Our Service Workflows

Our Facility offers a broad range of single-cell applications, providing expert knowledge, accessibility, and personalized support.

We continuously update our methods and instruments in collaboration with our users, ensuring that we stay in tune with the evolving needs of the research community.

We support end-to-end :

• 10x Genomics Chromium System (droplet-based) for fresh and fixed cells assays
• Parse Bioscience Evercode (plate-based)

We can also support Waters Bioscience BD Rhapsody assays (please contact us for more information).

Other user-made library types can be sequenced at the Facility.

Users are responsible for the preparation of their single cell suspensions and ensuring that sample quality meets the required standards. We can provide you with recommendations.

Our Facility takes care of your cell suspensions provided at one of our 3 locations (please inquire).

Genopode building Dorigny lab 1016 in GTF Facility	Agora building CHUV lab 227 in FCF Facility	Biopole SE-C building Epalinges lab 136 in FCF Facility

Schedule An Experiment

Samples should be processed as quickly as possible after the cell sorting. Accordingly, experiments must be carefully scheduled with our staff.

Please contactGTF@unil.ch  as early as possible when designing your project and provide us with as much information about your project by filling the following form :

Sample Preparation

Cell Preparation

Cells or nuclei preparation is user’s responsibility!

The cells/nuclei suspension quality is crucial for a successful single cell project. Cells/Nuclei must be perfectly dissociated, their density accurately quantified, and viability must be above 70% (for transcriptomics applications). Nuclei preparation is even more challenging since viability check does not apply .

Any manipulation (e.g. concentration by centrifugation) or waiting time can impact cells/nuclei quantity and quality. In particular, cell count and viability output metrics from cell sorters cannot be taken for granted. It is more than highly recommended that a final quality control step is performed on the very final material you provide us. You may want take advantage of our cell counter Luna-FX7 which relies on AO/PI staining to accurately distinguish cells from debris.

Failure to provide good quality starting material will inevitably result in suboptimal, sometimes useless, results. Data quality can only be assessed after sequencing, meaning that expensive single cell and sequencing reagents are engaged, whatever the outcome is.

In any case, we strongly recommend that pilot experiments are performed in order to validate the cell preparation procedure.

Popular links for sample preparation :

10X Genomics

• Generic Tech support
• Cell Preparation for single cell protocols
• Removal of dead cells
• Nuclei preparation for single cell protocols
• Tissu Fixation and dissociation protocol

Parse

• Sample preparation for single cell protocols
• Fixation protocols

Technology description

10x Genomics Chromium System (droplet-based)

For Fresh cells:

In addition to fresh material, cryopreserved cells are a suitable input if they retain high viability at thawing. 

3’ or 5’ gene expression with multiomic capabilities :

• 3’ gene expression with cell surface protein
• 5’ gene expression with BCR/TCR, cell surface protein, antigen specificity and CRISPR screening

• Cells/nuclei, fresh, frozen tissues or organoids
• Recovery of up to 20’000 cells/sample (for 30’000 cells input)
• Possibility for multiplexing with BioLegend hashtags (see TotalSeq product section on BioLegend’s website)
• Built-in multiplexing capabilities for fresh cells

• Recovery up to 20’000 cells/ 4 samples (5’000 recovered cells per sample for 8’000 cells per sample input)

GEM-X Epi Multiome :

• Some cells states are nearly identical at the transcript level but differ significantly in their epigenitic memory or regulatory landscape
• 3’ gene expression and chromatin accessibility in the same cell

• New Nuclei isolation kit with RNAase inhibitor v2
• Recovery : maximum 20’000 nuclei/sample

For Fixed cell : Flex v2 Apex

Enables to preserve the sample biology through fixation (PFA) at sample collection.

A probe-based solution targeting 18’000 transcripts (human and mouse) for the whole transcriptome gene expression (other custom probes available).

• In-line multiplexing for 1 up to 384 samples per emulsion for ultimate flexibility
• Cells/nuclei, fresh, frozen and FFPE tissues, organoids or fixed whole blood
• Multiomics capabilities : cell surface protein, intracellular protein, CRISPR screening
• Input as low as 100’000 cells/sample (less is possible, please inquire)
• Excluded genes :
  • TCR & IG variable/joining regions
  • Ribosomal & mitochondrial ribosomal proteins
  • Read-through genes
  • KIR & HLA genes (high allelic diversity)
  • Non-coding RNA

Parse Bioscience Evercode (plate-based)

Enables to preserve the sample biology through mild fixation at sample collection.

Whole transcriptome gene expression (oligoT + random primers) makes it suitable for any species.

Split-pool combinatorial barcoding (1 to 384 samples).

• Mild fixation for 100’000-300’000 cells/sample and even less with low input fixation kit
• Fresh cells/nuclei, FFPE tissues, fresh-frozen and fixed-frozen samples
• Multiomics capabilities: TCR, BCR, CRISPR screening
• Different sizes of kit :
  • Evercode WT – 1-48 samples – recovery 100K cells total
  • Evercode Mega – 1-384 samples – recovery 1M cells total
  • Evercode Penta – 1-384 samples – recovery 5M cells total

WATERS Biosciences (Former BD) (microwells-based)

• Whole Transcriptome
• Multiomics capabilities : TCR, BCR, CITE-Seq, Protein, ATACseq, Ag specificity
• This technology is not directly available at the GTF but inquire

Spatial Transcriptomics

GTF teams up with another facility to propose spatial transcriptomics and proteomics analysis (please inquire).

Sequencing

We perform 10X library sequencing on our Element Biosciences or Illumina sequencer, depending on the output required.

Depth can vary a lot depending on your need :

Assay	Minimum reads per cell recommended
10x 3’ or 5’ GEX	20’000
10x cell surface protein	5’000
10x BCR/TCR	5’000
10x CRISPR	5’000
10x ATACseq	25’000
10x FLEX V2	10’000
PARSE V4	10’000

A good practice is to request a single sequencing lane (600M) to start with. Further sequencing can then be requested after quality control for validating cell number, evaluating transcription saturation, and inspecting the presence of some genes of interest.

Pricing for sequencing is variable and is determined by multiple factors including :

• Technology you choose
• Number of samples
• Number of cells you aims to target per sample
• Read depth per cell
• Optional extensions

Data Analysis

Primary analysis with dedicated pipelines is included with our single cell service.

It may also be requested for user made libraries sequenced at GTF. Please contact us concerning pricing.

Note that analysis with custom genome reference (presence of a transgene, like GFP) or non-model organisms is also possible. Please contact us for further information and associated fees.

10x Genomics – Cell Ranger analysis pipeline

Parse Biosciences – Parse analysis pipeline

Example Parse pipeline output – Image adapted from Parse Biosciences