|
| Status |
Public on Jul 24, 2024 |
| Title |
Peri-injured 14d/injured 9_SP-C mutant lung tissue (non immune) |
| Sample type |
SRA |
| |
|
| Source name |
lung
|
| Organism |
Mus musculus |
| Characteristics |
tissue: lung
genotype: SP-CI73T mutant
Sex: Male
time point: day 14
treatment: tamoxifen treated
|
| Treatment protocol |
Single oral gavage treatment with tamoxifen (175mg/kg, in corn oil) excises neomycin cassette and boosts mutant SPC mutant expression. Corn oil gavage was used for
|
| Growth protocol |
all animals were kept in a germ free facility for the duration of their lives. Food and water was provided ad libitum. Sacrifice was performed according to IACUC protocol. Lungs were perfused through the heart with saline solution (0.9% sodium chloride). Lungs were then inflated with 10% Neutral buffered formalin at steady state pressure (25cmH2O). Tissue embedding in paraffin blocks was followed by sectioning immediately prior to immunofluorescent staining (CD45, CD68, DNA). Regions of interested were selected and staining threshold standardized across of samples.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Paraffin embedded blocks were sectioned at 6um of thickness
Spatial transcriptome sequencing libraries were prepared with NanoString Mouse Whole Transcriptome Kit (v1.0) and Reagents according to Nanostring protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
Peri--injured region_009_CD45- "other"
|
| Data processing |
Raw sequencing files were processed using Nanostring GeoMx NGS pipeline to generate DCC files
Sequences were aligned to mm10 genome within the NGS pipeline using NanoString oligo RTS_ID alignment
Aligned sequences were deduplicatedaccording to Nanostring oligo UNI sequences to generate final DCC
Assembly: mm10
Supplementary files format and content: 111_CTL (top) - 113_14d injured (bottom) [JPG]: tissue_hiresolution_image
Supplementary files format and content: file with barcodes, matrix, features
|
| |
|
| Submission date |
Apr 16, 2024 |
| Last update date |
Jul 24, 2024 |
| Contact name |
Alessandro Venosa |
| E-mail(s) |
Alessandro.venosa@pharm.utah.edu
|
| Organization name |
University of Utah
|
| Department |
Pharmacology and Toxicology
|
| Street address |
30 2000 E, Rm. 3952
|
| City |
Salt Lake City |
| State/province |
UT |
| ZIP/Postal code |
84112 |
| Country |
USA |
| |
|
| Platform ID |
GPL24247 |
| Series (1) |
| GSE264128 |
Spatial analysis of murine lungs exposed to fibrogenic stress |
|
| Relations |
| BioSample |
SAMN40985324 |
| SRA |
SRX24276215 |
