Single-cell RNA-seq analysis of Bronchpulmonary Dysplasia (BPD)

Xin Sun¹, Gloria Pryhuber², Allen Wang¹

¹University of California, San Diego, ²University of Rochester Medical Center, ^*Corresponding author

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Description Bronchopulmonary dysplasia (BPD) is a chronic lung disease characterized by alveolar dysplasia in newborns that are typically born prematurely. In this study, single-nucleus RNA-Sequencing was performed on BDPD infants (n=13) and age matched controls (n=11) who died from complications associated with BPD (4 months to 3 years of age).

Dataset ID LMEX0000004400

Assay Type Single-cell RNA-seq

Organism Human

Stages Infant | Child

Cell Count 250529

Technology 10x Genomics Chromium Single Cell Gene Expression

File	Description	Size
BPD-adata_combined.h5ad	HDF5 annotated format single-cell data matrix	4.3G
BPD_RNA_author-clusters.txt	Author clusters	16M
BPD_RNA_umap.txt	UMAP coordinates	17M
CellRef-cellbarcodes_to_clusters_umap.txt	CellRef cell barcodes to clusters UMAP coordinates	22M
CellRef-mapped.pdf	Predicted CellRef cell types	21K
CellRef-prediction_scores.pdf	CellRef prediction scores	11K
Donor-Metadata.xlsx	Donor metadata	14K
ViolinPlot.py	Code for generating violin plots	982

LungMAP ID	Alt ID	Species	Sex	Race	Age	Age Group	GA at Birth	CGA	Weight	Weight Percentile	Cause of Death	Type of Death
LMSP0000000134	D011	Homo sapiens	Female	White	20 months	Child	40 weeks		10.89 kg	53	Anoxic/Hypoxic Brain Injury - Drowning	DBD (after brain death)
LMSP0000000138	D015	Homo sapiens	Female	White	3 years	Child	25 weeks, 3 days	227.43 weeks	13 kg	6.4	Prematurity Complications - Other	DBD (after brain death)
LMSP0000000152	D031	Homo sapiens	Male	White	7 months	Infant	40 weeks		7.26 kg	7.4	Anoxic/Hypoxic Brain Injury - SIDS	DBD (after brain death)
LMSP0000000153	D032	Homo sapiens	Male	White	3 years	Child	40 weeks		18.14 kg	92	Trauma - Isolated Head Trauma	DBD (after brain death)
LMSP0000000160	D039	Homo sapiens	Female	Unknown or Not Reported	3 years	Child	23 weeks, 3 days	193.57 weeks	11 kg	0.6	Prematurity Complications - Hydrocephalus	DBD (after brain death)
LMSP0000000167	D046	Homo sapiens	Male	White	3 years	Child	40 weeks		15 kg	64	Trauma - Auto Accident	DCD (circulatory death)
LMSP0000000174	D053	Homo sapiens	Male	White	3 years	Child	24 weeks, 3 days	188.86 weeks	11.79 kg	2.1	Prematurity Complications - Hydrocephalus	DBD (after brain death)
LMSP0000000200	D079	Homo sapiens	Male	White	15 months	Child	40 weeks		9.98 kg	38	Trauma - Auto Accident	DBD (after brain death)
LMSP0000000207	D086	Homo sapiens	Female	White	8 months	Infant	25 weeks, 3 days	64.43 weeks	6.39 kg	1.7	Lung Disease - BPD/CLD	DCD (circulatory death)
LMSP0000000211	D090	Homo sapiens	Female	Unknown or Not Reported	14 months	Child	40 weeks	102.86 weeks	9.98 kg	66	Trauma - Firearm	DBD (after brain death)
LMSP0000000215	D094	Homo sapiens	Male	African American	11 months	Infant	40 weeks	91.71 weeks	11 kg	89	Trauma - Auto Accident	DBD (after brain death)
LMSP0000000216	D095	Homo sapiens	Female	White	21 months	Child	40 weeks, 3 days	134.57 weeks	11 kg	50	Trauma - Auto Accident	DBD (after brain death)
LMSP0000001012	D105	Homo sapiens	Female	White	6 months	Infant	40 weeks		8.7 kg	92	Trauma - Auto Accident	DBD (after brain death)
LMSP0000001020	D113	Homo sapiens	Male	African American	5 months	Infant	40 weeks	66.14 weeks	8.3 kg	65	Trauma - Other	DBD (after brain death)
LMSP0000001022	D115	Homo sapiens	Female	White	19 months	Child	26 weeks	110.14 weeks	12.5 kg	91	Lung Disease - BPD/CLD	DCD (circulatory death)
LMSP0000001046	D139	Homo sapiens	Female	White	3 years	Child	40 weeks		23.9 kg	99	Trauma - Auto Accident	DBD (after brain death)
LMSP0000001048	D141	Homo sapiens	Male	White	13 months	Child	25 weeks, 2 days	85 weeks	12.1 kg	96	Lung Disease - BPD/CLD	DCD (circulatory death)
LMSP0000001075	D169	Homo sapiens	Male	White	12 months	Child	28 weeks, 1 days	83.57 weeks	8.64 kg	12	Lung Disease - BPD/CLD	DCD (circulatory death)
LMSP0000001076	D170	Homo sapiens	Female	African American	21 months	Child	25 weeks, 3 days	119.57 weeks	8.62 kg	2.1	Lung Disease - BPD/CLD	DCD (circulatory death)
LMSP0000001090	D184	Homo sapiens	Male	White	15 months	Child	24 weeks	89.86 weeks	8.1 kg	1.3	Lung Disease - BPD/CLD	DBD (after brain death)
LMSP0000001389	D227	Homo sapiens	Female	White	18 months	Child	23 weeks, 3 days	109.57 weeks	11.79 kg	80	Prematurity Complications - Other	DCD (circulatory death)
LMSP0000001390	D251	Homo sapiens	Male	African American	316 days	Infant	25 weeks	70.29 weeks	10.43 kg	86	Lung Disease - BPD/CLD	DBD (after brain death)
LMSP0000001391	D319	Homo sapiens	Female	Unknown or Not Reported	4 months	Infant	25 weeks, 3 days	46.57 weeks	5.4 kg	85	Lung Disease - BPD/CLD	DCD (circulatory death)
LMSP0000001393	D352	Homo sapiens	Male	African American	3 years	Child	25 weeks	219 weeks	15 kg	35	Lung Disease - BPD/CLD	DBD (after brain death)

10 of this study's 24 samples were also assayed by 152 other LungMAP studies, across 10 modalities. Click any node to list those studies. The other 14 appear in no other study and are not drawn.

Shared samples by study