DLP+ Single Cell Whole Genome Sequencing
DLP+ is a high-throughput direct transposition single-cell whole-genome sequencing approach, based on commodity high-density nanowell arrays and picoliter-volume piezo-dispensing technology available “off the shelf”. DLP+ permits cost-effective shallow sequencing of thousands of cells, rather than sequencing fewer cells at greater depth. DLP+ data can be used to identify clonal populations and their genomic features, properties of individual cells including replication state and chromosomal mis-segregation, and relationships between genomic and morphological properties.
About the Data Data Levels Data Access
About the Data
Method and Protocol
Learn about this method and protocol in Laks, McPherson, et al. Cell (2019). DOI:10.1016/j.cell.2019.10.026
Data Visualization
An HTML report with preliminary analysis is available to explore. See Data Access and Visualization, below
Data Access
Access the data through:
- Level 1: FASTQ (By request with DUA)
- Level 2: BAM (EGA)
- Level 3: CSV, HTML (AWS)
For a description of the files see the table below.
About the Samples
The following are planned to be sequenced:
- 100 breast samples
Instruments
DLP+ uses a contactless piezoelectric dispensing platform, such as the sciFLEXARRAYER S3 or cellenONE
Reactions are carried out on a high-density nanowell chip, in this case a WaferGen (SmartChip) array
For more information, see Instrument Information (below)
About the Data Generators
This data was generated and analyzed in the lab of Sam Aparicio.
Data Levels:
| Data Level | Description | File Format | File Size (per sample) | Data Access |
|---|---|---|---|---|
| Raw sequences (Level 1) | Nucleotide sequence and quality scores | FASTQ | By request with DUA | |
| Aligned sequences (Level 2) | Sequencing data aligned to a reference genome | BAM | EGA | |
| Aggregated data (Level 3) | QC, analysis, and exploration of sequencing data | CSV, HTML | AWS | |
| All files | Total per sample | 130 GB |
Instrument Information
DLP+ uses a contactless piezoelectric dispensing platform to deposit single cells and reagents as picoliter-scale droplets into an open nanowell array, using commercially available instruments such as the sciFLEXARRAYER S3 or cellenONE. Reactions are carried out on a high-density nanowell chip, in this case a WaferGen (SmartChip) array, which serves as the physical substrate for parallelized single-cell library construction. The dispensing setup incorporates integrated imaging, including droplet and nozzle cameras, enabling image-based selection and quality control to avoid depositing doublets or debris. The spotter workstation also includes practical peripherals such as a chilled chip holder or target stage, a wash-solution reservoir, and an active wash station to support reliable dispensing and minimize carryover between deposits.
Data Access and Visualization
Several levels of primary and processed data are available via the data cards below:
- A summary report showing basic quality control and a preliminary analysis of the data.
- Processed CNA data including all single-cell copy number calls.
- Primary sequencing data available from the European Genome-Phenome Archive (EGA). A Data Access Agreement between your institution and EGA will be required.
