Project description:Microfluidic deterministic barcoding of mRNAs and proteins in tissue slides followed by high throughput sequencing enables the construction of high-spatial-resolution multi-omics atlas at the genome scale. Applying it to mouse embryo tissues revealed major tissue (sub)types in early-stage organogenesis, brain micro-vasculatures, and the fine structure of an optical vesicle at the single-cell-layer resolution.
Project description:This dataset contains proteomic analyses that validate the spatial proteomics technology, NicheProt. NicheProt is a 3D optical microscopy–guided, photobleaching-mediated cell barcoding approach designed to isolate intact cell types from specific microanatomical niches. We evaluate the proteomic profiles of samples processed using the multi-step NicheProt workflow and demonstrate that it does not introduce detectable protein artifacts.
Project description:This dataset contains proteomic analyses that validate the spatial proteomic technology, NicheProt, and its application to investigate dendritic cell phenotypes in inflammed mouse spleens. NicheProt is a 3D optical microscopy-guided, photobleaching-mediated cell barcoding approach to isolate intact cell types from specific microanatomical niches. Integrating with sequential bottom-up LC-MS/MS analysis we identified two distinct CD11c⁺ dendritic cell phenotypes defined by their spatial distribution. These compartment-specific populations displayed differential expression of 54 proteins. This approach enables cell-type and microregion-resolved proteomic insights, revealing previously unrecognized cell subtypes and their roles within distinct tissue compartments.
Project description:This dataset presents proteomic analyses validating the spatial proteomics technology, NicheProt. NicheProt is a 3D optical microscopy–guided, photobleaching-mediated cell barcoding approach for isolating intact cell types from defined microanatomical niches. Here, we evaluate whether tissue cryopreservation introduces protein artifacts by comparing proteomic profiles of mouse spleens processed immediately after fixation with those cryopreserved in 100% D-fructose at −80 °C prior to extraction. Our results demonstrate that D-fructose–based cryopreservation preserves protein integrity without introducing significant artifacts.
Project description:Spatial omics emerged as a new frontier of biological and biomedical research. Here, we present spatial-CUT&Tag for spatially resolved genome-wide profiling of histone modifications by combining in situ CUT&Tag chemistry, microfluidic deterministic barcoding, and next-generation sequencing. Spatially resolved chromatin states in mouse embryos revealed tissue-type-specific epigenetic regulations in concordance with ENCODE references and provide spatial information at tissue scale. Spatial-CUT&Tag revealed epigenetic control of the cortical layer development and spatial patterning of cell types determined by histone modification in mouse brain. Single-cell epigenomes can be derived in situ by identifying 20-micrometer pixels containing only one nucleus using immunofluorescence imaging. Spatial chromatin modification profiling in tissue may offer new opportunities to study epigenetic regulation, cell function, and fate decision in normal physiology and pathogenesis.
Project description:We present a new approach, Light-Seq, for multiplexed spatial indexing of intact biological samples using light-directed DNA barcoding in fixed cells and tissues followed by ex situ sequencing. Light-Seq combines spatially-targeted, rapid photocrosslinking of DNA barcodes onto cDNAs in situ with a novel one-step DNA stitching reaction to create pooled, spatially-indexed sequencing libraries. This light-directed barcoding enables in situ selection of multiple cell populations in intact fixed tissue samples for full transcriptome sequencing based on location, morphology, or protein stains, without cellular dissociation. Applying Light-Seq to mouse retinal sections, we recovered thousands of differentially enriched transcripts from three adjacent cellular layers and discovered new biomarkers for a very rare neuronal subtype, dopaminergic amacrine cells, from only 4-8 individual cells per section. Light-Seq provides an accessible workflow to combine in situ imaging and protein staining with next-generation sequencing of the same cells, leaving the sample intact sample for further analysis post-sequencing.
Project description:Deciphering the connectome, transcriptome and spatial-omics integrated multi-modal brain atlas and the underlying organization principles remains a great challenge. We developed a cost-effective Single-cell Projectome-transcriptome In situ Deciphering Sequencing (SPIDER-Seq) technique by combining viral barcoding tracing with single-cell sequencing and spatial-omics. This empowers us to delineate a comprehensive integrated single-cell spatial molecular, cellular and projectomic atlas of mouse prefrontal cortex (PFC). The projectomic and transcriptomic cell clusters display distinct modular organization principles, but are coordinately configured in the PFC. The projection neurons gradiently occupied different territories in the PFC aligning with their wiring patterns. Importantly, they show higher co-projection probability to the downstream nuclei with reciprocal circuit connections. Moreover, we integrated projectomic atlas with their distinct spectrum of neurotransmitter/neuropeptide and the receptors-related gene profiles and depicted PFC neural signal transmission network. By which, we uncovered potential mechanisms underlying the complexity and specificity of neural transmission. Finally, we predicted neuron projections with high accuracy by combining gene profiles and spatial information via machine learning. This study facilitates our understanding of brain multi-modal network and neural computation.
Project description:We present spatially resolved chromatin accessibility profiling of tissue sections via next-generation sequencing by combining in situ ATAC-seq chemistry and microfluidic deterministic barcoding. Mouse and human tissues were profiled by spatial-ATAC-seq.