Table 1.

Recommended tissue processing workflow

Tissue Type	Tissue processing	Volume (mm3)	Preferred Fixative	Blocking/Staining Buffer	Temp	Staining Time	Washing Time	Clearing Time
Lymph node	whole-mount	10	PLP/BD Cytofix	Conventional	37°C	4 days	3 days	1–2 days
Lung	whole-mount	1000	PLP/BD Cytofix	Conventional	37°C	4 days	2 days	1–2 days
Small Intestine	whole-mount	170	PLP/BD Cytofix	Conventional	4°C	12 hours	1 day	1 day
Thymus	whole-mount	60	PLP/BD Cytofix	Conventional	37°C	3 days	2 days	1–2 days
Bone	whole-mount (split longitudonally)	70	PLP/BD Cytofix	Conventional	37°C	1 day	1 day	1–2 days
Kidney	whole-mount	250	4% PFA Perfusion	Conventional	37°C	2–4 days	2–3 days	2–3 days
Liver	slice (500 um)	150	BD Cytofix/Cy toperm	Alternative	4°C	4 days	2–3 days	2–3 days
Brain	slice (up to 2mm)	200	BD Cytofix/Cy toperm	Alternative	37°C	2 days	2–3 days	1 day

This table provides general guidelines for effective tissue staining based on the indicated organ type and sample volume, and these can be modified further based on empirical testing. The preferred fixative, blocking buffer, staining time and temperature, as well as the approximate washing and clearing time requirements are indicated for various tested tissues. While most organs can be processed using the thick-slice methodology, certain tissues, indicated here, are more permissible for whole-mount antibody labeling. Optimal bone staining and clearing can be achieved by splitting the organ into two separate halves longitudinally after fixation but prior to blocking. Empirical testing also indicates that 4% PFA perfusion fixation is preferred for kidney processing. Similarly, rapid staining of the vascular endothelium can be achieved with perfusion-based labeling for various organ types.