|
| Status |
Public on Aug 08, 2018 |
| Title |
adult mourin lung GLI2+ stromal cells |
| Sample type |
SRA |
| |
|
| Source name |
adult mourin lung GLI2+ stromal cells
|
| Organism |
Mus musculus |
| Characteristics |
tissue: lung
developmental stage: adult
|
| 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 °C 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 °C and washed with FACS buffer. The following antibodies were used at 1:200 for staining: Rat anti-CD45-PE-Cy7 and Rat anti-Epcam-BV421. 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. Cells were sorted into FACS buffer. FACS analysis was performed by FACSDiva.
cDNA libraries were prepared for sequencing using standard protocol for the 10x Single Cell instrument.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
single cell RNA sequencing of adult mourin lung GLI2+ stromal cells
|
| Data processing |
Data were processed according to the 10x Cellranger pipeline.
BAM files were generated with v1.1 10X Genomics Cellranger software using default parameters.
Gene-barcode matrices were generated from Cellranger v1.1 using default parameteres.
Genome_build: mm10
Supplementary_files_format_and_content: Cellranger outputs a .mtx file with the gene-barcode matrix. This matrix contains the counts of molecules per cell (UMI/cell) as determined after filtering and counting by Cellranger. The matrix is in market exchange format while the row (gene names) and columns (cell barcodes) are provided as TSV files. File formats are documented in Cellranger software manual.
|
| |
|
| Submission date |
Aug 11, 2017 |
| Last update date |
May 15, 2019 |
| 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 |
GPL17021 |
| Series (2) |
| GSE102591 |
Hedgehog gradient in the stroma maintains niche diversity and organ function [Drop-seq] |
| GSE102592 |
Hedgehog gradient in the stroma maintains niche diversity and organ function |
|
| Relations |
| BioSample |
SAMN07501607 |
| SRA |
SRX3090437 |
