Results 241-250 of about 359
- Single-cell RNA and protein profiling of immune cells from the mouse brain and its border tissues new windowBrain–immune cross-talk and neuroinflammation critically shape brain physiology in health and disease. A detailed understanding of the brain immune landscape is essential for developing new treatments for neurological disorders. Single-cell
Date: (2022) Authors: Isabelle Scheyltjens , Hannah Van Hove , Karen De Vlaminck , Daliya Kancheva ... Kiavash Movahedi - 3D in vitro morphogenesis of human intestinal epithelium in a gut-on-a-chip or a hybrid chip with a cell culture insert new windowHuman intestinal morphogenesis establishes 3D epithelial microarchitecture and spatially organized crypt–villus characteristics. This unique structure is necessary to maintain intestinal homeostasis by protecting the stem cell niche in the basal
Date: (2022) Authors: Woojung Shin , Hyun Jung Kim - The SpliZ generalizes ‘percent spliced in’ to reveal regulated splicing at single-cell resolution new windowDetecting single-cell-regulated splicing from droplet-based technologies is challenging. Here, we introduce the splicing Z score (SpliZ), an annotation-free statistical method to detect regulated splicing in single-cell RNA sequencing. We applied the
Date: (2022) Authors: Julia Eve Olivieri , Roozbeh Dehghannasiri , Julia Salzman - Alevin-fry unlocks rapid, accurate and memory-frugal quantification of single-cell RNA-seq data new windowThe rapid growth of high-throughput single-cell and single-nucleus RNA-sequencing (scRNA-seq and snRNA-seq) technologies has produced a wealth of data over the past few years. The size, volume and distinctive characteristics of these data necessitate
Date: (2022) Authors: Dongze He , Mohsen Zakeri , Hirak Sarkar , Charlotte Soneson ... Rob Patro - Computational methods use different integrative strategies to tackle the challenges of spatially resolved transcriptomics data analysis.
Date: (2021) Authors: Shaina Lu , Daniel Fürth , Jesse Gillis - SpaGCN: Integrating gene expression, spatial location and histology to identify spatial domains and spatially variable g... new windowRecent advances in spatially resolved transcriptomics (SRT) technologies have enabled comprehensive characterization of gene expression patterns in the context of tissue microenvironment. To elucidate spatial gene expression variation, we present
Date: (2021) Authors: Jian Hu , Xiangjie Li , Kyle Coleman , Amelia Schroeder ... Mingyao Li - SEAM is a spatial single nuclear metabolomics method for dissecting tissue microenvironment new windowSpatial metabolomics can reveal intercellular heterogeneity and tissue organization. Here we report on the spatial single nuclear metabolomics (SEAM) method, a flexible platform combining high-spatial-resolution imaging mass spectrometry and a set of
Date: (2021) Authors: Zhiyuan Yuan , Qiming Zhou , Lesi Cai , Lin Pan ... Michael Q. Zhang - As single-cell omics continue to advance, the field of spatially resolved transcriptomics has emerged with a set of experimental and computational methods to map out the positions of cells and their gene expression profiles in space. Here we
Date: (2021) Authors: Ludvig Larsson , Jonas Frisén , Joakim Lundeberg - Coupled Transcriptomics for Differential Expression Analysis and Determination of Transcription Start Sites: Design and ... new windowThe term coupled transcriptomics is coined to describe a design of an RNA-seq experiment intended for both differential expression analysis and genome-wide determination of the transcription start sites (TSS). The minimal requirements for the first
Date: (2021) Authors: Antonio Rodríguez-García , Alberto Sola-Landa , Rosario Pérez-Redondo Ref: Antimicrobial Therapies - Deep learning and alignment of spatially resolved single-cell transcriptomes with Tangram new windowCharting an organs’ biological atlas requires us to spatially resolve the entire single-cell transcriptome, and to relate such cellular features to the anatomical scale. Single-cell and single-nucleus RNA-seq (sc/snRNA-seq) can profile cells
Date: (2021) Authors: Tommaso Biancalani , Gabriele Scalia , Lorenzo Buffoni , Raghav Avasthi ... Aviv Regev