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.

Oxford Nanopore Technologies

The Platform is also 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

SARS-CoV-2 whole genome sequencing using the amplicon-based Paragon Genomics panel.
RNA-seq: mRNA, non coding RNA, small RNA profiling. Isoforms, splice variants and fusion transcripts analysis.
mRNA-seq from single-cell is also available, allowing the identification of cell-to-cell differences within a population of cells. High-throughput analysis is available with the Chromium Controller system of 10x Genomics.
DNA-seq: genome assembly, re-sequencing (whole genome, exome or targeted -seq), structural variants identification.
ChIP-seq
ATAC-seq, MNase-seq
Direct detection of DNA and RNA modifications
4C & HiC-seq
...

Main protocols and input material recommendations

Protocol used and input material

RNA-seq

For classical library preparation, the Illumina TruSeq 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 100 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, Illumina TruSeq or Nextera sample preparation 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.

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.

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

Oxford Nanopore Technologies
MinION Mk1C
Photo ONT

Latest modification: 05/07/2023 - 09 h 53