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| Status |
Public on Oct 19, 2023 |
| Title |
Functional Pdgfra fibroblast heterogeneity in normal and fibrotic mouse lung |
| Organism |
Mus musculus |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
Using, scRNA Seq transcriptomic analysis, we report that Pdgra+ fibroblasts in mouse lung have significant heterogenity in normal and fibrotic lung, and key pathways involved in lipogenic and fibrogenic pathways govern the transition of normal lipofibroblasts from a normal to a myofibroblast phenotype following lung injury
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| Overall design |
Pdgfra-GFP reporter mice were dosed with either 2 U/Kg bleomycin or PBS. On day 14 post-exposure, lungs (3 mice/treatment) were harvested, cells enzymatically digested, and GFP+ cells sorted using FACS to prepare live cells for scRNA Seq. Sequencing was done using the 10X Genomics Chromium Platform, and following processing with Cell Ranger v3.0.1 was done to generate an initial cell by gene count matrix. Samples were combined in Seurat v3 and clustered into 11 unique clusters based on top gene marker expression. Data was analyzed using Ingenuity Pathway Analysis, Pseudotime trajectories prepared with SlingShot, and IF staining conducted for verification.
For repetive bleomyin exposure, Pdgfra-GFP mice were dosed with bleomycin or PBS once weekly for 3 weeks (bleomycin at 1, 1, and 0.5 U/Kg). Two weeks after the last exposure, lungs (3 mice/treatment) were harvested, cells enzymatically digested, and GFP+ cells sorted using FACS. Sequencing was done using the 10X Genomics Chromium Platform, and following processing with Cell Ranger v3.0.1 was done to generate an initial cell by gene count matrix. Samples were combined in Seurat v3 and clustered into 11 unique clusters based on top gene marker expression. Data was analyzed using Ingenuity Pathway Analysis, Pseudotime trajectories prepared with SlingShot, and IF staining conducted for verification.
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| Contributor(s) |
Garantziotis S, Trempus CS |
| Citation(s) |
37824216 |
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| Submission date |
Sep 04, 2021 |
| Last update date |
Oct 20, 2023 |
| Contact name |
Stavros Garantziotis |
| E-mail(s) |
garantziotis@nih.gov
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| Phone |
984-287-4412
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| Organization name |
NIH/NIEHS
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| Department |
DIR
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| Lab |
Clinical Research Branch
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| Street address |
111 TW Alexander Drive, Room 109
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| City |
Research Triangle Park |
| State/province |
NC |
| ZIP/Postal code |
27709 |
| Country |
USA |
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| Platforms (2) |
| GPL19057 |
Illumina NextSeq 500 (Mus musculus) |
| GPL24247 |
Illumina NovaSeq 6000 (Mus musculus) |
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| Samples (6)
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| GSM7585625 |
Alveolosphere fibrogenic PDGFRa fibroblasts |
| GSM7585626 |
Repetitve administration of PBS (control) |
| GSM7585627 |
Repetitve administration of Bleomycin (fibrosis) |
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| Relations |
| BioProject |
PRJNA760767 |
| SRA |
SRP335671 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE183423_RAW.tar |
113.7 Mb |
(http)(custom) |
TAR (of CSV) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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