LungMAP Data Explorer

Genomic, epigenomic, and biophysical cues controlling the emergence of the lung alveolus

All mouse experiments used CD-1 female mice with the age indicated in the libraries . Single-cell suspensions were prepared from whole mouse lungs. For all libraries, DAPI-negative cells were were sorted by flow cytometry to obtain heterogeneous whole lung sample. Human tissue was derived from normal peripheral lung tissue. Single cell suspension was depleted of CD45-positive cells by bead selection. All of the murine post-natal timepoints also had CD45-positive cells removed from cell sort. Single-cell barcoded droplets were produced using 10X Single Cell 3’ v2 chemistry. Libraries generated were sequenced using HiSeq2500 instrument in High-output mode. Reads were aligned and gene level unique molecular identifier (UMI) counts were obtained using the Cell Ranger pipeline.

Edward E. MorriseyUniversity of Pennsylvania
Jarod A. Zepp (Principal Investigator)1
Mike Morley (Data Analyst)1
Edward E. Morrisey (Principal Investigator)1
1University of Pennsylvania
None

To reference this project, please use the following link:

https://data-browser.lungmap.net/projects/00f056f2-73ff-43ac-97ff-69ca10e38c89
None
GEO Series Accessions:

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Analysis Portals

CZ CELLxGENECZ CELLxGENE
LungMAP AppsLungMAP Apps
ShinyShiny
ToppCellToppCell

Project Label

Genomic, epigenomic, and biophysical cues controlling the emergence of the lung alveolus

Species

Mus musculus

Sample Type

specimens

Anatomical Entity

Lung

Organ Part

Unspecified

Selected Cell Types

Unspecified

Disease Status (Specimen)

normal

Disease Status (Donor)

normal

Development Stage

2 development stages

Library Construction Method

10X 3' v2 sequencing

Nucleic Acid Source

single cell

Paired End

true

Analysis Protocol

1c145725-c287-45c8-b0d7-6b5ed78674fc, 823cb2ce-79ff-4737-82d8-c50c286ede54

File Format

4 file formats

Cell Count Estimate

Unspecified

Donor Count

7
csv2 file(s)fastq.gz138 file(s)h58 file(s)h5ad1 file(s)