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| Status |
Public on Feb 01, 2023 |
| Title |
Sample6_mRNA-derived cDNA_Symptomatic |
| Sample type |
SRA |
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| Source name |
human plaque isolated cells
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| Organism |
Homo sapiens |
| Characteristics |
cell type: human plaque isolated cells
library type: RNA
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| Extracted molecule |
total RNA |
| Extraction protocol |
For the citeseq sample, the Chromium Single Cell 3′ Library, Gel Bead and Multiplex Kit, and Chip Kit (10X Genomics)73,74 was used. The Chromium Single Cell 3′ v2 Reagent (10X Genomics, 120237) kit was used to prepare libraries according to the manufacturer’s instructions.
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| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 4000 |
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| Description |
10x Genomics
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| 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
Library strategy: CITE-seq (Cellular Indexing of Transcriptomes and Epitopes by sequencing)
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| Submission date |
Feb 01, 2023 |
| Last update date |
Jul 13, 2023 |
| Contact name |
Dr. Chiara Giannarelli |
| E-mail(s) |
Chiara.Giannarelli@nyulangone.org
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| Organization name |
NYU Langone Health
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| Department |
Cardiology
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| Street address |
435 E 30th St
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| City |
New York |
| State/province |
NY |
| ZIP/Postal code |
10016 |
| Country |
USA |
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| Platform ID |
GPL20301 |
| Series (1) |
| GSE224273 |
Single-cell immune landscape of human atherosclerotic plaques |
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| Relations |
| BioSample |
SAMN33008978 |
| SRA |
SRX19248913 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM7018585_Sample1G_barcodes.tsv.gz |
23.9 Kb |
(ftp)(http) |
TSV |
| GSM7018585_Sample1G_genes.tsv.gz |
297.9 Kb |
(ftp)(http) |
TSV |
| GSM7018585_Sample1G_matrix.mtx.gz |
22.0 Mb |
(ftp)(http) |
MTX |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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