High-Spatial-Resolution Multi-Omics Sequencing via Deterministic Barcoding in Tissue

Liu, Yang; Yang, Mingyu; Deng, Yanxiang; Su, Graham; Enninful, Archibald; Guo, Cindy C.; Tebaldi, Toma; Zhang, Di; Kim, Dongjoo; Bai, Zhiliang; Norris, Eileen; Pan, Alisia; Li, Jiatong; Xiao, Yang; Halene, Stephanie; Fan, Rong

doi:10.1016/j.cell.2020.10.026

Cited by 458 publications

(371 citation statements)

References 55 publications

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“…Based on the current library sequencing saturation rate, we prospect that we may be able to obtain up to 2,000 unique transcripts per 100 μm 2 area. This output is comparable to the most recent high-output ST technologies with 10 μm resolution, such as Slide-seqV2 (~550 per 100 μm 2 ) (Stickels et al, 2020) and DBiT-seq (1,320-4,900 per 100 μm 2 ) (Liu et al, 2020). Therefore, in addition to providing an unprecedented submicrometer resolution, Seq-Scope can reveal high-quality transcriptome information.…”

Section: Discussionmentioning

confidence: 56%

“…Among these three major methodologies, the spatial barcoding method is the most straightforward, comprehensive, widely-used and commercially available method easily accessible to many laboratories (Asp et al, 2020; Crosetto et al, 2015; Liao et al, 2020). Spatial barcoding is currently achieved by the microspotting of nucleotides (Salmen et al, 2018; Stahl et al, 2016), an array of split-pool-barcoded beads (Rodriques et al, 2019; Stickels et al, 2020; Vickovic et al, 2019), or a fabricated microfluidic channel (Liu et al, 2020). These methods, however, have an intrinsic limitation due to their low-resolution specifications.…”

Section: Introductionmentioning

confidence: 99%

“…Unlike former methods that use deterministic barcoding (Liu et al, 2020; Salmen et al, 2018; Stahl et al, 2016) or split-pool bead techniques (Rodriques et al, 2019; Stickels et al, 2020; Vickovic et al, 2019), our technique is based on the solid-phase amplification of a random barcode molecule, which can be conveniently achieved by the Illumina sequencing-by-synthesis (SBS) platform (Bentley et al, 2008). We show that this technology enables the generation of up to 1.5 million different spatially defined barcodes in a 1 mm 2 area, which is substantially higher than any currently existing technologies by several orders of magnitude (e.g., ~10,000 fold over VISIUM (Bergenstrahle et al, 2020), ~600 fold over DBiT-seq (Liu et al, 2020), ~120 fold over Slide-Seq (Rodriques et al, 2019; Stickels et al, 2020) and ~15 fold over HDST (Vickovic et al, 2019)). Seq-Scope has a center-to-center resolution of 0.5-1 μm, far superior to previous technologies and comparable to an optical microscope.…”

Section: Introductionmentioning

confidence: 99%

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Seq-Scope: Submicrometer-resolution spatial transcriptomics for single cell and subcellular studies

Cho

Park

et al. 2021

Preprint

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Spatial barcoding technologies have the potential to reveal histological details of transcriptomic profiles; however, they are currently limited by their low resolution. Here we report Seq-Scope, a spatial barcoding technology with a resolution almost comparable to an optical microscope. Seq-Scope is based on a solid-phase amplification of randomly barcoded single-molecule oligonucleotides using an Illumina sequencing-by-synthesis platform. The resulting clusters annotated with spatial coordinates are processed to expose RNA-capture moiety. These RNA-capturing barcoded clusters define the pixels of Seq-Scope that are approximately 0.5-1 μm apart from each other. From tissue sections, Seq-Scope visualizes spatial transcriptome heterogeneity at multiple histological scales, including tissue zonation according to the portal-central (liver), crypt-surface (colon) and inflammation-fibrosis (injured liver) axes, cellular components including single cell types and subtypes, and subcellular architectures of nucleus, cytoplasm and mitochondria. Seq-scope is quick, straightforward and easy-to-implement, and makes spatial single cell analysis accessible to a wide group of biomedical researchers.

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Section: Discussionmentioning

confidence: 56%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Seq-Scope: Submicrometer-resolution spatial transcriptomics for single cell and subcellular studies

Cho

Park

et al. 2021

Preprint

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“…As for the latter group, Slide-seq ( 16 ), spatial transcriptomics (ST, Visium) ( 17 ) and their optimized versions Slide-seqV2 and HDST (high-definition spatial transcriptome) ( 18, 19 ), respectively, use barcoded arrays and have attracted significant attention. Similarly, DBiT-seq (deterministic barcoding in tissue for spatial omics sequencing) uses microfluidic channels for delivering barcoded probes directly into tissues and can simultaneously capture transcripts and selected protein targets ( 20 ). Although unbiased in the nature of captured transcripts, barcoded probe-based techniques suffer from an inadequate balance between resolution, average numbers of gene/transcript per bin and capture rate across multiple bins.…”

Section: Main Textmentioning

confidence: 99%

Spatiotemporal transcriptomic atlas of mouse organogenesis using DNA nanoball patterned arrays

Chen¹,

Liao²,

Cheng³

et al. 2021

Preprint

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High-throughput profiling of in situ gene expression represents a major advance towards the systematic understanding of tissue complexity. Applied with enough capture area and high sample throughput it will help to define the spatio-temporal dynamics of gene expression in tissues and organisms. Yet, current technologies have considerable bottlenecks that limit widespread application. Here, we have combined DNA nanoball (DNB) patterned array chips and in situ RNA capture to develop Stereo-seq (Spatio-Temporal Enhanced REsolution Omics-sequencing). This approach allows high sample throughput transcriptomic profiling of histological sections at unprecedented (nanoscale) resolution with areas expandable to centimeter scale, high sensitivity and homogenous capture rate. As proof of principle, we applied Stereo-seq to the adult mouse brain and sagittal sections of E11.5 and E16.5 mouse embryos. Thanks to its unique features and amenability to additional modifications, Stereo-seq can pave the way for the systematic spatially resolved-omics characterization of tissues and organisms.

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“…Cell heterogeneity plays a critical role in shaping cell physiology and fates in most biological processes [1,2]. Different single-cell analysis technologies, including genomics [3], transcriptomics [4][5][6], and proteomics [7][8][9], etc. [10], are rapidly developing to decode cell heterogeneity at different levels.…”

mentioning

confidence: 99%

NOMA: a high-throughput microchip for robust, sequential measurements of secretions from the same single-cells

Zhu

et al. 2021

Preprint

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Despite advances in single-cell secretion analysis technologies, lacking simple methods to reliably keep the live single-cells traceable for longitudinal detection poses a significant obstacle. Here we developed the high-density NOMA (narrow-opening microwell array) microchip that realized the retention of ≥97% of trapped single cells during repetitive detection procedures, regardless of adherent or suspension cells. We demonstrated its use to decode the correlation of protein abundance between secreted extracellular vesicles (EVs) and its donor cells at the same single-cell level, in which we found that these two were poorly correlated with each other. We further applied it in monitoring single-cell protein secretions sequentially from the same single cells. Notably, we observed the digital protein secretion patterns dominate the protein secretion. We also applied the microchip for longitudinally tracking of the single-cell integrative secretions over days, which revealed the presence of “super secretors” within the cell population that could be more persistent to secrete protein or extracellular vesicle for an extended period. The NOMA platform reported here is simple, robust, and easy to operate for realizing sequential measurements from the same single cells, representing a novel and informative tool to inspire new observations in biomedical research.

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High-Spatial-Resolution Multi-Omics Sequencing via Deterministic Barcoding in Tissue

Cited by 458 publications

References 55 publications

Seq-Scope: Submicrometer-resolution spatial transcriptomics for single cell and subcellular studies

Seq-Scope: Submicrometer-resolution spatial transcriptomics for single cell and subcellular studies

Spatiotemporal transcriptomic atlas of mouse organogenesis using DNA nanoball patterned arrays

NOMA: a high-throughput microchip for robust, sequential measurements of secretions from the same single-cells

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