|
| Status |
Public on Nov 01, 2021 |
| Title |
Single-cell transcriptomes of macrophages isolated from atherosclerotic lesions of nt-LNA-treated mice |
| Sample type |
SRA |
| |
|
| Source name |
nt-LNA-treated CD45+/CD3- Cells
|
| Organism |
Mus musculus |
| Characteristics |
treatment: nt-LNA
|
| Treatment protocol |
Apoe-/- mice were treated with saline or nt-LNA (30 mg/kg) for 4 weeks in combination with a western diet. The aortic arch and thoracic aorta were removed and processed to yield a single cell suspension that was processed by FACS to yield a CD45+/CD3- population.
|
| Growth protocol |
n/a
|
| Extracted molecule |
total RNA |
| Extraction protocol |
10X Chromium system.
3' RNA Seq, P/N 1000006, 1000080, 1000020.
NovaSeq6000, 150 bp paired-end.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
RTA (version 2.4.11; Illumina) was used for base calling and analysis was completed using 10X Genomics Cell Ranger software v2.1.1.
scRNABatchQC software package was used for assessment of scSEQ data quality control,
Clustering analysis was generated by Seurat
Initial cell type classification (i.e. myeloid/macrophage, B cells, T cells, NK cells) of complete datasets was based on cell activity database (PanglaoDB).
Genome_build: mm9
Supplementary_files_format_and_content: Mouse_aortas_4187_2nd_ur.html: output from scRNABatchQC
Supplementary_files_format_and_content: Mouse_aortas_4187_2nd.cluster.summary.csv: # of cells from each treatment/cluster
Supplementary_files_format_and_content: Mouse_aortas_4187_2nd.cluster.csv: barcoding of individual cells and assignment to cluster by gene activity database
Supplementary_files_format_and_content: Mouse_aortas_4187_2nd.cluster.count.csv: raw gene expression in each cluster
Supplementary_files_format_and_content: Mouse_aortas_4187_2nd.cluster.normByUpQuantile.csv: normalized gene expression in each cluster
|
| |
|
| Submission date |
Nov 04, 2020 |
| Last update date |
Nov 01, 2021 |
| Contact name |
Ryan M Allen |
| E-mail(s) |
ryan.m.allen@vumc.org
|
| Phone |
3146109328
|
| Organization name |
Vanderbilt University Medical Center
|
| Department |
Medicine
|
| Lab |
Vickers
|
| Street address |
2220 Pierce Ave
|
| City |
Nashville |
| State/province |
TN |
| ZIP/Postal code |
37232 |
| Country |
USA |
| |
|
| Platform ID |
GPL24247 |
| Series (2) |
| GSE160791 |
The influence of nt-LNA on cell composition and phenotypees in the atherosclerotic lesion. |
| GSE206859 |
LDL delivery of microbial small RNAs drives atherosclerosis through macrophage TLR8 |
|
| Relations |
| BioSample |
SAMN16659285 |
| SRA |
SRX9430520 |
