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.
Select Tissue Sample
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Query Parameters
Species: Oculina patagonica •
Stage: Adult tissues/organs •
Emb/Org: Whole adults
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UMAP Visualization
UMAP — coloured by cluster
Only one UMAP is shown for this dataset.
For Oculina patagonica — Whole adults,
the cell-type–coloured projection was not deposited: the file previously displayed as a second panel was
byte-identical to the cluster-coloured one, so it is no longer shown twice.
Cell types in this dataset
(31 annotated cell types,
from the marker table
OPATA_cellmarker)
epidermis_like_2 2093 markers
neuron_Pou4_Gsx 2053 markers
immune_like_2 1948 markers
epidermis 1828 markers
immune_macrophage_like 1769 markers
neuron_Pou4_Otp_2 1759 markers
gastrodermis_muscle_like 1752 markers
epidermis_like_1 1697 markers
neuron_Pou4_Otp_1 1662 markers
germline_oocytes 1550 markers
gastrodermis_alga_hosting 1542 markers
immune_like_1 1448 markers
cnidocyte_1 1440 markers
neuron_Pou4_1 1410 markers
gastrodermis_like_2 1387 markers
calicoblast 1331 markers
gland_1_Xbp 1309 markers
neurosecretory_progenitors 1308 markers
gastrodermis_like_1 1263 markers
cnidocyte_2 1199 markers
gastrodermis 1185 markers
gland_8 1152 markers
gland_6 1150 markers
gland_3 1133 markers
gland_7 1110 markers
neuron_Pou4_2 1106 markers
neuron_Isl 1098 markers
gland_5 1069 markers
digestive_filaments 1042 markers
gland_2 1041 markers
gland_4 1010 markers
What this view shows.
Each point is one cell, positioned by UMAP so that transcriptionally similar cells sit together.
Colour encodes the cluster or cell type. Use it to judge how many distinct cell populations the sample
contains and how well separated they are; to find out what each population is, follow the cell-type chips
above into Cell Marker, which lists the genes that define it and links each
gene to its own FeaturePlot / VlnPlot.
Cells: 29,723 · Source: 41094138 · Species entry: CnidoSite
Cells: 29,723 · Source: 41094138 · Species entry: CnidoSite
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.
| Species | Stage / tissue | Cells | BioProject | Cell Atlas | Markers |
|---|---|---|---|---|---|
| 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).
