Cell Atlas

Every cell is one point. Drag to pan, scroll to zoom, shift-drag to select a region; click any group in the legend to isolate it. Use Colour cells by to switch between cell type, cluster, library, quality-control metric and the expression of a single gene.

Cell types in this dataset

Click a cell type to isolate it in the atlas above.

Cell type Cells Percent Markers
gastrodermis 7,328 33.65% marker genes
epidermis 3,078 14.14% marker genes
gastrodermis_alga_hosting 1,625 7.46% marker genes
calicoblast 1,024 4.70% marker genes
neuron_Isl 784 3.60% marker genes
epidermis_like_1 768 3.53% marker genes
gastrodermis_like_1 636 2.92% marker genes
digestive_filaments 587 2.70% marker genes
gastrodermis_like_2 552 2.54% marker genes
immune_1 507 2.33% marker genes
neurosecretory_progenitors 505 2.32% marker genes
neuron_Pou4_Otp_1 457 2.10% marker genes
gland_1_Xbp 442 2.03% marker genes
gland_6 362 1.66% marker genes
germline_oocytes 335 1.54% marker genes
gland_2 315 1.45% marker genes
gland_3 248 1.14% marker genes
cnidocyte_1 248 1.14% marker genes
immune_3 245 1.13% marker genes
immune_2 230 1.06% marker genes
gland_5 220 1.01% marker genes
neuron_Pou4_Gsx 218 1.00% marker genes
gland_7 215 0.99% marker genes
gland_4 156 0.72% marker genes
cnidocyte_2 127 0.58% marker genes
epidermis_like_2 124 0.57% marker genes
neuron_Pou4_1 97 0.45% marker genes
neuron_Pou4_Otp_2 97 0.45% marker genes
gastrodermis_muscle_like 88 0.40% marker genes
neuron_Pou4_2 84 0.39% marker genes
gland_8 73 0.34% marker genes

Quality control for this dataset

These are the figures actually applied to the cells shown above, not the values requested in a configuration file. Every dataset is filtered independently; see Single-cell Data for the full table across all datasets.

Source BioProject PRJNA1223412
SRA study SRP563749
GEO series GSE289546
Library type 10x Genomics Chromium (high confidence)
Libraries integrated 4
Cells reported by source 29723
Cells before filtering 29,723
Cells after cell filtering 21,794
Doublets removed 19 (0.09%)
Cells after filtering 21,775
Retained 73.3%
Filtering strategy Per-library MAD outlier detection (adaptive)
Thresholds applied adaptive: per-library MAD (5.0 MADs) on UMI, genes and MT%, floor 200 genes, floor 500 UMI
Mitochondrial genes found 0 — too few for a reliable MT% filter, so none was applied
Doublet method Scrublet (per library)
Integration method Harmony on sample (4 libraries)
Cell-type annotation Inherited from the source publication
Cell-type labels from GSE289546_Opat.cell_to_cts.csv.gz (100% of cells matched)
Pipeline version cnidosite-sc-1.0.0
Processed 2026-09-20T03:34:23+00:00
Clusters / cell types 55 / 31
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