The Crown Institute for Genomics Platform provides NGS (Next-Generation Sequencing) services for samples prepared by the Platform or for libraries submitted by external users.

Library preparation

The Crown Institute for Genomics supports a wide range of library preparation protocols and sequencing options.
In addition to standard Illumina kits, we developed and offer high quality in-house protocols for major applications at a reduced cost.
 

RNA-seq

  • Full length RNA-seq - polyA-based capturing
  • Full length RNA-seq - without polyA capture
  • 3' RNA-seq - Bulk MARS-seq
  • Turseq stranded RNA - Illumina
  • Full length RNA-seq low input - Bulk smart-seq2
  • FFPE bulk RNA seq

 

DNA-Seq

  • Whole Genome Sequencing

 

ChIP-seq

  • Chromatin Immunopercipitation

 

Amplicon-seq

  • Amplicons < 500bp

 

Bulk ATAC-seq

  • The bulk ATAC-seq is based on the OMNI-ATAC protocol (Grandi et al., Nature Protocols 2022). ATAC-seq (Assay for Transposase-Accessible Chromatin using sequencing) (Buenrostro et al, Nature Methods 2013) uses Tn5, a hyperactive transposase loaded with sequencing adapters, to map chromatin-accessible regions (nucleosome depleted), often containing regions of active genes and their promoters and enhancers. ATAC-seq is commonly used with other methods to infer regulatory regions in the genome.

    The OMNI-ATAC is a newer version of the ATAC-seq protocol that uses a combination of three detergents to lyse the cells and gives more robust results with a lower background. The recommended input is 50,000 cells, either freshly isolated or cryo-preserved.

 

Single Cell Genomics

  • Single cell 3' RNA-seq - 10x genomics
  • Cell Hashing
  • Single cell 5' RNA-seq - 10x genomics
  • Single cell immune profiling - TCR/BCR sequencing
  • Single cell ATAC-seq
  • Single cell multiome analysis

For more information visit https://www.10xgenomics.com/

 

Spatial transcriptomics

  • Visium fresh frozen
  • Visium FFPE
  • Visium HD

For more information visit https://www.10xgenomics.com/products/spatial-gene-expression

 

    Sequencing

    We sequence libraries that were prepared in our facility libraries or prepared by the researcher (Ready to Run).

    We offer a variety of sequencing instruments:

    • Novaseq X - high throughput sequencing, 1.6B, 10B, 25B reads per run
    • NextSeq 500 – medium throughput sequencing, 400M reads (HO) or 130M reads (MO) per run
    • MiSeq – low throughput sequencing, 1M, 4M, 12M, 22M reads per run