Tissue Block RNA Quality Check (OCT and FFPE)
The SCGF offers a service where clients submit tissue scrolls from OCT or FFPE tissue blocks, and the SCGF isolates and checks the RNA quality of that tissue. This service is most often used by clients interested in pursuing spatial transcriptomics assays through the SCGF.RNA Isolation Services
To determine the quality of the RNA within an embedded tissue, tissue scrolls need to be acquired from the block and submitted to the SCGF. Embedding material and presence of fixation will determine the number of scrolls and the RNA isolation kit used.Number of tissues scrolls, and section thickness needed per block based on embedding medium:
- Fresh-Frozen OCT blocks require: 9 scrolls at 10um per block
- Fixed-Frozen OCT blocks require: 9 scrolls at 10um per block
- FFPE blocks require: 3 scrolls at 10um per block
- Fresh-Frozen OCT blocks use: RNeasy Mini Kit (Optional: QIAshredder)
- Fixed-Frozen OCT blocks use: CELLDATA RNAstorm FFPE RNA Extraction Kit
- FFPE blocks use: RNeasy FFPE Kit
Quality Control Check
Once the RNA is isolated from the tissue scrolls, the SCGF will assess the quality using the Agilent TapeStation 4150 instrument.
TapeStation assays used:- RNA Assay: 25-500 ng/uL
- High Sensitivity RNA Assay: 0.1-25 ng/uL
- Fresh-Frozen OCT blocks require: RIN evaluation.
- Fixed-Frozen OCT blocks require: DV200 evaluation.
- FFPE blocks require: DV200 evaluation.
- RNA Integrity Number (RIN): Is an objective metric of total RNA quality ranging from 10 (highly intact RNA) to 1 (completely degraded RNA).
- DV200 calculation: Is the percentage of RNA fragments > 200 nucleotides. Higher percentages equal more intact RNA recovered from the sample.
