Human Developmental Lung Cell Atlas (pcw 5- pcw 14)

This portal serves as an accompanying resource of the Developmental origins of cell heterogeneity in the human lung , aiming to function as an interactive tool for exploring the human lung cellular diversity, found in the first trimester of gestation. It contains (1) all analyzed scRNA-Seq datasets, (2) spatial gene expression maps and predicted cell-type distributions, generated using Spatial Transcriptomics (ST), In Situ Sequencing (HybISS) and SCRINSHOT, on whole lung tissue sections from different developmental stages. Finally, (4) we integrate a CellChat-based viewer to further explore the communication patterns between cell-types that are consistently found in the same tissue "neighborhoods".

Single-cell RNA-Sequencing Spatial transcriptomics In situ sequencing Interactomes


Supplementary video



 Click on the images to go directly to the corresponding interactive data viewer. To download data, use the 'Regions' tab to draw a region, then 'Analyze' and 'Export', and a csv file with the corresponding datapoints can be downloaded. The csv file contains global coordinates, identities and (if applicable) sector values for pie charts.

ScRNA-Seq analysis

UMAP representation of single-cell clusters and sub-clusters, gene expression and metadata:

Link to repository Interactive views: Whole dataset
Endothelial cells Epithelial cells Immune cells Mesenchymal cells Neuronal cells

Supplementary data:  Differentially expressed genes in the single cell data.



Spatial Transcriptomics data

Per gene or pie chart view of gene expression.

Link to repository Interactive views: pcw 6 pcw 8 pcw 10 pcw 11



In situ sequencing data (ISS)

In situ sequencing data. Spot location + identity, per bin pie chart view of cell type probabilities and imputed genes.

Link to repository Interactive views: pcw 5 pcw 6 pcw 13

Supplementary data:  Sequences targeted via ISS.



SCRINSHOT data

SCRINSHOT data. Spot location + identity.

Link to repository Interactive views: pcw 6 pcw 8 pcw 11 pcw 14

Supplementary data:  Sequences targeted via SCRINSHOT.



Interactome analysis

Interactome analysis with R using Cellchat.

Interactive view




THE HUMAN DEVELOPMENTAL CELL ATLAS, A SWEDISH EFFORT WITHIN THE HUMAN CELL ATLAS INITIATIVE