Single-cell Data

Single-cell Data

In this module, a brief summary of single-cell RNA-seq datasets are listed as follows.

No dataset is listed for Heteractis aurora.

No row in the single-cell table names that species. The table below lists every species that does have one.

Class	Species	Project	Study Accession	Emb/Org	Stage	Number of Cells	Quality Control	Analyse	References
Hexacorallia	Acropora millepora	PRJNA1223412	SRP563749	Whole adults	Adult tissues/organs	28,736	10x Genomics Chromium 28,736 → 25,164 cells · 87.6% retained · doublets 0.04% full QC →	Atlas · Markers	41094138
Hexacorallia	Acropora muricata	PRJNA544778	SRP199550	Polyps	regeneration	17,277	not re-analysed — no count matrix in the public deposit	–	40269231
Hexacorallia	Montipora capricornis	PRJNA544778	SRP199550	Polyps	Adult tissues/organs	11,243	not re-analysed — no count matrix in the public deposit	–	Link
Hexacorallia	Montipora foliosa	PRJNA544778	SRP199550	Polyps	Adult tissues/organs	19,369	not re-analysed — no count matrix in the public deposit	–	Link
Hexacorallia	Nematostella vectensis	PRJNA1063743	SRP483247	2 month animal	Adult tissues/organs	2,032	10x Genomics Chromium 10,000 → 1,614 cells · 16.1% retained · doublets 0.00% full QC →	Atlas · Markers	39151009
Hexacorallia	Nematostella vectensis	PRJNA1217498	SRP560807	body wall with mesenteries	6-8 weeks adults	-	library type not stated in the deposit 12,352 → 11,742 cells · 95.1% retained · doublets 0.00% full QC →	Atlas · Markers	-
Hexacorallia	Nematostella vectensis	PRJNA1249376	SRP577940	whole-adult	Adult tissues/organs	~60,000	not re-analysed — no count matrix in the public deposit	–	-
Hexacorallia	Nematostella vectensis	PRJNA1291744	SRP601047	embryo	Developmental stages	-	10x Genomics Chromium 9,726 → 9,711 cells · 99.8% retained · doublets 0.15% full QC →	Atlas · Markers	-
Hexacorallia	Nematostella vectensis	PRJNA1327231	SRP619054	aggregates	Embryos treated	-	10x Genomics Chromium 36,568 → 36,550 cells · 100.0% retained · doublets 0.05% full QC →	Atlas · Markers	-
Hexacorallia	Nematostella vectensis	PRJNA1331670	SRP622332	neoplasm	Adult tissues/organs	-	10x Genomics Chromium 2,756 → 2,532 cells · 91.9% retained · doublets 0.08% full QC →	Atlas · Markers	-
Hexacorallia	Nematostella vectensis	PRJNA1331670	SRP622332	tentacle	Adult tissues/organs	-	10x Genomics Chromium 9,350 → 7,977 cells · 85.3% retained · doublets 0.04% full QC →	Atlas · Markers	-
Hexacorallia	Nematostella vectensis	PRJNA645134	SRP271116	Bodywall, Mesentery, Pharynx, Tentacle	Whole organism	2,032	not re-analysed — no count matrix in the public deposit	–	39151009
Hexacorallia	Nematostella vectensis	PRJNA823660	SRP367642	Blastula-gastrula intermediate	Developmental stages	55,042	10x Genomics Chromium 55,042 → 49,166 cells · 89.3% retained · doublets 0.06% full QC →	Atlas · Markers	36130520
Hexacorallia	Nematostella vectensis	PRJNA903823	SRP408911	Gastrula Cells	nervous system		not re-analysed — no count matrix in the public deposit	–	37244953
Hexacorallia	Oculina arbuscula	PRJNA1122932	SRP513328	whole organism	Symbiotic state	6,951	not re-analysed — no count matrix in the public deposit	–	40569035
Hexacorallia	Oculina patagonica	PRJNA1223412	SRP563749	Whole adults	Adult tissues/organs	29,723	10x Genomics Chromium 29,723 → 21,775 cells · 73.3% retained · doublets 0.09% full QC →	Atlas · Markers	41094138
Hexacorallia	Orbicella faveolata	PRJNA1180584	SRP542438	coral mucus and tissue	bleaching stages	12,719	not re-analysed — no count matrix in the public deposit	–	Link
Hexacorallia	Pocillopora verrucosa	PRJNA544778	SRP199550	Polyps	Adult tissues/organs	11,493	not re-analysed — no count matrix in the public deposit	–	Link
Hexacorallia	Stylophora pistillata	PRJNA1223412	SRP563749	Whole adults	Adult tissues/organs	15,053	10x Genomics Chromium 15,053 → 13,896 cells · 92.3% retained · doublets 0.06% full QC →	Atlas · Markers	41094138
Hydrozoa	Clytia hemisphaerica	PRJNA1220061	SRP562097	planula larva	Adult tissues/organs	-	not re-analysed — no count matrix in the public deposit	–	-
Hydrozoa	Hydra vulgaris	PRJNA614611	SRP253820	Whole polyp	Adult tissues/organs	1,152	not re-analysed — no count matrix in the public deposit	–	32647059
Hydrozoa	Hydra vulgaris	PRJNA614614	SRP253822	Whole polyp	Adult tissues/organs	1,152	not re-analysed — no count matrix in the public deposit	–	32647059
Hydrozoa	Hydractinia symbiolongicarpus	PRJNA1124116	SRP514108	Whole body	Adult tissues/organs	199,113	not re-analysed — no count matrix in the public deposit	–	40032860
Hydrozoa	Hydractinia symbiolongicarpus	PRJNA1263849	SRP587019	whole colony	Adult tissues/organs	47,000	not re-analysed — no count matrix in the public deposit	–	41382277
Hydrozoa	Hydractinia symbiolongicarpus	PRJNA807936	SRP360329	whole colony	Adult tissues/organs	-	not re-analysed — no count matrix in the public deposit	–	41262968
Hydrozoa	Turritopsis rubra	PRJNA1045549	SRP474384	whole animal	medusa	22,245	not re-analysed — no count matrix in the public deposit	–	39009560
Scyphozoa	Aurelia coerulea	PRJNA1011858	SRP458012	gastrodermis	Developmental stages	10000	not re-analysed — no count matrix in the public deposit	–	-
Scyphozoa	Aurelia coerulea	PRJNA1014937	SRP468849	whole organism	Developmental stages	not available	not re-analysed — no count matrix in the public deposit	–	38125018
Scyphozoa	Aurelia coerulea	PRJNA1041967	SRP472811	ephrya	oceanacid treatment	42,461	not re-analysed — no count matrix in the public deposit	–	Link
Scyphozoa	Aurelia coerulea	PRJNA1042913	SRP473863	podocysts	podocyst-forming polyps	17,978	not re-analysed — no count matrix in the public deposit	–	38133544
Scyphozoa	Aurelia coerulea	PRJNA1045549	SRP474384	whole animal	medusa	18,936	not re-analysed — no count matrix in the public deposit	–	39009560
Scyphozoa	Aurelia coerulea	PRJNA1287281	SRP598586	Rhopalium	Adult tissues/organs	-	not re-analysed — no count matrix in the public deposit	–	-
Scyphozoa	Aurelia coerulea	PRJNA884642	SRP400888	Whole adults	Developmental stages	45,286	not re-analysed — no count matrix in the public deposit	–	Link

Quality control. Each dataset is filtered on its own terms rather than by one fixed UMI window: where the source publication states thresholds they are reproduced exactly, and where it does not, outliers are called per library by median absolute deviation. The Cell Atlas records the figures actually applied to every dataset, including cells before and after filtering, doublet rates and the mitochondrial distribution.