I am currently working with 10x Genomics protocol CG000632 ("Sample Preparation from FFPE Tissue Sections for Chromium Fixed RNA Profiling") to process kidney biopsy samples obtained with an 18G needle. I am using 25 µm scrolls from FFPE blocks for this workflow.

However, I am facing an issue during the deparaffinization step. After the first xylene incubation, I am unable to see my scrolls or tissues, which makes me concerned that I am losing my sample at this stage.

Has anyone experienced similar challenges with small samples like kidney biopsies? Do you have suggestions on preventing tissue loss during deparaffinization or tips for adapting this protocol to handle small samples?