Center of Excellence in Stem Cell Genomics


Salk Institute for Biological Studies - Center of Excellence in Stem Cell Genomics - Resources


Key Components of Salk CESCG

Ultra high throughput Sequencing Capabilities

  • Whole genome bisulfite sequencing (MethylC-seq for DNA methylation profiling)
  • RNA-seq (transcriptome profiling)
  • Whole genome sequencing
  • ATAC-seq (TFBS – transcription factor binding sites profiling)
  • ChIP-seq (TFBS / histone modifications)
  • Hi-C (chromatin conformation pofiling)

Expert bioinformatics analysis

  • Uniform processing pipelines (mostly in sync with ENCODE standards)
  • High QC standards – assay dependent
  • In-house developed algorithms (eg., MethylPy) and other standard analysis software

State-of-the-art compute Infrastructure

  • 10 Cisco UCS server blades (expandable)
  • 240 Xeon processor cores (480 with hyper threading)
  • 2.56 terabytes of memory (256GB per blade)
  • 400 terabytes of disk storage (expandable)
  • Tape and cloud archival of raw and processed data

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We have streamlined the process of data generation, QC, analysis as outlined in the flowchart below:

Click to view a detailed view of the flowchart»