FLEX Single Cell RNA Sequencing 10x
About the Data Data Levels Data Visualization
FLEX single cell RNA sequencing 10X involves dissociating tissue into single cells and sequencing using the FLEX protocol for 10X scRNAseq where cells can be fixed and stored to run in batches of 8 or 16 samples at a time. This protocol greatly improves transcript detection and cell capture rate while reducing batch effects.
About the Data
Method and Protocol
Information forthcoming
Data Visualization
At this time, Level 3 data can 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: H5 and RDS (AWS)
For a description of the files see the table below.
About the Samples
60 normal breast tissue samples from reduction mammoplasties or prophylactic mastectomies have been run so far. Our goal is to sequence 135 samples that are matched by genotype, age, parity and menopause status.
Instruments
Information forthcoming
About the Data Generators
This data was generated and analyzed by teams in the labs of Joan Brugge 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 | GEO | |
| Aggregated data (Level 3) | QC, analysis, and exploration of single-cell RNA-seq data | H5 and RDS | 30 GB | AWS |
| All files | Total per sample | 80 GB |
Data Visualization
Below are private links to data visualizations accessible by members of the Gray BRCA Atlas Team.
