Human CellCards Multi-Study CellRef 1.0 Atlas

Minzhe Guo¹, Geremy Clair², Joshua N. Adkins², Gloria Pryhuber³, Ravi Misra³, Bruce Aronow¹, Timothy L. Tickle⁴, Nathan Salomonis¹, Xin Sun⁵, Edward E. Morrisey⁶, Jeffrey A. Whitsett¹, Yan Xu¹

¹Cincinnati Children's Hospital Medical Center, ²Pacific Northwest National Laboratory, ³University of Rochester Medical Center, ⁴The Broad Institute, ⁵University of California, San Diego, ⁶Perelman School of Medicine, University of Pennsylvania, ^*Corresponding author

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Description The "LungMAP Human Lung CellRef" atlas incorporates 48 well-defined lung cell types (CellCards) catalogued from diverse anatomic locations and stages of lung maturation. This atlas spans sc/snRNA-seq of 505,256 lung cells from 148 normal human lung samples from 104 donors from parenchyma, trachea, bonchi, bronchus SMG and small airway. This study includes 21 new lung samples. An accompanying R-shiny app (Azimuth) enables fast supervised annotation of user-provided single-cell RNA-Seq datasets (see below).

Dataset ID LMEX0000004396

Assay Type Single-cell RNA-seq

Organism Human

Stages Child | Adolescent | Adult | 65+ years

Cell Count 505256

Technology 10x Genomics Chromium Single Cell Gene Expression

Reference Guo, et al. (2022)

File	Description	Size
Cell.Metadata.txt	Cell Barcode-level metadata	38.5 MB
LungMAP_HumanLung_CellRef.v1.1.h5ad	HDF5 annotated format single-cell data matrix	4.7 GB
TopMarkers_celltype_level3.txt	Seurat ranked top marker genes (level 3 annotation)	104.8 KB
UMAP-coordinates.txt	UMAP Coordinates for the Human CellRef full dataset	21.1 MB

LungMAP ID	Alt ID	Species	Sex	Race	Age	Age Group	Weight	Cause of Death	Type of Death
LMSP0000001176	001C	Homo sapiens	Male	White	22 years	Adult
LMSP0000001177	002C	Homo sapiens	Female	White	25 years	Adult
LMSP0000001178	003C	Homo sapiens	Female	White	67 years	65+ years
LMSP0000001159	034C	Homo sapiens	Male	Asian	49 years	Adult
LMSP0000001172	065C	Homo sapiens	Female	White	66 years	65+ years
LMSP0000001182	081C	Homo sapiens	Male	White	20 years	Adult
LMSP0000001184	084C	Homo sapiens	Male	African American	46 years	Adult
LMSP0000001170	092C	Homo sapiens	Male	Hispanic/Latino	29 years	Adult
LMSP0000001163	098C	Homo sapiens	Female	White	41 years	Adult
LMSP0000001157	133C	Homo sapiens	Female	White	32 years	Adult
LMSP0000001158	1372C	Homo sapiens	Female	White	21 years	Adult
LMSP0000001183	137C	Homo sapiens	Male	White	54 years	Adult
LMSP0000001169	160C	Homo sapiens	Male	White	64 years	Adult
LMSP0000001174	192C	Homo sapiens	Female	White	62 years	Adult
LMSP0000001167	208C	Homo sapiens	Male	White	23 years	Adult
LMSP0000001160	218C	Homo sapiens	Male	White	29 years	Adult
LMSP0000001168	222C	Homo sapiens	Male	White	65 years	65+ years
LMSP0000001161	226C	Homo sapiens	Male	White	32 years	Adult
LMSP0000001162	244C	Homo sapiens	Male	White	50 years	Adult
LMSP0000001180	253C	Homo sapiens	Female	White	66 years	65+ years
LMSP0000001166	296C	Homo sapiens	Female	White	80 years	65+ years
LMSP0000001173	388C	Homo sapiens	Male	White	61 years	Adult
LMSP0000001165	396C	Homo sapiens	Female	White	37 years	Adult
LMSP0000001171	439C	Homo sapiens	Female	White	66 years	65+ years
LMSP0000001179	454C	Homo sapiens	Female	White	48 years	Adult
LMSP0000001164	465C	Homo sapiens	Male	White	56 years	Adult
LMSP0000001175	483C	Homo sapiens	Male	White	35 years	Adult
LMSP0000001181	484C	Homo sapiens	Male	White	31 years	Adult
LMSP0000001130	C51ctr	Homo sapiens	Female	White	70 years	65+ years
LMSP0000001131	C52ctr	Homo sapiens	Female	White	69 years	65+ years
LMSP0000001132	C53ctr	Homo sapiens	Male	Unknown or Not Reported	79 years	65+ years
LMSP0000001133	C54ctr	Homo sapiens	Female	Asian	72 years	65+ years
LMSP0000001134	C55ctr	Homo sapiens	Male	Unknown or Not Reported	69 years	65+ years
LMSP0000001135	C56ctr	Homo sapiens	Male	White	75 years	65+ years
LMSP0000001136	C57ctr	Homo sapiens	Male	White	68 years	65+ years
LMSP0000001305	CCHMC_Donor27	Homo sapiens	Male		47 years	Adult
LMSP0000001306	CCHMC_Donor28	Homo sapiens	Male		20 years	Adult
LMSP0000001307	CCHMC_Donor29	Homo sapiens	Female		13 years	Adolescent
LMSP0000001308	CCHMC_Donor33	Homo sapiens	Male		50 years	Adult
LMSP0000001309	CCHMC_Donor38	Homo sapiens	Female		39 years	Adult
LMSP0000001029	D122	Homo sapiens	Male	Unknown or Not Reported	31 years	Adult	109 kg	Trauma - Fall from Height	DBD (after brain death)
LMSP0000001081	D175	Homo sapiens	Female	White	29 years	Adult	89.1 kg	Trauma - Firearm	DCD (circulatory death)
LMSP0000001119	D231	Homo sapiens	Female	African American	33 years	Adult	103.87 kg	Anoxic/Hypoxic Brain Injury - Other	DCD (circulatory death)
LMSP0000001310	D322	Homo sapiens	Female		30 years	Adult
LMSP0000001311	D326	Homo sapiens	Male		31 years	Adult
LMSP0000001312	D339	Homo sapiens	Male		29 years	Adult
LMSP0000001313	D344	Homo sapiens	Female		26 years	Adult
LMSP0000001314	D353	Homo sapiens	Female		30 years	Adult
LMSP0000001315	D354	Homo sapiens	Male		33 years	Adult
LMSP0000001316	D363	Homo sapiens	Female		24 years	Adult
LMSP0000001317	D367	Homo sapiens	Male		27 years	Adult
LMSP0000001318	D372	Homo sapiens	Female		35 years	Adult
LMSP0000001284	Donor 1	Homo sapiens	Female	African American	63 years	Adult		Stroke
LMSP0000001285	Donor 2	Homo sapiens	Male	Asian	55 years	Adult		Intracranial hemorrhage
LMSP0000001286	Donor 3	Homo sapiens	Female	African American	29 years	Adult		Anoxic/Hypoxic Brain Injury
LMSP0000001287	Donor 4	Homo sapiens	Female	African American	57 years	Adult		Anoxic/Hypoxic Brain Injury
LMSP0000001288	Donor 5	Homo sapiens	Female	White	49 years	Adult		Intracranial hemorrhage
LMSP0000001289	Donor 6	Homo sapiens	Female	African American	22 years	Adult		Anoxic/Hypoxic Brain Injury
LMSP0000001290	Donor 7	Homo sapiens	Female	White	47 years	Adult		Intracranial hemorrhage
LMSP0000001291	Donor 8	Homo sapiens	Male	African American	21 years	Adult		Trauma
LMSP0000001359	EEM-scRNA-005	Homo sapiens	Female		29 years	Adult
LMSP0000001360	EEM-scRNA-006	Homo sapiens	Male		25 years	Adult
LMSP0000001361	EEM-scRNA-022	Homo sapiens	Male		17 years	Adolescent
LMSP0000001362	EEM-scRNA-026	Homo sapiens	Male		13 years	Adolescent
LMSP0000001363	EEM-scRNA-062	Homo sapiens	Female		57 years	Adult
LMSP0000001364	EEM-scRNA-067	Homo sapiens	Female		68 years	65+ years
LMSP0000001365	EEM-scRNA-073	Homo sapiens	Female		59 years	Adult
LMSP0000001366	EEM-scRNA-078	Homo sapiens	Female		12 years	Adolescent
LMSP0000001367	EEM-scRNA-079	Homo sapiens	Male		42 years	Adult
LMSP0000001348	EEM-scRNA-R05-1	Homo sapiens	Male		69 years	65+ years
LMSP0000001349	EEM-scRNA-R05-2	Homo sapiens	Male		69 years	65+ years
LMSP0000001346	EEM-scRNA-R06-1	Homo sapiens	Male		52 years	Adult
LMSP0000001347	EEM-scRNA-R06-2	Homo sapiens	Male		52 years	Adult
LMSP0000001350	EEM-scRNA-R07-1	Homo sapiens	Female		35 years	Adult
LMSP0000001351	EEM-scRNA-R07-2	Homo sapiens	Female		35 years	Adult
LMSP0000001352	EEM-scRNA-R15-1	Homo sapiens	Female		76 years	65+ years
LMSP0000001353	EEM-scRNA-R15-2	Homo sapiens	Female		76 years	65+ years
LMSP0000001354	EEM-scRNA-R20-1	Homo sapiens	Female		51 years	Adult
LMSP0000001355	EEM-scRNA-R20-2	Homo sapiens	Female		51 years	Adult
LMSP0000001356	EEM-scRNA-R36	Homo sapiens	Male		23 years	Adult
LMSP0000001357	EEM-scRNA-R39-1	Homo sapiens	Female		70 years	65+ years
LMSP0000001358	EEM-scRNA-R39-2	Homo sapiens	Female		70 years	65+ years
LMSP0000001334	F00409	Homo sapiens	Female		31 years	Adult
LMSP0000001335	F01157	Homo sapiens	Male		36 years	Adult
LMSP0000001336	F01174	Homo sapiens	Unknown		40 years	Adult
LMSP0000001337	F01365	Homo sapiens	Male			Adult
LMSP0000001338	F01366	Homo sapiens	Male			Adult
LMSP0000001339	F01367	Homo sapiens	Male			Adult
LMSP0000001340	F01394	Homo sapiens	Male		38 years	Adult
LMSP0000001341	HD65	Homo sapiens	Male		17 years	Adolescent
LMSP0000001342	HD66	Homo sapiens	Male		30 years	Adult
LMSP0000001343	HD67	Homo sapiens	Female		30 years	Adult
LMSP0000001344	HD68	Homo sapiens	Male		41 years	Adult
LMSP0000001345	HD70	Homo sapiens	Male		54 years	Adult
LMSP0000001120	Patient 1	Homo sapiens	Male		75 years	65+ years
LMSP0000001121	Patient 2	Homo sapiens	Male		46 years	Adult
LMSP0000001122	Patient 3	Homo sapiens	Female		51 years	Adult
LMSP0000001319	T101	Homo sapiens	Male		55 years	Adult
LMSP0000001320	T120	Homo sapiens	Female		57 years	Adult
LMSP0000001321	T121	Homo sapiens	Female		23 years	Adult
LMSP0000001322	T126	Homo sapiens	Female		35 years	Adult
LMSP0000001323	T137	Homo sapiens	Male		27 years	Adult
LMSP0000001324	T153	Homo sapiens	Male		38 years	Adult
LMSP0000001325	T154	Homo sapiens	Male		61 years	Adult
LMSP0000001326	T164	Homo sapiens	Male		66 years	65+ years
LMSP0000001327	T165	Homo sapiens	Male		64 years	Adult
LMSP0000001328	T166	Homo sapiens	Female		68 years	65+ years
LMSP0000001329	T167	Homo sapiens	Female		66 years	65+ years
LMSP0000001330	T84	Homo sapiens	Male		22 years	Adult
LMSP0000001331	T85	Homo sapiens	Male		59 years	Adult
LMSP0000001332	T89	Homo sapiens	Female		10 years	Child
LMSP0000001333	T90	Homo sapiens	Male		44 years	Adult

49 of this study's 112 samples were also assayed by 5 other LungMAP studies, across 1 modality. Click any node to list those studies. The other 63 appear in no other study and are not drawn.

Shared samples by study