|
| Status |
Public on May 14, 2024 |
| Title |
GLI1+ cells from hypoxic mouse lungs |
| Sample type |
SRA |
| |
|
| Source name |
lung
|
| Organism |
Mus musculus |
| Characteristics |
tissue: lung
cell type: TdTomato positive mesenchymal lung cells from Gli1Cre-ERT2 mice
genotype: Gli1CreERT2
treatment: Hypoxia
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Fresh isolated mouse lung samples were flushed with HBSS and then cut into small pieces and filtered two times with 70um and 40um filters. GLI1+ cells are lineage labeled cells with red fluorescent, we first use CD31, CD45 and Epcam to eliminate non-mesenchymal cells. Then PE is used to select RFP+ GLI1+ cell for the single cell analysis.
Library sample index sequences were incorporated as the sample index read and sequenced together on a Nextseq2000 sequencer. Raw reads were aligned against the mouse genome (mm10, ensemble assembly 104) and mapped and counted by StarSolo.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic single cell |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
10x Genomics scRNA-seq
|
| Data processing |
Reads were processed using the Cell Ranger 2.1.0 pipeline with default and recommended parameters.
Unsupervised clustering and differential gene analyses were performed using the Seurat package.
Assembly: mm10
Supplementary files format and content: CellRanger outputs (count matrix, genes, barcodes) as .gz
|
| |
|
| Submission date |
Mar 04, 2024 |
| Last update date |
May 14, 2024 |
| Contact name |
Marek Bartkuhn |
| E-mail(s) |
marek.bartkuhn@gen.bio.uni-giessen.de
|
| Organization name |
Justus-Liebig-University Giessen
|
| Department |
Biomedical Informatics and Systems Medicine
|
| Street address |
Aulweg 132
|
| City |
Giessen |
| State/province |
Hessen |
| ZIP/Postal code |
35392 |
| Country |
Germany |
| |
|
| Platform ID |
GPL13112 |
| Series (1) |
| GSE260788 |
GLI1+ cells contribute to vascular remodeling in hypoxia- and cigarette smoke-induced pulmonary hypertension |
|
| Relations |
| BioSample |
SAMN40253130 |
| SRA |
SRX23829368 |
