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NTRK3 / NT-3 growth factor receptor · IHC design guide
Design Immunohistochemistry for NTRK3
Plan NTRK3 IHC in paraffin sections using strongly stained cortical neurons as a reference (HPA tissue IHC). Assess the observed nuclear and cytoplasmic pattern alongside the receptor’s membrane topology, and check epitope coverage across its 5 isoforms (HPA tissue IHC; UniProt).
Evidence assembled Oct 2026 · For research use; verify linked source records and product datasheet before use
NTRK3 Immunohistochemistry Experimental Design Guide
Expected localisation, validated protocols, controls and antibodies — the at-a-glance facts below, then the full design guide.
Must know before staining
| Expected localisation | Nuclear and cytoplasmic in cerebral cortex (HPA tissue IHC) | |
| Staining pattern | Cortical neurons show strong nuclear and cytoplasmic staining (HPA tissue IHC) | |
| Antigen retrieval | Citrate pH 6.0 HIER, 95–98 °C, 20 min (rule: cytoplasmic / membrane antigen) | |
| Positive control | Cerebral cortex+4 more · see all | |
| Negative control | Adipose tissue+4 more · see all |
Important caveats
Reasons your staining may differ from the expected pattern.
| Fixation | Keep fixation consistent across sections (standard IHC practice; not target-specific) | |
| Caveat | Nuclear staining differs from membrane receptor topology (HPA tissue IHC; UniProt) | |
| Regulation | Isoform 2 is higher in adult than fetal brain (UniProt) | |
| Isoform / epitope | 5 isoforms; check extracellular vs cytoplasmic epitope coverage (UniProt) |
Section 1
Recommended NTRK3 IHC & IF Protocols
Compare the catalog antibody’s IHC-P protocol with a published TrkC IHC protocol for medullary thyroid cancer sections (PMC5299608).
| Sample | Tissue sections; selected-image fixative not specified (standard IHC workflow) |
| Fixation | Image fixative and duration unreported (datasheet PA1992-1); verify before use. |
| Sectioning | 4–5 µm sections on charged slides (standard) |
| Deparaffinisation | Xylene, graded ethanol series to water (standard) |
| Antigen retrieval | Heat-induced epitope retrieval in citrate buffer, pH 6.0, 20 min at 95–98 °C (standard rule: cytoplasmic / membrane antigen) |
| Peroxidase block | 3% H2O2, 10 min, room temperature (standard) |
| Blocking | 10% normal serum of the secondary host, 30 min, room temperature (standard) |
| Primary antibody | Rabbit anti-NTRK3, 0.5-1μg/ml (datasheet PA1992-1) |
| Primary incubation | Overnight at 4 °C (standard) |
| Detection | HRP-polymer secondary, DAB chromogen 5–10 min (standard) |
| Counterstain | Hematoxylin, blue, dehydrate and mount (standard) |
| Expected result | NTRK3-positive staining in neuronal cells of cerebral cortex (HPA tissue IHC: High). HPA tissue profile: High nuclear and cytoplasmic expression in cerebral cortex. No signal in the no-primary control. |
💡Decision noteStart with citrate pH 6.0 retrieval at 95–98 °C for 20 min (page retrieval); the published protocol used a high-pH buffer (PMC5299608).
Section 2
What Is the Expected NTRK3 Staining Pattern?
NTRK3 is a transmembrane receptor with an extracellular region and a cytoplasmic kinase region (UniProt Q16288 topology). In paraffin section IHC, expect the strongest reported staining in cerebral cortex neuronal cells, where HPA describes high nuclear and cytoplasmic expression (HPA tissue IHC). Interpret that distribution alongside the membrane annotation; HPA rates the tissue staining Approved, with medium consistency between antibody staining and RNA expression (HPA tissue IHC).
| Strong nuclear and cytoplasmic staining in cerebral cortex neuronal cells. | This matches HPA's reported high IHC pattern (HPA tissue IHC). UniProt places NTRK3 at the membrane, so describe the observed compartments without assuming every nuclear signal is receptor at the cell surface (UniProt Q16288 topology; HPA tissue IHC). |
| Staining appears only in a compartment unsupported by the reference patterns, especially if it also appears in controls. | Suspect an artefact and check the no primary control, tissue structure and antibody specificity (general IHC practice). Nuclear staining alone is not grounds for rejection: HPA reports it in cortex IHC and reports nucleolar locations in ICC-IF (HPA tissue IHC; HPA subcellular ICC-IF). |
| Strong staining appears in a cell population reported as not detected, such as adipocytes or bladder urothelial cells. | Investigate cross-reactivity or endogenous detection activity before assigning NTRK3 positivity (general IHC practice). HPA reports NTRK3 as not detected in those specific cell populations; that finding does not make every cell in either tissue a negative control (HPA tissue IHC). |
| Uniform color covers tissue, stroma and spaces between cells, obscuring cell boundaries. | Treat this as diffuse background until controls show otherwise. Check no primary staining, blocking, washing and chromogen development (general IHC practice). HPA's reported pattern is cell specific, with high staining in cortex neuronal cells and variable levels elsewhere (HPA tissue IHC). |
| Cerebral cortex neuronal cells show no detectable stain while the slide controls behave as expected. | The result conflicts with HPA's high cortical neuronal signal (HPA tissue IHC). Review whether the chosen antibody is validated for IHC, then check the section and detection workflow (general IHC practice). A blank slide alone cannot establish biological absence. |
💡Expected NTRK3 appearanceCall the IHC result concordant when cerebral cortex neuronal cells show high nuclear and cytoplasmic staining (HPA tissue IHC); broad, cell independent color or strong staining in HPA not detected cell populations is a warning to investigate, not an automatic NTRK3 positive call (HPA tissue IHC; general IHC practice).
| Membrane topology | NTRK3 has an extracellular region at residues 32–429, a transmembrane segment at 430–453 and a cytoplasmic region at 454–839 (UniProt Q16288 topology). Interpret a compartment claim in light of the antibody's known epitope, if available; this payload provides no epitope location. |
| Tissue and cell context | HPA reports high staining in cerebral cortex neuronal cells; medium staining includes caudate neuronal cells, cerebellar granular layer cells and heart cardiomyocytes (HPA tissue IHC). These observations provide comparison patterns, not guaranteed results for every section or antibody. |
| Negative comparison cells | HPA reports no detection in adipocytes, skin fibroblasts, tonsil germinal center cells and bladder urothelial cells, among other listed populations (HPA tissue IHC). Score the specified cells rather than labeling an entire mixed tissue negative. |
| Evidence strength | HPA calls its tissue IHC result Approved and describes medium consistency with RNA expression (HPA tissue IHC). Its listed IHC antibody CAB009233 is Approved; the two listed ICC antibodies are Approved for ICC, with no IHC status supplied (HPA antibodies). These labels do not validate a different catalog antibody. |
| IF/ICC pattern? | On its separate ICC-IF evidence, HPA reports mainly nucleoli and nucleoli rim, with additional nuclear membrane localization; images are listed for A-549, U-251MG and U2OS (HPA subcellular ICC-IF). This answers the IF/ICC localization question but does not prescribe an IF protocol or override tissue IHC observations. |
| Isoforms and processing | UniProt lists 5 isoforms and a signal peptide at residues 1–31, followed by a receptor chain at 32–839 (UniProt Q16288). An antibody's binding across isoforms or to processed material depends on its epitope; neither epitope coverage nor shedding is established here. |
| Situation | Likely cause | Next action |
|---|---|---|
| Cortex neuronal cells are blank. | The observation disagrees with HPA's high cortical neuronal staining; the cause cannot be assigned from a blank result alone (HPA tissue IHC). | Confirm the correct cells and a working positive control, then check IHC validation, retrieval conditions and detection reagents for the chosen antibody (general IHC practice). |
| Only weak staining appears in a proposed positive comparison tissue. | HPA reports medium, rather than high, staining for several comparison cells, including caudate neuronal cells and cardiomyocytes (HPA tissue IHC). | Compare the same cell type and score its actual intensity before changing the assay. Use cerebral cortex neuronal cells as the high signal reference when available (HPA tissue IHC; general IHC practice). |
| Nuclear color is dismissed as off target because NTRK3 is a membrane receptor. | UniProt annotates membrane topology, while HPA reports nuclear and cytoplasmic cortex IHC staining (UniProt Q16288 topology; HPA tissue IHC). | Record the compartments separately and compare cell specificity and controls. Do not infer surface localization or reject nuclear staining solely from receptor topology (general IHC practice). |
| The no primary control develops color. | Signal can arise from endogenous detection activity or other assay background without primary antibody (general IHC practice). | Resolve the control signal by checking blocking and the detection system, then repeat interpretation on a clean control set (general IHC practice). Do not count the affected stain as NTRK3 specific. |
| Strong color appears in adipocytes or bladder urothelial cells. | HPA reports NTRK3 as not detected in those cell types; unexpected color may reflect cross-reactivity or detection background (HPA tissue IHC; general IHC practice). | Verify cell identity and inspect no primary and negative comparison controls. Reassess antibody specificity before calling those cells positive (general IHC practice). |
| An ICC-IF image appears nucleolar, unlike the paraffin section pattern. | HPA's ICC-IF summary reports nucleoli and nucleoli rim, while its tissue IHC profile reports nuclear and cytoplasmic cortex staining (HPA subcellular ICC-IF; HPA tissue IHC). | Compare each result with its own application and cell context. Keep the ICC-IF observation as localization evidence; evaluate the paraffin section against tissue IHC controls (general IHC practice). |
Experiment evidence
IHC & IF images showing NTRK3 staining
PA1992-1 · IHCAnti-TrkC antibody, PA1992-1, IHC(P) IHC(P): Human Mammary Cancer Tissue
PA1992-1 · IHCAnti-TrkC antibody, PA1992-1, IHC(P) IHC(P): Rat Brain Tissue
HPA · Cerebral cortexHuman Protein Atlas IHC, Cerebral cortex. Source: https://www.proteinatlas.org/ENSG00000140538-NTRK3/tissue/cerebral+cortex#imid_3468528
HPA · ColonHuman Protein Atlas IHC, Colon. Source: https://www.proteinatlas.org/ENSG00000140538-NTRK3/tissue/colon#imid_3468462
HPA · LiverHuman Protein Atlas IHC, Liver. Source: https://www.proteinatlas.org/ENSG00000140538-NTRK3/tissue/liver#imid_3468471
HPA · KidneyHuman Protein Atlas IHC, Kidney. Source: https://www.proteinatlas.org/ENSG00000140538-NTRK3/tissue/kidney#imid_3468464
HPA · ICC-IF A-549Human Protein Atlas immunofluorescence, A-549, antibody HPA027484; green = NTRK3, blue = nucleus, red = microtubules.
HPA · ICC-IF A-549Human Protein Atlas immunofluorescence, A-549, antibody HPA027484; green = NTRK3, blue = nucleus, red = microtubules.
← swipe / scroll for more images →
Real IHC / IF data behind the staining-pattern expectations in this section.
Sample controls for NTRK3 IHC & IF
🧪Run cerebral cortex first and look for staining in neuronal cells (HPA: High in cerebral cortex neuronal cells); use adipose tissue adipocytes as the negative tissue (HPA: Not detected in adipocytes). On the positive slide, internal negative cells are those without specific chromogen staining and should show only the counterstain; confirm their status rather than assuming all non-neuronal cells are NTRK3-negative.
Positive control tissue: Cerebral cortex (Neuronal cells, HPA High)
Negative control tissue: Adipose tissue (HPA Not detected)
ICC-IF cell lines (HPA subcellular resource): HPA ICC-IF images show NTRK3 in A-549, U-251MG, U2OS, with annotated localisation: Nucleoli (supported), Nucleoli rim (supported) (HPA subcellular).
Technical controls: Include a no-primary, secondary-only control, a host- and clonality-matched isotype control, and NTRK3-knockout material as a biological negative. For chromogenic IHC, quench endogenous peroxidase and inspect cerebral cortex for pigment that could resemble staining; for IF, check tissue autofluorescence with a no-primary control (standard IHC/IF practice).
⚠️Feasibility: A target-specific fixation window and retrieval dependency are unreported in the supplied evidence; the selected PA1992-1 IHC(P) caption also does not report a fixative (selected-SKU tissue-IHC caption). Optimize antigen retrieval on matched paraffin sections, since the supplied evidence does not establish that frozen sections or IF are easier (standard IHC practice). Check cerebral cortex pigment as a possible chromogenic artefact and validate IF localization separately: the HPA ICC-IF summary reports nucleolar and nuclear-membrane localization, while UniProt describes NTRK3 as a membrane protein (HPA subcellular summary; UniProt Q16288 subcellular location).
HPA tissue IHC evidence for NTRK3
Comprehensive Human Protein Atlas IHC scoring per tissue (reliability: Approved — Medium consistency between antibody staining and RNA expression data.). Rows are taken directly from the HPA tissue chart — click any row's HPA link to view the source.
Positive expression · recommended positive controls
| Tissue | Cell type | Level | Evidence | Source |
|---|---|---|---|---|
| Cerebral cortex | Neuronal cells | High | Protein (IHC) | HPA → |
| Adrenal gland | Glandular cells | Medium | Protein (IHC) | HPA → |
| Bone marrow | Hematopoietic cells | Medium | Protein (IHC) | HPA → |
| Bronchus | Respiratory epithelial cells | Medium | Protein (IHC) | HPA → |
| Caudate | Neuronal cells | Medium | Protein (IHC) | HPA → |
Undetected expression · recommended negative controls
| Tissue | Cell type | Level | Evidence | Source |
|---|---|---|---|---|
| Adipose tissue | Adipocytes | Not detected | Protein (IHC) | HPA → |
| Appendix | Glandular cells | Not detected | Protein (IHC) | HPA → |
| Fallopian tube | Glandular cells | Not detected | Protein (IHC) | HPA → |
| Parathyroid gland | Glandular cells | Not detected | Protein (IHC) | HPA → |
| Seminal vesicle | Glandular cells | Not detected | Protein (IHC) | HPA → |
Section 3
Advanced NTRK3 IHC Tips
Troubleshooting NTRK3 staining in paraffin sections requires attention to retrieval, compartment, antibody epitope and cell type.
What should I change when NTRK3 staining is weak after retrieval?
Start with citrate pH 6.0 heat induced retrieval at 95–98 °C for 20 min (page retrieval setting). Compare a retrieval run against an adjacent section stained with the same antibody and detection reagents, using cerebral cortex neuronal cells as a positive tissue reference (HPA: High in cerebral cortex neuronal cells; standard IHC practice). If staining remains weak, optimise cooling and wash steps before trying an alternative retrieval buffer on paired sections; keep the original condition as the comparison (standard IHC practice). Record whether signal appears at the membrane or in other compartments, because NTRK3 has an extracellular region at residues 32–429 and a cytoplasmic region at 454–839 (UniProt Q16288 topology).
Could fixation explain inconsistent NTRK3 staining across paraffin blocks?
Target specific fixation sensitivity for NTRK3 is unknown from the supplied evidence, so do not assign a weak result to a particular fixative or fixation time (supplied evidence: no target specific fixation study). The selected antibody has a paraffin tissue IHC caption, but that caption does not state the fixative (PA1992-1 tissue IHC caption). Compare adjacent sections from blocks with documented processing histories using the same citrate pH 6.0, 95–98 °C, 20 min retrieval setting (page retrieval setting; standard IHC practice). Include a positive tissue control in each run and report processing differences alongside staining, without inferring a fixation effect from tissue expression patterns (HPA: High in cerebral cortex neuronal cells; standard IHC practice).
How should I assess NTRK3 staining that appears mainly nuclear?
Check membrane, cytoplasmic and nuclear staining separately, since NTRK3 is annotated as a membrane receptor with one transmembrane segment at residues 430–453 (UniProt Q16288 topology). Nuclear staining alone should not be dismissed automatically: tissue IHC reports high nuclear and cytoplasmic expression in cerebral cortex, while cell imaging supports nucleoli and nucleoli rim localisation (HPA tissue IHC profile; HPA subcellular). Those observations come from different assays, so record the compartment and cell type rather than treating their patterns as interchangeable (HPA tissue IHC; HPA subcellular; standard IHC practice). Compare serial sections, positive controls and negative reagent controls before calling an unexpected nuclear pattern NTRK3 specific (standard IHC practice).
Could antibody epitope choice explain different NTRK3 staining patterns?
Confirm the catalog antibody’s stated immunogen or epitope before comparing staining with another antibody; the supplied caption identifies tissue IHC use but gives no epitope location (PA1992-1 tissue IHC caption). NTRK3 has 5 annotated isoforms, so antibodies recognising different shared or isoform specific regions may produce different patterns (UniProt Q16288 isoforms; standard IHC practice). An extracellular epitope would fall within residues 32–429, whereas the cytoplasmic region spans 454–839; map any documented epitope against those boundaries (UniProt Q16288 topology). Also check whether a claim concerns total receptor or phosphorylation at a specified residue, because the record lists phosphorylated residues including 705, 709 and 710 (UniProt Q16288 modified residues).
How can IF help resolve an ambiguous NTRK3 IHC pattern?
Use IF as a separate validation experiment and multiplex NTRK3 with a neuronal marker when assessing cerebral cortex, where neuronal cells show high tissue IHC expression (HPA: High in cerebral cortex neuronal cells; standard IF practice). Choose fluorophores and imaging channels after measuring tissue autofluorescence in an unstained section, and include single stain controls to assess channel bleed through (standard IF practice). If the documented antibody epitope is cytoplasmic, permeabilise cells sufficiently to reach residues 454–839; an extracellular epitope lies at 32–429 and may need less permeabilisation (UniProt Q16288 topology; standard IF practice). Compare membrane and nuclear signals cautiously, since HPA cell imaging supports nucleoli and nucleoli rim localisation (HPA subcellular).
What causes diffuse brown signal in NTRK3 IHC sections?
First compare the stained section with a no primary antibody control and inspect pigment, folds, cut edges and necrotic areas before assigning diffuse brown signal to NTRK3 (standard IHC practice). Apply the routine endogenous peroxidase block when using enzyme based chromogenic detection, and check whether the DAB development time is producing background across both control and test sections (standard IHC practice). Titrate the primary antibody according to its validated IHC instructions; no working dilution is supplied in the selected caption (PA1992-1 tissue IHC caption). Evaluate background against the expected cell distribution and compartment, including cerebral cortex neuronal cells and the receptor’s membrane topology (HPA tissue IHC; UniProt Q16288 topology).
How should I quantify NTRK3 staining across paraffin sections? ⚠ ANSWER MARKED FOR VERIFICATION
Define the tissue region and eligible cell population before scoring, and keep section thickness, retrieval and chromogen development consistent across cases (standard IHC practice). For cellular staining, report the percentage of positive eligible cells and an H-score calculated from percentages at intensity grades 0–3, giving a possible range of 0–300 (standard IHC scoring practice). If counting positive cells by image analysis, report density per mm² of viable tissue and normalise to the eligible cell population or analysed area (standard IHC practice). Score membrane, cytoplasmic and nuclear compartments separately, and state the scoring threshold and tissue reference used (UniProt Q16288 topology; HPA tissue IHC profile; standard IHC practice).
When should an apparent NTRK3 positive cell be treated as artefact?
Interpret staining in its cell and tissue context: cerebral cortex neuronal cells are a high expression reference, while adipose tissue adipocytes are reported as not detected (HPA tissue IHC). NTRK3 is annotated as a membrane receptor, yet tissue IHC also reports nuclear and cytoplasmic cerebral cortex staining; an unexpected compartment therefore warrants confirmation rather than an automatic positive or negative call (UniProt Q16288 topology; HPA tissue IHC profile). Distrust isolated staining at section edges, in necrotic areas or where a no primary control shows comparable chromogen, and check endogenous enzyme blocking (standard IHC practice). Report compartment, cell type and control results alongside the score; HPA rates tissue staining and RNA consistency as medium (HPA reliability; standard IHC practice).
Boster reagents
Best NTRK3 / NT-3 growth factor receptor IHC Antibodies
PA1992-1 has IHC images of human mammary cancer and rat brain tissue (catalog image captions); A02502Y516 lists IF for human, mouse and rat (catalog applications and reactivity).
Real IHC data
Anti-TrkC/NTRK3 Antibody ®
Cat # PA1992-1
PA1992-1 is the card that will render, with a human mammary cancer paraffin-section IHC figure (card image caption). Its catalog also shows rat brain IHC and lists human, mouse and rat reactivity (catalog image caption and reactivity).
Which to pick: For tissue IHC, choose PA1992-1: its figure documents a human mammary cancer paraffin section, with a listed dilution of 0.5–1 μg/ml; the fixative is unreported (card image caption; catalog dilution). For IF, consider A02502Y516, a rabbit polyclonal antibody with IF listed at 1:50; ICC validation and an IF image are unreported (catalog applications, dilution and image fields). Both SKUs list human, mouse and rat reactivity for cross-species work; PA1992-1 also has a rat brain IHC image (catalog reactivity and image caption).
Each figure is that product's own IHC / IF validation image from its datasheet.
References
- UniProt Consortium. UniProt entry Q16288 (NTRK3_HUMAN, NT-3 growth factor receptor).
- Human Protein Atlas. NTRK3 tissue IHC expression (reliability: Approved).
- Human Protein Atlas. NTRK3 subcellular location (ICC-IF): Mainly localized to the nucleoli and nucleoli rim. In addition localized to the nuclear membrane..
- Human Protein Atlas. NTRK3 antibody validation summary (3 antibodies).
- Differences in the transcriptome of medullary thyroid cancer regarding the status and type of RET gene mutations. Scientific reports 2017 — PMC5299608.
- Identification of NTRK3 as a potential prognostic biomarker associated with tumor mutation burden and immune infiltration in bladder cancer. BMC cancer 2021 — PMC8070296.
- Primary Cutaneous Secretory Carcinoma: A Case Report and Literature Review. Cureus 2023 — PMC9957600.
- Clinicopathological analysis of 18 cases of secretory carcinoma of the salivary glands. Journal of dental sciences 2024 — PMC10829629.
- PubMed PMID:7806211 — UniProt-cited evidence.
- PubMed PMID:7823156 — UniProt-cited evidence.
- PubMed PMID:9778053 — UniProt-cited evidence.
Immunohistochemistry protocol sheet for NTRK3 (NT-3 growth factor receptor). Expected localisation Nuclear and cytoplasmic in cerebral cortex (HPA tissue IHC). Antigen retrieval: Citrate pH 6.0 HIER, 95–98 °C, 20 min (rule: cytoplasmic / membrane antigen). Validated IHC antibody: PA1992-1 at 0.5-1μg/ml (the product's own IHC validation image is shown). Controls (HPA): positive Cerebral cortex (Neuronal cells); negative Adipose tissue. IHC workflow; specimen preparation unspecified. Protocol steps: 1. Sample: Tissue sections; selected-image fixative not specified (standard IHC workflow); 2. Fixation: Image fixative and duration unreported (datasheet PA1992-1); verify before use.; 3. Sectioning: 4–5 µm sections on charged slides (standard); 4. Deparaffinisation: Xylene, graded ethanol series to water (standard); 5. Antigen retrieval: Heat-induced epitope retrieval in citrate buffer, pH 6.0 , 20 min at 95–98 °C…; 6. Peroxidase block: 3% H2O2, 10 min , room temperature (standard); 7. Blocking: 10% normal serum of the secondary host, 30 min , room temperature (standard); 8. Primary antibody: Rabbit anti-NTRK3, 0.5-1μg/ml (datasheet PA1992-1); 9. Primary incubation: Overnight at 4 °C (standard). Watch for: Fixation: Keep fixation consistent across sections (standard IHC practice; not target-specific); Caveat: Nuclear staining differs from membrane receptor topology (HPA tissue IHC; UniProt); Isoform / epitope: 5 isoforms; check extracellular vs cytoplasmic epitope coverage (UniProt); Regulation: Isoform 2 is higher in adult than fetal brain (UniProt). Evidence: UniProt Q16288, HPA tissue IHC · Approved, HPA ICC-IF · Mainly localized to the nucleoli and nucleoli rim. In addition…, Datasheet PA1992-1, PMC5299608. QR code links to https://www.bosterbio.com/bosterbio-gene-info-cards/NTRK3/immunohistochemistry-ihc-guide.