Frequently Answered Questions

Picoception is a highly sensitive 3’-end RNA sequencing platformoptimized for degraded RNA, such as in clinical biopsies from patients and all types of FFPE (formalin-fixed, paraffin-embedded) tissue. It is a high-throughput platform capable of rapidly profiling large cohorts of samples.

As a testament to its sensitivity, Picoception has consistently profiled RNA from decades-old tissue sections successfully,including tiny tissue sections from needle-core biopsies. Such small biopsiescannot be profiled with other standard methods.

Other RNA-seq platforms require fresh or recent tissue sections and far larger quantities of input. This is where Picoception offers adistinctive advantage.

The Picoception platform has successfully sequenced RNA from a wide range of eukaryotic species, ranging from humans and rodents to plants. The Picoception Tissue workflow has been used successfully with frozen and FFPE samples from human, mouse, and rat, including xenografts and viral infections. Any eukaryote with a published genome annotation is likely to be compatible with Picoception. We have had consistent success with FFPE tissue sections more than 20 years old.

Measuring the ERCC RNA standards with known concentrations over six orders of magnitude, the RNA-seq read count from Picoception is tightly correlated with the true copy number (r = 0.99).

Picoception is sensitive to picograms of RNA, the scale of a single cell. For the highest-quality data, we recommend providing 10 ng of total RNA or 0.1 mm² of tissue from a single FFPE slide section.

No, Picoception is specially optimized for degraded RNA. We have made successful libraries from samples with RIN and DV200 too low to measure.

Generally, no; because Picoception reads only a segment of each RNA transcript, the sequences are unlikely to contain useful information for genotyping. However, you can combine Picoception with your own separate assay, such as targeted DNA sequencing or shallow whole-genome sequencing to perform multi-omic analysis of the same sample.

As a service provider, we do not request authorship or citation in any professional publications based on the data wegenerate for you. Upon completion of your project, we will provide suggested text formatted for the Methods section of a scientific journal article, with your project’s specific technical details included. This text will include the specified procedures carried out by Picopoint Genomics.

Other spatial platforms scan a large area of a slide while testing for a limited number of target molecules across the entire area. This is useful for characterizing the overall landscape of the tissue. However, the trade-off is difficulty quantifying differential gene expression in specific regions, because the data complexity is less than bulk RNA-seq and the cost prevents testing many samples for statistical power. Most platforms also test a limited number of target genes.

Picoception targets specific regions of interest and performs a “microbulk” RNA-seq on each region, reading all mRNAs and some lncRNAs. This gives you the data complexity of bulk RNA-seq, but from spatially targeted areas of pure cellpopulations. If you already know the histology of your samples, Picoception lets you do deep gene-expression profiling in the regions you care about. This can be a complementary approach to other spatial platforms: you can use one tissue section to create the shallow spatial atlas, then use that to choose regions on a consecutive tissue section for deeper RNA-seq analysis.

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A single slide section is sufficient.

For the best view of histology, you may optionally mount a consecutive section on an ordinary glass slide, as the thicker section on the membrane slide may be slightly more difficult to read; you can select ROIs according to the glass slide and we will profile the corresponding areas on the membrane slide.

We recommend 7 µm for human tissue to provide additional RNA while still visualizing a single cell layer, but we can work with any thickness from 4 to 10 µm and possibly thicker if required.

Yes, absolutely! The Picoception Tissue platform is optimized for formalin-fixed, paraffin-embedded (FFPE) tissue sections. We have successfully profiled thousands of samples, many of which are decades-old.

Yes, your fixed tissue slide is safe to store at room temperature. In the long term we recommend storing it in a dry space, such asthe provided bag and desiccant.

Yes, the fixed tissue slides are safe to store for a few weeks before and after staining. You can wait to stain all your slides together in a batch.

The tissue we obtain from your region-of-interest (ROI) is fully consumed during our process. The remaining tissue on the slide may still be available to return to you in an emergency. However, if you want to perform any other analysis on the same tissue, you can plan ahead by reserving one or more sections for your own analysis and giving us a consecutive section.

Ultraviolet light is required to make the membrane adhesive, essentially to turn it into a charged slide, so you can mount a tissue section that stays flat without curling at the edges. It also sterilizes the slide of any contaminating nucleic acids.

Our system requires tissue to be mounted on a special membrane slide so it can be removed from the slide for profiling.

Staining, typically hematoxylin & eosin (H&E), is usually necessary to visualize histology and select ROIs. Contact us for a simplified workflow if you have tissue in which ROIs are identifiable without staining.

Yes, our protocol is just a guideline, but if you have a routine or optimized protocol for your type of tissue, you can use your protocol instead.

Some other kinds of stains may be compatible, e.g. simple alternatives to H&E like Nissl staining, but more complex treatment like immunohistochemistry (IHC) is likely to destroy the RNA. You can use a different slide for your other treatment and give us a consecutive section for RNA-seq, or contact us about a trial to validate your stain with our platform.

Pricing is per RNA-seq library and each library is made fromone or more ROIs. For example, if you want to compare one tumor region and one microenvironment region in the same tissue section, we can prepare them as two separate libraries. If you want to combine several regions of the same celltype from different areas, even areas on different slides, we can pool them tomake a single library.

No, we have made successful libraries from RNA with RIN toolow to measure and DV200 of zero.

You probably have more than enough RNA for our needs and weremeasure it before preparing libraries. Contact us to describe your sample source and extraction method so we can roughly estimate the expected yield.

The container has a stabilizer that protects RNA from degrading at room temperature, making it much safer and easier for you to send it to our lab.

The RNA storage container is validated for at least several months of storage of room temperature. We recommend storing it in a dry space,such as the provided bag and desiccant.

Clients based in Singapore may contact us to arrange handoff of your RNA samples. All others are strongly discouraged from shipping aqueous RNA as it can degrade quickly when thawed and international cold shipping is very costly and inconvenient.

We always provide a FASTQ file for every library, the raw sequence data that many journals require for manuscript submission. Depending on your needs we can also provide BAM files, a gene expression count matrix, and theoutput of other downstream analyses customized to your project such asdifferential gene expression, PCA/UMAP, GSEA, and survival analysis.

Deconvolution is usually not necessary because the sensitivity of the platform allows you to isolate and analyze a specific cell population, rather than pool multiple cell types as standard bulk RNA-seq may require. However, we have experience applying deconvolution algorithms to Picoception data from mixed cell populations and can include this analysis as an add-on to your project.