Citation Guidelines#
When using your fine-tuned model for your own research, we ask that you please cite the work of the authors who built the reference atlas you used for your mapping. Below you will find a list of references for each atlas found on ArchMap, as well as references of all demo datasets used.
Atlases#
HLCA Sikkema, L. et al. An integrated cell atlas of the lung in health and disease. Nat. Med. 29, 1563–1577 (2023).
HNOCA He, Z. et al. An integrated transcriptomic cell atlas of human neural organoids. bioRxiv 2023.10.05.561097 (2023) doi:10.1101/2023.10.05.561097.
HNOCA Extended He, Z. et al. An integrated transcriptomic cell atlas of human neural organoids. bioRxiv 2023.10.05.561097 (2023) doi:10.1101/2023.10.05.561097.
NSCLC Salcher, S. et al. High-resolution single-cell atlas reveals diversity and plasticity of tissue-resident neutrophils in non-small cell lung cancer. Cancer Cell 40, 1503–1520.e8 (2022).
Fetal brain Braun, E. et al. Comprehensive cell atlas of the first-trimester developing human brain. bioRxiv (2022) doi:10.1101/2022.10.24.513487.
Heart Litviňuková, M. et al. Cells of the adult human heart. Nature 588, 466–472 (2020).
Glioblastoma Ruiz-Moreno, C. et al. Harmonized single-cell landscape, intercellular crosstalk and tumor architecture of glioblastoma. bioRxiv 2022.08.27.505439 (2022) doi:10.1101/2022.08.27.505439.
HypoMap Steuernagel, L. et al. HypoMap—a unified single-cell gene expression atlas of the murine hypothalamus. Nature Metabolism 4, 1402–1419 (2022).
Fetal immune Suo, C. et al. Mapping the developing human immune system across organs. Science 376, eabo0510 (2022).
HEOCA Xu, Q. et al. An integrated transcriptomic cell atlas of human endoderm-derived organoids. bioRxiv 2023.11.20.567825 (2023) doi:10.1101/2023.11.20.567825.
Retina Chen, R. et al. Integrated multi-omics single cell atlas of the human retina. (2023) doi:10.21203/rs.3.rs-3471275/v1.
Breast Reed, A. D. et al. A single-cell atlas enables mapping of homeostatic cellular shifts in the adult human breast. Nat. Genet. 56, 652–662 (2024).
Pancreas Hrovatin, K., Bastidas-Ponce, A., Bakhti, M. et al. Delineating mouse β-cell identity during lifetime and in diabetes with a single cell atlas. Nat Metab 5, 1615–1637 (2023). https://doi.org/10.1038/s42255-023-00876-x
PBMC De Donno, C., Hediyeh-Zadeh, S., Moinfar, A.A. et al. Population-level integration of single-cell datasets enables multi-scale analysis across samples. Nat Methods 20, 1683–1692 (2023). https://doi.org/10.1038/s41592-023-02035-2
Plaque K. Traeuble, M. Munz, J. Pauli, N. Sachs, E. Vafadarnejad, T. Carrillo-Roa, L. Maegdefessel, P. Kastner, M. Heinig. Integrated single-cell atlas of human atherosclerotic plaques. bioRxiv 2024.09.11.612431; doi: https://doi.org/10.1101/2024.09.11.612431
Demo Datasets#
ArchMap offers demo query datasets for query-to-reference mapping for all atlases. All demo dataset references are provided below.
HLCA demo Subset of HLCA extended (https://cellxgene.cziscience.com/e/9f222629-9e39-47d0-b83f-e08d610c7479.cxg/) Dataset: Tsukui Tsukui, T. et al. Collagen-producing lung cell atlas identifies multiple subsets with distinct localization and relevance to fibrosis. Nat. Commun. 11, 1920 (2020).
HNOCA demo Subset of HNOCA extended (https://cellxgene.cziscience.com/collections/de379e5f-52d0-498c-9801-0f850823c847) 6 batches: [‘409b2-D70-Veh-C2’, ‘409b2-D70-Veh-V1’, ‘409b2-D90-Veh-Veh-C1’, ‘409b2-D90-Veh-Veh-C2’, ‘409b2-D90-Veh-Veh-V1’, ‘409b2-D90-Veh-Veh-V2’]
HNOCA Extended demo Subset of HNOCA extended (https://cellxgene.cziscience.com/collections/de379e5f-52d0-498c-9801-0f850823c847) 6 batches: [‘409b2-D70-Veh-C2’, ‘409b2-D70-Veh-V1’, ‘409b2-D90-Veh-Veh-C1’, ‘409b2-D90-Veh-Veh-C2’, ‘409b2-D90-Veh-Veh-V1’, ‘409b2-D90-Veh-Veh-V2’]
NSCLC demo Subset of NSCLC extended (https://cellxgene.cziscience.com/collections/edb893ee-4066-4128-9aec-5eb2b03f8287) dataset: “UKIM-V-2” Salcher, S. et al. High-resolution single-cell atlas reveals diversity and plasticity of tissue-resident neutrophils in non-small cell lung cancer. Cancer Cell 40, 1503–1520.e8 (2022).
Fetal brain demo Subset of HNOCA extended
Heart demo Maarten Hulsmans et al. ,Recruited macrophages elicit atrial fibrillation.Science381,231-239(2023).DOI:10.1126/science.abq3061 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE197518
Glioblastoma demo Subset of Glioblastomal atlas: Batch key: Author, Value: Ruiz2022 Ruiz-Moreno, C. et al. Harmonized single-cell landscape, intercellular crosstalk and tumor architecture of glioblastoma. bioRxiv 2022.08.27.505439 (2022) doi:10.1101/2022.08.27.505439.
HypoMap demo Romanov, R. A. et al. Molecular interrogation of hypothalamic organization reveals distinct dopamine neuronal subtypes. Nat. Neurosci. 20, 176–188 (2016).
Fetal immune demo HSC/progenitor cells (https://cellxgene.cziscience.com/collections/b1a879f6-5638-48d3-8f64-f6592c1b1561) Suo, C. et al. Mapping the developing human immune system across organs. Science 376, eabo0510 (2022).
HEOCA demo Subset of HEOCA extended (https://cellxgene.cziscience.com/collections/6282a908f162-44a2-99a3-8a942e4271b2) Xu, Q. et al. An integrated transcriptomic cell atlas of human endoderm-derived organoids. bioRxiv 2023.11.20.567825 (2023) doi:10.1101/2023.11.20.567825.
Retina demo scEiaD query Vinay S Swamy, Temesgen D Fufa, Robert B Hufnagel, David M McGaughey, Building the mega single-cell transcriptome ocular meta-atlas, GigaScience, Volume 10, Issue 10, October 2021, giab061, https://doi.org/10.1093/gigascience/giab061
Breast demo https://cellxgene.cziscience.com/collections/c9706a92-0e5f-46c1-96d8-20e42467f287
Pancreas demo Batch: Embryo_E14_5 Hrovatin, K., Bastidas-Ponce, A., Bakhti, M. et al. Delineating mouse β-cell identity during lifetime and in diabetes with a single cell atlas. Nat Metab 5, 1615–1637 (2023). https://doi.org/10.1038/s42255-023-00876-x
PBMC demo Subset of PBMC extended (https://figshare.com/projects/scPoli_data/155018) De Donno, C., Hediyeh-Zadeh, S., Moinfar, A.A. et al. Population-level integration of single-cell datasets enables multi-scale analysis across samples. Nat Methods 20, 1683–1692 (2023). https://doi.org/10.1038/s41592-023-02035-2
Plaque demo Query from Plaque atlas authors provided at https://github.com/kotr98/plaque-atlas-mapping?tab=readme-ov-file#example
Bladder (scvi-hub) demo Adult bladder immune subset from https://cellxgene.cziscience.com/collections/0e54d4de-44f0-4d50-8649-b5c2bbe8f5d1
Blood (scvi-hub) demo B cells – CV19 infection, vaccination and HC from https://cellxgene.cziscience.com/collections/ecb739c5-fe0d-4b48-81c6-217c4d64eec4
Blood (scvi-hub) demo healthy young bone marrow donor from https://cellxgene.cziscience.com/collections/93eebe82-d8c3-41bc-a906-63b5b5f24a9d
Eye (scvi-hub) demo Horizontal cells of the human fovea and peripheral retina from https://cellxgene.cziscience.com/collections/1d1c7275-476a-49e2-9022-ad1b1c793594
Fat (scvi-hub) demo snRNA-seq of human subcutaneous adipose tissue - adipocytes from https://cellxgene.cziscience.com/collections/ba84c7ba-8d8c-4720-a76e-3ee37dc89f0b
Heart (scvi-hub) demo dataset of ‘High-resolution single-cell transcriptomic survey of cardiomyocytes from patients with hypertrophic cardiomyopathy’ from https://cellxgene.cziscience.com/collections/1e313b15-4aca-4e5a-94a3-1093c4c42abd
Liver (scvi-hub) demo B cells from human healthy donor liver samples from https://cellxgene.cziscience.com/collections/0c8a364b-97b5-4cc8-a593-23c38c6f0ac5
Lymph node (scvi-hub) demo scRNA-seq of adult gamma delta T cells from https://cellxgene.cziscience.com/collections/ec691f5f-0aac-433c-8f78-e7f4b85a05e0
Mammary (scvi-hub) demo Breast cancer 4 patients archival FFPE samples profiling with Chromium FLEX from https://cellxgene.cziscience.com/collections/bd552f76-1f1b-43a3-b9ee-0aace57e90d6
Muscle (scvi-hub) demo Immune Cells of Human skeletal muscle ageing atlas from https://cellxgene.cziscience.com/collections/2d40e6a7-f2fd-49ba-9db9-6b97e4c6dad5
Pancreas (scvi-hub) demo Single cell transcriptome analysis of human pancreas reveals transcriptional signatures of aging and somatic mutation patterns from https://cellxgene.cziscience.com/collections/a238e9fa-2bdf-41df-8522-69046f99baff
Prostate (scvi-hub) demo A Cellular Anatomy of the Normal Adult Human Prostate and Prostatic Urethra - Human Fibromuscular Stromal Cells from https://cellxgene.cziscience.com/collections/e2a4a67f-6a18-431a-ab9c-6e77dd31cc80
Salivary gland (scvi-hub) demo Gland Immune Atlas from https://cellxgene.cziscience.com/collections/065ad318-59fd-4f8c-b4b1-66caa7665409
Skin (scvi-hub) demo Single-cell transcriptomes of the human skin reveal age-related loss of fibroblast priming from https://cellxgene.cziscience.com/collections/c353707f-09a4-4f12-92a0-cb741e57e5f0
Spleen (scvi-hub) demo scRNA-seq of adult gamma delta T cells from https://cellxgene.cziscience.com/collections/ec691f5f-0aac-433c-8f78-e7f4b85a05e0
Thymus (scvi-hub) demo thymus scRNA-seq atlas - B cell subset from https://cellxgene.cziscience.com/collections/fc19ae6c-d7c1-4dce-b703-62c5d52061b4
Tongue (scvi-hub) demo Oral and Craniofacial Atlas subset from https://cellxgene.cziscience.com/collections/065ad318-59fd-4f8c-b4b1-66caa7665409
Trachea (scvi-hub) demo B cells (trachea) from https://cellxgene.cziscience.com/collections/c1241244-b22d-483d-875b-75699efb9f3c
Uterus (scvi-hub) demo Non-pregnant Uterus (Endometrium - Epithelial) from https://cellxgene.cziscience.com/collections/32f2fd23-ec74-486f-9544-e5b2f41725f5
Vasculature (scvi-hub) demo scRNA-seq data analysis of endothelium-enriched mesenteric arterial tissues from human donors from https://cellxgene.cziscience.com/collections/db468083-041c-41ca-8f6f-bf991a070adf