|
| Status |
Public on Sep 12, 2024 |
| Title |
T3_ARC_144 |
| Sample type |
SRA |
| |
|
| Source name |
left atrial tissue
|
| Organism |
Mus musculus |
| Characteristics |
tissue: left atrial tissue
cell type: nuclei
treatment: anti-Trem2-siSpp1
|
| Extracted molecule |
nuclear RNA |
| Extraction protocol |
Left atrial tissues from vehicle- and anti-Trem2-siSpp1-treated HOMER mice were microdissected using a dissection microscope and subsequently snap-frozen in liquid nitrogen. Nuclei were then isolated using the 10X Chromium Nuclei Isolation kit according to the manufacturer’s protocol. In detail, frozen samples were homogenized using a pestle and lysis buffer and passed through a column. Next, debris was removed via centrifugation in debris removal buffer. The nuclei were then washed, resuspended and visualized under a microscope to determine nuclei concentration and quality. The isolated nuclei were immediately loaded on a 10X Genomics Chromium Single Cell G chip as outlined by the 10X Genomics Chromium Single Cell 3’ Reagent kit v3.1 user guide. As nuclei have a lower RNA content than whole cells, the cDNA amplification cycles were increased by 1-2 cycles, as recommended by 10X Genomics.
Libraries were prepared as outlined by the 10X Genomics Chromium Single Cell 3’ Reagent kit v3.1 user guide with appropriate modifications to the PCR cycles based on the cDNA concentration. Constructed libraries were validated and quantified with the Agilent High Sensitivity DNA chip and by real-time qPCR and subsequently sequenced on an Illumina NovaSeq 6000 system as recommended by 10X Genomics.
snRNA-seq
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic single cell |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
10x Genomics
|
| Data processing |
The demultiplexing, barcoded processing and gene counting were made using the 10X Genomics Cell Ranger software v7.1.0.
Assembly: mm10
Supplementary files format and content: Raw count matrices in H5 format
|
| |
|
| Submission date |
Jul 17, 2024 |
| Last update date |
Sep 12, 2024 |
| Contact name |
I-Hsiu Lee |
| Organization name |
Mass General Hospital/Harvard University
|
| Department |
Center for Systems Biology
|
| Street address |
185 Cambridge Street
|
| City |
Boston |
| State/province |
Massachusetts |
| ZIP/Postal code |
02114 |
| Country |
USA |
| |
|
| Platform ID |
GPL24247 |
| Series (1) |
| GSE272503 |
Therapeutic silencing Spp1 in cardiac macrophages suppresses atrial fibrillation |
|
| Relations |
| BioSample |
SAMN42564449 |
| SRA |
SRX25366300 |
