|
| Status |
Public on Sep 06, 2022 |
| Title |
Oasl1/Apoe WT rep2 (scRNA-Seq) |
| Sample type |
SRA |
| |
|
| Source name |
Aortic arch
|
| Organism |
Mus musculus |
| Characteristics |
strain: Apoe-/-
tissue: Aorta
genotype: Oasl1+/+Apoe-/-
disease state: Atherosclerosis
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Each cell suspension was subjected to 3’ single-cell RNA sequencing using the GemCode system (10x Genomics), following the manufacturer’s instructions. Libraries were sequenced on an Illumina HiSeq and mapped to the mouse mm10 reference genome using the Cell Ranger toolkit (version 3.1.0).
RNA libraries were prepared for sequencing using Chromium Single Cell 3’ Library v2 kit.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
A_22
|
| Data processing |
Alignment was performed using the Cell Ranger toolkit (version 3.1.0).
For each cell, filtered gene-cell-barcode matrix was obtained by appling two quality measures: mitochondrial genes (<10%) and gene count count (>200) using Seurat v4.0.3.
The doublets were detected and removed by using DoubletFinder.
The remaining data was log-normalized and then used in downstream analysis after z-transformation.
Genome_build: mm10
Supplementary_files_format_and_content: scRNA_normalized_count.txt
|
| |
|
| Submission date |
Oct 21, 2021 |
| Last update date |
Sep 06, 2022 |
| Contact name |
GooTaeg Oh |
| E-mail(s) |
gootaeg@ewha.ac.kr
|
| Phone |
82-10-4766-4128
|
| Organization name |
Ewha Womans University
|
| Department |
Department of Life Sciences
|
| Street address |
52, Ewhayeodae-gil
|
| City |
Seoul |
| ZIP/Postal code |
03760 |
| Country |
South Korea |
| |
|
| Platform ID |
GPL17021 |
| Series (1) |
| GSE186355 |
Single cell RNA sequencing analysis for atherosclerotic aortas in Oasl1/Apoe WT and Oasl1/Apoe DKO mice |
|
| Relations |
| BioSample |
SAMN22486924 |
| SRA |
SRX12729044 |
