360° Transcriptomics: bulk, single-cell, spatial

What each modality tells you, and what it cannot

The three are not competing methods. They are three angles on the same biology, and the gap between them is usually where the answer sits.

Bulk RNA-seq

The population average, reliably and at scale: robust differential expression, enough depth for low-abundance transcripts, and the statistical power that comes with sequencing many samples. It cannot tell you which cells produced the signal.

Single-cell

Resolves the average into the cell populations that make it up: which subsets shift, which appear, which disappear. It cannot tell you where those cells were sitting in the tissue.

Spatial transcriptomics

Puts expression back into the tissue with its architecture intact: what is next to what, at the tumour margin, inside a niche. It trades depth for position.

Why buying the three separately costs you the answer

Each modality is available on its own from someone. Bought that way, the three never quite line up.

Three designs instead of one

Group sizes and time points chosen for a bulk experiment are rarely the ones a single-cell or spatial run needs. Two of the three datasets end up underpowered for their own question.

Three sample sets

Different aliquots, different handling, sometimes different animals or patients. The modalities then disagree, and you cannot tell whether that is biology or logistics.

Three interpretations

Three reports, each internally consistent, that you are left to reconcile. The cross-modality reading, which is the reason you ran all three, is the one nobody delivers.

Who runs what

One modality each, one design, one sample set, one project lead accountable for the whole chain.

GenXMap — bulk RNA-seq

Extraction, library preparation and sequencing on our Marseille platforms, then the bioinformatics, statistics and AI-assisted integration that pulls the three modalities into one reading.

Parean Biotechnologies — single-cell

Based in Saint-Malo, specialised in deep immune phenotyping and multi-omics data analysis, with wet laboratories and a data science unit.

Explicyte — spatial transcriptomics

A precision oncology and immuno-oncology CRO in Bordeaux, bringing spatial transcriptomics alongside its oncology and immuno-oncology models.

The chain, end to end

One design covering all three modalities, one sample set split across them, and methods, parameters and thresholds documented across the whole chain.

01

Question

What the programme must establish, and which of the three modalities actually bears on it.

02

One design

Groups, time points and controls chosen so bulk, single-cell and spatial are each adequately powered.

03

One sample set

Material collected once and split across the three routes, with a documented chain of custody.

04

Three runs

Bulk in Marseille, single-cell in Saint-Malo, spatial in Bordeaux, on a shared timeline.

05

Integration

Versioned pipelines, cross-modality integration and AI-assisted prioritisation.

06

One interpretation

A single report that reads the three together and answers the question you started from.

The bulk platforms behind it are the ones published on OMICS4, where the offering is also listed as a combo platform. See also our wet-lab platforms and computational biology and AI.

Who this is for

Immuno-oncology programmes

Where the treatment effect has to be read in the tumour microenvironment: which immune subsets shift, and where they sit relative to the tumour. See immuno-oncology.

Translational and precision medicine

Where a signature has to survive contact with clinical metadata and an independent cohort, and be traceable to a cell type and a location. See precision medicine.

Teams without an in-house chain

Biotechs and academic groups that need all three modalities contracted once, with a PhD-level scientist accountable for the reading.

Questions we get asked

Common questions about running bulk, single-cell and spatial together.

Which do I need: bulk, single-cell or spatial transcriptomics?

It depends on the question, not on which method is newest. Bulk RNA-seq gives you the population average with the depth and statistical power that come from sequencing many samples, and it is the right answer more often than people expect. Single-cell resolves that average into the cell populations behind it. Spatial puts expression back into the tissue with its architecture intact. If your question spans two of those, running them on separate designs usually costs you the comparison.

Can the three be run on the same samples?

That is the point of the 360° programme. One experimental design is agreed up front so bulk, single-cell and spatial are each adequately powered, material is collected once and split across the three routes, and the chain of custody is documented throughout. Buying the three separately normally means three designs and three sample sets that no longer compare.

Does anyone in France offer all three transcriptomic modalities in one programme?

That is precisely what GenXMap set out to make available. Bulk RNA-seq runs on our own platforms in Marseille, single-cell with Parean Biotechnologies in Saint-Malo, spatial transcriptomics with Explicyte in Bordeaux, under one contract with one PhD-level project lead accountable for the whole chain and for the final interpretation. The full transcriptomic spectrum, designed and read as one thing, is the offering — not three services sold side by side.

Who is accountable if the modalities disagree?

One project lead, at GenXMap, for the whole programme. Disagreement between modalities is often the most informative part of the result, and reading it requires knowing how each sample was generated. That is why the interpretation is not split three ways.

Can you work on transcriptomic data we already have?

Yes. An existing dataset, from an earlier study or another provider, is analysed on its own terms. What decides the work is the biological question and the metadata that came with the data, not who ran the sequencer.

Where is the work done, and does the material leave the EU?

Bulk sequencing runs in our Marseille laboratories, hosted at the Méditerranée Infection building. Single-cell runs in Saint-Malo and spatial in Bordeaux. Samples and data stay in the European Union, with a documented chain of custody from intake to delivery.

Three views of the same transcriptome, in one programme