Which sample types have been validated using SeekSpace?
2026-06-23
Answer:
SeekSpace assays have been tested across a broad range of tissue types and species.
Validation status definitions:
- ✅ Validated: Consistently reliable performance under standard workflow conditions
- ⚠️ Caution / Conditional: Performance may be strongly influenced by tissue characteristics, sectioning difficulty, RNA stability, or nuclei recovery
- ❌ Not Recommended: Current workflow compatibility is limited due to low nuclei recovery, severe degradation, high debris levels, or poor transcriptomic performance
Observed performance reflects typical project experience and may vary depending on sample quality, handling, embedding conditions, and tissue pathology.
Representative validated sample types
Validated tissues include human, mouse, rat, monkey, pig, fish, and avian samples.
Representative validated tissues include:
Species | Validated Tissue |
Human | Liver Cancer |
Human | Breast Cancer |
Human | Brain Glioma / Brain Tumor |
Human | Testis |
Human | Eye |
Human | Kidney / Kidney Cancer |
Human | Prostate Cancer |
Human | Liver |
Human | Lung / Lung Cancer |
Human | Uterine Tumor |
Human | Stomach / Gastric Cancer |
Human | Embryo |
Human | Brain |
Human | Oral Cancer |
Human | Pancreatic Cancer |
Human | Cholangiocarcinoma |
Human | Nasopharyngeal Carcinoma Brain Metastasis |
Human | Skin / Skin Tumor |
Human | Lymph Node |
Human | Head and Neck Cancer |
Human | Hypopharyngeal Cancer |
Human | Thyroid Cancer |
Human | Adrenal Nodules |
Human | Gallbladder Adenocarcinoma |
Human | Dental Follicle |
Human | Melanoma |
Human | Cervical Cancer |
Human | Spinal Tumor |
Human | Lower Limb Tissue |
Human | Spleen |
Human | Intestinal Cancer |
Human | Bladder Cancer |
Human | Adenoid |
Human | Endometrium with Myometrium |
Human | Decidua |
Human | Placenta |
Human | Adenoma |
Mouse | Brain |
Mouse | Brain Tumor |
Mouse | Testis |
Mouse | Subcutaneous Tumor |
Mouse | Ovary |
Mouse | Tongue Cancer |
Mouse | Kidney Capsule Tumor Model |
Mouse | CKD Kidney |
Mouse | Pancreatic Cancer |
Mouse | Kidney |
Mouse | Thymus |
Mouse | Eye |
Mouse | Pancreatic Tumor |
Mouse | Patella |
Mouse | Hippocampus |
Mouse | Penile Corpus Cavernosum |
Mouse | Embryo Shoulder |
Mouse | B16F10 Melanoma |
Mouse | Lung |
Mouse | Bladder |
Mouse | Gastric Ulcer |
Mouse | Spleen |
Rat | Fetal Jaw Bone |
Rat | Brain |
Rat | Fetal Tooth Germ |
Rat | Gastric Ulcer |
Rat | Embryo |
Rat | Ovary |
Monkey | Testis |
Monkey | Brain |
Carp | Gonad |
Pig | Ovary |
Pig | Kidney |
Bird | Brain |
Caution / conditional sample types
The following sample types may be feasible but are considered high-risk or may require workflow optimization.
Tissue Type | Main Challenge | Explanation | Recommended Handling |
Adult zebrafish | Difficult sectioning | Sections may contain gaps or fail to remain intact | High risk. Isopentane + liquid nitrogen embedding strongly recommended. Pre-screen samples before submission. |
Placenta, aquatic, and marine samples | High water content | Ice crystal formation may damage tissue structure and reduce nuclei and gene capture efficiency | High risk. Use isopentane + liquid nitrogen embedding and minimize freeze-thaw cycles. |
Grouper gonad | Large cell diameter | Gonadal cells may exceed 20 μm and frequently rupture during sectioning, leading to very low cell capture | High risk. Increased section thickness may be considered for large-cell studies. |
Certain human or mouse glioma samples, snake venom gland, embryonic brain | Tissue detachment risk | Soft and fragile tissues with high water content are prone to floating or detachment during processing | High risk. Optimize embedding and handling conditions. |
Low-fat tissues where adipose tissue is not the focus (e.g., lymph node, breast cancer, prostate, skin) | Difficult sectioning | Tissue may tear easily, detach after sectioning, exhibit low nuclei counts after H&E staining, or show reduced median gene counts | High risk. Some datasets may require force-processing during downstream analysis. |
Placental villi, placenta, decidua | RNA instability | RNA degradation may continue during processing, often resulting in low nuclei recovery and reduced median gene counts | High risk. Rapid freezing and minimal handling are critical. |
Tendon and Achilles tendon | High debris content | Elongated nuclei and highly fibrous tissue structure may lead to debris accumulation, partial capture area loss, and severe clogging risk | High risk. Careful preprocessing is required. |
Uterine fibroid, gastric ulcer, skin tumor, kidney cancer | Low cell capture efficiency | Fibrous architecture and spindle-shaped nuclei may reduce nuclei recovery in certain regions | High risk. Lower cell capture efficiency should be anticipated. |
Necrotic, fibrotic, calcified, or mechanically tough tissues | Low nuclei recovery | Tissue fragmentation, RNA degradation, low nuclei yield, and excessive debris are common | High risk. Lower capture efficiency is expected. |
Biopsy punch samples | Small tissue area | Limited tissue area may reduce nuclei capture efficiency | High risk. Samples with punch diameter >1.2 mm may benefit from thicker sections (~30 μm) or multi-tissue embedding. |
Mouse liver and liver cancer | Low gene counts | Ribosomal blocking may be less effective, increasing the risk of low median gene counts | High risk. Lower transcript complexity should be anticipated. |
Neonatal mouse patella | Tissue floating risk | Soft bone tissue may section successfully but frequently detaches during processing | High risk. Handle sections carefully during mounting. |
❌ Not Recommended Sample Types
The following sample types are currently not recommended due to substantial technical limitations.
Tissue Type | Main Limitation | Explanation |
Hair follicle, zebrafish heart, organoids, dorsal root ganglion (DRG) | Small tissue area | Small section size (<3 × 3 mm or thickness <500 μm) results in insufficient nuclei recovery. If attempted, multiple tissues should be embedded together on the same plane. |
Tympanic membrane, trabecular meshwork, retina, yolk sac membrane, and other membrane-like tissues (<30 μm) | Extremely thin tissue | Tissue quantity is insufficient for both QC and downstream gene expression analysis. |
Bone and rotator cuff | Difficult sectioning | Bone tissue is difficult to section, prone to detachment, and contains excessive debris. Rotator cuff samples often contain bone and exhibit very low nuclei recovery with high clogging risk. |
Adipose tissue or highly fat-rich tissue where adipose biology is the main focus | Difficult sectioning and poor nuclei recovery | Tissue is difficult to section, prone to detachment, exhibits low nuclei counts after H&E staining, and often yields extremely poor cell capture after gene expression analysis. |
Plant samples | Difficult nuclei isolation | Nuclei extraction differs substantially from standard animal tissue workflows and is currently not optimized. |
Vessel, plaque, synovium, muscle, optic nerve, heart, and spinal cord | Excessive debris and extremely low nuclei abundance | Samples are difficult to section, contain extensive debris, and often show severe RNA degradation and poor gene detection performance. High clogging risk is common. |
Pancreas | Severe RNA degradation | RNA degradation frequently continues throughout sectioning and enzymatic processing. Samples are generally not recommended for submission. |
Bone marrow | Extremely low gene detection | Median gene counts are typically extremely low after spatial processing. |
Intestine | Severe degradation risk | Digestive enzyme activity often causes rapid degradation during nuclei isolation and processing. |
Snake lung and gonad | Poor platform compatibility | Based on project experience, nuclei capture efficiency is extremely low. |
Mouse lung (asthma or fungal infection models) | Low median gene counts | Ribosomal blocking is often insufficient, resulting in low transcript complexity and poor median gene counts. |
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