SCANPY: large-scale single-cell gene expression data analysis

Novel Alzheimer risk genes determine the microglia response to amyloid‐β but not to TAU pathology

Sierksma1, Lu2, Mancuso3 et al. 2020EMBO Mol Med251111804Get access via publisherAdd to dashboardCite Exaggerated anticipatory anxiety is common in social anxiety disorder (SAD). Neuroimaging studies have revealed altered neural activity in response to social stimuli in SAD, but fewer studies have examined neural activity during anticipation of feared social stimuli in SAD. The current study examined the time course and magnitude of activity in threat processing brain regions during speech anticipation in socially anxious individuals and healthy controls (HC). Method Participants (SAD n = 58; HC n = 16) underwent functional magnetic resonance imaging (fMRI) during which they completed a 90s control anticipation task and 90s speech anticipation task. Show abstract Exaggerated anticipatory anxiety is common in social anxiety disorder (SAD). Neuroimaging studies have revealed altered neural activity in response to social stimuli in SAD, but fewer studies have examined neural activity during anticipation of feared social stimuli in SAD. The current study examined the time course and magnitude of activity in threat processing brain regions during speech anticipation in socially anxious individuals and healthy controls (HC). Method Participants (SAD n = 58; HC n = 16) underwent functional magnetic resonance imaging (fMRI) during which they completed a 90s control anticipation task and 90s speech anticipation task. show abstract“…The raw BCL files were demultiplexed and aligned with Cellranger (v3. 1. 0) against a joint database with the mouse genome (mm10, GRCm38), the rat genome (Rnor_6. 0), and the human genome (GRCh38). Cells from each experimental group were clustered using Scanpy (v1. 4. 4;Wolf et al, 2018). Cells were separated, as expected, in clusters per organism. …”Section: Single Microglia Sequencingmentioningconfidence: 98%

Novel Alzheimer risk genes determine the microglia response to amyloid‐β but not to TAU pathology

Sierksma1, Lu2, Mancuso3 et al. 2020EMBO Mol Med251111804Get access via publisherAdd to dashboardCite Exaggerated anticipatory anxiety is common in social anxiety disorder (SAD). Neuroimaging studies have revealed altered neural activity in response to social stimuli in SAD, but fewer studies have examined neural activity during anticipation of feared social stimuli in SAD. The current study examined the time course and magnitude of activity in threat processing brain regions during speech anticipation in socially anxious individuals and healthy controls (HC). Method Participants (SAD n = 58; HC n = 16) underwent functional magnetic resonance imaging (fMRI) during which they completed a 90s control anticipation task and 90s speech anticipation task. Show abstract Exaggerated anticipatory anxiety is common in social anxiety disorder (SAD). Neuroimaging studies have revealed altered neural activity in response to social stimuli in SAD, but fewer studies have examined neural activity during anticipation of feared social stimuli in SAD. The current study examined the time course and magnitude of activity in threat processing brain regions during speech anticipation in socially anxious individuals and healthy controls (HC). Method Participants (SAD n = 58; HC n = 16) underwent functional magnetic resonance imaging (fMRI) during which they completed a 90s control anticipation task and 90s speech anticipation task. show abstract“…The most common biological data correction is to remove the effects of the cell cycle on the transcriptome. This data correction can be performed by a simple linear regression against a cell cycle score as implemented in the Scanpy and Seurat platforms Wolf et al, 2018) or in specialized packages with more complex mixture models such as scLVM or f-scLVM . Lists of marker genes to compute cell cycle scores are obtained from the literature (Macosko et al, 2015). …”Section: Regressing Out Biological Effectsmentioningconfidence: 99%

Current best practices in single‐cell RNA‐seq analysis: a tutorial

Luecken1, Theis2 2019Molecular Systems Biology1,945131,7930Get access via publisherAdd to dashboardCite Exaggerated anticipatory anxiety is common in social anxiety disorder (SAD). Neuroimaging studies have revealed altered neural activity in response to social stimuli in SAD, but fewer studies have examined neural activity during anticipation of feared social stimuli in SAD. The current study examined the time course and magnitude of activity in threat processing brain regions during speech anticipation in socially anxious individuals and healthy controls (HC). Method Participants (SAD n = 58; HC n = 16) underwent functional magnetic resonance imaging (fMRI) during which they completed a 90s control anticipation task and 90s speech anticipation task. Show abstract Exaggerated anticipatory anxiety is common in social anxiety disorder (SAD). Neuroimaging studies have revealed altered neural activity in response to social stimuli in SAD, but fewer studies have examined neural activity during anticipation of feared social stimuli in SAD. The current study examined the time course and magnitude of activity in threat processing brain regions during speech anticipation in socially anxious individuals and healthy controls (HC). Method Participants (SAD n = 58; HC n = 16) underwent functional magnetic resonance imaging (fMRI) during which they completed a 90s control anticipation task and 90s speech anticipation task. show abstract“…Using a modified workflow described previously in (39), samples were filtered by Gaussian fit of read count, expressed gene count, and number of cells in which a gene is expressed. Counts were normalized by cell, log transformed, principle component analysis performed with 15 components, and k-nearest neighbors computed using SCANPY (40), and then the full data set normalized with R package 'scran' (41). Batch correction by individual and sample region was performed with SCANPY. …”Section: Single-cell Rna-seqmentioningconfidence: 99%“…ACE2 mRNA expression is shown for comparison in upper panel. UMAP dimensionality reduction plot was computed and visualized in ScanPy (40). Figure 5. …”Section: Author Contributionsmentioningconfidence: 99%“…Trachea expression data is taken from GSE103354 (37) and intestinal epithelia data is derived from GSE92332(61). Visualized in ScanPy(40). …”mentioningconfidence: 99%See 1 more Smart Citation

Bioinformatic characterization of angiotensin-converting enzyme 2, the entry receptor for SARS-CoV-2

Barker1, Parkkila2 2020Preprint140110Get access via publisherAdd to dashboardCite Exaggerated anticipatory anxiety is common in social anxiety disorder (SAD) VSports app下载. Neuroimaging studies have revealed altered neural activity in response to social stimuli in SAD, but fewer studies have examined neural activity during anticipation of feared social stimuli in SAD. The current study examined the time course and magnitude of activity in threat processing brain regions during speech anticipation in socially anxious individuals and healthy controls (HC). Method Participants (SAD n = 58; HC n = 16) underwent functional magnetic resonance imaging (fMRI) during which they completed a 90s control anticipation task and 90s speech anticipation task. Show abstract Exaggerated anticipatory anxiety is common in social anxiety disorder (SAD). Neuroimaging studies have revealed altered neural activity in response to social stimuli in SAD, but fewer studies have examined neural activity during anticipation of feared social stimuli in SAD. The current study examined the time course and magnitude of activity in threat processing brain regions during speech anticipation in socially anxious individuals and healthy controls (HC). Method Participants (SAD n = 58; HC n = 16) underwent functional magnetic resonance imaging (fMRI) during which they completed a 90s control anticipation task and 90s speech anticipation task. show abstractScite is an AI-powered research tool that helps researchers better discover and evaluate scientific literature through Smart Citations—a revolutionary system that shows whether articles support, contrast, or simply mention a given claim. Founded in 2018, and now part of Research Solutions, Scite has indexed over 1. 4 billion citations and partnered with more than 30 major publishers to provide researchers with unparalleled access to scientific literature. With its Scite Assistant, Smart Citation Index, and advanced search capabilities, the platform addresses critical challenges such as information overload and research reproducibility. Trusted by two million active users worldwide, Scite is reshaping how researchers interact with scholarly content—building ethical, transparent AI tools that support rigorous, copyright-compliant research.