Ex vivo modeling of precision immuno-oncology responses in lung cancer

Single-cell RNA-sequencing (scRNA-seq) data from paired lung cancer organoids and immune cells. The experiment was performed using the Single Cell 5' solution of 10X Genomics. 

The dataset includes 15 samples from 4 multiplexed experiments. The multiplexing was performed using the Feature Barcoding technology of 10X Genomics.

Sample name
Multiplexed experiment
Donor
Hashtag name
Description

1-PBMCs_lung-19
PBMCs_demux
Lung-19
Hashtag_1
Untreated, baseline PBMCs for Lung-19

2-PBMCs_lung-35
PBMCs_demux
Lung-35
Hashtag_2
Untreated, baseline PBMCs for Lung-35

3-PBMCs_Lung-25
PBMCs_demux
Lung-25
Hashtag_3
Untreated, baseline PBMCs for Lung-25

4-T_cells_Lung-19
PBMCs_demux
Lung-19
Hashtag_4
Tumor-stimulated immune cells for Lung-19

5-T_cells_Lung-35
PBMCs_demux
Lung-35
Hashtag_5
Tumor-stimulated immune cells for Lung-35

6-T_cells_Lung-25
PBMCs_demux
Lung-25
Hashtag_6
Tumor-stimulated immune cells for Lung-25

1-Lung-19_tumor_cells
Tumor_cells_1_demux
Lung-19
Hashtag_1
Tumor cells alone for Lung-19

2-Lung-35_T_tumor_cells
Tumor_cells_1_demux
Lung-35
Hashtag_2
Tumor cells alone for Lung-35

3-Lung-25_tumor_cells
Tumor_cells_1_demux
Lung-25
Hashtag_3
Tumor cells alone for Lung-25

1-Lung-19_tumor_cells_T_cells
Tumor_cells_2_demux
Lung-19
Hashtag_7
Tumor cells and ts-immune cells for Lung-19

2-Lung-35_T_tumor_cells_T_cells
Tumor_cells_2_demux
Lung-35
Hashtag_8
Tumor cells and ts-immune cells for Lung-35

3-Lung-25_tumor_cells_T_cells
Tumor_cells_2_demux
Lung-25
Hashtag_9
Tumor cells and ts-immune cells for Lung-25

1-Lung-19_tumor_cells_T_cells_Nivolumab
Tumor_cells_3_demux
Lung-19
Hashtag_10
Tumor cells and ts-immune cells + Nivolumab for Lung-19

2-Lung-35_T_tumor_cells_T_cells_Nivolumab
Tumor_cells_3_demux
Lung-35
Hashtag_12
Tumor cells and ts-immune cells + Nivolumab for Lung-35

3-Lung-25_tumor_cells_T_cells_Nivolumab
Tumor_cells_3_demux
Lung-25
Hashtag_13
Tumor cells and ts-immune cells + Nivolumab for Lung-25

This Zenodo repository provides:

Processed RNA-seq and hashtag oligo sequencing (HTO-seq) data (feature_bc_matrices.zip)

Hashtag names and sequences (Custom_CMO_set.csv), which are needed to rerun Cellranger

Seurat v5 objects (seurat_object_all_tumor_cells.rds, seurat_object_all_immune_cells.rds, seurat_object_PBMCs_demux.rds)

This Zenodo repository does not provide:

Sensitive raw sequencing data

Sensitive metadata

The raw data generated from the scRNA sequencing is available at the European Genome-phenome Archive (EGA; https://ega-archive.org) under accession number EGAD50000000845.

To cite our work:

Bassel Alsaed et al. Ex vivo modeling of precision immuno-oncology responses in lung cancer.Sci. Adv.10,eadq6830(2024).DOI:10.1126/sciadv.adq6830