Single cell copy number and spatial transcriptomics of ovarian cancer specimens

This data is supplementary to the report "Integrated single-cell whole genome sequencing and spatial transcriptomics reveal intra-tumoral heterogeneity in ovarian cancer" by Bassiouni et al.

Background

Ovarian tumors often comprise clonal mixtures arising from chromosomal instability. To characterize intra-tumoral heterogeneity, we performed single cell whole genome sequencing (scWGS) of five ovarian cencer specimens using the 10x Genomics Chromium Single Cell DNA Reagent Kit. For four of these, we also performed spatial transcriptomics using the 10x Genomics Visium FFPE Spatial Gene Expression Kit. Sample OV773 was not subject to spatial transcriptomics due to sample scarcity.

Archived here are the processed data files (ie, 10x Genomics pipeline outputs) for these experiments. Further details on the files includes are below.

Single cell copy number

Libraries comprising individually-barcoded and amplified single cell DNA were sequenced on an Illumina NovaSeq 6000 instrument. Sequencing data was then processed with the 10x Genomics Cell Ranger DNA pipeline (v. 1.0.0) to generate processed single cell copy number data and associated metrics. Archived here are the following pipeline output files for each sample: 

• cnv_data.h5
• node_cnv_calls.bed
• mappable_regions.bed
• per_cell_summary_metrics.csv

Detailed information about these outputs can be found on the 10x Genomics website: https://support.10xgenomics.com/single-cell-dna/software/pipelines/latest/output/overview

Corresponding scWGS BAM files are archived with controlled access at the European Genome-Phenome Archive (EGA) at accession EGAD50000002102. Access to the dataset is controlled by the Data Access Committee EGAC50000000834 and governed by policy EGAP50000000783. 

Also archived here are the following R scripts for analysing and plotting the single cell copy number data:

• scDNA_cleanup_and_clustering.R [for cleaning up the data, clustering, and plotting heatmaps]
• cluster_lineplots.R [for creating cluster-average copy number line plots]
• BAF_with_ideogram.R [for binning and plotting B allele frequencies per cluster]

For convenience, we also include the following Python script for splitting single-cell copy number BAM files, which are archived in the European-Genome Phenome Archive under controlled access.

• template-single-cell_splitBam.py [for splitting the BAM file by cell barcodes]

Spatial transcriptomics

DNA libraries representing spatially barcoded, probe-captured RNA molecules were sequenced on an Illumina NextSeq 2000 instrument. Sequencing data was processed with the 10x Genomics Space Ranger pipelines (v. 3.0.1) to generate processed spatially-resolved gene expression data. Archived here are the following pipeline output files for each sample:

• cloupe.cloupe
• filtered_feature_bc_matrix.h5
• scalefactors_json.json
• tissue_hires_image.png
• tissue_positions.csv

Detailed information about these files can be found on the 10x Genomics website: https://www.10xgenomics.com/support/software/space-ranger/latest/analysis/outputs/output-overview.

Corresponding spatial transcriptomics BAM files are archived in the European Nucleotide Archive with project accession number PRJEB102074.