|
| Status |
Public on Sep 16, 2022 |
| Title |
NoBleo |
| Sample type |
SRA |
| |
|
| Source name |
Normal mouse lung
|
| Organism |
Mus musculus |
| Characteristics |
number: n=1
tissue: lung
treatment: Normal untreated
|
| Treatment protocol |
For single cell RNAseq, adult mice were treated or untreated with bleomycin every week for total 4 weeks. Mice lung were collected. Fresh lung tissue was minced and incubated in an enzymatic cocktail containing 60 ml dispase (5U/ml, Stemcell Technologies), 900 µl liberase (1g/l, Sigma Aldrich), 0.03 g DNase (Sigma Aldrich) at 37 ℃ for 45 minutes. Suspensions were washed with media, cell counts were performed and cells were resuspended in RPMI at a final concentration of 100 cells/ml.
|
| Growth protocol |
Mice were housed in barrier and all experiments were performed in accordance with approved IACUC protocols
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Single-cell suspensions were processed through the 10X Chromium to generate single-cell cDNA libraries attached to microbeads.
Microbeads were counted, and amplified by PCR, and the 3' end of the cDNA was prepared for sequencing using a modified Nextera XT protocol.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic single cell |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
10x 3' v2 scRNA-seq
|
| Data processing |
Read alignment and gene-expression quantification of mouse single-cell RNA-seq (scRNA-seq) were performed using Cell Ranger version 2.0.0 pipeline (10x Genomics).
For scRNA-seq alignment and quantification, Cell Ranger pre-built mouse (mm10) reference package was used.
Assembly: mm10
Supplementary files format and content: Raw Feature Barcode Matrix and 10x Cell Ranger filtered Feature Barcode Matirx in HDF5 format
|
| |
|
| Submission date |
Sep 09, 2022 |
| Last update date |
Sep 16, 2022 |
| Contact name |
Yan Xu |
| E-mail(s) |
[email protected]
|
| Phone |
513-6368921
|
| Organization name |
Cincinnati Children's Hospital Medical Center
|
| Street address |
3333 Burnet Ave
|
| City |
Cincinnati |
| State/province |
OH |
| ZIP/Postal code |
45229 |
| Country |
USA |
| |
|
| Platform ID |
GPL24247 |
| Series (2) |
| GSE213016 |
Lung endothelial cells regulate pulmonary fibrosis through FOXF1/R-Ras signaling (Mouse I). |
| GSE213018 |
Lung endothelial cells regulate pulmonary fibrosis through FOXF1/R-Ras signaling |
|
| Relations |
| BioSample |
SAMN30755552 |
| SRA |
SRX17507005 |
