 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Apr 16, 2024 |
| Title |
2042GFPPOS |
| Sample type |
SRA |
| |
|
| Source name |
Lung
|
| Organism |
Mus musculus |
| Characteristics |
tissue: Lung
cell type: Fibroblasts
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Dissected mouse lung was 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) after perfusion with PBS and removed from the chest. The lung was incubated in digestion cocktail for 45 mins at 37C with continuous shaking. The mixture was then washed with FACS buffer (2% FBS and 1% Penicillin-Streptomycin in DMEM). The mixture was passed through a 70 μm cell strainer and resuspended in red blood cell (RBC) lysis buffer, then passed through a 40 μm cell strainer. Cell suspensions were incubated with the appropriate conjugated antibodies in sorting buffer for 30 min at 4C and washed with FACS buffer. Doublets and dead cells were excluded based on forward and side scatter and SYTOX Blue (Invitrogen, S34857), respectively. The following antibodies were used for staining: CD45-BV421 (BD, 563890), CD31-BV421 (Invitrogen, 48-0311-82), EpCAM-BV421 (BD, 563214). Immune (CD45-biotin, Biolgened, Cat#103104), epithelial (CD326-biotin, Biolegend, Cat#118204) and endothelial (CD31-Biotin, Biolegend, Cat#102404) cells are removed with EasySep mouse streptavidin RapidShperes (StemCell, 19860A). FACS was performed on a BD FACS Aria using FACSDiva Software. CD45- CD31- EpCAM- cells were sorted for mesenchymal cells, the GFP+ fibroblasts were further separated and were sorted into FACS buffer.
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 |
10x Genomics
|
| Data processing |
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v2.1.1.
Assembly: 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 |
Jun 20, 2023 |
| Last update date |
Apr 16, 2024 |
| Contact name |
Jinyoung Lee |
| E-mail(s) |
[email protected]
|
| Organization name |
UCSF
|
| Street address |
513 Parnassus Avenue
|
| City |
San Francisco |
| ZIP/Postal code |
94143 |
| Country |
USA |
| |
|
| Platform ID |
GPL17021 |
| Series (1) |
| GSE235352 |
Gene expression profile at single cell level of p16INK4a+ fibroblasts from fibrotic mouse lung |
|
| Relations |
| BioSample |
SAMN35815552 |
| SRA |
SRX20733147 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM7500884_barcodes.tsv.gz |
40.7 Kb |
(ftp)(http) |
TSV |
| GSM7500884_features.tsv.gz |
284.1 Kb |
(ftp)(http) |
TSV |
| GSM7500884_matrix.mtx.gz |
103.5 Mb |
(ftp)(http) |
MTX |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
|
|
|
|
 |
