Cell dissociation from nasal and bronchial brushings withcold-active protease for single-cell RNA-seq v2

Zaragosi, Laure-Emmanuelle; Barbry, Pascal

doi:10.17504/protocols.io.qubdwsn

Cited by 1 publication

(1 citation statement)

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“…The curette tip was then cut and placed in 2 ml of hypothermosol and stored at 4C until processing. Single cell suspension was generated using cold-active dispase protocol reported by Deprez, Zaragosi and colleagues 18, 82 with slight modification. Specifically, EDTA was omitted and cells were dispersed by pipetting 20 times every 5 min using a 1ml tip instead of trituration using a 21/23G needle, the final concentration of protease from Bacillus Licheniformis was 10 mg/ml.…”

Section: Methodsmentioning

confidence: 99%

An integrated cell atlas of the human lung in health and disease

Sikkema

Strobl

Zappia

et al. 2022

Preprint

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126

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Organ- and body-scale cell atlases have the potential to transform our understanding of human biology. To capture the variability present in the population, these atlases must include diverse demographics such as age and ethnicity from both healthy and diseased individuals. The growth in both size and number of single-cell datasets, combined with recent advances in computational techniques, for the first time makes it possible to generate such comprehensive large-scale atlases through integration of multiple datasets. Here, we present the integrated Human Lung Cell Atlas (HLCA) combining 46 datasets of the human respiratory system into a single atlas spanning over 2.2 million cells from 444 individuals across health and disease. The HLCA contains a consensus re-annotation of published and newly generated datasets, resolving under- or misannotation of 59% of cells in the original datasets. The HLCA enables recovery of rare cell types, provides consensus marker genes for each cell type, and uncovers gene modules associated with demographic covariates and anatomical location within the respiratory system. To facilitate the use of the HLCA as a reference for single-cell lung research and allow rapid analysis of new data, we provide an interactive web portal to project datasets onto the HLCA. Finally, we demonstrate the value of the HLCA reference for interpreting disease-associated changes. Thus, the HLCA outlines a roadmap for the development and use of organ-scale cell atlases within the Human Cell Atlas.

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Section: Methodsmentioning

confidence: 99%