GZNL's Respiratory Data Centre, GZNL-RDC

Developmental lung data

Developmental Lung Cell Atlas

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Data Viewer Portrait Genes Exploration Dataset

Developmental Lung Cell Atlas is a comprehensive and unified atlas of the lung that was built across studies, regions and sequencing platforms. We integrated the majority of the single-nuclei/single-cell transcriptomic datasets published from 2017 to present from a diverse source of lung samples that provide a unified cell type and manually curated metadata annotated framework for lung cell research in the development.

Data Viewer

The Data Viewer page features the UMAP that presents the sample characteristics and gene expressions in the Developmental Lung Cell Atlas. From the “Data Viewer” tab, you can choose to view a particular UMAP of lung.

(1) By clicking the selection from “Cell Metadata”, you can view coloured cells from a certain attribute for the cells. Several other dimiensions to view the UMAP are described as below: A list of selectable attributes to display the UMAPs are shown in the left column.

Name Description
sample_ID Sample ID of the cells or nuclei.
donor_ID Author specified donor IDs, which are indicated in the original publications.
donor_gender F = Female; M = Male; Unclassified = Unknown.
donor_age For postnatal individuals, 6 months old is denoted by 6mo; 21 years old is denoted by "21yr". For prenatal individuals, 9w stands for 9 gestational weeks (GW). For organoids, use d (days in culture) Eg. 10d.
donor_status Each donor's disease status corresponds to common names appearing in MONDO Diseased Ontology.
DEGregion Anatomical structure level 1 (Please find details in the first table of the Help Page).
sample_status Each disease status corresponds to common names appearing in MONDO Diseased Ontology.
project_code Project codes are the data accession codes or strings of abbreviation of the study provided by the authors. Eg. GSE/SCP/E-MTAB-/PRJNA/EGAS/phs/PRJEB/SDY/SRP.
seq_method Sequencing method of the cells or nuclei.
seq_tech Sequencing technology of the cells or nuclei.



Portrait

The interactive viewer shows the human lung and includes all the major regions from the data used in Developmental Lung Cell Atlas. You can click on the relevant label and the page will direct to the data viewer page to display information about that area.

Concrete Region Broad Region Anatomical Region
Distal airway Distal airway Distal airway
Lung Whole lung Whole lung
Peripheral lung Periphery Bronchioles/alveoli
d_LowLeftPar Parenchyma Bronchioles/alveoli
e_TopLeftPar Parenchyma Bronchioles/alveoli
c_Bronchi.4 Bronchi Bronchi
Distal lung Distal lung Bronchioles/alveoli
Whole lung Whole lung Whole lung
Right lobes Right lobes Right lobes
Middle airway Middle airway Middle airway
Proximal airway epithelium Proximal airway Proximal airway
a_Trachea Trachea Trachea
Right middle lobe Right middle lobe Right middle lobe
Left lower lobe periphery region Periphery Bronchioles/alveoli
Right upper lobe periphery region Periphery Bronchioles/alveoli
b_Bronchi.2.3 Bronchi Primary bronchus
Not applicable Trachea Trachea
Proximal lung Proximal lung Proximal lung
Right upper lobe mid-bronchial region Bronchi Bronchi
Left lower lobe bronchus region Bronchi Bronchi
Left upper lobe periphery Periphery Bronchioles/alveoli
Bronchus Bronchi Bronchi
Bronchiole Bronchiole Bronchioles

The table shows the information of regions. The Concrete Region is the original annotation of studies; the Broad Region is rough region; the Anatomical Region is the anatomical division of the region.



Gene

Users can obtain a list of differentially expressed genes of the cell types from a selected lung region.
The cell type name is defined by the most scored prediced cell type computed from the 8 machine-learning-based annotation methods:

To calculate candidate markers within a specific region by selecting tabs By Region or find candidate markers of a cell type by selecting the tab By Cell type. After selection and click on the tab Markers, a volcano plot will be shown

For example, if you click By Region, the search box will show the region and cell type, you can select a region and a cell type, this function is to show the differential genes of your selected cell type and other cell types under the same region, and clicking the marker button will show the volcano map and the csv table of the differential genes.

Region DEG & Cell type DEG

Region DEG (Differential expression Genes) compares different cell types from the same region. A violin plot of the top 3 DEGs for each different cell types of the region will be shown after selection of the input.

Cell type DEG compares the same cell type from different regions. Likewise, a violin plot of the top 3 DEGs for this cell type across different region will be shown after selection of the input.



Exploration

This page present the statistics of Developmental Lung Cell Atlas with various of plots.
You can locate the lung region to get summary information about the relevant resources in the Developmental Lung Cell Atlas. From the “Data Viewer” tab, you can choose the Atlas from Developmental Lung. Then, select some meta information from the “Cell Metadata” tab and click on the “COMPOSITION” button to view the statistics information. For example, in “Cell Metadata”, select “donor_gender” and “donor_age”, and then click “COMPOSITION” to see the gender ratio for each age.

  • Cell Proportion
    The bar plot shows the proportion of different donor gender in the different ages. The cell types are annotated with scAnnot.



Dataset

The Dataset page includes all the datasets used in the Developmental Lung Cell Atlas, a full list of the studies and authors from this page can be found here. Processed data with re-annotated cell type metadata will be avaiable for download upon publication. All data can be downloaded by four buttons: Copy, CSV, Excel, PDF etc.