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Sample GSM7790999 Query DataSets for GSM7790999
Status Public on Feb 06, 2024
Title YU-003 PDX, residual
Sample type SRA
Source name Patient-derived xenograft
Organism Homo sapiens
Characteristics tissue: Patient-derived xenograft
cell type: Tumor cells
treatment: Osimertinib for 6 weeks
Treatment protocol Mice were treated with with osimertinib at 25mg/kg for five consecutive days each week. The treatment lasted for 6 weeks before drug tolerant residual tumor was excised.
Growth protocol Dissociated PDX tissues were implanted subcutaneously into NSG mice. Treatment was started as the tumors grew to appropriate size.
Extracted molecule total RNA
Extraction protocol Subcutaneous PDX tumors were resected from mice and processed with tumor dissociation kit (Miltenyi Biotech, 130-095-929). The single-cell suspension was stained with human EpCAM antibody (BioLegend, 324209, 1:100) and LIVE/DEAD cell stain (invitrogen, L34971, 1:250), and subjected to FACS to isolate live tumor cells.
The sorted cells were re-suspended in FACS buffer and loaded on the Single Cell A Chip together with RT Master Mix and barcoded gel beads to form nanoliter-scale Gel Beads in Emulsions (GEMs) through Chromium Controller. The single-cell cDNA libraries were constructed using 3’ library prep kit v3 (10X genomics).
Library strategy RNA-Seq
Library source transcriptomic single cell
Library selection cDNA
Instrument model Illumina HiSeq 4000
Description 10X Genomics
Data processing The single-cell sequencing raw data were processed and mapped to a human-mouse hybrid genome to distinguish between human and mouse cells.
Gene expression matrix for human cells is generated by Cell Ranger pipeline and analyzed using Seurat package.
Genes whose expression is identified in at least three cells will be considered as features and cells with number of feature genes greater than 200 but smaller than 7000 and percentage of mitochondria reads less than 50% were included in the following analyses.
The single-cell expression data were normalized by SCTransform embedded in Seurat and then underwent linear dimensional reduction through PCA. The first 100 principal components were used to cluster cells, with a resolution of 0.4.
The clustering results were visualized in UMAP plot.
Assembly: hg38
Supplementary files format and content: matrix files
Submission date Sep 19, 2023
Last update date Feb 06, 2024
Contact name Bomiao Hu
Organization name Yale University
Street address 310 Cedar Street
City New Haven
State/province CT
ZIP/Postal code 06519
Country USA
Platform ID GPL20301
Series (2)
GSE243562 ASCL1 Drives Tolerance to Osimertinib in EGFR Mutant Lung Cancer in Permissive Cellular Contexts [scRNA-seq]
GSE243569 ASCL1 Drives Tolerance to Osimertinib in EGFR Mutant Lung Cancer in Permissive Cellular Contexts
BioSample SAMN37459355
SRA SRX21827404

Supplementary file Size Download File type/resource
GSM7790999_320_barcodes.tsv.gz 28.2 Kb (ftp)(http) TSV
GSM7790999_320_features.tsv.gz 813.5 Kb (ftp)(http) TSV
GSM7790999_320_matrix.mtx.gz 42.9 Mb (ftp)(http) MTX
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Raw data are available in SRA

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