Single-Cell Analysis for Whole-Organism Datasets

Pisco, Angela Oliveira; Tojo, Bruno; McGeever, Aaron

doi:10.1146/annurev-biodatasci-092820-031008

Cited by 9 publications

(12 citation statements)

References 138 publications

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“…Although such efforts are yielding insights ( 5 – 7 ), one caveat to current approaches is that individual organs are often collected at different locations or from different donors ( 8 ), are processed using different protocols, or lack replicate data ( 9 ). Controlled comparisons of cell types between different tissues and organs are especially difficult when donors differ in genetic background, age, environmental exposure, and epigenetic effects.…”

mentioning

confidence: 99%

The Tabula Sapiens: A multiple-organ, single-cell transcriptomic atlas of humans

Jones¹,

Karkanias²,

Bulthaup³

et al. 2022

Science

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407

145

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Molecular characterization of cell types using single-cell transcriptome sequencing is revolutionizing cell biology and enabling new insights into the physiology of human organs. We created a human reference atlas comprising nearly 500,000 cells from 24 different tissues and organs, many from the same donor. This atlas enabled molecular characterization of more than 400 cell types, their distribution across tissues, and tissue-specific variation in gene expression. Using multiple tissues from a single donor enabled identification of the clonal distribution of T cells between tissues, identification of the tissue-specific mutation rate in B cells, and analysis of the cell cycle state and proliferative potential of shared cell types across tissues. Cell type–specific RNA splicing was discovered and analyzed across tissues within an individual.

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mentioning

confidence: 99%

The Tabula Sapiens: A multiple-organ, single-cell transcriptomic atlas of humans

Jones¹,

Karkanias²,

Bulthaup³

et al. 2022

Science

Self Cite

407

145

View full text Add to dashboard Cite

show abstract

“…We collected multiple tissues from individual human donors (designated TSP [1][2][3][4][5][6][7][8][9][10][11][12][13][14][15] and performed coordinated single cell transcriptome analysis on live cells (12). We collected 17 tissues from one donor, 14 tissues from a second donor, and 5 tissues from two other donors (Fig.…”

Section: Data Collection and Cell Type Representationmentioning

confidence: 99%

“…While such efforts are yielding insights and producing data (5)(6)(7), one caveat to current approaches is that individual organs are often collected at different locations, from different donors (8) and processed using different protocols, or lack replicate data (9).…”

Section: Introductionmentioning

confidence: 99%

“…While such efforts are yielding insights ( 5–7 ), one caveat to current approaches is that individual organs are often collected at different locations, from different donors ( 8 ) and processed using different protocols, or lack replicate data ( 9 ). Controlled comparisons of cell types between different tissues and organs are especially difficult when donors differ in genetic background, age, environmental exposure, and epigenetic effects.…”

Section: Introductionmentioning

confidence: 99%

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The Tabula Sapiens: a multiple organ single cell transcriptomic atlas of humans

Quake

2021

Preprint

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In recent years there has been tremendous progress towards deep molecular characterization of cell types using single cell transcriptome sequencing. Here we report a single cell transcriptomic atlas comprising nearly 500,000 cells from 24 different human tissues and organs. In several instances multiple organs were analyzed from the same donor. Analyzing organs from the same individual controls for genetic background, age, environment, and epigenetic effects, and enables a detailed comparison of cell types that are shared between tissues. This resource provides a rich molecular characterization of more than 400 cell types, their distribution across tissues, and detailed information about tissue specific variation in gene expression. We have used the fact that multiple tissues came from the same donor to study the clonal distribution of T cells between tissues, to understand the tissue specific mutation rate in B cells, and to analyze the cell cycle state and proliferative potential of shared cell types across tissues. Finally, we have also used this data to characterize cell type specific RNA splicing and how such splicing varies across tissues within an individual.

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“…[3,4] Unlike classical methods that can analyze multiple cells, such as DOI: 10.1002/adma.202300486 macroscopic tissue analysis, a key advantage of single-cell analysis is that it elucidates gene expression in individual cells. [5][6][7] Dispensing or spatially isolating the desired number of cells to be analyzed is required before single cell analysis. Techniques contributing to such single-cell level manipulation have been developed.…”

Section: Introductionmentioning

confidence: 99%

Drycells: Cell‐Suspension Micro Liquid Marbles for Single‐Cell Picking

2023

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Cell-picking technology is essential for cell culturing. Although the recently developed tools enable single-cell-level picking, they rely on special skills or additional devices. In this work, a dry powder that encapsulates single to several cells with a >95% aqueous culture medium, thereby acting as a powerful cell-picking tool, is reported. The proposed "drycells" are formed by spraying a cell suspension onto a powder bed of hydrophobic fumed silica nanoparticles. The particles adsorb to the droplet surface and form a superhydrophobic shell, which prevents the drycells from coalescence. The number of encapsulated cells per drycell can be controlled by adjusting the drycell size and cell-suspension concentration. Moreover, it is possible to encapsulate a pair of normal or cancerous cells and create several cell colonies within a single drycell. A sieving process can be used to sort the drycells according to size. The size of the droplet can range from one to hundreds of micrometers. The drycells are sufficiently stiff to be collected using tweezers; however, centrifugation separates them into nanoparticles and cell-suspension layers, with the separated particles being recyclable. Various handling techniques, such as splitting coalescence and inner liquid replacement, can be used. It is believed that the application of the proposed drycells will greatly improve the accessibility and productivity of single-cell analysis.

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Single-Cell Analysis for Whole-Organism Datasets

Cited by 9 publications

References 138 publications

The Tabula Sapiens: A multiple-organ, single-cell transcriptomic atlas of humans

The Tabula Sapiens: A multiple-organ, single-cell transcriptomic atlas of humans

The Tabula Sapiens: a multiple organ single cell transcriptomic atlas of humans

Drycells: Cell‐Suspension Micro Liquid Marbles for Single‐Cell Picking

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