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    1. Immunology and Inflammation
    2. Neuroscience

    Spatial transcriptomics of meningeal inflammation reveals inflammatory gene signatures in adjacent brain parenchyma

    Sachin P Gadani, Saumitra Singh ... Pavan Bhargava
    Leptomeningeal inflammation in a mouse model of multiple sclerosis triggers deeply penetrating gene changes in underlying brain tissue, described using spatial transcriptomics.
    Version of Record
    Short Report
    • Important
    • Solid
    1. Cancer Biology

    A chronic signaling TGFb zebrafish reporter identifies immune response in melanoma

    Haley R Noonan, Alexandra M Thornock ... Leonard I Zon
    An in vivo reporter of TGFb signaling in zebrafish reveals that melanoma cells undergoing chronic TGFb signaling up-regulate extracellular matrix genes, down-regulate IFN, and are preferentially phagocytosed by macrophages compared to non-TGFb responsive melanoma cells.
    1. Immunology and Inflammation
    2. Microbiology and Infectious Disease

    Chemokine expression profile of an innate granuloma

    Megan E Amason, Cole J Beatty ... Edward A Miao
    A successful innate granuloma requires CCR2 to organize the macrophage ring, and without CCR2, mice succumb to Chromobacterium violaceum infection.
    1. Neuroscience

    Three-dimensional single-cell transcriptome imaging of thick tissues

    Rongxin Fang, Aaron Halpern ... Xiaowei Zhuang
    By integrating multiplexed error-robust fluorescence in situ hybridization (MERFISH), deep learning, optical sectioning, and protocol optimization, thick-tissue 3D MERFISH allows volumetric single-cell transcriptome imaging of thick-tissue samples, broadening the scope of applications of spatial genomics.
    1. Developmental Biology

    Spatial transcriptomics in adult Drosophila reveals new cell types in the brain and identifies subcellular mRNA patterns in muscles

    Jasper Janssens, Pierre Mangeol ... Frank Schnorrer
    Not revised
    Reviewed Preprint v1
    • Valuable
    • Solid
    1. Ecology
    2. Evolutionary Biology

    Phylogenomic and mitogenomic data can accelerate inventorying of tropical beetles during the current biodiversity crisis

    Michal Motyka, Dominik Kusy ... Ladislav Bocak
    Integrated phylogenomics and mitochondrial DNA inventory of net-winged beetles across three continents suggest ~1000 undescribed species, biodiversity hot spots, and phylogeny-based classification that sets up the basis for further research.
    1. Cell Biology

    Science Forum: Vision, challenges and opportunities for a Plant Cell Atlas

    Plant Cell Atlas Consortium, Suryatapa Ghosh Jha ... Seung Y Rhee
    A Plant Cell Atlas that shows the location and organization of molecules at cellular and tissue levels could have far-reaching consequences for plant sciences.
    1. Chromosomes and Gene Expression
    2. Genetics and Genomics

    Comparative analysis of multiplexed in situ gene expression profiling technologies

    Austin Hartman, Rahul Satija
    Not revised
    Reviewed Preprint v1
    • Important
    • Incomplete
    1. Neuroscience

    The subiculum is a patchwork of discrete subregions

    Mark S Cembrowski, Lihua Wang ... Nelson Spruston
    Pyramidal cells of the subiculum, a major output cell type of the hippocampus, can be deconstructed into distinct subtypes that exhibit a patchwork-like organization in space.
    1. Neuroscience

    Single-cell RNAseq analysis of spinal locomotor circuitry in larval zebrafish

    Jimmy J Kelly, Hua Wen, Paul Brehm
    Single-cell transcriptomics of larval zebrafish spinal cord reveal ion channels and exocytotic machinery that enhance transmitter release in neuronal types shown to mediate high-speed swimming and escape behavior.