|
| Status |
Public on Apr 16, 2024 |
| Title |
WT_VD_1 |
| Sample type |
SRA |
| |
|
| Source name |
aorta
|
| Organism |
Mus musculus |
| Characteristics |
tissue: aorta
genotype: Tet2flox/flox
Sex: male
treatment: vD3
age: 8 weeks old
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
The aorta was washed three times in PBS, incubated at 37 °C for 40 minutes with an enzymatic dissociation cocktail (0.55 mg/mL collagenase I, 0.15 mg/mL collagenase IV and 0.07 mg/mL hyaluronidase in RPMI-1640 medium) and minced. The cell suspensions were filtered through 70 µm strainers and then pelleted by centrifugation at 400g for 5 minutes. The enzyme solution was then discarded and cells were resuspended in fresh PBS containing 0.04% BSA.
Cell suspension was loaded onto the Chromium single cell controller (10x Genomics) to generate single-cell gel beads-in-emulsion (GEMs). Captured cells were lysed and the released RNA were barcoded through reverse transcription in individual GEMs. Reverse transcription was performed on a Thermal Cycler. Libraries were constructed using Single Cell 3’ Library and Gel Bead Kit V3.1 according to the manufacturer’s protocol.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic single cell |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
10x Genomics
|
| Data processing |
Alignment, filtering, barcode counting, and unique molecular identifier (UMI) counting were performed with Cell Ranger count module to generate feature-barcode matrix and determine clusters.
Assembly: mm10
Supplementary files format and content: barcodes files, features files, matrix files
|
| |
|
| Submission date |
Apr 11, 2024 |
| Last update date |
Apr 16, 2024 |
| Contact name |
Xuejiao Fan |
| Organization name |
Guangzhou Women and Children’s Medical Centre
|
| Department |
Institute of Pediatrics
|
| Street address |
Tianhe District, Jinsui Road
|
| City |
Guangzhou |
| State/province |
Guangdong |
| ZIP/Postal code |
510623 |
| Country |
China |
| |
|
| Platform ID |
GPL24247 |
| Series (1) |
| GSE263739 |
Single cell RNA-seq of aortas from Tet2flox/flox and Tet2SMC-KO mice receiving high-dosed cholecalciferol |
|
| Relations |
| BioSample |
SAMN40927008 |
| SRA |
SRX24222540 |
