Gene Expression Core Facility
DNA molecules (Adobe education license)
Mission
We provide 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, 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
Illumina (MiSeq, NextSeq, NovaSeq) or Elembio (Aviti) short reads. Oxford Nanopore long reads (MinION, Promethion)
Single cells genomics/ transcriptomics
10X Genomics ChromiumX, Parse…
Spatial Transcriptomics
10X Genomics Visium / CytAssist
Quantitative and digital PCR
Classical qPCR (Applied Biosystems QuantStudio), microfluidics-based qPCR (Fluidigm BioMark), and digital PCR (Qiagen Qiacuity)
Nucleic acids QC
Profiling (TapeStation 4200 and Fragment Analyzer) and quantification (Qubit, Nanodrop One)
ORF & cDNA Collections
We manage and distribute several large collections of ORFs
News
November 2024
- New price list available here.
- TotalSeq multiplexing for 10X Genomics
- Parse single cell method available.
- A warm welcome to our new collaborator Guillaume Fabre
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
- A warm welcome to our new collaborator Michael Stock.
November 2023
- New price list available here, with decrease of fixed RNA 10XG (FLEX) prices
October 2023
- Launch of our PromethION long reads service.
July 2023
- New price list available here! Many new services included. Price decrease of NovaSeq runs.
June 2023
- We have launched the 10X Genomics https://www.epfl.ch/research/facilities/gene-expression-core-facility/page-112636-en-html/page-153363-en-html/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
- Our new CytAssist instrument now allows us to process FFPE slides for spatial transcriptomics analysis of human and mouse tissues with improved sensitivity, flexibility and robustness.
- Our new QIAcuity One 5plex digital PCR system is up and running.
2022
- From now on please use our team email address [email protected] 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
- Our new QuantStudio 7 is now operational.
2019
- Our 10X Genomics Visium spatial transcriptomics service is launched. A fruitful collaboration with the HCF.
- Our 10X Genomics single cell ATAC-seq service is operational.
2018
- Our new HiSeq 4000 sequencer just arrived! Service will begin later in January.
- We released libraries submission guidelines for NextSeq sequencing. They are available here.
- We released RNA submission guidelines for RNA-seq, and gDNA submission guidelines for whole genome sequencing or exome sequencing. They are available here.
- A slightly updated version of our price list is available here.
- Our new 10X Genomics Chromium instrument is operational. This allows scaling up single cells transcriptomics experiments to thousands of cells.
- New user-friendly short protocols are available for the TapeStation 4200.
2017
- The GECF now provides bioinformatics services, presented in a dedicated web site. More news soon.
- New method available on our Fragment Analyzer for gDNA and large DNA fragments (up to 50 Kb).
- Release of user friendly quick start guides for our QuantStudio 6 and 7900HT qPCR instruments.
- New more user-friendly releases of our ORFs databases.
- A warm welcome to our new team members Elisa Cora and Lionel Ponsonnet!
2016
- Initial release of our new MOUSAIC collection of murine ORFs.
- New improved versions of the Fragment Analyzer kits were released.
- Our new Agilent TapeStation 4200 has arrived. This RNA/DNA profiling instrument nicely complements our Fragment Analyzer. Please contact us for more details.
2015
- Our next-generation Illumina NextSeq 500 sequencer is now operational. Please contact us for more details.
- New user-friendly short protocols are available for the Fragment Analyzer.
- Our service of automated 96-well plate minipreps is now available. Please inquire for further details.
- The new FlexSix system is available on our BioMark HD, allowing for much more flexible samples/genes combinations.
- CAHOS database v1.004 released, including 32 new human ZNF ORFs.
- Our new QuantStudio 6 Flex qPCR instrument is available for booking (only with a 384w block for now).