embedding_id	dataset	species	scope	served	api_status	cells	runs	input_read_type	batch_integration	coordinate_built	labels_event	coordinate_verified	limitations
shared_sampled_atlas	(21-dataset sampled atlas)	human+mouse (joint coordinate space; portal displays one species at a time)	sampled	True	available	141313	123	long-read ONT/PacBio cDNA	Harmony by run	2026-07-30	cell_type rewritten from cell_map_repair_20260819_final overlay on 2026-08-21; coordinates unchanged		Joint human+mouse coordinate space: cross-species separation is verified in the diagnostics record, but the shared map must not be read as a cross-species biological alignment. | Sampling caps each run x cell type at 250 cells; absolute abundances are not preserved. | Labels mix granularity levels (broad type, subtype, developmental state, technical/context strings); see the label hierarchy audit. | Exploratory display embedding; not a trajectory or integration benchmark product.
full:GSE178175:human	GSE178175	human	full	True	available	70688	16	long-read ONT/PacBio cDNA	Harmony by run applied	2026-08-19	labels transferred from the matched FCtx1 paper-recipe 10x matrix (7,314 QC nuclei; FCtx2 left as context-only because GEO lacks its 10x matrix)	True	FCtx2 nuclei carry context-only labels because GEO lacks the FCtx2 10x matrix; context strings are not cell types.
full:GSE212945:human	GSE212945	human	full	True	available	21996	5	long-read ONT/PacBio cDNA	Harmony by run applied	2026-07-30	cell_type rewritten from cell_map_repair_20260819_final overlay (map_display_label) on 2026-08-22; coordinates unchanged (relabel script rewrites only the cell_type column)		
full:GSE214231:human	GSE214231	human	full	False	blocked:matrix_mismatch_policy	44638	6	long-read ONT/PacBio cDNA	Harmony by run applied	2026-08-04	cell_type rewritten from cell_map_repair_20260819_final overlay (map_display_label) on 2026-08-22; coordinates unchanged (relabel script rewrites only the cell_type column)		Withheld by portal policy: the processed matrix does not contain the annotated cells (matrix/annotation mismatch).
full:GSE224045:human	GSE224045	human	full	True	available	8756	1	long-read ONT/PacBio cDNA	no batch integration (single run or <50 cells)	2026-07-30	cell_type rewritten from cell_map_repair_20260819_final overlay (map_display_label) on 2026-08-22; coordinates unchanged (relabel script rewrites only the cell_type column)		
full:GSE248118:human	GSE248118	human	full	True	available	2224	1	long-read ONT/PacBio cDNA	no batch integration (single run or <50 cells)	2026-07-30	cell_type rewritten from cell_map_repair_20260819_final overlay (map_display_label) on 2026-08-22; coordinates unchanged (relabel script rewrites only the cell_type column)		
full:GSE252344:human	GSE252344	human	full	False	blocked:matrix_mismatch_policy	28956	1	long-read ONT/PacBio cDNA	no batch integration (single run or <50 cells)	2026-08-04	cell_type rewritten from cell_map_repair_20260819_final overlay (map_display_label) on 2026-08-22; coordinates unchanged (relabel script rewrites only the cell_type column)		Withheld by portal policy: the processed matrix does not contain the annotated cells (matrix/annotation mismatch).
full:GSE252416:human	GSE252416	human	full	False	blocked:matrix_mismatch_policy	18933	1	long-read ONT/PacBio cDNA	no batch integration (single run or <50 cells)	2026-08-04	cell_type rewritten from cell_map_repair_20260819_final overlay (map_display_label) on 2026-08-22; coordinates unchanged (relabel script rewrites only the cell_type column)		Withheld by portal policy: the processed matrix does not contain the annotated cells (matrix/annotation mismatch).
full:GSE274249:human	GSE274249	human	full	True	available	32253	4	long-read ONT/PacBio cDNA	Harmony by run applied	2026-07-30	labels from the active annotation release at build time; no v2 overlay relabel recorded for this dataset		
full:GSE276974:human	GSE276974	human	full	True	available	113023	16	long-read ONT/PacBio cDNA	Harmony by run applied	2026-08-21	cell_type rewritten from cell_map_repair_20260819_final overlay (map_display_label) on 2026-08-22; coordinates unchanged (relabel script rewrites only the cell_type column)	True	
full:GSE283629:human	GSE283629	human	full	True	available	58984	4	long-read ONT/PacBio cDNA	Harmony by run applied	2026-07-30	labels from the active annotation release at build time; no v2 overlay relabel recorded for this dataset		
full:GSE283658:human	GSE283658	human	full	True	available	17571	3	long-read ONT/PacBio cDNA	Harmony by run applied	2026-07-30	labels from the active annotation release at build time; no v2 overlay relabel recorded for this dataset		
full:GSE288222:human	GSE288222	human	full	True	available	29053	12	long-read ONT/PacBio cDNA	Harmony by run applied	2026-07-30	labels from the active annotation release at build time; no v2 overlay relabel recorded for this dataset		
full:GSE289428:human	GSE289428	human	full	False	blocked:smartseq2_policy	3	3	long-read ONT/PacBio cDNA	no batch integration (single run or <50 cells)	2026-08-04	labels from the active annotation release at build time; no v2 overlay relabel recorded for this dataset		Smart-seq2 / one-library-per-file route (IsoQuant file_name grouping on ONT long reads of full-length libraries); each displayed 'cell' is one library file. Map exists on disk but is withheld by portal policy (no joint structure in one-cell-per-well maps). | Runs are bulk HeLa TLDR-seq libraries (library-level records, R2m1); the 3 displayed 'cells' are libraries, not cells.
full:GSE289790:human	GSE289790	human	full	True	available	3915	2	long-read ONT/PacBio cDNA	Harmony by run applied	2026-07-30	cell_type rewritten from cell_map_repair_20260819_final overlay (map_display_label) on 2026-08-22; coordinates unchanged (relabel script rewrites only the cell_type column)		
full:GSE292324:human	GSE292324	human	full	True	available	55507	8	long-read ONT/PacBio cDNA	Harmony by run applied	2026-07-30	labels from the active annotation release at build time; no v2 overlay relabel recorded for this dataset		
full:GSE295932:human	GSE295932	human	full	True	available	8951	4	long-read ONT/PacBio cDNA	Harmony by run applied	2026-07-30	cell_type rewritten from cell_map_repair_20260819_final overlay (map_display_label) on 2026-08-22; coordinates unchanged (relabel script rewrites only the cell_type column)		
full:GSE301658:human	GSE301658	human	full	True	available	3353	1	long-read ONT/PacBio cDNA	no batch integration (single run or <50 cells)	2026-07-30	labels from the active annotation release at build time; no v2 overlay relabel recorded for this dataset		
full:GSE303762:human	GSE303762	human	full	True	available	71466	2	long-read ONT/PacBio cDNA	Harmony by run applied	2026-07-30	cell_type rewritten from cell_map_repair_20260819_final overlay (map_display_label) on 2026-08-22; coordinates unchanged (relabel script rewrites only the cell_type column)		
full:GSE307660:human	GSE307660	human	full	True	available	44988	18	long-read ONT/PacBio cDNA	Harmony by run applied	2026-07-30	cell_type rewritten from cell_map_repair_20260819_final overlay (map_display_label) on 2026-08-22; coordinates unchanged (relabel script rewrites only the cell_type column)		
full:benagen_human_ovary:human	benagen_human_ovary	human	full	True	available	28921	2	long-read ONT/PacBio cDNA	Harmony by run applied	2026-08-04	labels from the active annotation release at build time; no v2 overlay relabel recorded for this dataset		
full:GSA_mouse_testis_11week:mouse	GSA_mouse_testis_11week	mouse	full	True	available	26792	2	long-read ONT/PacBio cDNA	Harmony by run applied	2026-07-30	labels from the active annotation release at build time; no v2 overlay relabel recorded for this dataset		
full:GSE114157:mouse	GSE114157	mouse	full	False	blocked:smartseq2_policy	5	5	long-read ONT/PacBio cDNA	no batch integration (single run or <50 cells)	2026-08-04	labels from the active annotation release at build time; no v2 overlay relabel recorded for this dataset		Smart-seq2 / one-library-per-file route (IsoQuant file_name grouping on ONT long reads of full-length libraries); each displayed 'cell' is one library file. Map exists on disk but is withheld by portal policy (no joint structure in one-cell-per-well maps).
full:GSE130708:mouse	GSE130708	mouse	full	True	available	3687	5	long-read ONT/PacBio cDNA	Harmony by run applied	2026-07-30	labels from the active annotation release at build time; no v2 overlay relabel recorded for this dataset		
full:GSE158450:mouse	GSE158450	mouse	full	True	available	35753	4	paired short-read (10x) gene counts; the study's long-read runs quantify the same cells but do not provide this map's input matrix	Harmony by run applied	2026-08-24	labels from the author-deposited paired 10x annotation (gse158450_paper_10x_20260824) applied at build time		
full:GSE178175:mouse	GSE178175	mouse	full	True	available	2106	1	long-read ONT/PacBio cDNA	no batch integration (single run or <50 cells)	2026-07-30	labels assigned by Scanpy Leiden (resolution 0.6) on the long-read gene matrix with canonical hippocampal markers; unresolved cells hidden		
full:GSE185554:mouse	GSE185554	mouse	full	False	blocked:smartseq2_policy	42	42	long-read ONT/PacBio cDNA	no batch integration (single run or <50 cells)	2026-08-04	cell_type rewritten from cell_map_repair_20260819_final overlay (map_display_label) on 2026-08-22; coordinates unchanged (relabel script rewrites only the cell_type column)		Smart-seq2 / one-library-per-file route (IsoQuant file_name grouping on ONT long reads of full-length libraries); each displayed 'cell' is one library file. Map exists on disk but is withheld by portal policy (no joint structure in one-cell-per-well maps).
full:GSE250381:mouse	GSE250381	mouse	full	True	available	230	4	long-read ONT/PacBio cDNA	Harmony by run applied	2026-08-19	cell_type rewritten from cell_map_repair_20260819_final overlay (map_display_label) on 2026-08-22; coordinates unchanged (relabel script rewrites only the cell_type column)	True	
full:GSE255520:mouse	GSE255520	mouse	full	True	available	5069	2	long-read ONT/PacBio cDNA	Harmony by run applied	2026-07-30	labels from the active annotation release at build time; no v2 overlay relabel recorded for this dataset		
full:GSE274527:mouse	GSE274527	mouse	full	False	blocked:smartseq2_policy	24	24	long-read ONT/PacBio cDNA	no batch integration (single run or <50 cells)	2026-08-04	labels from the active annotation release at build time; no v2 overlay relabel recorded for this dataset		Smart-seq2 / one-library-per-file route (IsoQuant file_name grouping on ONT long reads of full-length libraries); each displayed 'cell' is one library file. Map exists on disk but is withheld by portal policy (no joint structure in one-cell-per-well maps).
full:GSE295352:mouse	GSE295352	mouse	full	True	available	12528	6	long-read ONT/PacBio cDNA	Harmony by run applied	2026-07-30	labels from the active annotation release at build time; no v2 overlay relabel recorded for this dataset		
full:GSE295353:mouse	GSE295353	mouse	full	True	available	19036	6	long-read ONT/PacBio cDNA	Harmony by run applied	2026-08-19	cell_type rewritten from cell_map_repair_20260819_final overlay (map_display_label) on 2026-08-22; coordinates unchanged (relabel script rewrites only the cell_type column)	True	
full:GSE309071:mouse	GSE309071	mouse	full	False	blocked:smartseq2_policy	212	212	long-read ONT/PacBio cDNA	Harmony by run applied	2026-08-04	cell_type rewritten from cell_map_repair_20260819_final overlay (map_display_label) on 2026-08-22; coordinates unchanged (relabel script rewrites only the cell_type column)		Smart-seq2 / one-library-per-file route (IsoQuant file_name grouping on ONT long reads of full-length libraries); each displayed 'cell' is one library file. Map exists on disk but is withheld by portal policy (no joint structure in one-cell-per-well maps).
full:GSE314176:mouse	GSE314176	mouse	full	True	available	25325	3	long-read ONT/PacBio cDNA	Harmony by run applied	2026-08-04	labels from the active annotation release at build time; no v2 overlay relabel recorded for this dataset		
full:GSE76026:mouse	GSE76026	mouse	full	False	blocked:smartseq2_policy	12	12	long-read ONT/PacBio cDNA	no batch integration (single run or <50 cells)	2026-08-04	labels from the active annotation release at build time; no v2 overlay relabel recorded for this dataset		Smart-seq2 / one-library-per-file route (IsoQuant file_name grouping on ONT long reads of full-length libraries); each displayed 'cell' is one library file. Map exists on disk but is withheld by portal policy (no joint structure in one-cell-per-well maps).
full:OWN_ASE_scONT:mouse	OWN_ASE_scONT	mouse	full	True	available	55729	6	coordinates not recomputed by scTHREAD; overlays are ONT long-read IsoQuant assignment counts	Seurat Harmony (inside the authoritative object; exact parameters not re-derivable from portal artifacts)	not recomputable from portal artifacts (authoritative in-house object)	REANNOTATION_LEVEL2 six-stage reannotation shipped with the object		Coordinates are taken from the authoritative Seurat object; the portal cannot re-derive them from the published build script. | Overlay join keys are run-wise barcode matches; unmatched cells would be absent rather than estimated.