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| Status |
Public on Apr 15, 2024 |
| Title |
control replicate 2 |
| Sample type |
SRA |
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| Source name |
lung primary cells
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| Organism |
Mus musculus |
| Characteristics |
cell type: whole lung digest
time point: control
genotype: SP-CI73T
treatment: oil treated
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| Treatment protocol |
Two oral gavage treatments with tamoxifen (175mg/kg, in corn oil, three days apart) excises neomycin cassette and boosts mutant SPC mutant expression. Corn oil gavage was used for controls
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| Extracted molecule |
total RNA |
| Extraction protocol |
Lungs were lavaged with ice cold saline solution. This was followed by saline perfusion through the heart. Lungs were then incubated in collagenase D for 30 min (2mg/ml, 37C, 5%CO2), followed by single cell suspension through a 70um strainer. Red blood cells were lyzed, cells were counted, and submitted for library preparation and sequencing following the 10x genomics protocol.
Libraries were prepped according to the 10X Genomics scRNA-seq 3’ v3.1 Next GEM protocol, NovaSeq Reagent Kit v1.5_150x150 bp Sequencing (400 M read-pairs)
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic single cell |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
20624X3
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| Data processing |
10x genomics Cell Ranger was used to process raw sequencing data, and produce counts
Genes that were detected in less than 3 cells were removed. Cell with a minimum 200 detected genes were used for analysis.
PCA analysis and differential gene expression analysis was performed using hciR package, using Seurat (version 4.0.4).
Assembly: mm10, M_musculus_Jun_2020, GRCm38
Supplementary files format and content: file with barcodes, matrix, features
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| Submission date |
Nov 11, 2023 |
| Last update date |
Apr 15, 2024 |
| Contact name |
Alessandro Venosa |
| E-mail(s) |
Alessandro.venosa@pharm.utah.edu
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| Organization name |
University of Utah
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| Department |
Pharmacology and Toxicology
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| Street address |
30 2000 E, Rm. 3952
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| City |
Salt Lake City |
| State/province |
UT |
| ZIP/Postal code |
84112 |
| Country |
USA |
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| Platform ID |
GPL24247 |
| Series (1) |
| GSE247520 |
Single cell analysis of mutant Surfactant Protein-C injury and remodeling |
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| Relations |
| BioSample |
SAMN38208233 |
| SRA |
SRX22489197 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
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