|
| Status |
Public on Sep 29, 2023 |
| Title |
CD3ζ-TIR-CAR-iMAC, scRNAseq |
| Sample type |
SRA |
| |
|
| Source name |
human iPSC-derived CAR-macrophage
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: human iPSC-derived CAR-macrophage
|
| Treatment protocol |
Before co-incubation with U87MGEGFRvIII cells, CAR-iMACs were maintained in StemSpanXF medium containing IFN-γ/LPS for 24 hours. MEM medium containing 10% FBS, 1×Non-Essential Amino Acids , 1mM Sodium Pyruvate, and 1×Pen Strep was used as a medium for the co-incubation of CAR-iMACs with U87MGEGFRvIII cells.
|
| Growth protocol |
Matured CAR-iMACs growed in StemSpanXF medium containing M-CSF (100 ng/mL) and GM-CSF (100 ng/mL). U87MGEGFRvIII cells were cultured in MEM medium supplemented with 10% FBS, 1×Non-Essential Amino Acids , 1mM Sodium Pyruvate, and 1×Pen Strep.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
After co-incubation of CAR-iMACs with U87MGEGFRvIII cells for 24 hours, cells were harvested through trypsin digestion. DPBS was used to wash the cells 3 times to remove the residual medium. Subsequently, the cells were processed with 10X Single Cell 3' Solution Reagents V2 to construct an RNA library.
We used 10X Single Cell 3' Solution Reagents V2 following the manufacturer’s protocol (10x Genomics)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
10x Genomics
|
| Data processing |
The "cellrange count" program, a subcommand included in the 10×single-cell gene expression analysis pipeline (https://support.10xgenomics.com/single-cell-gene-expression/), was used to produce a gene-cell barcode expression matrix.
The single-cell gene expression matrix was analyzed with Seurat v3.2.1 (https://satijalab.org/seurat/). To guarantee the quality of genes and cells used for downstream analysis, we excluded genes expressed in fewer than 3 cells and cells expressing less than 200 genes or more than 30000.
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files
|
| |
|
| Submission date |
Sep 25, 2022 |
| Last update date |
Sep 29, 2023 |
| Contact name |
Hua Yu |
| E-mail(s) |
yuhua@westlake.edu.cn
|
| Phone |
18758008246
|
| Organization name |
Westlake University
|
| Street address |
No.18 Shilongshan Road
|
| City |
Hangzhou |
| ZIP/Postal code |
310024 |
| Country |
China |
| |
|
| Platform ID |
GPL18573 |
| Series (1) |
| GSE214140 |
The Second Generation of CAR-iMACs with Enhanced Polarization, CAR-mediated Efferocytosis and Superior Potency against Solid Tumors |
|
| Relations |
| BioSample |
SAMN31011209 |
| SRA |
SRX17699625 |
