What are the characteristics of different tissue types, and what are the recommended handling strategies?

Tissue Category

Representative Tissue

Characteristics

Recommendations

Digestive system

Intestinal or gastric tumors

High tendency for cell aggregation

Standard dissociation protocols can be applied

Digestive system

Normal intestine (colon, jejunum, ileum) and gastric mucosa

Rapid loss of viability and strong aggregation tendency

Samples should be transferred into tissue preservation solution immediately after collection if transport is required. In such cases, intestinal contents should not be removed prior to preservation, as this may disrupt the native microbial environment. If the sample is processed immediately for tissue dissociation, washing steps can be performed as needed.

Functional organs

Spleen, lung, kidney

High blood content

Thorough washing is required; for mouse samples, perfusion is recommended if blood cells are not the focus

Functional organs

Heart

Cardiomyocytes are large and irregular, and are prone to loss during dissociation

If cardiomyocytes are of interest, nuclei isolation is recommended; otherwise, fresh dissociation may be used

Functional organs

Liver

Hepatocytes are large (20–40 μm) and are underrepresented in standard dissociation workflows

Nuclei isolation is recommended if hepatocyte representation is important; RNA quality assessment is required for frozen samples

Secretory glands

Thyroid, mammary gland, salivary gland

High aggregation tendency

For small glands, pooling multiple samples is recommended

Bone and cartilage

Hard bone and cartilage

High impurity content and calcified structure

Sterile sampling is required; prolonged digestion may be necessary

Muscle

Skeletal and smooth muscle

Elongated cells with relatively low viability

Extended digestion time is recommended

Adipose tissue

White and brown adipose tissue

High lipid content

Nuclei isolation is recommended for mature adipocytes

Brain tissue

Cortex, hippocampus, brain tumors

Enriched in neuronal cells

Nuclei isolation is recommended if neurons are the primary focus

Body fluids

Cerebrospinal fluid, ascites, urine

Low cell numbers and/or high impurity levels

A minimum of 100,000 live cells is recommended whenever possible

Reproductive

Testis

Extremely low transcriptional activity and mRNA abundance

Not recommended for scRNA-seq applications

Non-mammalian samples

-

Presence of nucleated red blood cells, which are difficult to remove

Additional optimization may be required