High depth targeted DNA sequencing
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.
About the Data Data Levels Data Visualization
About the Data
Method and Protocol
DNA is extracted from fresh tissue using the Qiagen DNeasy Blood and Tissue kit. DNA libraries are completed using IDT xGen library prep kits and hybridized (10-plexed) overnight to a custom IDT 149-gene panel. The samples are then sequenced with a targeted mean depth of 2,000x.
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.
