Single-cell RNA-seq analysis of Interstitial Lung Disease (ILD) subtypes

Jonathan A. Kropski¹, Nicholas E. Banovich²

¹Vanderbilt University Medical Center, ²Translational Genomics Research Institute, ^*Corresponding author

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Description ScRNA-seq profiles for 114 individuals, including 66 (58%) with ILD and 48 (42%) unaffected donors. The ILD lungs included samples from 39 individuals with IPF and 27 with other forms of pulmonary fibrosis, including sarcoidosis (n = 4), connective tissue disease-associated ILD (n = 3), idiopathic nonspecific interstitial pneumonia (n = 3), coal worker’s pneumoconiosis (n = 3), chronic hypersensitivity pneumonitis (n = 2), interstitial pneumonia with autoimmune features (n = 2) and unclassifiable ILD (n = 10). Most (67%) the lung samples were from individuals with self-reported ethnicity of European ancestry; 53 (46%) reported past or present tobacco use.

Dataset ID LMEX0000004403

Assay Type Single-cell RNA-seq

Organism Human

Stages Adult | 65+ years

Cell Count 475047

Technology 10x Genomics Chromium Single Cell Gene Expression

Reference Natri, et al. (2024)

External databases dbGaP: phs003521.v1.p1 GEO: GSE227136

File	Description	Size
ILD_manual_annotation_1.h5ad	Analysis object for the interstitial lung disease viewers, HDF5 AnnData, gzip compressed. 475,047 cells x 33,538 genes over the authors' 43 `manual_annotation_1` states in 9 lineages, across 120 samples and 10 diagnoses. X holds log2 counts per ten thousand, converted exactly from the authors' natural-log matrix; the source carries no raw counts, so none is shipped. obs carries the annotation and its two coarser levels, the diagnosis, the disease status, the donor covariates and the processing site; obsm carries the UMAP.	2272.2 MB
ILD_sample_metadata.tsv	Sample metadata for this study, one row per sample and covariate combination, 166 rows over 120 samples, with the diagnosis, disease status, sample source and type, sex, age, ethnicity, tobacco history and processing site. The rows account for all 475,047 cells in the analysis object.	13.2 KB

LungMAP ID	Alt ID	Species	Sex	Race	Age	Age Group
LMSP0000001419	THD0001	Homo sapiens	Male	European	36 years	Adult
LMSP0000001420	THD0002	Homo sapiens	Female	American Indian/Alaska Native	39 years	Adult
LMSP0000001421	THD0005	Homo sapiens	Male	European	59 years	Adult
LMSP0000001430	THD0006	Homo sapiens	Male	European	35 years	Adult
LMSP0000001431	THD0007	Homo sapiens	Male	European	57 years	Adult
LMSP0000001432	THD0008	Homo sapiens	Male	European	53 years	Adult
LMSP0000001433	THD0009	Homo sapiens	Female	European	54 years	Adult
LMSP0000001445	THD0010	Homo sapiens	Male	Hispanic/Latino	47 years	Adult
LMSP0000001434	THD0012	Homo sapiens	Male	European	40 years	Adult
LMSP0000001450	THD0014	Homo sapiens	Male	European	64 years	Adult
LMSP0000001454	THD0015	Homo sapiens	Male	European	58 years	Adult
LMSP0000001472	THD0016	Homo sapiens	Male	Unknown or Not Reported	45 years	Adult
LMSP0000001473	THD0017	Homo sapiens	Male	Unknown or Not Reported		Adult
LMSP0000001474	THD0019	Homo sapiens	Male	Unknown or Not Reported		Adult
LMSP0000001475	THD0020	Homo sapiens	Male	Unknown or Not Reported		Adult
LMSP0000001480	THD0021	Homo sapiens	Female	Unknown or Not Reported	60 years	Adult
LMSP0000001481	THD0022	Homo sapiens	Male	Unknown or Not Reported	50 years	Adult
LMSP0000001482	THD0023	Homo sapiens	Female	Unknown or Not Reported	44 years	Adult
LMSP0000001483	THD0026	Homo sapiens	Unknown	Unknown or Not Reported		Adult
LMSP0000001495	TILD001	Homo sapiens	Male	Hispanic/Latino	65 years	65+ years
LMSP0000001422	TILD006	Homo sapiens	Female	Hispanic/Latino	72 years	65+ years
LMSP0000001423	TILD010	Homo sapiens	Female	European	74 years	65+ years
LMSP0000001424	TILD015	Homo sapiens	Male	European	67 years	65+ years
LMSP0000001425	TILD019	Homo sapiens	Male	European	56 years	Adult
LMSP0000001426	TILD028	Homo sapiens	Female	European	54 years	Adult
LMSP0000001427	TILD030	Homo sapiens	Male	European	68 years	65+ years
LMSP0000001497	TILD037	Homo sapiens	Male	European	63 years	Adult
LMSP0000001498	TILD039	Homo sapiens	Male	European	70 years	65+ years
LMSP0000001499	TILD041	Homo sapiens	Male	European	69 years	65+ years
LMSP0000001435	TILD049	Homo sapiens	Male	European	67 years	65+ years
LMSP0000001436	TILD051	Homo sapiens	Male	European	71 years	65+ years
LMSP0000001437	TILD055	Homo sapiens	Female	European	43 years	Adult
LMSP0000001438	TILD059	Homo sapiens	Male	European	70 years	65+ years
LMSP0000001455	TILD060	Homo sapiens	Unknown	Unknown or Not Reported		Adult
LMSP0000001439	TILD062	Homo sapiens	Male	European	62 years	Adult
LMSP0000001451	TILD074	Homo sapiens	Male	European	60 years	Adult
LMSP0000001456	TILD080	Homo sapiens	Male	Unknown or Not Reported	63 years	Adult
LMSP0000001452	TILD084	Homo sapiens	Male	European	69 years	65+ years
LMSP0000001453	TILD102	Homo sapiens	Unknown	Unknown or Not Reported		Adult
LMSP0000001476	TILD103	Homo sapiens	Female	Unknown or Not Reported		Adult
LMSP0000001507	TILD109	Homo sapiens	Male	European	71 years	65+ years
LMSP0000001508	TILD111	Homo sapiens	Male	European	70 years	65+ years
LMSP0000001509	TILD113	Homo sapiens	Unknown	Unknown or Not Reported		Adult
LMSP0000001477	TILD116	Homo sapiens	Unknown	Unknown or Not Reported		Adult
LMSP0000001484	TILD123	Homo sapiens	Male	European	50 years	Adult
LMSP0000001478	TILD126	Homo sapiens	Male	Unknown or Not Reported		Adult
LMSP0000001485	TILD136	Homo sapiens	Male	European	73 years	65+ years
LMSP0000001428	VUHD071	Homo sapiens	Male	European	38 years	Adult
LMSP0000001500	VUHD072	Homo sapiens	Female	European	71 years	65+ years
LMSP0000001501	VUHD073	Homo sapiens	Female	European	55 years	Adult
LMSP0000001502	VUHD077	Homo sapiens	Female	European	55 years	Adult
LMSP0000001503	VUHD078	Homo sapiens	Male	European	27 years	Adult
LMSP0000001510	VUHD101	Homo sapiens	Male	Unknown or Not Reported	25 years	Adult
LMSP0000001461	VUHD103	Homo sapiens	Male	European	55 years	Adult
LMSP0000001462	VUHD104	Homo sapiens	Male	African American	29 years	Adult
LMSP0000001463	VUHD106	Homo sapiens	Male	European	49 years	Adult
LMSP0000001464	VUHD107	Homo sapiens	Male	European	25 years	Adult
LMSP0000001486	VUHD108	Homo sapiens	Unknown	Unknown or Not Reported		Adult
LMSP0000001487	VUHD111	Homo sapiens	Unknown	Unknown or Not Reported		Adult
LMSP0000001488	VUHD112	Homo sapiens	Male	European	19 years	Adult
LMSP0000001489	VUHD113	Homo sapiens	Female	European	40 years	Adult
LMSP0000001490	VUHD114	Homo sapiens	Unknown	Unknown or Not Reported		Adult
LMSP0000001491	VUHD115	Homo sapiens	Female	European	60 years	Adult
LMSP0000001492	VUHD117	Homo sapiens	Male	European	50 years	Adult
LMSP0000001512	VUHD65	Homo sapiens	Male	European	17 years	Adult
LMSP0000001513	VUHD66	Homo sapiens	Male	European	30 years	Adult
LMSP0000001515	VUHD67	Homo sapiens	Female	Unknown or Not Reported	30 years	Adult
LMSP0000001516	VUHD68	Homo sapiens	Male	European	41 years	Adult
LMSP0000001496	VUHD69	Homo sapiens	Female	African American	31 years	Adult
LMSP0000001519	VUHD70	Homo sapiens	Male	European		Adult
LMSP0000001440	VUHD84	Homo sapiens	Female	European	34 years	Adult
LMSP0000001441	VUHD85	Homo sapiens	Male	African American	53 years	Adult
LMSP0000001457	VUHD92	Homo sapiens	Male	African American	55 years	Adult
LMSP0000001458	VUHD94	Homo sapiens	Male	Caucasian	62 years	Adult
LMSP0000001459	VUHD95	Homo sapiens	Female	European	64 years	Adult
LMSP0000001460	VUHD98	Homo sapiens	Male	European	69 years	65+ years
LMSP0000001479	VUILD100	Homo sapiens	Male	European	56 years	Adult
LMSP0000001493	VUILD102	Homo sapiens	Male	European	58 years	Adult
LMSP0000001494	VUILD104	Homo sapiens	Male	European	69 years	65+ years
LMSP0000001520	VUILD48	Homo sapiens	Male	European	52 years	Adult
LMSP0000001522	VUILD53	Homo sapiens	Female	European	56 years	Adult
LMSP0000001521	VUILD54	Homo sapiens	Male	African American	57 years	Adult
LMSP0000001523	VUILD55	Homo sapiens	Male	African American	46 years	Adult
LMSP0000001514	VUILD57	Homo sapiens	Female	African American	58 years	Adult
LMSP0000001524	VUILD58	Homo sapiens	Male	European	60 years	Adult
LMSP0000001517	VUILD59	Homo sapiens	Male	European	69 years	65+ years
LMSP0000001518	VUILD60	Homo sapiens	Male	African American	59 years	Adult
LMSP0000001525	VUILD61	Homo sapiens	Male	European	66 years	65+ years
LMSP0000001526	VUILD62	Homo sapiens	Female	European	55 years	Adult
LMSP0000001527	VUILD63	Homo sapiens	Female	African American	64 years	Adult
LMSP0000001429	VUILD64	Homo sapiens	Male	European	68 years	65+ years
LMSP0000001504	VUILD67	Homo sapiens	Male	African American	64 years	Adult
LMSP0000001505	VUILD68	Homo sapiens	Male	European	69 years	65+ years
LMSP0000001506	VUILD69	Homo sapiens	Male	European	64 years	Adult
LMSP0000001443	VUILD73	Homo sapiens	Male	Other	65 years	65+ years
LMSP0000001444	VUILD77	Homo sapiens	Male	Hispanic/Latino	62 years	Adult
LMSP0000001442	VUILD79	Homo sapiens	Female	European	59 years	Adult
LMSP0000001465	VUILD82	Homo sapiens	Male	South Asian	56 years	Adult
LMSP0000001466	VUILD83	Homo sapiens	Male	European	67 years	65+ years
LMSP0000001467	VUILD84	Homo sapiens	Male	European	61 years	Adult
LMSP0000001528	VUILD85	Homo sapiens	Male	European	55 years	Adult
LMSP0000001529	VUILD86	Homo sapiens	Male	European	64 years	Adult
LMSP0000001530	VUILD87	Homo sapiens	Female	European	68 years	65+ years
LMSP0000001468	VUILD88	Homo sapiens	Female	European	65 years	65+ years
LMSP0000001511	VUILD89	Homo sapiens	Male	European	50 years	Adult
LMSP0000001469	VUILD90	Homo sapiens	Female	European	53 years	Adult
LMSP0000001470	VUILD91	Homo sapiens	Male	European	65 years	65+ years
LMSP0000001471	VUILD92	Homo sapiens	Female	European	56 years	Adult
LMSP0000001446	VUILD93	Homo sapiens	Male	European	61 years	Adult
LMSP0000001447	VUILD95	Homo sapiens	Female	European	64 years	Adult
LMSP0000001448	VUILD96	Homo sapiens	Female	African American	61 years	Adult
LMSP0000001449	VUILD97	Homo sapiens	Male	European	70 years	65+ years
LMSP0000001531	VUILD98	Homo sapiens	Male	European	59 years	Adult
LMSP0000001532	VUILD99	Homo sapiens	Male	European	65 years	65+ years

7 of this study's 114 samples were also assayed by 1 other LungMAP studies, across 1 modality. Click any node to list those studies. The other 107 appear in no other study and are not drawn.

Shared samples by study