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:Mapping the molecular identities and functions of cells alongside their spatial tissue context is key to understanding the complex interplay within and between their tissue neighbourhoods. A wide range of methods enable spatial profiling of regions, some down to the level of individual cells, in their anatomical context, via different barcoding schemes that encode either the location or the identity of target molecules. However, all these technologies face a trade-off between spatial resolution, depth of profiling, and scalability. Here, we present Barcoding by Activated Linkage of Indexes (BALI), a method that uses light to write combinatorial spatial molecular barcodes directly onto target molecules in situ, enabling multi-omics profiling by next generation sequencing. A unique feature of BALI is that the user can define the number, size, and shape of the spatial locations to be interrogated, with the potential to profile millions of distinct regions down to subcellular scale. As a proof of concept, we used BALI to capture the transcriptome, chromatin accessibility, or both, from distinct areas of the mouse brain in single tissue sections, demonstrating strong concordance with publicly available datasets. BALI therefore combines high spatial resolution, high throughput, histological adaptability, and workflow accessibility to enable powerful spatial multi-omics profiling.
Project description:Mapping the molecular identities and functions of cells alongside their spatial tissue context is key to understanding the complex interplay within and between their tissue neighbourhoods. A wide range of methods enable spatial profiling of regions, some down to the level of individual cells, in their anatomical context, via different barcoding schemes that encode either the location or the identity of target molecules. However, all these technologies face a trade-off between spatial resolution, depth of profiling, and scalability. Here, we present Barcoding by Activated Linkage of Indexes (BALI), a method that uses light to write combinatorial spatial molecular barcodes directly onto target molecules in situ, enabling multi-omics profiling by next generation sequencing. A unique feature of BALI is that the user can define the number, size, and shape of the spatial locations to be interrogated, with the potential to profile millions of distinct regions down to subcellular scale. As a proof of concept, we used BALI to capture the transcriptome, chromatin accessibility, or both, from distinct areas of the mouse brain in single tissue sections, demonstrating strong concordance with publicly available datasets. BALI therefore combines high spatial resolution, high throughput, histological adaptability, and workflow accessibility to enable powerful spatial multi-omics profiling.
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:This dataset consists of two individual sample-multiplexing (MULTI-seq) single-cell RNA sequencing experiments, MB10x01 and MB10x02. Single-cell RNA sequencing (10X Genomics) analyses were performed on a microfluidic 3D in vitro blood-brain-barrier model (containing primary human brain microvascular endothelial cells, brain vascular pericytes, and astrocytes) perfused with P. falciparum egress product (MB10x01) or P. falciparum-infected red blood cells (RBC) (MB10x02). Dataset MB10x01 included two samples multiplexed by MULTI-seq sample barcoding (TCCTCGAA for control RBC lysate, ATGCGATG for P. falciparum egress product). P. falciparum egress product was obtained by letting tightly synchronized P. falciparum-infected RBC egress in media used for perfusions (5x10^7 infected RBC/ml). 3D blood-brain-barrier models perfused with P. falciparum egress products were incubated for 24 hours and compared to a control perfused with uninfected red blood cell lysate. MULTI-seq barcoding (McGinnis et al.Ê2019) was used for sample-barcoding of these two conditions, and the dataset contains cDNA (transcriptome) and sample barcode read files. Dataset MB10x02 included three samples multiplexed by MULTI-seq sample barcoding (GCTATGCA for control RBC, CGATACTG for Trophozoite stage, TACGCAGT for Schizont stage). 3D blood-brain-barrier models were perfused for 30 minutes with P. falciparum-infected RBC in the Trophozoite stage (26-34 hours post invasion) or Schizont stage (42-48 hours post invasion) (5x10^7 infected RBC/ml). After a 20-minute wash, the 3D blood-brain-barrier models were incubated with the bound P. falciparum-infected RBC for 6 hours and compared to uninfected RBC perfused controls. MULTI-seq barcoding was used for sample-barcoding of the three conditions, and the dataset contains cDNA (transcriptome) and sample barcode read files.
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:Mapping the molecular identities and functions of cells alongside their spatial tissue context is key to understanding the complex interplay within and between their tissue neighbourhoods. A wide range of methods enable spatial profiling of regions, some down to the level of individual cells, in their anatomical context, via different barcoding schemes that encode either the location or the identity of target molecules. However, all these technologies face a trade-off between spatial resolution, depth of profiling, and scalability. Here, we present Barcoding by Activated Linkage of Indexes (BALI), a method that uses light to write combinatorial spatial molecular barcodes directly onto target molecules in situ, enabling multi-omics profiling by next generation sequencing. A unique feature of BALI is that the user can define the number, size, and shape of the spatial locations to be interrogated, with the potential to profile millions of distinct regions down to subcellular scale. As a proof of concept, we used BALI to capture the transcriptome, chromatin accessibility, or both, from distinct areas of the mouse brain in single tissue sections, demonstrating strong concordance with publicly available datasets. BALI therefore combines high spatial resolution, high throughput, histological adaptability, and workflow accessibility to enable powerful spatial multi-omics profiling.