Description
This track displays data from A
molecular cell atlas of the human lung from single-cell RNA
sequencing. Using droplet-based and plate-based single-cell RNA
sequencing (scRNA-seq), 58 lung cell type populations were identified:
15 epithelial, 9 endothelial, 9 stromal, and 25 immune. This dataset
covers ~75,000 human cells across all lung tissue compartments and
circulating blood.
This track collection contains 19 bar chart tracks of RNA expression in the human lung where cells
are grouped such as by cell type (Lung Cells,
Lung Cells FACS), tissue compartments
(Lung Compart,
Lung Compart FACS),
detailed cell type (Lung Detail,
Lung Detail FACS),
organ donor (Lung Donor,
Lung Donor FACS), halfway detailed cell type
(Lung Half Det,
Lung Half Det FACS),
sample location (Lung Locat,
Lung Locat FACS), or organ
(Lung Organ,
Lung Organ FACS).
The default track displayed is Lung Cells.
Display Conventions
The cell types are colored by which class they belong to according to the following table.
| Color |
Cell classification |
| fibroblast |
| immune |
| muscle |
| secretory |
| ciliated |
| epithelial |
| endothelial |
Cells that fall into multiple classes will be colored by blending the colors
associated with those classes. The colors will be purest in the Lung Cells subtrack, where
the bars represent relatively pure cell types. They can give an overview of the
cell composition within other categories in other subtracks as well.
Data Access
The raw bar chart data can be
explored interactively with the Table
Browser, or the Data Integrator. For
automated analysis, the data may be queried from our REST API. Please refer to our mailing
list archives for questions, or our Data Access FAQ for more
information.
Method
Healthy lung tissue and peripheral blood was surgically removed from 2 male
patients (ages 46 and 75) and 1 female patient (age 51) undergoing lobectomy
for focal lung tumors. Lung tissue was sampled from the bronchi (proximal),
bronchiole (medial), and alveolar (distal) regions. Lung samples were
dissociated and enriched with magnetic columns before being sorted into
epithelial, endothelial/immune, and stromal cell suspensions. Lung and
peripheral blood libraries were prepared using the 10x Genomics 3' v2 kit. In
parallel, Smart-Seq2 (SS2) cDNA libraries were prepared using the Nextera XT
library kit. Both 10x and SS2 libraries were sequenced on a NovaSeq 6000.
The cell/gene matrix and cell-level metadata was downloaded from the
UCSC Cell Browser.
The UCSC command line utility matrixClusterColumns, matrixToBarChart, and bedToBigBed were used
to transform these into a bar chart format bigBed file that can be visualized. The coloring
was done by defining colors for the broad level cell classes and then using another UCSC utility,
hcaColorCells, to interpolate the colors across all cell types. The UCSC utilities can be found on
our download server.
Data Access
The raw bar chart data can be
explored interactively with the Table
Browser or the Data Integrator. For
automated analysis, the data may be queried from our REST API. Please refer to our mailing
list archives for questions, or our Data Access FAQ for more
information.
Credit
Thanks to Kyle J. Travaglini, Ahmad N. Nabhan, and to the many authors who worked on
producing and publishing this data set. The data were integrated into the UCSC
Genome Browser by Jim Kent and Brittney Wick then reviewed by Gerardo Perez. The
UCSC work was paid for by the Chan Zuckerberg Initiative.
References
Travaglini KJ, Nabhan AN, Penland L, Sinha R, Gillich A, Sit RV, Chang S, Conley SD, Mori Y, Seita J
et al.
A molecular cell atlas of the human lung from single-cell RNA sequencing.
Nature. 2020 Nov;587(7835):619-625.
PMID: 33208946; PMC: PMC7704697
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