A whole brain was harvested from an adult mouse (male C57BL/6, 66 days old) and fixed with 10% neutral-buffered formalin overnight at 4°C. Each hemisphere was then separately processed in-house into formalin-fixed paraffin-embedded (FFPE) blocks. Six, 50 micron FFPE curls (coronal section, forebrain) were collected near the hippocampus region. Cells were isolated following the demonstrated protocol Isolation of Cells from FFPE Tissue Sections for Chromium Fixed RNA Profiling (CG000632), using the gentleMACS Octo Dissociator option.
The Fixed RNA Gene Expression library was generated as described in the Chromium Fixed RNA Profiling for Singleplexed Samples with Feature Barcode technology for Cell Surface Protein User Guide (CG000477). The resulting library was sequenced on an Illumina NovaSeq6000 with approximately 16k read pairs per cell.
- Total 11,629 cells detected
- Paired-end, dual indexing: 28 cycles Read 1, 10 cycles i7, 10 cycles i5, 90 cycles Read 2
Brightfield and propidium iodide fluorescence images of the resulting cell suspensions after dissociation are provided, as well as images of the final pooled sample (also shown below).
| Brightfield | Fluorescence |
|---|---|
 |  |