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Related Experiment Video

Updated: Sep 9, 2025

Production of Tissue Microarrays, Immunohistochemistry Staining and Digitalization Within the Human Protein Atlas

Production of Tissue Microarrays, Immunohistochemistry Staining and Digitalization Within the Human Protein Atlas

Published on: May 31, 2012

Constructing and Using Cell Type Populations of the Human Reference Atlas.

Andreas Bueckle¹, Bruce W Herr¹, Lu Chen²

¹Department of Intelligent Systems Engineering, Luddy School of Informatics, Computing, and Engineering, Indiana University, Bloomington, IN, 47408, USA.

Biorxiv : the Preprint Server for Biology

|September 2, 2025

Summary

This summary is machine-generated.

The Human Reference Atlas Cell Type Population (HRApop) quantifies human cell types within anatomical structures. This resource enables prediction of cell populations in 3D body volumes and tissue origins.

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Area of Science:

Human Anatomy
Cell Biology
Bioinformatics

Background:

The human body comprises trillions of cells across diverse types and anatomical structures.
Existing atlases offer limited quantitative cell type population data within specific anatomical contexts.
Scalable and reproducible methods are needed to map cell types across the human body.

Purpose of the Study:

To develop a quantitative 3D framework of human cell type populations within anatomical structures.
To create the Human Reference Atlas Cell Type Population (HRApop) dataset.
To enable prediction of cell type distributions in 3D volumes and tissue origins.

Main Methods:

Utilized high-quality single-cell (sc) transcriptomics and proteomics data.
Employed scalable and reproducible workflows for cell type annotation (CTann) using Azimuth, CellTypist, and popV.
Integrated 662 sc-transcriptomics and 104 sc-proteomics datasets, totaling over 27 million cells.
Spatially registered data to 230 locations across 17 organs.

Main Results:

HRApop v1.0 provides reference cell type populations for 73 anatomical structures (112 sex-specific).
Quantified cell types and biomarker expression for over 11 million cells from transcriptomics data.
Integrated proteomics data demonstrated generalizability of the annotation methods.
The HRApop dataset includes a total of 27,619,613 cells.

Conclusions:

HRApop offers a quantitative 3D map of human cell type populations.
This resource facilitates predictions of cell distributions within the human body.
HRApop enables determination of the spatial origin of tissue samples based on cell populations.