Gene Expression Core Facility

DNA molecules (Adobe education license)

Mission

The GECF provides a diverse set of tools for the functional and quantitative analysis of genomes and transcriptomes, both at single cells level or on bulk cell populations. This comprises in particular next-generation sequencing (NGS), classical or high-throughput microfluidics-based qPCR technologies, digital PCR, and spatial transcriptomics analyses. In addition, we enable manipulation of the cellular gene expression program by providing different genome-wide collections of ORFs. Because new technologies constantly emerge, we are eager to discuss means to further improve and develop our toolbox.

Expertise

Next generation sequencing (NGS)

Illumina (MiSeq, NextSeq, NovaSeq) or Elembio (Aviti) short reads. Oxford Nanopore long reads (MinION, Promethion)

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Single cells genomics/ transcriptomics

10X Genomics ChromiumX, Parse…

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Spatial Transcriptomics

10X Genomics Visium / CytAssist

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Quantitative and digital PCR

Classical qPCR (Applied Biosystems QuantStudio), microfluidics-based qPCR (Fluidigm BioMark), and digital PCR (Qiagen Qiacuity)

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Nucleic acids QC

Profiling (TapeStation 4200 and Fragment Analyzer) and quantification (Qubit, Nanodrop One)

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ORF & cDNA Collections

We manage and distribute several large collections of ORFs

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News

March 2025

  • Our f.sight.omics, i.dot and c.wash instruments for Plate-seq are available for booking.
  • New multiplexing options for 10XG available (“On-chip multiplexing”).
  • Decrease of Aviti prices! And new 100mio 150 cycles run under 1’000CHF.

November 2024

July 2024

  • New price list available here.

April 2024

  • Visium HD is here! Spatial transcriptomics resolution is now down to single cell scale. More info here!

March 2024

  • Our new Aviti sequencer is operational. Please inquire. More news soon anyway.

January 2024

November 2023

  • New price list available here, with decrease of fixed RNA 10XG (FLEX) prices

October 2023

July 2023

  • New price list available here! Many new services included. Prices decrease of NovaSeq runs.

June 2023

  • We have launched the 10X Genomics FLEX (fixed RNA profiling) service, based on fixed cells. Ideal for evening or weekend processing of samples since fixed cells can be stored.

April 2023

  • We have just launched a HiC libraries prep service, based on Arima workflow. Inquire for pricing and details.
  • A new libraries submission form is available here (together with updated guidelines).

February 2023

2022

  • From now on please use our team email address gecf@epfl.ch for projects submissions and other demands.
  • New versions of our libraries submission form/guidelines are available here.
  • We have launched our NovaSeq 6000 service! Please inquire.

2021

  • We have launched a Visium FFPE spatial transcriptomics service, in collaboration with HCF.
  • A NovaSeq 6000 will soon replace our HiSeq 4000! More news in December.
  • A warm welcome to our new collaborator Chiara Sartori.
  • The replacement process for our HiSeq 4000 sequencer has begun, more news in 2 months.
  • Our new 10X Genomics single cell multiome (scATAC-seq+scRNA-seq) and CellPlex services are operational.
  • Our new QuantStudio 6 instrument is now operational.
  • Our new web tool CloneMap for ORFs browsing and QC is operational (thanks Fabrice David).
  • A warm welcome to our new collaborator Patricia Hornitschek.

2020

2019