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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Jan 25, 2024 |
| Title |
bri_1618_vdj |
| Sample type |
SRA |
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| Source name |
tumor
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| Organism |
Homo sapiens |
| Characteristics |
cell type: CD45+ immune cells
tissue: tumor
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| Extracted molecule |
total RNA |
| Extraction protocol |
Renal tumor samples were dissociated into single cells by a semi-automated combined mechanical/enzymatic process. The tumor tissue was cut into pieces of (2-3mm) in size and transferred to C Tubes (Miltenyi Biotech) containing a mix of Enzymes H, R and A (Tumor Dissociation Kit, human; Miltenyi Biotech). Mechanical dissociation was accomplished by performing a program (37C_h_TDK_1) on the gentleMAC Octo Dissociator with Heaters (Miltenyi Biotech). Single cell suspensions generated from ccRCC tumor samples were FACS sorted on a SONY MA900 sorter (SONY) for viable human CAR-T cells (Zombie- mCD45- hCD45+ CD3+, BioLegend).
Sorted cells were stained with a distinct barcoded antibody (Cell-Hashing antibody, TotalSeq-A, Biolegend). Next, 7,500 cells from each condition were resuspended in 0.4% BSA in PBS at a concentration of 1,000 cells per μl, pooled together, then loaded onto a single lane (Chromium chip B, 10X Genomics) followed by encapsulation in a lipid droplet (Single Cell 5′ kit V3, 10X Genomics) followed by cDNA and library generation according to the manufacturer’s protocol. mRNA library was sequenced to an average of 50,000 reads per cell, and HTO (Cell Hashing antibodies) library sequenced to an average of 5,000 reads per cell, both using Illumina Novaseq.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic single cell |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
10x Genomics
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| Data processing |
Sample demultiplexing, barcode processing, alignment, filtering, UMI counting, and aggregation of multiple sequencing runs were performed using the Cell Ranger analysis pipeline (v6.1.2)
Background and non-cellular barcodes are removed
Assembly: GRCh38
Supplementary files format and content: .tsv: barcodes, genes, .mtx: count matrix, .csv: tcr sequence
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| Submission date |
Aug 06, 2022 |
| Last update date |
Jan 25, 2024 |
| Contact name |
JAE WON CHO |
| Organization name |
Brigham and Women's Hospital
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| Department |
Neurology
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| Lab |
Hemberg's lab
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| Street address |
60 Fenwood Road
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| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02215 |
| Country |
USA |
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| Platform ID |
GPL24676 |
| Series (1) |
| GSE210664 |
Immune Restoring (IR) CAR-T Cells Display Superior Antitumor Activity and Reverse Immunosuppressive TME in a Humanized ccRCC Orthotopic Mouse Model |
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| Relations |
| BioSample |
SAMN30173632 |
| SRA |
SRX16930696 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM6435223_bri_1618_filtered_contig_annotations.csv.gz |
194.0 Kb |
(ftp)(http) |
CSV |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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