|
| Status |
Public on Feb 01, 2023 |
| Title |
Sample5_scRNAseq_Asymptomatic |
| Sample type |
SRA |
| |
|
| Source name |
human plaque isolated cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: human plaque isolated cells
|
| Extracted molecule |
total RNA |
| Extraction protocol |
The single-cell suspensions of scRNA-seq samples were converted to barcoded scRNA-seq libraries using the Chromium Single Cell 3′ Library, Gel Bead and Multiplex Kit, and Chip Kit (10X Genomics)73,74.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic single cell |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
10x Genomics
|
| Data processing |
scRNA-seq used the Cell Ranger Single-Cell Software Suite (version 2.1.1, 10X Genomics) to quality control the single-cell expression data.
Pre-processing of sequencing results to generate count matrices (gene expression, ADT and HTO barcode counts) was performed using the 10x genomics Cell Ranger pipeline where ADT and HTO sequences were concatenated and treated as Custom library with default settings (v2.1.1) and aligning to the hg38 genome.
Further processing was done with Seurat v3.0.0 (cell and gene filtering, hashtag identification, clustering, differential gene expression analysis).
CITE-seq used the Cell Ranger Single-Cell Software Suite (version 2.1.1, 10X Genomics) to quality control the expression data.
Assembly: hg38
Supplementary files format and content: Tab-separated values files and matrix files
|
| |
|
| Submission date |
Feb 01, 2023 |
| Last update date |
Jul 13, 2023 |
| Contact name |
Dr. Chiara Giannarelli |
| E-mail(s) |
Chiara.Giannarelli@nyulangone.org
|
| Organization name |
NYU Langone Health
|
| Department |
Cardiology
|
| Street address |
435 E 30th St
|
| City |
New York |
| State/province |
NY |
| ZIP/Postal code |
10016 |
| Country |
USA |
| |
|
| Platform ID |
GPL20301 |
| Series (1) |
| GSE224273 |
Single-cell immune landscape of human atherosclerotic plaques |
|
| Relations |
| BioSample |
SAMN33008979 |
| SRA |
SRX19248912 |
