Technologies

Next Gen Sequencing (NGS)

Illumina

The Genomics Platform is equipped with the NovaSeq 6000 from Illumina.

This highly robust and accurate sequencing platform is based on massively parallel sequencing of million of reads using proprietary reversible terminator-based sequencing chemistry (see method description in Illumina website).

The system enables sequencing of 100 to 250 bases from one end (single read; SR) or both ends (paired-end; PE) of DNA inserts.

10x genomics

The Platform is equipped with the high throughput Chromium X system as well as the CytAssist system from 10x Genomics.

Oxford Nanopore Technologies

The Platform is equipped with the MinION Mk1C of Oxford Nanopore Technologies.

This portable device for real-time DNA and RNA sequencing generates ultra-long reads (longest > 4 Mb) while keeping bases modification information.

This nanopore based sequencing system allows direct sequencing (without amplification or cDNA preparation) if needed.
 

Applications

  • RNA-seq:
    • Bulk RNA-seq: mRNA, non coding RNA, small RNA profiling.
    • Single cell RNA-seq with the Chromium X system of 10x Genomics, for the identification of cell-to-cell differences within a population of cells. Tens of thousands of single cells can be analysed at a time thanks to the Gel Bead-in-Emulsion (GEM) technology (gel bead partitions in which barcoded cDNA is prepared). The preparation of NGS libraries is then carried out in bulk reaction (see further details in 10x Genomics website). Workflow compatible with fresh and fixed cells as well as FFPE tissues.

    • Spatial transcriptomics with the Visium system of 10x Genomics. A CytAssist - for transfering transcriptomics probes from standard glass slides to Visium slides - is made available for users. HD slides allow single-cell spatial resolution, enhancing the ability to analyse cells within their native spatial contexte. Workflow compatible with fresh frozen and FFPE tissue sections.

  • DNA-seq: genome assembly, re-sequencing (whole genome, exome or targeted -seq), structural variants identification.
  • ChIP-seq
  • ATAC-seq
  • Direct detection of DNA and RNA modifications
  • 4C & HiC-seq

Before bringing samples to the Platform, please submit them in the genomics Laboratory Information Management System (LIMS) to help sample processing, monitoring and data retrieval.

Protocol used and input material
RNA-seq
  • For classical library preparation, the Illumina Stranded mRNA Prep, Ligation protocol is applied.
  • Poly A selection or ribo-depletion strategy can be applied to get rid of ribosomic RNA.
  • For classical protocol, a minimum of 25 ng of total RNA is required. A special protocol can be applied for lower input quantity (down to few ng).
  • A protocol of RNA exome capture is also available; ideal for low-quality samples such as FFPE samples.
  • Single-cell RNA-seq is available.
DNA-seq
  • For whole genome sequencing, the Illumina DNA prep, Tagmentation & TruSeq DNA Nano protocols are applied. 50 ng of DNA input is required, or 1 ng for smaller genomes.
  • For targeted sequencing, enrichment is performed with IDT, Agilent or Twist captures.
ChIP-seq
  • For classical library preparation, the Illumina TruSeq protocol is applied.
  • Just a few ng are needed.
Illumina NovaSeq 6000

 Illumina NovaSeq 6000
 We are grateful to the Société
 Académique de Genève for its support.
 Photo Illumina

10x Genomics Chromium X

10x Genomics Chromium X

 We are grateful to the  Ernst et Lucie Schmidheiny  & Carlos et Elsie de Reuter Fondations  for their support.
 Photo 10x Genomics

10x Genomics CytAssist
 Photo 10x Genomics

Oxford Nanopore Technologies MinION Mk1C

 Oxford Nanopore Technologies
 MinION Mk1C
 Photo ONT

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