FFPE Transcriptional Activation Profiling Grant Program
Are you working with archival or low-quality FFPE?
Your FFPE archive holds years of biology – but RNA doesn’t last that long.
Apply for a chance to win a free CUTANA™ FFPE Transcriptional Activation Profiling service project and access the gene regulatory data locked in your samples! Tell us how CUTANA™ FFPE would advance your research. The winner will receive complete end-to-end services: expert project design, on-slide FFPE sample processing, library prep, sequencing, and data delivery – at no cost. The submission window closes June 23rd at 11:59 PM Pacific Daylight Time (GMT-7).
What's included in this project?
Meet with our science team
Consultation with our scientific team on a project design best suited to your experimental goals.
Sample Processing
Processing of up to 12 slide-mounted FFPE tissue samples with CUTANA™ FFPE targeting RNAPII.
Data Analysis
Sequencing and data analysis including alignment, peak calling, and enrichment profiles at select target loci to confirm assay success.
Data Delivery
Personalized data presentation and delivery of both raw and analyzed files.
Why CUTANA™ FFPE?
RNA-seq is the standard tool for studying gene expression, but it fails on most archival FFPE material. Formalin fixation degrades RNA over time, and older blocks or resource-limited collections are often unusable for transcriptomic analysis. The result is that decades of clinically annotated tissues, the substrates for retrospective cohort studies and biomarker discovery, remain inaccessible to the methods researchers rely on most. ATAC-seq faces similar constraints: it requires substantially more tissue than a routine FFPE section and lacks the transcriptional specificity needed to interpret regulatory activity.
Figure 1. CUTANA™ FFPE Transcriptional Activation Profiling workflow for slide mounted FFPE tissue sections. FFPE sections are deparaffinized, subjected to antigen retrieval, and incubated with an RNAII antibody. A modified CUT&Tag method inserts sequencing adapters at RNAPII-occupied sites. DNA is recovered, PCR amplified, and sequenced at approximately 10 million reads per sample.
EpiCypher’s CUTANA™ Transcriptional Activation Profiling takes a different approach: rather than relying on RNA, it reads the transcriptional machinery itself. RNA Polymerase II (RNAPII), the enzyme responsible for transcribing protein-coding and regulatory genes, remains stably associated with chromatin through FFPE fixation. Using CUT&Tag, the assay targets the transcriptionally active form of RNAPII (Figure 1). The assay provides a quantitative readout of active transcription (Figure 2) and resolves tissue-specific expression profiles (Figure 3). Because DNA is far more stable than RNA in archival tissue, this approach works across a wide range of archive ages and sample qualities, opening cohorts that are closed to RNA-based methods. By targeting the RNAPII C-Terminal Domain, which contains multiple repeating epitopes, the assay benefits from substantial signal amplification. The result is high-resolution mapping of active promoters and enhancers from a single 5 µm section with signal that outperforms even standard ATAC-seq on fresh tissue (Figure 4).
The scientific basis for this assay was published in Science by Henikoff et al. (2025). EpiCypher holds exclusive commercial rights to this technology and has optimized it for routine use — FFPE Transcriptional Activation Profiling is available only from EpiCypher. Read the paper: doi.org/10.1126/science.ads2169
Figure 2. CUTANA™ FFPE is transcription-coupled; ATAC-seq is not. Metagene profiles centered on the TSS for human colon FFPE sections, with genes ranked into deciles by RNA-seq expression level. ATAC-seq signal (left) shows minimal separation across top expression deciles, reflecting an inability to differentiate nuances in high levels of expression. CUTANA™ FFPE (right) resolves clear signal stratification across all ten deciles, confirming that RNAPII targeting quantitatively couples the readout to active transcription. Data from the Sheikh laboratory, UNC-Chapel Hill (samples collected 2019-2021).
Figure 3. Tissue-specific transcriptional profiles resolved by CUTANA™ FFPE. (A) Metagene profiles centered on transcription start sites (TSS) demonstrate quantitative coupling between CUTANA™ FFPE and RNA-seq across liver, colon, and brain sections. (B) Genome browser tracks show RNAPII occupancy at tissue-specific genes in liver (Ahsg), colon (Epcam), and brain (Mir124a-1hg), alongside a ubiquitously expressed housekeeping gene (Tubb5) with signal across all tissues. These patterns indicate that the assay captures biologically meaningful, tissue-specific transcriptional activity.
For researchers working with archival FFPE samples, CUTANA™ FFPE Transcriptional Activation Profiling offers practical advantages over other genomic approaches:
- Maps transcriptional activity onto DNA rather than RNA, enabling transcriptomic analysis of archival FFPE samples that are inaccessible to RNA-seq
- Profiles active enhancers, key drivers of gene expression that RNA-seq cannot detect
- Generates stronger signal than both FFPE-ATAC and standard ATAC-seq on fresh tissue
- Requires a single 5 µm section per sample – 10-fold less than ATAC-seq and RNA-seq
- Requires only ~10 million reads per sample compared to 30-70 million for FFPE RNA-seq
Figure 4. CUTANA™ FFPE produces higher signal intensity than ATAC-based methods. TSS-centered heatmaps comparing signal across assays show the strongest enrichment with CUTANA™ FFPE in mouse liver, followed by Omni-ATAC in fresh mouse liver, compared to substantially lower signal from FFPE-ATAC.
Application Details
What the winner receives
An end-to-end service project to pilot the utility of this assay in your research, including:
- Consultation with our scientific team on a project design best suited to your experimental goals
- Processing of up to 12 slide-mounted FFPE tissue samples with CUTANA™ FFPE targeting RNAPII
- Sequencing and data analysis including alignment, peak calling, and enrichment profiles at select target loci to confirm assay success
- Personalized data presentation and delivery of both raw and analyzed files
Who should apply
We welcome applications from researchers at any career stage. This grant is particularly relevant if you:
- Use FFPE RNA-seq and want to extend your findings to active regulatory elements, including promoters and enhancers, that RNA-seq cannot capture.
- Are studying cancer, inflammatory disease, or other conditions where your primary resource is an archival biobank, including older collections where RNA quality is limiting or unknown.
- Have limited or precious FFPE blocks that must also support pathology review and other molecular tests. CUTANA™ Transcriptional Activation Profiling requires only a single standard 5 µm section.
- Are designing retrospective cohort studies where prospective fresh-tissue collection is not feasible and want to access transcriptional biology in samples that RNA-based methods cannot reach.
- Are working on biomarker discovery or patient stratification in translational oncology and need genome-wide transcriptional activation data from clinical FFPE specimens, including active enhancers that RNA-seq cannot detect.
How to apply
Step 1. Fill out the short form on this page. In order to submit the form, you must read the terms and conditions to ensure your samples and project are aligned with the guidelines.
Step 2. Our scientific team will evaluate all submissions and select a winner based on scientific merit, clarity of research question, and potential impact. The submission window closes June 23rd at 11:59 PM Pacific Daylight Time (GMT-7).
Step 3. The winner will be contacted directly to begin project scoping, and all other applicants will be notified of the final decision.
If you have any questions, please email our science team at [email protected].