|
| Status |
Public on Jan 16, 2024 |
| Title |
Epithelial cells AT2- and ciliated-depleted and dividing epithelial cells, SRC mice, injured lung, day2 |
| Sample type |
SRA |
| |
|
| Source name |
lung
|
| Organism |
Mus musculus |
| Characteristics |
tissue: lung
cell type: epithelial
genotype: Scgb1a1-CreER x Rosa26R-DTA x CycB1-GFP
treatment: 2 x 4mg tamoxifen
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
PBS-perfused lungs were inflated with 2 ml of digestion cocktail containing 50 U/ml dispase (Corning), 250 U/ml collagenase type I (Worthington), 5 U/ml elastase (Worthington), and 60 U/ml DNAse I (Roche). Trachea was clipped distally and lungs were dissected in a petri dish on ice to remove extrapulmonary airways (trachea and main bronchi). Lung lobes were placed in a C tube (Miltenyi) containing 3 ml of digestion cocktail, and the m_lung_01 program was run on gentleMACS (Miltenyi). C tubes were placed in a rotating incubation oven at 37ºC for 30 minutes. The m_lung_02 program was run again, and the tubes were placed on ice for the next steps. The lung cells were passed through a 70 µm cell strainer (Corning) and centrifuged at 400 g for 5 minutes. The pellet was resuspended in a red blood lysis buffer solution (0.15 M NH4Cl, 10 mM KHCO3, 0.1 mM EDTA), incubated for 2 minutes on ice, and washed with EasySep buffer (STEMCELL Technologies) at 400 g for 5 minutes. To isolate mesenchymal cells, a milder digestion cocktail was used containing only 375 U/ml collagenase and 60 U/ml DNase I.
Libraries were prepared using Chromium Next GEM Single Cell 3’ v2 (samples 1 to11) or Chromium Next GEM Single Cell 3’ v3.1 (samples 12 to16) and following the manufacturer’s protocol (10x Genomics)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic single cell |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
SRC Epithelial AT2- and ciliated- depleted day2
|
| Data processing |
Raw sequencing data was processed with 10x Genomics Cell Ranger v3.1.0
Supplementary files format and content: Tab-separated value files and matrix files
|
| |
|
| Submission date |
Jan 30, 2023 |
| Last update date |
Jan 16, 2024 |
| Contact name |
Cihan Erkut |
| E-mail(s) |
cihan.erkut@nct-heidelberg.de
|
| Organization name |
German Cancer Research Center
|
| Department |
Applied Functional Genomics
|
| Street address |
Im Neuenheimer Feld 581
|
| City |
Heidelberg |
| ZIP/Postal code |
69120 |
| Country |
Germany |
| |
|
| Platform ID |
GPL24247 |
| Series (1) |
| GSE223816 |
Single-cell division tracing and transcriptomics reveal cell types and differentiation paths in the regenerating lung |
|
| Relations |
| BioSample |
SAMN32963631 |
| SRA |
SRX19221801 |
