|
| Status |
Public on Nov 02, 2022 |
| Title |
GFPpos time 7 rep 2 |
| Sample type |
SRA |
| |
|
| Source name |
lung
|
| Organism |
Mus musculus |
| Characteristics |
cell type: Lung mesenchyme
genotype/variation: CD45-Epcam-CD31-PDGFRa+GFP+ (p16INK4a+)
tissue: lung
developmental stage: adult
treatment: 7 days post Naphthalene injury
|
| Treatment protocol |
Naphthalene was dissolved in corn oil at 300mg/ml at 37C nutating for 1 hour and administered intraperitoneally once at 200mg/kg. Corn oil was injected to solvent control animals.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Whole lung was dissected from the adult mouse and tracheally perfused with a digestion cocktail of Collagenase Type I (225 U/ml, Thermo Fisher), Dispase (15 U/ml, Thermo Fisher) and Dnase (50 U/ml, Sigma) and removed from the chest. The lung was further diced with razor blades and the mixture was incubated for 45 mins at 37 ºC and vortexed intermittently. The mixture was then washed with FACS buffer (2% FBS in DMEM-F12). The mixture was passed through a 70 µm cell strainer and resuspended in RBC lysis buffer, before passing through a 40 µm cell strainer. Cells suspensions were incubated with the appropriate antibodies in FACS buffer for 30 min at 4 ºC and washed with FACS buffer. DAPI (0.2 µg/ml) was used to exclude dead cells. Doublets and dead cells were excluded based on forward scatter, side scatter and DAPI fluorescence. CD45-Epcam-CD31-PDGFRa+GFP- or CD45-Epcam-CD31-PDGFRa+GFP+ cells were sorted . Cells were sorted into FACS buffer. FACS analysis was performed by FACSDiva (BD Biosciences). The RNA was extracted by PicoPure RNA Isolation Kit (Applied Biosystems) from the sorted cells, and the amount and quality of extracted RNA was measured by RNA 6000 Pico Kit (Agilent). The Bulk RNA-seq was done in GENEWIZ.
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
H2B-eGFP
7308-GFPpos
|
| Data processing |
FASTQC for quality control, Cuadapt and Sickle for triming adaptors
reads were aligned and mapped using HISAT and Stringtie
DESeq was use to call differential gene expression, in Rstudio
Genome_build: UCSC mus musculus mm10
|
| |
|
| Submission date |
Nov 19, 2019 |
| Last update date |
Nov 02, 2022 |
| Contact name |
Peng Tien |
| E-mail(s) |
tien.peng@ucsf.edu
|
| Phone |
4155144180
|
| Organization name |
University of California San Francisco
|
| Department |
Department of Pulmonary Medicine
|
| Lab |
Dr. Tien Peng
|
| Street address |
513 Parnassus Ave, Health Sciences East 1350
|
| City |
San Francisco |
| State/province |
CA |
| ZIP/Postal code |
94143 |
| Country |
USA |
| |
|
| Platform ID |
GPL13112 |
| Series (2) |
| GSE140654 |
Sentinel p16INK4a+ cells in the basement membrane form a reparative niche in the lung [RNA-Seq] |
| GSE140657 |
Sentinel p16INK4a+ cells in the basement membrane form a reparative niche in the lung |
|
| Relations |
| BioSample |
SAMN13326848 |
| SRA |
SRX7182790 |
