|
| Status |
Public on Aug 04, 2020 |
| Title |
aorta adventitia Cd45+ at steady state |
| Sample type |
SRA |
| |
|
| Source name |
adventitia
|
| Organism |
Mus musculus |
| Characteristics |
condition: steady state
cell type: Advenitital immune cells
strain: RankCreRosa26eYFP
tissue: adventitia
age: 16 weeks
|
| Treatment protocol |
no treatment or treatment with Angiotensin II (1.8 µg AngII/kg/min )
|
| Growth protocol |
Animals were approximately 16 weeks old
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
After sorting CD45-positive immune cells from whole aortas, viable cells were proceeded for single cell capture using the Chromium Controller (10X Genomics).
Barcoding and library preparation was done using Chromium Next GEM single cell 3’ (v3.1, 10x Genomics). The resulting 3‘ Gene Expression libraries were sequenced on an Illumina HiSeq 1500 (Illumina, San Diego, USA) in paired-end mode with asymmetric read length of 28+91 bp and a single indexing read of 8bp, to reach approximately 50.000 reads per single-cell.
Single cell RNA sequencing
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 1500 |
| |
|
| Description |
single cell 3' mRNA library (10x Genomics)
|
| Data processing |
RTA1.18.66.3, bcl2fastq for basecalling and fastq conversion
Je-demultiplex-illu (v1.2) to demultiplex fastq files
cellranger count (v3.1.0, 10x Genomics) for alignment, filtering, barcode counting, and UMI counting
Genome_build: NCBI Mouse Build 38 patch release 6 (GRCm38.p6), Gencode annotation M24, modified to include eYFP transgene
Supplementary_files_format_and_content: Feature-Barcode Matrices from cellranger (10x Genomics)
|
| |
|
| Submission date |
Aug 03, 2020 |
| Last update date |
Aug 04, 2020 |
| Contact name |
Dena Esfandyari |
| E-mail(s) |
[email protected], [email protected]
|
| Phone |
08941403286
|
| Organization name |
Technical University of Munich
|
| Department |
Institute of Pharmacology and Toxicology
|
| Street address |
Haus 607, Biedersteiner Str. 29, IPT
|
| City |
Munich |
| State/province |
Bavaria |
| ZIP/Postal code |
80802 |
| Country |
Germany |
| |
|
| Platform ID |
GPL18480 |
| Series (1) |
| GSE155569 |
Single-cell RNA sequencing of Cd45+ adventitial cells from mice at steady state or treated with AngiotensinII |
|
| Relations |
| BioSample |
SAMN15702847 |
| SRA |
SRX8870423 |
