Bronchiolitis Obliterans Syndrome Airway scRNA-Seq
1Cincinnati Children's Hospital Medical Center, *Corresponding author
Description
In as many as half of all lung transplant patients, Bronchiolitis Obliterans Syndrome or BOS, can develop, resulting in a progress deterioration of lung function. In this experiment, scRNA-Seq was performed on a series of 5 distal and proximal airway regions of the removed lung, prior to transplantation. The patient was a a male 9 year old, with BOS confirmed upon biopsy, which occurred after a bone marrow transplantation (graft versus host rejection). The sample was prepared from flash frozen sample, processed using a cold activated protease protocol in the laboratory of Anne Karina Perl (Cincinnati Children's Hospital - IRB 2013-3309). The dataset was processed using the Terra Optimus and Cumulus pipelines to produce unsupervised louvain clusters as well as in the software ICGS2 (unsupervised) and cellHarmony (supervised) to identify cell population identities relative to prior published studies.
Dataset ID
LMEX0000004409
Assay Type
Single-cell RNA-seq
Organism
Human
Stages
Child
Cell Count
15801
Technology
10x Genomics Chromium Single Cell Gene Expression
| File | Description | Size |
|---|---|---|
| BOS_library_metadata.tsv | Harmonized library metadata for the five libraries, all 68 columns, one row per library. The Samples tab above shows only the fourteen columns the site defines for a human sample, so this file is where the rest live: anatomic region, assay, cell counts, smoking status, pulmonary function, source accession and provenance. 35 of the 68 columns carry a value for this study; 33 are empty because the released file is censored. | 5.1 KB |
| BOS_release_counts.h5ad | Release object for this study, HDF5 AnnData, gzip compressed. 15,801 cells x 31,782 genes over 24 author cell states and 5 libraries of one donor. X holds RAW INTEGER COUNTS, not a normalized matrix, so a reader can normalize as they choose. obs carries the author annotation (ICGS-Annotations), the library, the region, the donor covariates and the UMAP coordinates. The site's heatmap and chart viewers read a log2 counts-per-ten-thousand matrix rebuilt from these counts. | 99.4 MB |
| LungMAP ID | Alt ID | Species | Sex | Age | Age Group | Health Status |
|---|---|---|---|---|---|---|
| LMSPBOS0000001 | Run2651-distal-CTRL | Homo sapiens | Male | 9.4 years | Child | Known lung disease |
| LMSPBOS0000002 | Run2652 | Homo sapiens | Male | 9.4 years | Child | Known lung disease |
| LMSPBOS0000003 | Run2655 | Homo sapiens | Male | 9.4 years | Child | Known lung disease |
| LMSPBOS0000004 | Run2661 | Homo sapiens | Male | 9.4 years | Child | Known lung disease |
| LMSPBOS0000005 | Run2663 | Homo sapiens | Male | 9.4 years | Child | Known lung disease |