Cell Atlas

In this module, we provide cell atlases from single-cell and single-nucleus transcriptomes, which include information on cell type composition. The distance between different cell types is visualized in two-dimensional space using the UMAP method.

A cell atlas is provided for six species only: AMILL Acropora millepora, AMURI Acropora muricata, NVECT Nematostella vectensis, OARBU Oculina arbuscula, OPATA Oculina patagonica, SPIST Stylophora pistillata. There is no atlas for Pocillopora verrucosa; its dataset, if any, is listed in Single-cell Data with the source BioProject/SRA links. See the species portal for everything this species does provide.
Select Tissue Sample
Species:
Stages:
Emb/Org:
Dataset coverage of the Cell Atlas

The Single-cell Data module indexes 33 datasets across 15 species. An interactive atlas is shown here only when the study deposited a processed UMAP embedding and a cell-type marker table; for the remaining datasets CnidoSite provides the sample metadata and the link to the original study, but no projection can be recomputed from the deposited raw reads. The table below makes this explicit per dataset.

SpeciesStage / tissueCellsBioProject Cell AtlasMarkers
Acropora millepora Whole adults 28,736 PRJNA1223412 available browse
Acropora muricata Polyps 17,277 PRJNA544778 available browse
Aurelia coerulea ephrya 42,461 PRJNA1041967 not deposited –
Aurelia coerulea gastrodermis 10000 PRJNA1011858 not deposited –
Aurelia coerulea podocysts 17,978 PRJNA1042913 not deposited –
Aurelia coerulea Rhopalium - PRJNA1287281 not deposited –
Aurelia coerulea Whole adults 45,286 PRJNA884642 not deposited –
Aurelia coerulea whole animal 18,936 PRJNA1045549 not deposited –
Aurelia coerulea whole organism not available PRJNA1014937 not deposited –
Clytia hemisphaerica planula larva - PRJNA1220061 not deposited –
Hydra vulgaris Whole polyp 1,152 PRJNA614614 not deposited –
Hydra vulgaris Whole polyp 1,152 PRJNA614611 not deposited –
Hydractinia symbiolongicarpus Whole body 199,113 PRJNA1124116 not deposited –
Hydractinia symbiolongicarpus whole colony - PRJNA807936 not deposited –
Hydractinia symbiolongicarpus whole colony 47,000 PRJNA1263849 not deposited –
Montipora capricornis Polyps 11,243 PRJNA544778 not deposited –
Montipora foliosa Polyps 19,369 PRJNA544778 not deposited –
Nematostella vectensis 2 month animal 2,032 PRJNA1063743 available browse
Nematostella vectensis aggregates - PRJNA1327231 available browse
Nematostella vectensis Blastula-gastrula intermediate 55,042 PRJNA823660 available browse
Nematostella vectensis body wall with mesenteries - PRJNA1217498 available browse
Nematostella vectensis Bodywall, Mesentery, Pharynx, Tentacle 2,032 PRJNA645134 available browse
Nematostella vectensis embryo - PRJNA1291744 available browse
Nematostella vectensis Gastrula Cells - PRJNA903823 available browse
Nematostella vectensis neoplasm - PRJNA1331670 available browse
Nematostella vectensis tentacle - PRJNA1331670 available browse
Nematostella vectensis whole-adult ~60,000 PRJNA1249376 available browse
Oculina arbuscula whole organism 6,951 PRJNA1122932 available browse
Oculina patagonica Whole adults 29,723 PRJNA1223412 available browse
Orbicella faveolata coral mucus and tissue 12,719 PRJNA1180584 not deposited –
Pocillopora verrucosa Polyps 11,493 PRJNA544778 not deposited –
Stylophora pistillata Whole adults 15,053 PRJNA1223412 available browse
Turritopsis rubra whole animal 22,245 PRJNA1045549 not deposited –

Atlas embeddings currently deposited: AMILL (1), AMURI (1), NVECT (5), OARBU (1), OPATA (1), SPIST (1).

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