INTRODUCTION

The Pig Single Cell RNA Atlas (PCA) database is created to facilitate the application of pigs in biomedical research and applications. Pigs have been used as large animals for modelling human diseases, testing and development of treatments. Recently, there are growing interests in using genetically modified pigs for human organ transplantation. And breakthroughs in kidney and heart transplantation have been achieved. However, it is yet to fully understand the cellular compositions and similarity between pig and human organs. Other remaining challenges such as chronic immune rejections are still the major challenges to be overcome. The PCA is thus created as a fully open access resource to facilitate the understanding of cell and organ functions in pigs using single cell RNA sequencing.

In this first release of PCA (v.2022.1), we have performed single cell and single nucleic RNA sequencing of 20 tissues (from 10 major organs). Over 200,000 single cells are sequenced using single cell or single nuclei RNA sequencing technologies. The composition of cell types within tissues/organs is annotated according to the expression of cell type-specific markers.

To enable the usage of this vast amount of transcriptome data, we have created an interactive database, allowing free exploration of cell type specific gene expression, co-expression analysis, generation of various gene expression plots, and analysis of tissue and cell type specific gene expression.

Overview of tissues included in the first release of Pig Single Cell RNA Atlas.

ABOUT TEAM AND THE PIG ATLAS CONSORTIUM

About

The Pig Atlas Project was initiated by Associate Professor Yonglun Luo and Professor Lars Bolund, from the Lars Bolund Institute of Regenerative Medicine (LBI, BGI-Research and Department of Biomedicine, Aarhus University; Professor Mathias Uhlen, from the Human Protein Atlas and the SciLifeLab; and Professor Huanming Yang, from BGI-Research. The aim of this project is to gain better genomic and biomedical insights into pig gene expression, cell and organs functions using the next generation sequencing technologies. The biomedical aim of this project is to facilitate the application of pigs in biomedicine.

The brain-wide classification of protein-coding gene expression has been released in 2020¹. The brain-wide RNA editing landscape was released in 2021². The body-wide classification of pig gene expression (based on bulk RNA sequencing) specificity and distribution has been released in 20223. The latest organ-wide profiling of pig cell heterogeneity and gene expression is now released in Q2 of 2022 (submitted for publication).

Signing ceremony of the Pig Atlas

PUBLICATIONS

Sjöstedt E, Zhong W, Fagerberg L, Karlsson M, Mitsios N, Adori C, Oksvold P, Edfors F, Limiszewska A, Hikmet F, Huang J, Du Y, Lin L, Dong Z, Yang L, Liu X, Jiang H, Xu X, Wang J, Yang H, Bolund L, Mardinoglu A, Zhang C, von Feilitzen K, Lindskog C, Pontén F, Luo Y, Hökfelt T, Uhlén M, Mulder J. An atlas of the protein-coding genes in the human, pig, and mouse brain. Science. 2020 Mar 6;367(6482):eaay5947. doi: 10.1126/science.aay5947. PMID: 32139519.
Huang J, Lin L, Dong Z, Yang L, Zheng T, Gu W, Zhang Y, Yin T, Sjöstedt E, Mulder J, Uhlén M, Kristiansen K, Bolund L, Luo Y. A porcine brain-wide RNA editing landscape. Commun Biol. 2021 Jun 10;4(1):717. doi: 10.1038/s42003-021-02238-3. PMID: 34112917; PMCID: PMC8192503.
Karlsson M, Sjöstedt E, Oksvold P, Sivertsson Å, Huang J, Álvez MB, Arif M, Li X, Lin L, Yu J, Ma T, Xu F, Han P, Jiang H, Mardinoglu A, Zhang C, von Feilitzen K, Xu X, Wang J, Yang H, Bolund L, Zhong W, Fagerberg L, Lindskog C, Pontén F, Mulder J, Luo Y, Uhlen M. Genome-wide annotation of protein-coding genes in pig. BMC Biol. 2022 Jan 25;20(1):25. doi: 10.1186/s12915-022-01229-y. PMID: 35073880; PMCID: PMC8788080.