- [Resource Hub](/) - [Resource](/?resource-type=video#library) - Tissue Transcriptomics with CyteFinder® II Instruments # Tissue Transcriptomics with CyteFinder® II Instruments How RareCyte principal scientist Jennifer Chao uses the CyteFinder II instrument and the PicSeq workflow to read one tissue section at three levels: its spatial organization, its cell phenotypes, and the RNA inside chosen regions. RareCyte principal scientist Jennifer Chao shows how the CyteFinder II instrument and the PicSeq workflow bring RNA-level profiling to an imaged tissue section, pairing whole-slide multiplex fluorescence imaging with needle-based retrieval of chosen regions of interest for downstream RNA sequencing. Working through breast-cancer and tonsil examples on both fresh-frozen and FFPE tissue, she demonstrates PicSeq characterizing one section at three levels at once: its spatial organization, the phenotype of individual cells, and the RNA profile of the small regions picked for sequencing. Each pick recovers roughly 10 to 20 cells, and CIBERSORT deconvolution returns cell-type expression signatures that match the imaging, carrying the workflow from immune-cell profiling to RNA-driven biomarker discovery. In this video: - PicSeq, end to end: stain with fluorescent antibodies, image on CyteFinder II, mark ROIs in CyteHub, retrieve with CytePicker Retrieval Module for RNA-seq with commercial kits. - Precise, small-region retrieval: a 40-micron needle lifts each region of interest at roughly 10 to 20 cells, so sequencing reflects a defined location, not a bulk homogenate. - Three levels from one precious section: tissue architecture, single-cell phenotype, and molecular RNA profile; the talk’s case for oncology and immuno-oncology studies. - Fresh-frozen breast-cancer example: T-cell and tumor regions are picked; CIBERSORT shows T-cell picks dominated by T-cell signatures, tumor picks by tumor signatures. - FFPE via adjacent sections: antigen retrieval blocks efficient RNA extraction from the stained slide, so picks come from a serial section guided by CD3/CD20 on its neighbor. - RNA-driven biomarker discovery: PicSeq flagged CD21 as differentially expressed between two adjacent tonsil follicles, then confirmed by immunofluorescence on a serial section. Full transcript Hi, my name is Jennifer Chao, principal scientist at RareCyte. I will present an overview of RareCyte’s tissue applications, and how our technology enables transcriptomics research for a wide variety of applications, including immune profiling and biomarker discovery. Discovery applications using the RareCyte platform involve the CyteFinder instrument, which integrates whole-slide, multiple parameter imaging with needle based retrieval. This workflow termed PicSeq enables deep sample characterization at multiple levels from large scale tissue organization to individual cellular interactions and phenotypes to DNA and RNA profiling of small regions of interest. Because sample integrity is preserved and DNA and RNA can be profiled in an unbiased manner, PicSeq enables many applications including tumor microenvironment characterization and biomarker discovery. Our multiplex tissue imaging and PicSeq workflow involves staining the tissue sample with fluorescently labeled antibodies, followed by imaging on the CyteFinder II instrument. Images are reviewed and regions of interest identified using our CyteHub software. These regions of interest can then be retrieved with the CytePicker Retrieval Module and further characterized by RNA sequencing using commercially available kits. PicSeq can be performed on fresh-frozen, or FFPE tissue types. In this first example, T-cell infiltration in breast cancer was characterized in fresh-frozen tissue stained with T-cell and tumor markers. The T-cells of interest were chosen based on staining and distribution within the tumor and are circled in the left panel. Each of the regions were retrieved with a 40 micron diameter needle and the tissue after picking is shown in the inset. The narrow needle bore allows for very precise retrieval, each containing approximately 10 to 20 cells. After retrieval RNA was extracted and sequenced from each of the picked regions. Cibersort is a computational method to quantify cell fractions from a mixed population and was used to deconvolve the RNA signatures. The results are shown on the right. As expected, the T-cell picks are largely made up of T-cell expression signatures, while the tumor picks are largely comprised of tumor signatures. The tumor infiltrating lymphocytes had a mixture signature of tumor and TIL that corresponded to the number of T-cells identified during imaging. These results demonstrate the power of the PicSeq workflow to deeply characterize your tissue of interest from the spatial organization and the cellular phenotyping right down to molecular profiling. CyteFinder II and PicSeq also enable immune cell profiling and biomarker discovery applications. The following experiment was performed on FFPE tonsil tissue. The section was first stained to identify the T-cell and B-cell zones with CD3 and CD20 respectively. Unlike frozen tissue, FFPE sections require extensive antigen retrieval for staining, which precludes efficient RNA extraction. Therefore, RNA sequencing from FFPE tissue requires the retrieval and staining to be done on adjacent sections. In this experiment, all picks for RNA sequencing were taken from section 2 guided by staining on section 1. Cibersort RNA sequencing deconvolution of the tonsil picks revealed expression signatures of multiple different immune cell types within each of the T-cell zone and B-cell zone picks as indicated in the graph on the right. This demonstrates that even with the extensive fixation in FFPE tissue sections, we can extract and sequence RNA from PicSeq retrieved regions to identify and characterize immune cell populations. Principal component analysis of the RNA data from the retrieved regions revealed that the ROIs from the two follicles clustered differently from each other as well as from the T-cell zone. Gene expression analysis based on the frequency of mapped reads revealed that CD21 was one of the genes differentially expressed between the adjacent follicles. To validate the RNA sequencing results, we performed immunofluorescent staining on a serial tonsil section with CD21, the gene identified to be differentially expressed in the two B cell follicles by RNA sequencing. As you can see, the differential staining of CD21 was confirmed by immunofluorescence. This example demonstrates the utility of PicSeq as a powerful method of RNA driven biomarker discovery in tissue. To conclude, oncology and immuno-oncology studies require investigation at multiple levels, architectural, morphological and molecular. The CyteFinder II system and the PicSeq workflow enable comprehensive characterization at all of these levels to obtain the maximum information from each precious tissue section. Transcript reproduced from RareCyte’s captured video transcript and lightly edited only for obvious transcription artifacts (a stray comma, a mistyped connective word, missing hyphens and spaces, and one homophone term); the presenter’s words and all technical details, quantities, and product names are otherwise verbatim. [Back to all resources](/#library) ## Related resources [Article](https://www.selectscience.net/product-news/measuring-versus-reading-transforming-the-field-of-quantitative-pathology?artid=58733) CyteFinder SelectScience ### Measuring versus reading – transforming the field of quantitative pathology [Read Article](https://www.selectscience.net/product-news/measuring-versus-reading-transforming-the-field-of-quantitative-pathology?artid=58733) [Spec Sheet](https://go.pardot.com/l/455452/2019-11-18/7mzyyz/455452/220141/TS20_103.pdf) CyteFinder ### CyteFinder II HT [View Spec Sheet](https://go.pardot.com/l/455452/2019-11-18/7mzyyz/455452/220141/TS20_103.pdf) [Spec Sheet](https://go.pardot.com/l/455452/2019-11-18/7mzyz2/455452/220143/TS20_104.pdf) CyteFinder ### CyteFinder II [View Spec Sheet](https://go.pardot.com/l/455452/2019-11-18/7mzyz2/455452/220143/TS20_104.pdf) [Publication](https://doi.org/10.1200/JCO.2026.44.16_suppl.5041) CyteFinder Journal of Clinical Oncology 2026 ### Clinical validation of circulating tumor cell synaptophysin and androgen receptor expression in metastatic prostate cancer phenotypes. [View Publication](https://doi.org/10.1200/JCO.2026.44.16_suppl.5041) [Video](https://www.youtube.com/watch?v=_oGC1KRVN2U) CyteFinder 2026 ### Dr. Pashtoon Kasi on the impact of circulating tumor cells on clinical research [Watch Video](https://www.youtube.com/watch?v=_oGC1KRVN2U) [Publication](https://doi.org/10.1038/s41587-026-03099-z) CyteFinder Nature Biotechnology 2026 ### mRNA vaccine immunity is enhanced by hepatocyte detargeting and not dependent on dendritic cell expression [View Publication](https://doi.org/10.1038/s41587-026-03099-z) [Publication](https://pmc.ncbi.nlm.nih.gov/articles/PMC7618831/) CyteFinder Cancer Immunology Research 2026 ### Ex Vivo Immuno-Oncology Platform Reveals Spatial T Cell Infiltration Patterns Linked to ATR Inhibition Responses in High-Grade Serous Ovarian Cancer [View Publication](https://pmc.ncbi.nlm.nih.gov/articles/PMC7618831/) [Publication](https://doi.org/10.1097/pai.0000000000001311) CyteFinder Applied Immunohistochemistry & Molecular Morphology 2026 ### Quantitative Assays for TROP2 Measurement in Breast Cancer and Comparison to H-Score [View Publication](https://doi.org/10.1097/pai.0000000000001311) [Publication](https://pmc.ncbi.nlm.nih.gov/articles/PMC12881594/) CyteFinder Nature Communications 2026 ### Extracellular matrix mediates circulating tumor cell clustering in triple-negative breast cancer metastasis [View Publication](https://pmc.ncbi.nlm.nih.gov/articles/PMC12881594/) [Publication](https://doi.org/10.1016/j.ejso.2025.111357) CyteFinder European Journal of Surgical Oncology 2026 ### Circulating tumor cells predict relapse in head and neck mucosal squamous cell carcinoma [View Publication](https://doi.org/10.1016/j.ejso.2025.111357) [Publication](https://pmc.ncbi.nlm.nih.gov/articles/PMC12805936/) CyteFinder Cancer Research Communications 2026 ### Surface Marker Identification to Capture Live Circulating Tumor Cells in Metastatic Triple-Negative Breast Cancer [View Publication](https://pmc.ncbi.nlm.nih.gov/articles/PMC12805936/) [Publication](https://doi.org/10.1158/1078-0432.CCR-25-0244) CyteFinder Clinical Cancer Research 2025 ### Pre-clinical Modeling of Navtemadlin Pharmacokinetics, Pharmacodynamics, and Efficacy in IDH-wildtype Glioblastoma [View Publication](https://doi.org/10.1158/1078-0432.CCR-25-0244)