|
| Status |
Public on Sep 24, 2021 |
| Title |
scRNA-seq of TdTomato+ cells from Cont1 mouse |
| Sample type |
SRA |
| |
|
| Source name |
lung
|
| Organism |
Mus musculus |
| Characteristics |
condition: Cont
replicate: 1
experiment: experiment 2
|
| Treatment protocol |
To induce PAH for experiment 2, mice were injected once weekly with SU5416 at 20 mg/kg body weight per dose for a total of 3 weeks. Stock Sugen 5416 powder was suspended at 4mg/ml in a solution of 0.5% [w/v] carboxymethylcellulose sodium, 0.9% [w/v] sodium chloride, 0.5% [v/v] polysorbate 80 and 0.9% [v/v] benzyl alcohol in saline, with sonication to aid suspension. During the 3-week period the mice were exposed to chronic hypobaric hypoxia inside a ventilated plexiglass chamber under a controlled atmosphere at 10% oxygen. Ammonia was removed by ventilation and activated charcoal filtration through an air purifier. Control mice were exposed to room air for 3 weeks.
|
| Growth protocol |
Cdh5-CreERT2-TdTomato mice were generated by breeding Cdh5-CreERT2 (Tg(Cdh5-cre/ERT2)1Rha) (transgene obtained by inserting the tamoxifen-inducible cre/ERT2 sequence was inserted into a P1 artificial chromosome containing the Cdh5 gene, Ralf H Adams, MGI:3848982) with ROSA-TdTomato(B6.Cg-Gt(ROSA)26Sortm9(CAG-tdTomato)Hze) (JAX stock #007909 from the Jackson laboratory). To achieve induction of Cre gene, female Cdh5-CreERT2-TdTomato mice were gavaged with 400mg/kg of tamoxifen, followed by a two week wash out period.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Endothelial mouse lung cells were isolated as previously described (Fehrenbach et al, Am J Physiol Lung Cell Mol Physiol 2009). Cells were then separated using the BD FACSAria II cell sorter based their TdTomato+ status.
Single cell RNA-sequencing libraries were prepared using the Single Cell 3′ Reagent Kit User Guide v2 (10x Genomics)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
fastq files obtained from Edinburgh Genomics
Read mapping and generation of the expression matrix was done using CellRanger version 3.1.0 on a custom annotation based on mm10 and including the TdTomato transcript.
Genome_build: mm10 + TdTomato transcript
Supplementary_files_format_and_content: h5 file from CellRanger output
|
| |
|
| Submission date |
Jul 23, 2020 |
| Last update date |
Sep 24, 2021 |
| Contact name |
Julie Rodor |
| E-mail(s) |
Julie.Rodor@ed.ac.uk
|
| Phone |
+44 (0)7580200884
|
| Organization name |
UNIVERSITY OF EDINBURGH
|
| Department |
Centre for Cardiovascular Science
|
| Street address |
47 Little France Crescent
|
| City |
Edinburgh |
| State/province |
NA |
| ZIP/Postal code |
EH16 4TJ |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL24247 |
| Series (1) |
| GSE154959 |
Single cell RNA-seq profiling of murine endothelial cells in response to pulmonary hypertension |
|
| Relations |
| BioSample |
SAMN15617984 |
| SRA |
SRX8805998 |
