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Sample GSM6435221 Query DataSets for GSM6435221
Status Public on Jan 25, 2024
Title bri_1066_vdj
Sample type SRA
 
Source name tumor
Organism Homo sapiens
Characteristics cell type: CD45+ immune cells
tissue: tumor
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.
 
Library strategy RNA-Seq
Library source transcriptomic single cell
Library selection cDNA
Instrument model Illumina NovaSeq 6000
 
Description 10x Genomics
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
 
Submission date Aug 06, 2022
Last update date Jan 25, 2024
Contact name JAE WON CHO
Organization name Brigham and Women's Hospital
Department Neurology
Lab Hemberg's lab
Street address 60 Fenwood Road
City Boston
State/province MA
ZIP/Postal code 02215
Country USA
 
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
Relations
BioSample SAMN30173634
SRA SRX16930694

Supplementary file Size Download File type/resource
GSM6435221_bri_1066_filtered_contig_annotations.csv.gz 511.1 Kb (ftp)(http) CSV
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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