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- Pick-Seq®: Spatial tissue analysis via multi-parameter imaging and RNA sequencing of micro-regions

# Pick-Seq®: Spatial tissue analysis via multi-parameter imaging and RNA sequencing of micro-regions

Imaging tells you where protein markers sit in a tissue but not the wider gene-expression program behind them; this SITC 2019 poster from RareCyte and Harvard Medical School introduces Pick-Seq®, a workflow that maps multi-parameter fluorescence on the CyteFinder® instrument and then RNA-sequences 40-micron micro-regions that the CytePicker® module retrieves from sites chosen in those images.

Presented by RareCyte and Harvard Medical School.

Read or download to see:

- Pick-Seq® couples multi-parameter fluorescence imaging with RNA sequencing of targeted tissue micro-regions. Tissue sections are stained by immunofluorescence and scanned on the CyteFinder® instrument to map regions of interest; 40-micron-diameter micro-regions are then retrieved with the integrated CytePicker® module, and their RNA is amplified and sequenced for differential gene expression, cell-composition, and T-cell-receptor readouts.

- In tonsil tissue, sequencing of picked micro-regions told two adjacent B-cell follicles apart. Micro-regions were selected from a 5-color immunofluorescence image (CD3, CD4, CD8, CD20, SYTOX Orange); RNA sequencing found the neighboring follicles differed in CD19 and CD21 expression, and a targeted re-stain confirmed that only one of them contained a germinal center.

- In frozen breast carcinoma, the same workflow sorted micro-regions into 3 architecture classes and resolved tumor–immune interactions. Regions of tumor, tumor mixed with infiltrating lymphocytes, and adjacent lymphoid aggregates were picked separately; differential expression and hierarchical clustering separated the 3 classes, and CIBERSORT deconvolution found a T-cell transcriptomic signal that scaled with the number of T cells retrieved.

[Download poster](https://cdn.sanity.io/files/s3p6uqps/production/9c2a61a02e4d30eac944a8f8a0d21827cd326a4b.pdf)

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