High depth targeted DNA sequencing
About the Data Data Levels Data Visualization
About the Data
Method and Protocol
The tissues were bulk sequenced by the Nathanson lab using a custom panel of 149 genes commonly altered in breast cancer. The list was curated from existing clinical panels and literature reviews.
Data Visualization
Level 3 data can currently be explored on the Broad Single Cell Portal by members of the Gray BRCA Atlas Team
Data Access
Access the data through:
- Level 1: FASTQ (by request with DUA)
- Level 2: BAM (GEO)
- Level 3: VCF (AWS)
For a description of the files see the table below.
About the Samples
The following have been sequenced:
- 118 samples from 116 individuals
Instruments
Information forthcoming
About the Data Generators
This data was generated and analyzed by a team in the lab of Kate Nathanson.
Data Levels:
| Data Level | Description | File Format | File Size (per file) | Data Access |
|---|---|---|---|---|
| Raw sequences (Level 1) | Nucleotide sequence and quality scores | FASTQ | 400-700 MB | by Request with DUA |
| Aligned sequences (Level 2) | sequencing data aligned to a reference genome | BAM | 1.5 GB | GEO |
| Aggregated data (Level 3) | QC, analysis, and exploration of single-cell RNA-seq data | VCF | 50 KB | AWS |
Data Visualization
Below are private links to data visualizations accessible by members of the Gray BRCA Atlas Team.
High Depth Targeted DNA Sequencing of Breast Tissues
