Asian Immune Diversity Atlas (AIDA)

Version 0, updated 19 March 2025

Thank you for your interest in the Asian Immune Diversity Atlas (AIDA). AIDA is a multi-national single-cell reference atlas of circulating immune cells from donors from diverse populations. Data generation is on-going as of 2025, and AIDA comprises multiple phases and data freezes. We appreciate your patience in navigating the various AIDA resources and data freezes, especially since each AIDA member country has their own data access regulations.

AIDA Publications, Protocols, and Media

Publications

The paper describing the AIDA Phase 1 resource (Asian diversity in human immune cells) has been published open access (Kock et al., Cell, 2025), and can be accessed via https://www.cell.com/cell/fulltext/S0092-8674(25)00202-8 and https://doi.org/10.1016/j.cell.2025.02.017.

For further details on this paper, please contact the corresponding authors: Dr Jay W. Shin (jay_shin@gis.a-star.edu.sg), Dr Woong-Yang Park (woongyang.park@samsung.com), and Dr Shyam Prabhakar (prabhakars@gis.a-star.edu.sg)

Quantification of escape from X chromosome inactivation with single-cell omics data reveals heterogeneity across cell types and tissues
(Tomofuji et al., Cell Genomics, 2024, https://doi.org/10.1016/j.xgen.2024.100625, open access)

For further details on this paper, please contact the corresponding authors: Dr Yoshihiko Tomofuji (ytomofuji@sg.med.osaka-u.ac.jp) and Dr Yukinori Okada (yuki-okada@m.u-tokyo.ac.jp)

Single-cell RNA sequencing of peripheral blood links cell-type-specific regulation of splicing to autoimmune and inflammatory diseases (Tian et al., Nature Genetics, 2024, https://doi.org/10.1038/s41588-024-02019-8, open access)

For further details on this paper, please contact the corresponding author: Dr Boxiang Liu (boxiangliu@nus.edu.sg)

(The list above will be updated periodically.)

Protocols

Our PBMC isolation protocol is available via protocols.io: https://www.protocols.io/view/pbmcs-isolation-from-cpt-tube-b8r9rv96
Our sample multiplexing and cell preparation protocol is available via protocols.io: https://www.protocols.io/view/demuxlet-cell-preparation-protocol-b8sdrwa6

Media

Our AIDA Phase 1 press releases include:

Singapore Scientists to Help Develop Asian Immune Diversity Atlas; A*STAR: https://www.a-star.edu.sg/News/astarNews/news/press-releases/singapore-scientists-to-help-develop-asian-immune-diversity-atlas
RIKEN IMS Receives CZI Ancestry Network Grant to Investigate Immune Diversity in Japan and Asia; RIKEN: https://www.ims.riken.jp/english/2021/12/004329.php
Scientists from the Genome Institute of Singapore awarded CZI Ancestry Network grant to investigate immune diversity in Singapore and Asia; A*STAR: https://www.a-star.edu.sg/docs/librariesprovider11/gis-publicity/t1/20211211_press_release-astar_gis_receives_czi_ancestry_network_grant-dec_9_ls_sp.pdf

AIDA is supported by the Chan Zuckerberg Initiative (CZI):

CZI Seed Networks: https://chanzuckerberg.com/science/programs-resources/cell-science/seednetworks/asian-immune-diversity-atlas/
CZI Ancestry Networks: https://chanzuckerberg.com/science/programs-resources/cell-science/ancestry-networks/immune-cell-atlas-of-asian-populations/

AIDA Resources

We recommend our AIDA Phase 1 visualisations at the Chan Zuckerberg (CZ) CELLxGENE data portal as a starting point for exploring AIDA resources: https://cellxgene.cziscience.com/collections/ced320a1-29f3-47c1-a735-513c7084d508.

AIDA Phase 1 Data Freeze v1

The AIDA Phase 1 Data Freeze v1 object comprises 1,058,909 peripheral blood mononuclear cells (PBMCs) from 503 healthy donors from Japan, Singapore, and South Korea alongside 5 common controls. This first AIDA data freeze was released to the research community pre-publication (including via the Human Cell Atlas (HCA) Data Portal, and CZ CELLxGENE), and was also part of the first CZ CELLxGENE Census assembled in May 2023.

AIDA Phase 1 Data Freeze v1 Please cite Kock et al., Cell, 2025, https://doi.org/10.1016/j.cell.2025.02.017, if you use/analyse any of these datasets. For X chromosome inactivation escape analyses, please also cite Tomofuji et al., Cell Genomics, 2024, https://doi.org/10.1016/j.xgen.2024.100625. For splicing analyses, please also cite Tian et al., Nature Genetics, 2024, https://doi.org/10.1038/s41588-024-02019-8.
Gene-cell matrix and metadata	CZ CELLxGENE: https://cellxgene.cziscience.com/collections/ced320a1-29f3-47c1-a735-513c7084d508
Pre-processing and data analysis code	GitHub: https://github.com/prabhakarlab/AIDA_Phase1/ Zenodo: https://doi.org/10.5281/zenodo.14722571
Japan 10x 5’ v2 gene expression FASTQ files	Open access at Human Cell Atlas Data Portal: https://data.humancellatlas.org/explore/projects/f0f89c14-7460-4bab-9d42-22228a91f185
Singapore 10x 5’ v2 gene expression FASTQ files	The Singapore donor data are not publicly available due to data privacy regulations; please e-mail helios_science@ntu.edu.sg for the HELIOS Data Access Committee (DAC) data access application.
South Korea 10x 5’ v2 gene expression FASTQ files	Open access at Human Cell Atlas Data Portal: https://data.humancellatlas.org/explore/projects/f0f89c14-7460-4bab-9d42-22228a91f185

AIDA Phase 1 Data Freeze v2

The AIDA Phase 1 Data Freeze v2 object comprises 1,265,624 PBMCs from 619 donors, spanning 7 population groups across 5 Asian countries (India, Japan, Singapore, South Korea, and Thailand), and 6 common controls. Going from Data Freeze v1 to Data Freeze v2, we added additional healthy Asian donor samples and control samples. We excluded 5 Asian donors (SG_HEL_H141, SG_HEL_H185, SG_HEL_H203, SG_HEL_H239, and SG_HEL_H347) from AIDA Phase 1 Data Freeze v1 with ambiguous medication data. We added 121 new Asian donors (32 Singapore donors, 59 Thailand Thai donors, and 30 India Indian donors). These new Asian donors included donors SG_HEL_H262 and SG_HEL_H269, as well as donors profiled in experimental batches SG_HEL_B023, SG_HEL_B024, TH_MAH_B001, TH_MAH_B002, TH_MAH_B003, TH_MAH_B004, IN_NIB_B001, and IN_NIB_B002. We also removed two libraries with high doublet rates (SG_HEL_B011_L002 and SG_HEL_B021_L001). Please see our paper (Kock et al., Cell, 2025) for further details. This second AIDA data freeze was also released to the research community pre-publication.

AIDA Phase 1 Data Freeze v2 Please cite Kock et al., Cell, 2025, https://doi.org/10.1016/j.cell.2025.02.017, if you use/analyse any of these datasets. For X chromosome inactivation escape analyses, please also cite Tomofuji et al., Cell Genomics, 2024, https://doi.org/10.1016/j.xgen.2024.100625. For splicing analyses, please also cite Tian et al., Nature Genetics, 2024, https://doi.org/10.1038/s41588-024-02019-8.
Gene-cell matrix and metadata	CZ CELLxGENE: https://cellxgene.cziscience.com/collections/ced320a1-29f3-47c1-a735-513c7084d508
Cell annotation metadata	Cell Annotation Platform: https://celltype.info/project/336/dataset/591
Pre-processing and data analysis code	GitHub: https://github.com/prabhakarlab/AIDA_Phase1/ Zenodo: https://doi.org/10.5281/zenodo.14722571
India 10x 5’ v2 gene expression FASTQ files	Open access at Human Cell Atlas Data Portal: https://data.humancellatlas.org/explore/projects/f0f89c14-7460-4bab-9d42-22228a91f185
Japan 10x 5’ v2 gene expression FASTQ files and Illumina GSAv3 genotype data	Managed access at Human Cell Atlas Data Portal: https://explore.data.humancellatlas.org/projects/35d5b057-3daf-4ccd-8112-196194598893
Singapore 10x 5’ v2 gene expression FASTQ files and Illumina GSAv3 genotype data	The Singapore donor data are not publicly available due to data privacy regulations; please e-mail helios_science@ntu.edu.sg for the HELIOS Data Access Committee (DAC) data access application.
South Korea 10x 5’ v2 gene expression FASTQ files and Illumina GSAv3 genotype data	Transiting to HCA Managed Access and will be available for application via the Human Cell Atlas Data Portal: https://data.humancellatlas.org/hca-bio-networks/genetic-diversity/datasets
Thailand 10x 5’ v2 gene expression FASTQ files	Transiting to HCA Managed Access and will be available for application via the Human Cell Atlas Data Portal: https://data.humancellatlas.org/hca-bio-networks/genetic-diversity/datasets

AIDA Acknowledgements

Inclusion and Ethics

We included local researchers in India, Japan, Singapore, South Korea, and Thailand in every aspect of research, including study design, study implementation, data ownership, and authorship. Community engagement has been led by authors and collaborators in each country with expertise in epidemiology and population genetics.
All study protocols were approved by the Institutional Review Boards (IRBs) of the institutions our laboratories are affiliated with (Genome Institute of Singapore: IRBs 2020-012 and 2022-051; Nanyang Technological University: IRB-2016-11-030-01, IRB-2016-11-030, and 18IC4698; RIKEN: IRB H30-9; Samsung Genome Institute, Samsung Medical Center: IRB 2019-09-121; Yongin Severance Medical Center: IRB 9-2020-0109; Faculty of Medicine Siriraj Hospital, Mahidol University: IRB 725/2563(IRB3); National Institute of Biomedical Genomics: IRB NIBMG/2022/1/0022) prior to dataset generation.

Data Generation

AIDA data generation was supported by:

Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR) in Singapore; Samsung Genome Institute, Samsung Medical Center in South Korea; RIKEN in Japan; Mahidol University in Thailand; and the John C. Martin Centre for Liver Research and Innovations (JCMLRI) in India.
Grants CZF2019-002446 (Shyam Prabhakar, Woong-Yang Park, Jay W. Shin, John C. Chambers) and CZF2021-238829 (5022) (Shyam Prabhakar, Woong-Yang Park, Jay W. Shin) from Chan Zuckerberg Foundation, and 2020-224570 (Shyam Prabhakar, Varodom Charoensawan, Ponpan Matangkasombut, Partha P. Majumder), 2021-240178 (Shyam Prabhakar, Woong-Yang Park, Jay W. Shin, John C. Chambers, Varodom Charoensawan, Ponpan Matangkasombut, Partha P. Majumder) from Chan Zuckerberg Initiative (CZI) DAF, an advised fund of Silicon Valley Community Foundation.
Singapore donor samples were obtained through the Health for Life in Singapore (HELIOS) Study (Lee Kong Chian School of Medicine (LKCMedicine), Nanyang Technological University (NTU); National Healthcare Group (NHG), Singapore; Imperial College London). We would like to express our gratitude to HELIOS study participants, and the HELIOS operation team for recruitment, organisation, and data and sample collection, including Yoke Yin Terry Tong, Swat Kim Kerk, Guo Liang Low, and Halimah Binte Ibrahim (HELIOS Biobanking team).
Singapore Ministry of Health’s National Medical Research Council (OF-LCG: MOH-000271-00) and intramural funding (NTU; LKCMedicine; NHG); A*STAR Industry Alignment Fund (Pre-Positioning): H17/01/a0/007, and H18/01/a0/020 (Shyam Prabhakar); Japan Ministry of Education, Culture, Sports, Science and Technology (MEXT) to RIKEN Center for Integrative Medical Sciences; Thailand Program Management Unit for Competitiveness Enhancement (PMU-C) (C10F650132) (Varodom Charoensawan, Ponpan Matangkasombut, Manop Pithukpakorn, Bhoom Suktitipat); and Mahidol University’s Basic Research Fund: fiscal year 2021 (BRF1-017/2564) (Varodom Charoensawan, Bhoom Suktitipat) and Fundamental Fund: fiscal years 2021, 2024 (Ponpan Matangkasombut).

We would like to thank Jennifer Zamanian, Jennifer Chien, and Jason Hilton (HCA Lattice, Stanford University) for data deposits and community access to scRNA-seq datasets; and members of our laboratories; Jonah Cool, Norbert Tavares, Bailey Marshall, Garabet Yeretssian, and CZI Cell Science; Sudhagar Samydurai and GIS S2GP; and Mohamad Amin Honardoost.

AIDA Phase 1 data generation – AIDA Network members

Atlas assembly authors are arranged by area of contribution and ordered alphabetically by last name.

Single-cell experimental dataset generation leads: Varodom Charoensawan, Chung-Chau Hon, Partha P. Majumder, Ponpan Matangkasombut, Woong-Yang Park, Shyam Prabhakar, Jay W. Shin

Cohort and sample collection leads: Piero Carninci, John C. Chambers, Marie Loh, Manop Pithukpakorn, Bhoom Suktitipat, Kazuhiko Yamamoto

Overall study design and protocol development: Deepa Rajagopalan, Nirmala Arul Rayan, Shvetha Sankaran

Sample isolation and processing, single-cell experimental data generation: Juthamard Chantaraamporn, Ankita Chatterjee, Supratim Ghosh, Kyung Yeon Han, Damita Jevapatarakul, Sarintip Nguantad, Sumanta Sarkar, Narita Thungsatianpun

Sample isolation and processing: Mai Abe, Seiko Furukawa, Gyo Inoue, Keiko Myouzen, Jin-Mi Oh, Akari Suzuki

Single-cell experimental data generation: Yoshinari Ando, Miki Kojima, Tsukasa Kouno, Jinyeong Lim, Arindam Maitra, Le Min Tan, Prasanna Nori Venkatesh

Single-cell experimental data generation and analysis: Murim Choi, Jong-Eun Park

Single-cell data analysis up to cell type annotation: Eliora Violain Buyamin, Kian Hong Kock, Quy Xiao Xuan Lin, Jonathan Moody, Radhika Sonthalia

Genotype quality control and imputation: Kazuyoshi Ishigaki, Masahiro Nakano, Yukinori Okada, Yoshihiko Tomofuji

Document Change Log

Version	Notes
Version 0, 19 March 2025	First version, prepared prior to online publication of resource paper (Kock et al., Cell, 2025)

Shyam Prabhakar Lab