2023
DOI: 10.1038/s41592-023-01884-1
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Simultaneous profiling of spatial gene expression and chromatin accessibility during mouse brain development

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Cited by 30 publications
(22 citation statements)
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“…SIMS, being based on TabNet, and therefore optimized for tabular data [30], can work well with over 45K features (Figure 2). This property would allow, in principle, SIMS to be trained simultaneously on references of multiple species, species with large genomes such as the axolotl [87], as well as multimodal data including combined single cell gene expression and gene accessibility sequencing datasets [88].…”
Section: Discussionmentioning
confidence: 99%
“…SIMS, being based on TabNet, and therefore optimized for tabular data [30], can work well with over 45K features (Figure 2). This property would allow, in principle, SIMS to be trained simultaneously on references of multiple species, species with large genomes such as the axolotl [87], as well as multimodal data including combined single cell gene expression and gene accessibility sequencing datasets [88].…”
Section: Discussionmentioning
confidence: 99%
“…This microfluidics-based combinatorial barcoding strategy also significantly reduces the variety of deterministic DNA barcodes, thereby reducing spatial barcoding costs. This strategy has been subsequently adopted for other spatial omics and spatial multiomics by transforming these omic molecules into DNA sequences and spatially barcoding them. DNA-barcoded antibodies can label and barcode target proteins with specific DNA tags for protein sequencing. ,, Tn5 transposition chemistry and CUT&Tag (Cleavage Under Targets and Tagmentation) chemistry can be utilized to tag DNAs, chromatin accessibility, and histone modification for genome and epigenome sequencing, respectively. ,,, For example, both DBiT-Seq and spatial CITE-seq enabled simultaneous spatial protein and transcriptomics profiling with protein throughput of 273 and the resolution of near-cellular level . As for joint spatial profiling of the epigenome and transcriptome, Fan’s group further developed spatial assay for transposase-accessible chromatin and RNA using sequencing (spatial ATAC-RNA-seq) and spatial assay of cleavage under targets and tagmentation and RNA using sequencing (spatial CUT&Tag-RNA-seq) .…”
Section: Dna Array-barcoded Spatial Indexing Methodsmentioning
confidence: 99%
“…49 Similarly, Peng's group developed microfluidic indexingbased spatial assay for transposase-accessible chromatin and RNA sequencing (MISAR-seq), which allowed investigation of spatiotemporal regulatory logics during mouse brain development. 52 To achieve multiplexed analysis of tissue samples, Wirth et al developed the Multiplexed Deterministic Barcoding in Tissue (xDBiT) workflow (Figure 10B). 44 Serpentine microchannel chips were designed to spatially barcode nine tissue sections in parallel (Figure 10B-i).…”
Section: Microfluidics-based Barcodingmentioning
confidence: 99%
“…The development of genome-wide assays at increasingly refined cell resolution has greatly enabled biologists to characterize chromatin dynamics and to investigate its biological function [3][4][5][6][7][8][9][10][11][12] . On the other hand, few studies have examined the spatial context of chromatin dynamics [13][14][15][16][17][18] . As such, the role of the tissue environment in mediating chromatin dynamics remains poorly understood.…”
Section: Introductionmentioning
confidence: 99%
“…Recently, several technologies have been developed to profile genome-wide chromatin states while maintaining the spatial information 11,[13][14][15][16][17][18] , thereby providing a great opportunity to systematically characterize the tissue-wide spatial organization of chromatin states and to further investigate the underlying mechanisms. On the other hand, previous analyses of such data have been limited to spatial mapping of various cell-types, whereas the relationship between spatially adjacent cell neighborhoods has not been systematically investigated.…”
Section: Introductionmentioning
confidence: 99%