The Immunoregulatory Architecture of the Adult Oral Cavity
Cite
Matuck, B.F., Huynh, K., Pereira, D., Zhang, X., Kunz, M., Kumar, N., Easter, Q.T., Fernandes, A., Ghodke, A., Predeus, A. and Szabo, L., 2024. The Immunoregulatory Architecture of the Adult Oral Cavity. bioRxiv.
https://doi.org/10.1101/2024.12.01.626279
Abstract
The oral cavity is a critical barrier with immunosurveillance capabilities. A detailed understanding of its cellular, molecular, and spatial architecture is essential for advancing precision medicine across aerodigestive tissues. Here, we present the first integrated atlas of human adult oral and craniofacial tissues, derived from single-cell RNA sequencing of ∼250,000 cells from 70 samples across 13 niches, including salivary glands and oral mucosae. Complementary spatial atlases using a 40-plex protein and 300-plex transcriptomics panels were developed, covering >2 million cells. Using our new AstroSuite package, we identified 8 tissue cellular neighborhoods (TCNs) and 17 multicellular interaction modules (MCIMs) across gland and mucosae in health. Diverse fibrovascular TCNs emerged as centralized hubs, coordinating immune cell migration and activation. Mucosal hubs within stroma displayed higher immune cell density, diversity, and activation than glands, underscoring differences in functional architecture. In keratinized and nonkeratinized mucosae, common fibrovascular hubs, and MCIMs revealed a specialized biogeography of immunoregulation. Under chronic inflammation, mucosal TCNs were fragmented, and MCIMs involving fibroblasts and immune cells were reorganized and expanded. Focused analysis of tertiary lymphoid structures (TLS) and fibroblasts identified TLS-associated MCIMs and drug candidates targeting these spatial interactions, offering a foundational framework for broadly dissecting mucosal immunity to guide precision medicine approaches.
Datasets
1. Oral and Craniofacial Atlas
ExploreAuthor cell type
Sample ID
Study
Niche
Subject ID
Protocol url
Institute
Sample collection site
Collection relative time point
Library ID
GEO accession
Manner of death
Sample source
Sample collection method
Sampled site condition
Tooth region
Sample preservation method
Sample collection year
Library preparation batch
Library sequencing run
Sequenced fragment
Reference genome
Gene annotation version
Alignment software
Intron inclusion
Ancestry
Age
Cell type
Assay
Disease
Sex
Tissue
Ethnicity
Leiden clustering
Epithelial cells62,303 cells
Vasculature58,065 cells
Lymphoid cells49,863 cells
Fibroblasts46,247 cells
Myeloid cells19,492 cells
Neural Crest-derived9,664 cells
Mineralized443 cells
Muscle cells26 cells
P513,265 cells
DP1010,895 cells
MSG710,842 cells
P29,837 cells
SMG18,952 cells
B78,738 cells
B48,734 cells
HP28,233 cells
DP17,725 cells
G97,436 cells
DP26,639 cells
G56,461 cells
MSG66,023 cells
G125,974 cells
Tong25,679 cells
G115,487 cells
SMG25,191 cells
SLG15,180 cells
DP35,098 cells
DP65,005 cells
G74,564 cells
MSG94,345 cells
Tong44,221 cells
Tong33,933 cells
G103,796 cells
DP53,720 cells
B83,512 cells
DP73,434 cells
P13,385 cells
DP43,229 cells
G153,059 cells
B53,032 cells
Tong12,999 cells
G132,916 cells
DP82,803 cells
MSG82,800 cells
G22,559 cells
P32,526 cells
G182,221 cells
MSG52,198 cells
G172,002 cells
G12,002 cells
G81,991 cells
P41,970 cells
B31,904 cells
MSG31,855 cells
G31,626 cells
B61,475 cells
MSG21,473 cells
G161,455 cells
DP121,445 cells
Pd41,074 cells
MSG41,033 cells
MSG1904 cells
SP1835 cells
L5748 cells
L4738 cells
DP11579 cells
HP1574 cells
G19498 cells
B2480 cells
Pd3472 cells
Pd2467 cells
L3393 cells
DP9393 cells
G14389 cells
Pd5322 cells
L1175 cells
L2156 cells
Pd129 cells
Williams et al.72,687 cells
Tabula Sapiens35,234 cells
Pagella et al.28,775 cells
Costa-da-Silva et al.24,010 cells
Krivanek et al.22,530 cells
Horeth et al.14,143 cells
Huang et al.13,639 cells
Chen et al.13,265 cells
Ko et al.8,807 cells
Pringle et al.4,496 cells
Caetano et al.3,448 cells
Warner et al.2,210 cells
Opasawatchai et al.2,024 cells
Kretzschmar et al.835 cells
Gingival Mucosa54,436 cells
Dental Pulp50,965 cells
Minor Salivary Gland31,473 cells
Parotid Salivary Gland30,983 cells
Buccal Mucosa27,875 cells
Dorsal Tongue16,832 cells
Submandibular Gland14,143 cells
Hard Palate8,807 cells
Sublingual Gland5,180 cells
Periodontium2,364 cells
Labial Mucosa2,210 cells
Soft Palate835 cells
Tabula Sapiens_TSP1423,171 cells
Chen_parotid gland 113,265 cells
Tabula Sapiens_TSP712,063 cells
Krivanek_510,895 cells
Costa-da-Silva_HV210,842 cells
Horeth_Submandibular Gland 128,952 cells
Williams_BM1688,738 cells
Williams_BM1578,734 cells
Ko_replicate 28,233 cells
Pagella_Pulp17,725 cells
Williams_GM2387,436 cells
Pagella_Pulp26,639 cells
Williams_GM1486,461 cells
Costa-da-Silva_HV16,023 cells
Williams_GM2835,974 cells
Williams_GM2425,487 cells
Horeth_Submandibular Gland 155,191 cells
Pagella_Pulp35,098 cells
Krivanek_15,005 cells
Williams_GM1834,564 cells
Costa-da-Silva_HV44,345 cells
Williams_GM2413,796 cells
Pagella_Pulp53,720 cells
Williams_BM1693,512 cells
Krivanek_23,434 cells
Pagella_Pulp43,229 cells
Caetano_Healthy23,059 cells
Williams_BM1583,032 cells
Williams_GM2892,916 cells
Krivanek_32,803 cells
Costa-da-Silva_HV32,800 cells
Williams_GM1432,559 cells
Pringle_12,526 cells
Huang_ATL0032,221 cells
Huang_MSG132,198 cells
Williams_GM1362,002 cells
Huang_ATL0022,002 cells
Williams_GM1841,991 cells
Pringle_21,970 cells
Williams_BM1561,904 cells
Huang_MSG91,855 cells
Williams_GM1441,626 cells
Williams_BM1651,475 cells
Huang_MSG81,473 cells
Huang_ATL0011,455 cells
Opasawatchai_Donor C1,445 cells
Pagella_Perio41,074 cells
Huang_MSG111,033 cells
Huang_MSG7904 cells
Kretzschmar_1835 cells
Warner_3633748 cells
Warner_3632738 cells
Opasawatchai_Donor A579 cells
Ko_replicate 1574 cells
Huang_ATL005498 cells
Williams_BM152480 cells
Pagella_Perio3472 cells
Pagella_Perio2467 cells
Krivanek_4393 cells
Warner_3631393 cells
Caetano_Healthy1389 cells
Pagella_Perio5322 cells
Warner_3629175 cells
Warner_3630156 cells
Pagella_Perio129 cells
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8359928/72,687 cells
https://www.science.org/stoken/author-tokens/ST-495/full35,234 cells
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8099559/28,775 cells
https://www.sciencedirect.com/science/article/pii/S2589004221015625?via%3Dihub24,010 cells
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7511944/22,530 cells
https://journals.sagepub.com/doi/10.1177/00220345221147908?url_ver=Z39.88-2003&rfr_id=ori:rid:crossref.org&rfr_dat=cr_pub%20%200pubmed14,143 cells
https://www.nature.com/articles/s41591-021-01296-813,639 cells
https://journals.sagepub.com/doi/full/10.1177/0022034522107606913,265 cells
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9827523/8,807 cells
Unassigned7,541 cells
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7781605/3,448 cells
https://www.frontiersin.org/articles/10.3389/fdmed.2021.806294/full2,024 cells
National Institute of Dental and Craniofacial Research (NIDCR)112,546 cells
Chan-Zuckerberg BioHub35,234 cells
University of Zurich26,411 cells
Medical University of Vienna22,530 cells
University at Buffalo14,143 cells
Sichuan University13,265 cells
University of Pennsylvania8,807 cells
University Medical Center Groningen4,496 cells
King's College London3,448 cells
University of Zurich (UZH)2,364 cells
Mahidol University2,024 cells
MSNZ University of Würzburg835 cells
site_1_USA110,336 cells
site_2_USA35,234 cells
site_1_Switzerland28,775 cells
site_1_Austria22,530 cells
site_3_USA14,143 cells
site_1_China13,265 cells
site_4_USA8,807 cells
site_1_Netherlands4,496 cells
site_1_UK3,448 cells
Unassigned2,210 cells
site_1_Thailand2,024 cells
site_1_Germany835 cells
Unassigned210,869 cells
day135,234 cells
TSP1423,171 cells
parotid gland 113,265 cells
TSP712,063 cells
Donor510,895 cells
HV210,842 cells
Submandibular Gland 12 scRNA8,952 cells
BM1688,738 cells
BM1578,734 cells
replicate 28,233 cells
Pulp17,725 cells
GM2387,436 cells
Pulp26,639 cells
GM1486,461 cells
HV16,023 cells
GM2835,974 cells
GM2425,487 cells
N/A5,331 cells
Submandibular Gland 15 scRNA5,191 cells
Pulp35,098 cells
Donor15,005 cells
GM1834,564 cells
HV44,345 cells
GM2413,796 cells
Pulp53,720 cells
BM1693,512 cells
Donor23,434 cells
Pulp43,229 cells
Healthy23,059 cells
BM1583,032 cells
GM2892,916 cells
Donor32,803 cells
HV32,800 cells
GM1432,559 cells
ATL0032,221 cells
MSG132,198 cells
GM1362,002 cells
ATL0022,002 cells
GM1841,991 cells
BM1561,904 cells
MSG91,855 cells
GM1441,626 cells
BM1651,475 cells
MSG81,473 cells
ATL0011,455 cells
DTP_041,445 cells
Perio41,074 cells
MSG111,033 cells
MSG7904 cells
Muc26748 cells
Muc25738 cells
DTP_01579 cells
replicate 1574 cells
ATL005498 cells
BM152480 cells
Perio3472 cells
Perio2467 cells
Donor4393 cells
Muc24393 cells
Healthy1389 cells
Perio5322 cells
Muc22175 cells
Muc23156 cells
Perio129 cells
Unassigned56,414 cells
GSM5683602 13,265 cells
GSM4365610 10,895 cells
GSM5464616 10,842 cells
GSM5965738 8,952 cells
GSM51770378,738 cells
GSM50050468,734 cells
GSM67254568,233 cells
GSM49984577,725 cells
GSM50050557,436 cells
GSM49984586,639 cells
GSM50050526,461 cells
GSM54646156,023 cells
GSM51770405,974 cells
GSM50050575,487 cells
GSM5965739 5,191 cells
GSM49984595,098 cells
GSM4365608 5,005 cells
GSM50050534,564 cells
GSM54646184,345 cells
GSM50050563,796 cells
GSM49984613,720 cells
GSM51770383,512 cells
GSM43656073,434 cells
GSM49984603,229 cells
GSM46008973,059 cells
GSM50050473,032 cells
GSM51770412,916 cells
GSM43656022,803 cells
GSM54646172,800 cells
GSM50050492,559 cells
GSM50050482,002 cells
GSM50050541,991 cells
GSM50050451,904 cells
GSM50050501,626 cells
GSM51770361,475 cells
GSM56084291,445 cells
GSM4904137 1,074 cells
GSM5608427579 cells
GSM6725455574 cells
GSM5005044480 cells
GSM4904136 472 cells
GSM4904135 467 cells
GSM4365603 393 cells
GSM4600896389 cells
GSM4904138 322 cells
GSM4904134 29 cells
not applicable210,869 cells
235,234 cells
surgical donor210,869 cells
postmortem donor35,234 cells
biopsy175,226 cells
surgical resection42,102 cells
scraping28,775 cells
healthy228,342 cells
adjacent17,761 cells
Unassigned89,009 cells
Labial minor salivary gland24,010 cells
Third molar22,530 cells
Parotid salivary gland17,718 cells
Submandibular gland14,143 cells
Lower pole of the parotid salivary gland 13,265 cells
Posterior tongue: circumvallate papilla anterior to sulcus terminalis9,900 cells
Rugous Area anterior Hard palate8,807 cells
Mandibular labial minor salivary glands7,463 cells
Anterior tongue: tongue dorsum 6,932 cells
13-146,461 cells
Palatal side, interdental papilla #14 distal/15 mesial 6,176 cells
Sublingual gland5,180 cells
Buccal gingival margin UR3/UL33,059 cells
Mandibular labial mucosa3,045 cells
Apical two-thirds of the roots of extracted third molars2,364 cells
Tooh number 18 (upper maxillary right third molar)2,024 cells
14-162,002 cells
16-171,626 cells
Buccal gingival margin UR6
389 cells
fresh238,562 cells
frozen at -80C6,706 cells
frozen at -150C835 cells
Unassigned239,927 cells
20196,176 cells
Unassigned177,783 cells
batch0145,138 cells
batch0223,182 cells
Unassigned137,005 cells
run180,237 cells
run220,707 cells
run44,221 cells
run33,933 cells
3 prime tag246,103 cells
GRCh38246,103 cells
v98246,103 cells
STAR v2.7.10a_alpha_220818 / STARsolo246,103 cells
no246,103 cells
N/A121,017 cells
White84,843 cells
Asian29,785 cells
Black6,465 cells
Latino2,002 cells
American Indian1,991 cells
18-39157,412 cells
50-5941,064 cells
60-6934,622 cells
40-4913,005 cells
epithelial cell62,303 cells
lymphocyte49,863 cells
fibroblast46,247 cells
endothelial cell of vascular tree43,549 cells
myeloid cell19,492 cells
mural cell14,516 cells
Schwann cell9,366 cells
odontoblast443 cells
melanocyte298 cells
muscle cell26 cells
10x 3' v3183,135 cells
10x 3' v262,968 cells
normal246,103 cells
male102,224 cells
female92,574 cells
Unassigned51,305 cells
gingiva54,436 cells
dental pulp50,965 cells
minor salivary gland31,473 cells
parotid gland30,983 cells
buccal mucosa27,875 cells
mucosa of dorsum of tongue16,832 cells
submandibular gland14,143 cells
hard palate8,807 cells
sublingual gland5,180 cells
periodontium2,364 cells
mucosa of lip2,210 cells
soft palate835 cells
Unassigned121,017 cells
European84,843 cells
Asian29,785 cells
African6,465 cells
Hispanic or Latin American2,002 cells
Native American1,991 cells
Cluster 1147,060 cells
Cluster 336,771 cells
Cluster 832,567 cells
Cluster 431,273 cells
Cluster 122,836 cells
Cluster 716,806 cells
Cluster 515,303 cells
Cluster 210,982 cells
Cluster 96,695 cells
Cluster 66,099 cells
Cluster 105,176 cells
Cluster 123,074 cells
Cluster 142,797 cells
Cluster 132,342 cells
Cluster 191,506 cells
Cluster 161,107 cells
Cluster 18568 cells
Cluster 25497 cells
Cluster 15491 cells
Cluster 22459 cells
Cluster 23434 cells
Cluster 21388 cells
Cluster 24327 cells
Cluster 17245 cells
Cluster 20210 cells
Cluster 2690 cells
2. Mucosal Atlas
ExploreAuthor cell type
Sample ID
Study
Niche
Subject ID
Protocol url
Institute
Sample collection site
Library ID
GEO accession
Manner of death
Sample source
Sample collection method
Sampled site condition
Tooth region
Sample preservation method
Library sequencing run
Sequenced fragment
Reference genome
Gene annotation version
Alignment software
Intron inclusion
Ancestry
Age
Cell type
Assay
Disease
Sex
Tissue
Ethnicity
Leiden clustering
Vascular endothelial cells23,920 cells
Fibroblasts19,235 cells
CD4 T cells7,644 cells
Mural cells7,375 cells
Keratinocytes6,802 cells
CD8 T cells5,367 cells
Plasma cells2,768 cells
Lymphatic endothelial cells2,278 cells
Mast cells1,960 cells
Monocytes/Macrophages1,925 cells
Natural Killer cells1,604 cells
B cells1,544 cells
Dendritic cells1,497 cells
Neutrophils814 cells
Langerhans cells618 cells
Acinar cells558 cells
Melanocytes374 cells
Schwann cells323 cells
Ductal epithelial cells265 cells
Merkel cells52 cells
Muscle cells51 cells
Myoepithelial cells26 cells
B48,611 cells
B78,456 cells
HP27,863 cells
G97,435 cells
G56,461 cells
G125,974 cells
G115,487 cells
G74,564 cells
G103,796 cells
B83,425 cells
G153,059 cells
B53,012 cells
G132,916 cells
G22,559 cells
G12,002 cells
G81,991 cells
B31,870 cells
G31,626 cells
B61,455 cells
SP1831 cells
L5745 cells
L4732 cells
HP1569 cells
B2460 cells
G14389 cells
L3388 cells
L1174 cells
L2150 cells
Williams et al.72,100 cells
Ko et al.8,432 cells
Caetano et al.3,448 cells
Warner, et al.2,189 cells
Kretzschmar et al.831 cells
Gingival Mucosa48,259 cells
Buccal Mucosa27,289 cells
Hard Palate8,432 cells
Labial Mucosa2,189 cells
Soft Palate831 cells
Williams_BM1578,611 cells
Williams_BM1688,456 cells
Ko_replicate 27,863 cells
Williams_GM2387,435 cells
Williams_GM1486,461 cells
Williams_GM2835,974 cells
Williams_GM2425,487 cells
Williams_GM1834,564 cells
Williams_GM2413,796 cells
Williams_BM1693,425 cells
Caetano_Healthy23,059 cells
Williams_BM1583,012 cells
Williams_GM2892,916 cells
Williams_GM1432,559 cells
Williams_GM1362,002 cells
Williams_GM1841,991 cells
Williams_BM1561,870 cells
Williams_GM1441,626 cells
Williams_BM1651,455 cells
Kretzschmar_1831 cells
Warner_3633745 cells
Warner_3632732 cells
Ko_replicate 1569 cells
Williams_BM152460 cells
Caetano_Healthy1389 cells
Warner_3631388 cells
Warner_3629174 cells
Warner_3630150 cells
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8359928/72,100 cells
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9827523/8,432 cells
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7781605/3,448 cells
Unassigned3,020 cells
National Institute of Dental and Craniofacial Research (NIDCR)74,289 cells
University of Pennsylvania8,432 cells
King's College London3,448 cells
MSNZ University of Würzburg831 cells
site_1_USA72,100 cells
site_4_USA8,432 cells
site_1_UK3,448 cells
Unassigned2,189 cells
site_1_Germany831 cells
BM1578,611 cells
BM1688,456 cells
replicate 27,863 cells
GM2387,435 cells
GM1486,461 cells
GM2835,974 cells
GM2425,487 cells
GM1834,564 cells
GM2413,796 cells
BM1693,425 cells
Healthy23,059 cells
BM1583,012 cells
GM2892,916 cells
GM1432,559 cells
GM1362,002 cells
GM1841,991 cells
BM1561,870 cells
GM1441,626 cells
BM1651,455 cells
N/A831 cells
Muc26745 cells
Muc25732 cells
replicate 1569 cells
BM152460 cells
Healthy1389 cells
Muc24388 cells
Muc22174 cells
Muc23150 cells
GSM50050468,611 cells
GSM51770378,456 cells
GSM67254567,863 cells
GSM50050557,435 cells
GSM50050526,461 cells
GSM51770405,974 cells
GSM50050575,487 cells
GSM50050534,564 cells
GSM50050563,796 cells
GSM51770383,425 cells
GSM46008973,059 cells
Unassigned3,020 cells
GSM50050473,012 cells
GSM51770412,916 cells
GSM50050492,559 cells
GSM50050482,002 cells
GSM50050541,991 cells
GSM50050451,870 cells
GSM50050501,626 cells
GSM51770361,455 cells
GSM6725455569 cells
GSM5005044460 cells
GSM4600896389 cells
not applicable87,000 cells
surgical donor87,000 cells
biopsy82,721 cells
surgical resection4,279 cells
healthy87,000 cells
Unassigned62,011 cells
Rugous Area anterior Hard palate8,432 cells
13-146,461 cells
Buccal gingival margin UR3/UL33,059 cells
Mandibular labial mucosa3,020 cells
14-162,002 cells
16-171,626 cells
Buccal gingival margin UR6
389 cells
fresh83,980 cells
frozen at -80C2,189 cells
frozen at -150C831 cells
Unassigned78,568 cells
run18,432 cells
3 prime tag87,000 cells
GRCh3887,000 cells
v9887,000 cells
STAR v2.7.10a_alpha_220818 / STARsolo87,000 cells
no87,000 cells
White40,663 cells
Asian29,483 cells
Unassigned8,432 cells
Black4,429 cells
Latino2,002 cells
American Indian1,991 cells
18-3970,060 cells
50-5912,856 cells
60-694,084 cells
blood vessel endothelial cell23,920 cells
fibroblast19,235 cells
CD4-positive helper T cell7,644 cells
mural cell7,375 cells
keratinocyte6,802 cells
CD8-positive, alpha-beta T cell5,367 cells
plasma cell2,768 cells
endothelial cell of lymphatic vessel2,278 cells
mast cell1,960 cells
macrophage1,925 cells
natural killer cell1,604 cells
B cell1,544 cells
dendritic cell1,497 cells
neutrophil814 cells
Langerhans cell618 cells
acinar cell of salivary gland558 cells
melanocyte374 cells
Schwann cell323 cells
salivary gland glandular cell265 cells
Merkel cell52 cells
adult skeletal muscle myoblast51 cells
myoepithelial cell26 cells
10x 3' v351,079 cells
10x 3' v235,921 cells
normal87,000 cells
female59,388 cells
male27,612 cells
gingiva48,259 cells
buccal mucosa27,289 cells
hard palate8,432 cells
mucosa of lip2,189 cells
soft palate831 cells
European40,663 cells
Asian29,483 cells
Unassigned8,432 cells
African4,429 cells
Hispanic or Latin American2,002 cells
Native American1,991 cells
Cluster 519,901 cells
Cluster 319,271 cells
Cluster 414,697 cells
Cluster 77,314 cells
Cluster 16,761 cells
Cluster 106,648 cells
Cluster 24,683 cells
Cluster 63,599 cells
Cluster 82,203 cells
Cluster 91,923 cells
3. Pulp Atlas
ExploreAuthor cell type
Sample ID
Study
Niche
Subject ID
Protocol url
Institute
Sample collection ite
Library ID
GEO accession
Manner of death
Sample source
Sample collection method
Sampled site condition
Tooth region
Sample preservation method
Sequenced fragment
Reference genome
Gene annotation version
Alignment software
Intron inclusion
Age
Cell type
Assay
Disease
Sex
Tissue
Leiden clustering
Fibroblasts23,077 cells
Vascular endothelial cells10,658 cells
Mural cells6,281 cells
Schwann cells6,166 cells
Monocytes/Macrophages1,555 cells
CD4 T cells1,060 cells
CD8 T cells1,053 cells
Odontoblasts620 cells
Natural Killer cells217 cells
Neutrophils89 cells
Dendritic cells81 cells
Peripherial neurons51 cells
B cells19 cells
DP1010,895 cells
DP17,725 cells
DP26,619 cells
DP35,077 cells
DP65,005 cells
DP53,722 cells
DP73,434 cells
DP43,230 cells
DP82,803 cells
DP121,445 cells
DP11579 cells
DP9393 cells
Pagella et al.26,373 cells
Krivanek et al.22,530 cells
Opasawatchai et al.2,024 cells
Dental Pulp50,927 cells
Krivanek_510,895 cells
Pagella_Pulp17,725 cells
Pagella_Pulp26,619 cells
Pagella_Pulp35,077 cells
Krivanek_15,005 cells
Pagella_Pulp53,722 cells
Krivanek_23,434 cells
Pagella_Pulp43,230 cells
Krivanek_32,803 cells
Opasawatchai_Donor C1,445 cells
Opasawatchai_Donor A579 cells
Krivanek_4393 cells
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8099559/26,373 cells
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7511944/22,530 cells
https://www.frontiersin.org/articles/10.3389/fdmed.2021.806294/full2,024 cells
University of Zurich26,373 cells
Medical University of Vienna22,530 cells
Mahidol University2,024 cells
site_1_Switzerland26,373 cells
site_1_Austria22,530 cells
site_1_Thailand2,024 cells
Donor510,895 cells
Pulp17,725 cells
Pulp26,619 cells
Pulp35,077 cells
Donor15,005 cells
Pulp53,722 cells
Donor23,434 cells
Pulp43,230 cells
Donor32,803 cells
DTP_041,445 cells
DTP_01579 cells
Donor4393 cells
GSM4365610 10,895 cells
GSM49984577,725 cells
GSM49984586,619 cells
GSM49984595,077 cells
GSM4365608 5,005 cells
GSM49984613,722 cells
GSM43656073,434 cells
GSM49984603,230 cells
GSM43656022,803 cells
GSM56084291,445 cells
GSM5608427579 cells
GSM4365603 393 cells
not applicable50,927 cells
surgical donor50,927 cells
scraping26,373 cells
surgical resection24,554 cells
healthy50,927 cells
Unassigned26,373 cells
Third molar22,530 cells
Tooh number 18 (upper maxillary right third molar)2,024 cells
fresh50,927 cells
3 prime tag50,927 cells
GRCh3850,927 cells
v9850,927 cells
STAR v2.7.10a_alpha_220818 / STARsolo50,927 cells
no50,927 cells
18-3950,927 cells
fibroblast23,077 cells
blood vessel endothelial cell10,658 cells
mural cell6,281 cells
Schwann cell6,166 cells
macrophage1,555 cells
CD4-positive helper T cell1,060 cells
CD8-positive, alpha-beta T cell1,053 cells
odontoblast620 cells
natural killer cell217 cells
neutrophil89 cells
dendritic cell81 cells
peripheral nervous system neuron51 cells
B cell19 cells
10x 3' v326,286 cells
10x 3' v224,641 cells
normal50,927 cells
Unassigned48,903 cells
female2,024 cells
dental pulp50,927 cells
Cluster 112,408 cells
Cluster 610,323 cells
Cluster 29,783 cells
Cluster 76,349 cells
Cluster 53,761 cells
Cluster 82,320 cells
Cluster 42,226 cells
Cluster 91,704 cells
Cluster 31,648 cells
Cluster 10356 cells
Cluster 1149 cells
4. Gland Atlas
ExploreAuthor cell type
Sample ID
Study
Niche
Subject ID
Protocol url
Institute
Sample collection site
Sample collection relative time point
Library ID
GEO accession
Manner of death
Sample source
Sample collection method
Sample site condition
Tooth region
Sample preservation method
Library preparation batch
Library sequencing run
Sequenced fragment
Reference genome
Gene annotation version
Alignment software
Intron inclusion
Ancestry
Age
Cell type
Assay
Disease
Sex
Tissue
Ethnicity
Leiden clustering
Acinar cells29,997 cells
Ductal epithelial cells3,846 cells
Fibroblasts3,630 cells
Plasma cells2,979 cells
Vascular endothelial cells2,205 cells
CD8 T cells2,063 cells
Monocytes/Macrophages1,092 cells
Mural cells778 cells
Neutrophils665 cells
CD4 T cells657 cells
Keratinocytes586 cells
Schwann cells529 cells
Dendritic cells331 cells
Ionocytes315 cells
Myoepithelial cells220 cells
Natural Killer cells155 cells
Lymphatic endothelial cells81 cells
Muscle cells56 cells
B cells55 cells
MSG710,842 cells
SMG18,952 cells
MSG66,023 cells
SMG25,190 cells
MSG94,345 cells
MSG82,798 cells
P32,526 cells
MSG52,198 cells
P41,958 cells
MSG31,853 cells
MSG21,472 cells
MSG41,033 cells
MSG1904 cells
P2104 cells
P142 cells
Costa-da-Silva et al.24,008 cells
Horeth et al.14,142 cells
Huang et al.7,460 cells
Pringle et al.4,484 cells
Tabula Sapiens146 cells
Minor Salivary Gland31,468 cells
Submandibular Gland14,142 cells
Parotid Salivary Gland4,630 cells
Costa-da-Silva_HV210,842 cells
Horeth_Submandibular Gland 128,952 cells
Costa-da-Silva_HV16,023 cells
Horeth_Submandibular Gland 155,190 cells
Costa-da-Silva_HV44,345 cells
Costa-da-Silva_HV32,798 cells
Pringle_12,526 cells
Huang_MSG132,198 cells
Pringle_21,958 cells
Huang_MSG91,853 cells
Huang_MSG81,472 cells
Huang_MSG111,033 cells
Huang_MSG7904 cells
Tabula Sapiens_TSP14104 cells
Tabula Sapiens_TSP742 cells
https://www.sciencedirect.com/science/article/pii/S2589004221015625?via%3Dihub24,008 cells
https://journals.sagepub.com/doi/10.1177/00220345221147908?url_ver=Z39.88-2003&rfr_id=ori:rid:crossref.org&rfr_dat=cr_pub%20%200pubmed14,142 cells
https://www.nature.com/articles/s41591-021-01296-87,460 cells
Unassigned4,484 cells
https://www.science.org/stoken/author-tokens/ST-495/full146 cells
National Institute of Dental and Craniofacial Research (NIDCR)31,468 cells
University at Buffalo14,142 cells
University Medical Center Groningen4,484 cells
Chan-Zuckerberg BioHub146 cells
site_1_USA31,468 cells
site_3_USA14,142 cells
site_1_Netherlands4,484 cells
site_2_USA146 cells
Unassigned50,094 cells
day1146 cells
HV210,842 cells
Submandibular Gland 12 scRNA8,952 cells
HV16,023 cells
Submandibular Gland 15 scRNA5,190 cells
N/A4,484 cells
HV44,345 cells
HV32,798 cells
MSG132,198 cells
MSG91,853 cells
MSG81,472 cells
MSG111,033 cells
MSG7904 cells
TSP14104 cells
TSP742 cells
Unassigned12,090 cells
GSM5464616 10,842 cells
GSM5965738 8,952 cells
GSM54646156,023 cells
GSM5965739 5,190 cells
GSM54646184,345 cells
GSM54646172,798 cells
not applicable50,094 cells
2146 cells
surgical donor50,094 cells
postmortem donor146 cells
biopsy50,240 cells
healthy45,756 cells
adjacent4,484 cells
Labial minor salivary gland24,008 cells
Submandibular gland14,142 cells
Mandibular labial minor salivary glands7,460 cells
Parotid salivary gland4,630 cells
fresh45,756 cells
frozen at -80C4,484 cells
Unassigned35,952 cells
batch018,994 cells
batch025,294 cells
run140,462 cells
run25,294 cells
Unassigned4,484 cells
3 prime tag50,240 cells
GRCh3850,240 cells
v9850,240 cells
STAR v2.7.10a_alpha_220818 / STARsolo50,240 cells
no50,240 cells
Unassigned45,610 cells
White4,630 cells
18-3926,870 cells
40-4913,003 cells
60-695,232 cells
50-595,135 cells
acinar cell of salivary gland29,997 cells
salivary gland glandular cell3,846 cells
fibroblast3,630 cells
plasma cell2,979 cells
blood vessel endothelial cell2,205 cells
CD8-positive, alpha-beta T cell2,063 cells
macrophage1,092 cells
mural cell778 cells
neutrophil665 cells
CD4-positive helper T cell657 cells
keratinocyte586 cells
Schwann cell529 cells
dendritic cell331 cells
ionocyte315 cells
myoepithelial cell220 cells
natural killer cell155 cells
endothelial cell of lymphatic vessel81 cells
adult skeletal muscle myoblast56 cells
B cell55 cells
10x 3' v350,240 cells
normal50,240 cells
male33,636 cells
female16,604 cells
minor salivary gland31,468 cells
submandibular gland14,142 cells
parotid gland4,630 cells
Unassigned45,610 cells
European4,630 cells
Cluster 714,525 cells
Cluster 17,160 cells
Cluster 36,387 cells
Cluster 25,610 cells
Cluster 103,551 cells
Cluster 62,734 cells
Cluster 92,319 cells
Cluster 112,187 cells
Cluster 52,064 cells
Cluster 81,522 cells
Cluster 12804 cells
Cluster 13779 cells
Cluster 4598 cells
5. Minor Salivary Gland Atlas
ExploreAuthor cell type
Sample ID
Study
Niche
Subject ID
Protoco url
Institute
Sample collection site
Library ID
GEO accession
Manner of death
Sample source
Sample collection method
Sampled site condition
Tooth region
Sample preservation method
Library sequencing run
Sequenced fragment
Reference genome
Gene annotation version
Alignment software
Intron inclusion
Age
Cell type
Assay
Disease
Sex
Tissue
Leiden clustering
Acinar cells18,786 cells
Fibroblasts2,800 cells
Plasma cells2,455 cells
Ductal epithelial cells2,361 cells
Vascular endothelial cells1,513 cells
CD8 T cells1,025 cells
Mural cells606 cells
Myoepithelial cells431 cells
Monocytes/Macrophages416 cells
CD4 T cells300 cells
Keratinocytes214 cells
Dendritic cells168 cells
Ionocytes110 cells
Neutrophils92 cells
Lymphatic endothelial cells78 cells
Muscle cells47 cells
B cells35 cells
Natural Killer cells31 cells
MSG710,842 cells
MSG66,023 cells
MSG94,345 cells
MSG82,798 cells
MSG52,198 cells
MSG31,853 cells
MSG21,472 cells
MSG41,033 cells
MSG1904 cells
Costa-da-Silva et al.24,008 cells
Huang et al.7,460 cells
Minor Salivary Gland31,468 cells
Costa-da-Silva_HV210,842 cells
Costa-da-Silva_HV16,023 cells
Costa-da-Silva_HV44,345 cells
Costa-da-Silva_HV32,798 cells
Huang_MSG132,198 cells
Huang_MSG91,853 cells
Huang_MSG81,472 cells
Huang_MSG111,033 cells
Huang_MSG7904 cells
https://www.sciencedirect.com/science/article/pii/S2589004221015625?via%3Dihub24,008 cells
https://www.nature.com/articles/s41591-021-01296-87,460 cells
National Institute of Dental and Craniofacial Research (NIDCR)31,468 cells
site_1_USA31,468 cells
HV210,842 cells
HV16,023 cells
HV44,345 cells
HV32,798 cells
MSG132,198 cells
MSG91,853 cells
MSG81,472 cells
MSG111,033 cells
MSG7904 cells
GSM5464616 10,842 cells
Unassigned7,460 cells
GSM54646156,023 cells
GSM54646184,345 cells
GSM54646172,798 cells
not applicable31,468 cells
surgical donor31,468 cells
biopsy31,468 cells
healthy31,468 cells
Labial minor salivary gland24,008 cells
Mandibular labial minor salivary glands7,460 cells
fresh31,468 cells
run131,468 cells
3 prime tag31,468 cells
GRCh3831,468 cells
v9831,468 cells
STAR v2.7.10a_alpha_220818 / STARsolo31,468 cells
no31,468 cells
18-3924,912 cells
40-494,051 cells
50-592,505 cells
acinar cell of salivary gland18,786 cells
fibroblast2,800 cells
plasma cell2,455 cells
salivary gland glandular cell2,361 cells
blood vessel endothelial cell1,513 cells
CD8-positive, alpha-beta T cell1,025 cells
mural cell606 cells
myoepithelial cell431 cells
macrophage416 cells
CD4-positive helper T cell300 cells
keratinocyte214 cells
dendritic cell168 cells
ionocyte110 cells
neutrophil92 cells
endothelial cell of lymphatic vessel78 cells
adult skeletal muscle myoblast47 cells
B cell35 cells
natural killer cell31 cells
10x 3' v331,468 cells
normal31,468 cells
male20,096 cells
female11,372 cells
minor salivary gland31,468 cells
Cluster 310,604 cells
Cluster 15,986 cells
Cluster 23,721 cells
Cluster 52,784 cells
Cluster 111,680 cells
Cluster 41,597 cells
Cluster 91,565 cells
Cluster 61,326 cells
Cluster 8686 cells
Cluster 12641 cells
Cluster 10632 cells
Cluster 7246 cells
6. Buccal and Labial Atlas
ExploreAuthor cell type
Sample ID
Study
Niche
Subject ID
Protocol url
Institute
Sample collection site
Library ID
GEO accession
Manner of death
Sample source
Sample collection method
Sampled site condition
Tooth region
Sample preservation method
Sequenced fragment
Reference genome
Gene annotation version
Alignment software
Intron inclusion
Ancestry
Age
Cell type
Assay
Disease
Sex
Tissue
Ethnicity
Leiden clustering
Vascular endothelial cells9,788 cells
Fibroblasts6,524 cells
Mural cells2,641 cells
CD4 T cells2,167 cells
CD8 T cells1,932 cells
Keratinocytes1,738 cells
Lymphatic endothelial cells877 cells
Dendritic cells744 cells
Monocytes/Macrophages699 cells
Natural Killer cells603 cells
Acinar cells451 cells
Langerhans cells365 cells
Plasma cells203 cells
Melanocytes202 cells
Ductal epithelial cells176 cells
Neutrophils171 cells
Mast cells105 cells
Schwann cells70 cells
Myoepithelial cells22 cells
B48,611 cells
B78,456 cells
B83,425 cells
B53,012 cells
B31,870 cells
B61,455 cells
L5745 cells
L4732 cells
B2460 cells
L3388 cells
L1174 cells
L2150 cells
Williams et al.27,289 cells
Warner, et al.2,189 cells
Buccal Mucosa27,289 cells
Labial Mucosa2,189 cells
Williams_BM1578,611 cells
Williams_BM1688,456 cells
Williams_BM1693,425 cells
Williams_BM1583,012 cells
Williams_BM1561,870 cells
Williams_BM1651,455 cells
Warner_3633745 cells
Warner_3632732 cells
Williams_BM152460 cells
Warner_3631388 cells
Warner_3629174 cells
Warner_3630150 cells
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8359928/27,289 cells
Unassigned2,189 cells
National Institute of Dental and Craniofacial Research (NIDCR)29,478 cells
site_1_USA27,289 cells
Unassigned2,189 cells
BM1578,611 cells
BM1688,456 cells
BM1693,425 cells
BM1583,012 cells
BM1561,870 cells
BM1651,455 cells
Muc26745 cells
Muc25732 cells
BM152460 cells
Muc24388 cells
Muc22174 cells
Muc23150 cells
GSM50050468,611 cells
GSM51770378,456 cells
GSM51770383,425 cells
GSM50050473,012 cells
Unassigned2,189 cells
GSM50050451,870 cells
GSM51770361,455 cells
GSM5005044460 cells
not applicable29,478 cells
surgical donor29,478 cells
biopsy29,478 cells
healthy29,478 cells
Unassigned27,289 cells
Mandibular labial mucosa2,189 cells
fresh27,289 cells
frozen at -80C2,189 cells
3 prime tag29,478 cells
GRCh3829,478 cells
v9829,478 cells
STAR v2.7.10a_alpha_220818 / STARsolo29,478 cells
no29,478 cells
White18,692 cells
Asian8,916 cells
Black1,870 cells
18-3927,463 cells
60-691,627 cells
50-59388 cells
blood vessel endothelial cell9,788 cells
fibroblast6,524 cells
mural cell2,641 cells
CD4-positive helper T cell2,167 cells
CD8-positive, alpha-beta T cell1,932 cells
keratinocyte1,738 cells
endothelial cell of lymphatic vessel877 cells
dendritic cell744 cells
macrophage699 cells
natural killer cell603 cells
acinar cell of salivary gland451 cells
Langerhans cell365 cells
plasma cell203 cells
melanocyte202 cells
salivary gland glandular cell176 cells
neutrophil171 cells
mast cell105 cells
Schwann cell70 cells
myoepithelial cell22 cells
10x 3' v329,478 cells
normal29,478 cells
female15,604 cells
male13,874 cells
buccal mucosa27,289 cells
mucosa of lip2,189 cells
European18,692 cells
Asian8,916 cells
African1,870 cells
Cluster 68,140 cells
Cluster 56,579 cells
Cluster 44,737 cells
Cluster 72,627 cells
Cluster 101,918 cells
Cluster 31,716 cells
Cluster 11,597 cells
Cluster 21,061 cells
Cluster 8855 cells
Cluster 9207 cells
Cluster 1141 cells
7. Major Salivary Gland Atlas
ExploreAuthor cell type
Sample ID
Study
Niche
Subject ID
Protocol url
Institute
Sample collection site
Sample collection relative time point
Library ID
GEO accession
Manner of death
Sample source
Sample collection method
Sampled site condition
Tooth region
Sample preservation method
Library preparation batch
Library sequencing run
Sequenced fragment
Reference genome
Gene annotation version
Alignment software
Intron inclusion
Ancestry
Age
Cell type
Assay
Disease
Sex
Tissue
Ethnicity
Leiden clustering
Acinar cells11,211 cells
Ductal epithelial cells1,485 cells
CD8 T cells1,038 cells
Fibroblasts830 cells
Vascular endothelial cells741 cells
Monocytes/Macrophages676 cells
Neutrophils572 cells
Plasma cells523 cells
Myoepithelial cells381 cells
CD4 T cells357 cells
Keratinocytes274 cells
Ionocytes205 cells
Mural cells172 cells
Dendritic cells163 cells
Natural Killer cells124 cells
B cells20 cells
SMG18,952 cells
SMG25,190 cells
P32,526 cells
P41,958 cells
P2104 cells
P142 cells
Horeth et al.14,142 cells
Pringle et al.4,484 cells
Tabula Sapiens146 cells
Submandibular Gland14,142 cells
Parotid Salivary Gland4,630 cells
Horeth_Submandibular Gland 128,952 cells
Horeth_Submandibular Gland 155,190 cells
Pringle_12,526 cells
Pringle_21,958 cells
Tabula Sapiens_TSP14104 cells
Tabula Sapiens_TSP742 cells
https://journals.sagepub.com/doi/10.1177/00220345221147908?url_ver=Z39.88-2003&rfr_id=ori:rid:crossref.org&rfr_dat=cr_pub%20%200pubmed14,142 cells
Unassigned4,484 cells
https://www.science.org/stoken/author-tokens/ST-495/full146 cells
University at Buffalo14,142 cells
University Medical Center Groningen4,484 cells
Chan-Zuckerberg BioHub146 cells
site_3_USA14,142 cells
site_1_Netherlands4,484 cells
site_2_USA146 cells
Unassigned18,626 cells
day1146 cells
Submandibular Gland 12 scRNA8,952 cells
Submandibular Gland 15 scRNA5,190 cells
N/A4,484 cells
TSP14104 cells
TSP742 cells
GSM5965738 8,952 cells
GSM5965739 5,190 cells
N/A4,630 cells
not applicable18,626 cells
2146 cells
surgical donor18,626 cells
postmortem donor146 cells
biopsy18,772 cells
healthy14,288 cells
adjacent4,484 cells
Submandibular gland14,142 cells
Parotid salivary gland4,630 cells
fresh14,288 cells
frozen at -80C4,484 cells
batch018,994 cells
batch025,294 cells
Unassigned4,484 cells
run18,994 cells
run25,294 cells
Unassigned4,484 cells
3 prime tag18,772 cells
GRCh3818,772 cells
v9818,772 cells
STAR v2.7.10a_alpha_220818 / STARsolo18,772 cells
no18,772 cells
Unassigned14,142 cells
White4,630 cells
40-498,952 cells
60-695,232 cells
50-592,630 cells
18-391,958 cells
acinar cell of salivary gland11,211 cells
salivary gland glandular cell1,485 cells
CD8-positive, alpha-beta T cell1,038 cells
fibroblast830 cells
blood vessel endothelial cell741 cells
macrophage676 cells
neutrophil572 cells
plasma cell523 cells
myoepithelial cell381 cells
CD4-positive helper T cell357 cells
keratinocyte274 cells
ionocyte205 cells
mural cell172 cells
dendritic cell163 cells
natural killer cell124 cells
B cell20 cells
10x 3' v318,772 cells
normal18,772 cells
male13,540 cells
female5,232 cells
submandibular gland14,142 cells
parotid gland4,630 cells
Unassigned14,142 cells
European4,630 cells
Cluster 55,338 cells
Cluster 113,340 cells
Cluster 31,858 cells
Cluster 91,474 cells
Cluster 41,258 cells
Cluster 101,177 cells
Cluster 8832 cells
Cluster 6807 cells
Cluster 12657 cells
Cluster 13607 cells
Cluster 1591 cells
Cluster 7347 cells
Cluster 2273 cells
Cluster 14213 cells
8. Palate Atlas
ExploreAuthor cell type
Sample ID
Study
Niche
Subject ID
Protocol url
Institute
Sample collection site
Library ID
GEO accession
Manner of death
Sample source
Sample collection method
Sampled site condition
Tooth region
Sample preservation method
Library sequencing run
Sequenced fragment
Reference genome
Gene annotation version
Alignment software
Intron inclusion
Ancestry
Age
Cell type
Assay
Disease
Sex
Tissue
Ethnicity
Leiden clustering
Fibroblasts2,814 cells
Mural cells1,512 cells
Vascular endothelial cells1,057 cells
Keratinocytes889 cells
CD4 T cells858 cells
CD8 T cells412 cells
Dendritic cells284 cells
Plasma cells241 cells
Neutrophils209 cells
Monocytes/Macrophages203 cells
Lymphatic endothelial cells190 cells
Schwann cells175 cells
Natural Killer cells154 cells
B cells75 cells
Merkel cells71 cells
Langerhans cells64 cells
Melanocytes29 cells
Mast cells26 cells
HP27,863 cells
SP1831 cells
HP1569 cells
Ko et al.8,432 cells
Kretzschmar et al.831 cells
Hard Palate8,432 cells
Soft Palate831 cells
Ko_replicate 27,863 cells
Kretzschmar_1831 cells
Ko_replicate 1569 cells
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9827523/8,432 cells
Unassigned831 cells
University of Pennsylvania8,432 cells
MSNZ University of Würzburg831 cells
site_4_USA8,432 cells
site_1_Germany831 cells
replicate 27,863 cells
Unassigned831 cells
replicate 1569 cells
GSM67254567,863 cells
Unassigned831 cells
GSM6725455569 cells
not applicable9,263 cells
surgical donor9,263 cells
biopsy8,432 cells
surgical resection831 cells
healthy9,263 cells
Rugous Area anterior Hard palate8,432 cells
Mandibular labial mucosa831 cells
fresh8,432 cells
frozen at -150C831 cells
run18,432 cells
Unassigned831 cells
3 prime tag9,263 cells
GRCh389,263 cells
v989,263 cells
STAR v2.7.10a_alpha_220818 / STARsolo9,263 cells
no9,263 cells
Unassigned8,432 cells
White831 cells
18-398,432 cells
60-69831 cells
fibroblast2,814 cells
mural cell1,512 cells
blood vessel endothelial cell1,057 cells
keratinocyte889 cells
CD4-positive helper T cell858 cells
CD8-positive, alpha-beta T cell412 cells
dendritic cell284 cells
plasma cell241 cells
neutrophil209 cells
macrophage203 cells
endothelial cell of lymphatic vessel190 cells
Schwann cell175 cells
natural killer cell154 cells
B cell75 cells
Merkel cell71 cells
Langerhans cell64 cells
melanocyte29 cells
mast cell26 cells
10x 3' v39,263 cells
normal9,263 cells
female7,863 cells
male1,400 cells
hard palate8,432 cells
soft palate831 cells
Unassigned8,432 cells
European831 cells
Cluster 41,670 cells
Cluster 71,421 cells
Cluster 151,348 cells
Cluster 11953 cells
Cluster 2707 cells
Cluster 5685 cells
Cluster 1646 cells
Cluster 6456 cells
Cluster 10413 cells
Cluster 3276 cells
Cluster 14153 cells
Cluster 12152 cells
Cluster 9144 cells
Cluster 8120 cells
Cluster 13119 cells
9. Mucosal Immune Atlas
ExploreAuthor cell type
Sample ID
Study
Niche
Subject ID
Protocol url
Institute
Sample collection site
Library ID
GEO accession
Manner of death
Sample source
Sample collection method
Sampled site condition
Tooth region
Sample preservation method
Sample collection year
Library preparation batch
Library sequencing run
Sequenced fragment
Reference genome
Gene annotation version
Alignment software
Intron inclusion
Ancestry
Age
Cell type
Assay
Disease
Sex
Tissue
Ethnicity
Leiden clustering
CD8 T cells6,617 cells
CD4 T cells6,151 cells
Innate lymphoid cells2,149 cells
Mast cells1,982 cells
Dendritic cells1,928 cells
Monocytes/Macrophages1,878 cells
B cells1,516 cells
Neutrophils533 cells
Plasma cells310 cells
GSM50050552,905 cells
GSM51770402,657 cells
GSM50050462,119 cells
GSM67254561,763 cells
GSM50050571,274 cells
ATL0011,218 cells
GSM50050471,196 cells
GSM51770371,018 cells
GSM50050531,012 cells
ATL002882 cells
GSM5005052841 cells
GSM5177041793 cells
ATL003756 cells
GSM5005056610 cells
GSM4600897524 cells
GSM5005048500 cells
GSM5005045481 cells
GSM5005049441 cells
GSM5177036395 cells
GSM5005050389 cells
GSM5005054337 cells
GSM5177038285 cells
GSM4600896228 cells
ATL005123 cells
GSM6725455112 cells
Palate 1104 cells
GSM5005044101 cells
Williams et al.17,354 cells
Huang et al.2,979 cells
Ko et al.1,875 cells
Caetano et al.752 cells
Kretzschmar et al.104 cells
Gingival Mucosa15,490 cells
Buccal Mucosa5,595 cells
Hard Palate1,875 cells
Soft Palate104 cells
Williams_GM2382,905 cells
Williams_GM2832,657 cells
Williams_BM1572,119 cells
Ko_replicate 21,763 cells
Williams_GM2421,274 cells
Huang_ATL0011,218 cells
Williams_BM1581,196 cells
Williams_BM1681,018 cells
Williams_GM1831,012 cells
Huang_ATL002882 cells
Williams_GM148841 cells
Williams_GM289793 cells
Huang_ATL003756 cells
Williams_GM241610 cells
Caetano_Healthy2524 cells
Williams_GM136500 cells
Williams_BM156481 cells
Williams_GM143441 cells
Williams_BM165395 cells
Williams_GM144389 cells
Williams_GM184337 cells
Williams_BM169285 cells
Caetano_Healthy1228 cells
Huang_ATL005123 cells
Ko_replicate 1112 cells
Kretzschmar_1104 cells
Williams_BM152101 cells
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8359928/17,354 cells
https://www.nature.com/articles/s41591-021-01296-82,979 cells
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9827523/1,875 cells
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7781605/752 cells
Unassigned104 cells
National Institute of Dental and Craniofacial Research (NIDCR)20,333 cells
University of Pennsylvania1,875 cells
King's College London752 cells
MSNZ University of Würzburg104 cells
site_1_USA20,333 cells
site_4_USA1,875 cells
site_1_UK752 cells
site_1_Germany104 cells
GM2382,905 cells
GM2832,657 cells
BM1572,119 cells
replicate 21,763 cells
GM2421,274 cells
ATL0011,218 cells
BM1581,196 cells
BM1681,018 cells
GM1831,012 cells
ATL002882 cells
GM148841 cells
GM289793 cells
ATL003756 cells
GM241610 cells
Healthy2524 cells
GM136500 cells
BM156481 cells
GM143441 cells
BM165395 cells
GM144389 cells
GM184337 cells
BM169285 cells
Healthy1228 cells
ATL005123 cells
replicate 1112 cells
Unassigned104 cells
BM152101 cells
Unassigned3,083 cells
GSM50050552,905 cells
GSM51770402,657 cells
GSM50050462,119 cells
GSM67254561,763 cells
GSM50050571,274 cells
GSM50050471,196 cells
GSM51770371,018 cells
GSM50050531,012 cells
GSM5005052841 cells
GSM5177041793 cells
GSM5005056610 cells
GSM4600897524 cells
GSM5005048500 cells
GSM5005045481 cells
GSM5005049441 cells
GSM5177036395 cells
GSM5005050389 cells
GSM5005054337 cells
GSM5177038285 cells
GSM4600896228 cells
GSM6725455112 cells
GSM5005044101 cells
not applicable23,064 cells
surgical donor23,064 cells
biopsy22,208 cells
surgical resection856 cells
healthy23,064 cells
Unassigned15,624 cells
Palatal side, interdental papilla #14 distal/15 mesial 2,979 cells
Rugous Area anterior Hard palate1,875 cells
13-14841 cells
Buccal gingival margin UR3/UL3524 cells
14-16500 cells
16-17389 cells
Buccal gingival margin UR6
228 cells
Mandibular labial mucosa104 cells
fresh22,960 cells
frozen at -150C104 cells
Unassigned20,085 cells
20192,979 cells
Unassigned20,208 cells
batch012,856 cells
Unassigned18,210 cells
run14,854 cells
3 prime tag23,064 cells
GRCh3823,064 cells
v9823,064 cells
STAR v2.7.10a_alpha_220818 / STARsolo23,064 cells
no23,064 cells
White11,304 cells
Asian7,244 cells
Unassigned1,875 cells
Black1,804 cells
Latino500 cells
American Indian337 cells
18-3920,537 cells
50-592,034 cells
60-69493 cells
CD8-positive, alpha-beta T cell6,617 cells
CD4-positive helper T cell6,151 cells
innate lymphoid cell2,149 cells
mast cell1,982 cells
dendritic cell1,928 cells
macrophage1,878 cells
B cell1,516 cells
neutrophil533 cells
plasma cell310 cells
10x 3' v314,755 cells
10x 3' v28,309 cells
normal23,064 cells
female15,310 cells
male7,754 cells
gingiva15,490 cells
buccal mucosa5,595 cells
hard palate1,875 cells
soft palate104 cells
European11,304 cells
Asian7,244 cells
Unassigned1,875 cells
African1,804 cells
Hispanic or Latin American500 cells
Native American337 cells
Cluster 37,729 cells
Cluster 44,830 cells
Cluster 63,865 cells
Cluster 22,335 cells
Cluster 11,979 cells
Cluster 71,589 cells
Cluster 5451 cells
Cluster 8286 cells
10. Gland Immune Atlas
ExploreAuthor cell type
Sample ID
Study
Niche
Subject ID
Protocol url
Institute
Sample collection site
Library ID
GEO accession
Manner of death
Sample source
Sample collection method
Sampled site condition
Tooth region
Sample preservation method
Library preparation batch
Library sequencing run
Sequenced fragment
Reference genome
Gene annotation version
Alignment software
Intron inclusion
Ancestry
Age
Cell type
Assay
Disease
Sex
Tissue
Ethnicity
Leiden clustering
Plasma cells2,892 cells
CD8 T cells1,325 cells
Monocytes/Macrophages832 cells
CD4 T cells587 cells
Neutrophils370 cells
Innate lymphoid cells146 cells
Dendritic cells120 cells
B cells90 cells
MSG61,179 cells
P4959 cells
P3873 cells
MSG9527 cells
MSG5508 cells
SMG1399 cells
MSG3391 cells
MSG7384 cells
SMG2367 cells
MSG8298 cells
MSG2207 cells
MSG1148 cells
MSG4122 cells
Costa-da-Silva et al.2,388 cells
Pringle et al.1,832 cells
Huang et al.1,376 cells
Horeth et al.766 cells
Minor Salivary Gland3,764 cells
Parotid Salivary Gland1,832 cells
Submandibular Gland766 cells
Costa-da-Silva_HV11,179 cells
Pringle_2959 cells
Pringle_1873 cells
Costa-da-Silva_HV4527 cells
Huang_MSG13508 cells
Horeth_Submandibular Gland 12399 cells
Huang_MSG9391 cells
Costa-da-Silva_HV2384 cells
Horeth_Submandibular Gland 15367 cells
Costa-da-Silva_HV3298 cells
Huang_MSG8207 cells
Huang_MSG7148 cells
Huang_MSG11122 cells
https://www.sciencedirect.com/science/article/pii/S2589004221015625?via%3Dihub2,388 cells
Unassigned1,832 cells
https://www.nature.com/articles/s41591-021-01296-81,376 cells
https://journals.sagepub.com/doi/10.1177/00220345221147908?url_ver=Z39.88-2003&rfr_id=ori:rid:crossref.org&rfr_dat=cr_pub%20%200pubmed766 cells
National Institute of Dental and Craniofacial Research (NIDCR)3,764 cells
University Medical Center Groningen1,832 cells
University at Buffalo766 cells
site_1_USA3,764 cells
site_1_Netherlands1,832 cells
site_3_USA766 cells
Unassigned1,832 cells
HV11,179 cells
HV4527 cells
MSG13508 cells
Submandibular Gland 12 scRNA399 cells
MSG9391 cells
HV2384 cells
Submandibular Gland 15 scRNA367 cells
HV3298 cells
MSG8207 cells
MSG7148 cells
MSG11122 cells
Unassigned3,208 cells
GSM54646151,179 cells
GSM5464618527 cells
GSM5965738 399 cells
GSM5464616 384 cells
GSM5965739 367 cells
GSM5464617298 cells
not applicable6,362 cells
surgical donor6,362 cells
biopsy6,362 cells
healthy4,530 cells
adjacent1,832 cells
Labial minor salivary gland2,388 cells
Parotid salivary gland1,832 cells
Mandibular labial minor salivary glands1,376 cells
Submandibular gland766 cells
fresh4,530 cells
frozen at -80C1,832 cells
Unassigned5,596 cells
batch01399 cells
batch02367 cells
run14,163 cells
Unassigned1,832 cells
run2367 cells
3 prime tag6,362 cells
GRCh386,362 cells
v986,362 cells
STAR v2.7.10a_alpha_220818 / STARsolo6,362 cells
no6,362 cells
Unassigned4,530 cells
White1,832 cells
18-393,495 cells
40-491,298 cells
50-591,202 cells
60-69367 cells
plasma cell2,892 cells
CD8-positive, alpha-beta T cell1,325 cells
macrophage832 cells
CD4-positive helper T cell587 cells
neutrophil370 cells
innate lymphoid cell146 cells
dendritic cell120 cells
B cell90 cells
10x 3' v36,362 cells
normal6,362 cells
male4,424 cells
female1,938 cells
minor salivary gland3,764 cells
parotid gland1,832 cells
submandibular gland766 cells
Unassigned4,530 cells
European1,832 cells
Cluster 11,212 cells
Cluster 51,171 cells
Cluster 41,021 cells
Cluster 7870 cells
Cluster 9728 cells
Cluster 3575 cells
Cluster 11273 cells
Cluster 10177 cells
Cluster 8135 cells
Cluster 6110 cells
Cluster 290 cells
Alias names
Human Oral and Craniofacial Cell Atlas