Single Cell RNA Sequencing 10x 3’
About the Data Data Levels Data Visualization
About the Data
Method and Protocol
Fresh tissue is collected from pathology and preserved using MACS media. Tissue is minced down and dissociated in the lab to a single cell suspension in freezing media (90% FBS + 10% DMSO) using the Miltenyi Biotec human dissociation kit and then stored at -80C. Samples are later thawed, washed, filtered and counted before being run on the 10x Chromium Controller following the 10x 3’ GEM-X protocol.
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 (By request with DUA)
- Level 3: H5 (AWS)
For a description of the files see the table below.
About the Samples
The following are planned to be sequenced:
- 45-56 breast samples from reduction mammoplasties or prophylactic mastectomies
Instruments
10x Chromium Controller following the 10x 3’ GEM-X protocol
About the Data Generators
This data was generated and analyzed by teams in the labs of Kate Nathanson and Henry Long.
Data Levels:
| Data Level | Description | File Format | File Size (per patient) | 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 | By request with DUA | |
| Aggregated data (Level 3) | QC, analysis, and exploration of ATAC sequencing data | H5 | 10-30 MB | AWS |
| All files | Total per sample | 16 GB |
Data Visualization
Below are private links to data visualizations accessible by members of the Gray BRCA Atlas Team.
