expression profiles and has revealed many distinct cell populations in the brain 1-3 . Single-cell epigenomic profiling 4,5 further provides information on gene-regulatory signatures of different cell types. Understanding how different cell types contribute to brain function, however, requires knowledge of their spatial organization and connectivity, which is not preserved in sequencing-based methods that involve cell dissociation 3,6 . Here, we used an in situ single-cell transcriptome-imaging method, multiplexed error-robust fluorescence in situ hybridization (MERFISH) 7 , to generate a molecularly defined and spatially resolved cell atlas of the mouse primary motor cortex (MOp). We profiled

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Scrublet: Computational Identification of Cell Doublets in Single-Cell Transcriptomic Data

Cited by 1,659 publications

References 30 publications

An Atlas of Gene Regulatory Elements in Adult Mouse Cerebrum

An Atlas of Gene Regulatory Elements in Adult Mouse Cerebrum

Non-neuronal expression of SARS-CoV-2 entry genes in the olfactory system suggests mechanisms underlying COVID-19-associated anosmia

Molecular, spatial and projection diversity of neurons in primary motor cortex revealed by in situ single-cell transcriptomics

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