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SLITRK1 / SLIT and NTRK-like protein 1 · IHC design guide
Design Immunohistochemistry for SLITRK1
Plan chromogenic SLITRK1 IHC on paraffin sections with the catalog antibody, starting at 2.5 μg/mL (datasheet). Use cortical glia as a strong staining reference and interpret cytoplasmic CNS staining with the reported secreted variant in mind (HPA tissue IHC).
Evidence assembled Oct 2026 · For research use; verify linked source records and product datasheet before use
SLITRK1 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 | Cytoplasmic staining in CNS cells (HPA tissue IHC) | |
| Staining pattern | Selective cytoplasmic CNS staining, strongest in cortical glia (HPA tissue IHC) | |
| Antigen retrieval | Citrate pH 6.0 HIER, 95–98 °C, 20 min (rule: cytoplasmic / membrane antigen) | |
| Positive control | Cerebral cortex+2 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 paraffin sections. (standard IHC practice; not target-specific) | |
| Caveat | A secreted variant may shift protein from RNA-positive cells (HPA tissue IHC) | |
| Regulation | Predominant expression in frontal cortex (UniProt) | |
| Isoform / epitope | No listed isoforms; extracellular versus cytoplasmic epitope matters (UniProt) |
Section 1
Recommended SLITRK1 IHC & IF Protocols
The catalog antibody has an IHC-P protocol (datasheet); one published brain-section DAB protocol provides a comparison (PMC3292218).
| Sample | Tissue sections; selected-image fixative not specified (standard IHC workflow) |
| Fixation | Image fixative and duration unreported (datasheet A07507); 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-SLITRK1, 2.5 μg/mL (datasheet A07507) |
| 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 | SLITRK1-positive staining in glial cells of cerebral cortex (HPA tissue IHC: High). HPA tissue profile: Selective cytoplasmic expression in CNS. No signal in the no-primary control. |
💡Decision noteFor paraffin sections, start with citrate pH 6.0 HIER at 95–98 °C for 20 min (page retrieval rule: membrane antigen). The published method does not specify retrieval (PMC3292218).
Section 2
What Is the Expected SLITRK1 Staining Pattern?
SLITRK1 is annotated at the membrane, synapse and in secreted form, with an extracellular region at residues 18–622, a transmembrane segment at 623–643 and a cytoplasmic tail at 644–696 (UniProt Q96PX8 topology). In tissue IHC, expect selective cytoplasmic CNS staining: high in cerebral-cortex glia and medium in cerebellar Purkinje cells and hippocampal neurons (HPA tissue IHC). HPA rates the tissue pattern Enhanced, while reporting medium RNA–protein consistency (HPA tissue IHC).
| Cerebral-cortex glia show strong cytoplasmic chromogen; cerebellar Purkinje cells and hippocampal neurons show weaker staining. | This matches the reported high cortical-glial and medium Purkinje-cell and hippocampal-neuronal levels (HPA tissue IHC). Compare the named cells within each region; a uniformly dark section does not establish this selective pattern (general IHC interpretation). |
| Predominantly nuclear staining appears in the expected positive cells. | A nuclear-only pattern does not match HPA’s selective cytoplasmic tissue profile or UniProt’s membrane, synapse and secreted annotations (HPA tissue IHC; UniProt Q96PX8). Check nuclear counterstain overlap and detection controls before interpreting it as SLITRK1 (general IHC practice). |
| Strong signal appears in an unexpected cell type, or in adipocytes used as a negative comparison. | HPA reports adipocytes as not detected in adipose tissue and breast, while its named CNS positives are specific cell classes (HPA tissue IHC). Unexpected staining may reflect cross-reactivity or endogenous detection activity; morphology alone cannot distinguish these causes (general IHC interpretation). |
| Chromogen spreads across tissue compartments and obscures cell boundaries. | Diffuse staining prevents a reliable call on HPA’s selective cytoplasmic pattern (HPA tissue IHC). Review background in a no-primary control and inspect the detection chemistry before scoring cells (general IHC practice). A diffuse result alone does not demonstrate secreted SLITRK1 (UniProt Q96PX8). |
| No signal is visible in the expected cells of a cerebral-cortex section. | That conflicts with HPA’s high cortical-glial result, but one negative slide cannot establish absent protein (HPA tissue IHC; general IHC interpretation). Verify that glia are present, the positive control and detection reagents work, and the IHC-validated antibody was used under its documented conditions (general IHC practice). |
💡Expected SLITRK1 appearanceCall a positive when cytoplasmic chromogen is strongest in cerebral-cortex glia, with medium staining in cerebellar Purkinje cells or hippocampal neurons; isolated nuclear staining or equally strong staining throughout unrelated cells warrants control checks (HPA tissue IHC; general IHC interpretation).
| Epitope location | SLITRK1 spans an extracellular region, one transmembrane segment and a cytoplasmic tail (UniProt Q96PX8 topology). The supplied evidence does not locate the IHC antibody’s epitope, so topology alone cannot predict which compartment that antibody will highlight. |
| Secreted annotation | UniProt lists secreted SLITRK1, and HPA notes that at least one protein variant is secreted; RNA and tissue protein locations may therefore differ (UniProt Q96PX8; HPA tissue IHC). Do not treat diffuse extracellular color by itself as proof of secretion (general IHC interpretation). |
| Strength of the tissue reference | HPA labels the tissue IHC result Enhanced and notes external characterization, medium RNA–protein consistency and presumed off-target binding that was disregarded (HPA tissue IHC). Use the named cell and region pattern with controls when judging a new stain (general IHC practice). |
| Antigen retrieval | Target-specific fixation effects are not established by the supplied assay evidence. Verify with a matched IHC source before attributing a result to fixation. |
| IF/ICC Q&A: Is a cell-line staining pattern established? | No ICC-IF image-bearing cell line or main subcellular location is supplied by HPA (HPA subcellular). Its membrane/secreted summary and UniProt’s topology provide context, but do not validate an IF/ICC pattern or a protocol option (HPA subcellular; UniProt Q96PX8). |
| Situation | Likely cause | Next action |
|---|---|---|
| Cortical glia are unstained. | A failed detection step, unsuitable antibody conditions or a section lacking the expected cells can mimic a negative result (general IHC practice); HPA reports high cortical-glial staining (HPA tissue IHC). | Confirm glial morphology and section quality, run a documented positive section, and check antibody use and detection reagents before changing retrieval (general IHC practice). No SLITRK1-specific retrieval condition is supplied (HPA tissue IHC; UniProt Q96PX8). |
| The whole section has brown haze. | Background from detection reagents or inadequate blocking can obscure selective cytoplasmic staining (general IHC practice; HPA tissue IHC). | Compare a no-primary section, adjust blocking or washes, and inspect the chromogen reaction according to the detection system (general IHC practice). Score SLITRK1 only where cells and compartments remain distinguishable (HPA tissue IHC). |
| Nuclei are the dominant positive compartment. | The pattern is discordant with reported cytoplasmic tissue staining and annotated membrane/synapse localization; counterstain or nonspecific detection may confuse interpretation (HPA tissue IHC; UniProt Q96PX8; general IHC practice). | Review an unstained or no-primary control and examine cells at higher magnification before calling nuclear positivity (general IHC practice). |
| Adipocytes stain as strongly as cortical glia. | HPA reports adipocytes as not detected in adipose tissue and breast, versus high cortical-glial staining (HPA tissue IHC). Cross-reactivity or detection background is possible, not proven (general IHC interpretation). | Compare the tissues in the same staining run and review no-primary controls; reassess antibody specificity if the unexpected cellular signal persists (general IHC practice). |
| Cerebellum or hippocampus looks weaker than cortex. | Medium Purkinje-cell and hippocampal-neuronal staining versus high cortical-glial staining is the reported relationship (HPA tissue IHC). | Judge the named cell populations against their own background before increasing signal development; stronger cortex alone does not imply failure in the other regions (HPA tissue IHC; general IHC practice). |
| A negative comparison shows a few faint cells. | Duodenal and small-intestinal enterocytes are reported at low levels, so they are unsuitable as absolute negatives; adipose-tissue adipocytes are reported not detected (HPA tissue IHC). | Choose a reported not-detected cell population for the negative comparison, confirm its morphology, and interpret faint staining alongside a no-primary control (HPA tissue IHC; general IHC practice). |
Experiment evidence
IHC & IF images showing SLITRK1 staining
A07507 · IHCImmunohistochemistry of Slitrk1 in human brain tissue with Slitrk1 antibody at 2.5 μg/mL.
A07507 · IFImmunofluorescence of slitrk1 in human brain tissue with slitrk1 antibody at 20 μg/mL.
HPA · Cerebral cortexHuman Protein Atlas IHC, Cerebral cortex. Source: https://www.proteinatlas.org/ENSG00000178235-SLITRK1/tissue/cerebral+cortex#imid_20919063
HPA · ColonHuman Protein Atlas IHC, Colon. Source: https://www.proteinatlas.org/ENSG00000178235-SLITRK1/tissue/colon#imid_20918989
HPA · LiverHuman Protein Atlas IHC, Liver. Source: https://www.proteinatlas.org/ENSG00000178235-SLITRK1/tissue/liver#imid_20918998
HPA · KidneyHuman Protein Atlas IHC, Kidney. Source: https://www.proteinatlas.org/ENSG00000178235-SLITRK1/tissue/kidney#imid_20918991
← swipe / scroll for more images →
Real IHC / IF data behind the staining-pattern expectations in this section.
Sample controls for SLITRK1 IHC & IF
🧪Run cerebral cortex first and look for staining in glial cells (High; HPA: cerebral cortex, glial cells); use adipose tissue adipocytes as the negative tissue (HPA: adipose tissue, adipocytes, Not detected). On the cortex slide, cells without specific signal should remain at background levels; do not assume all nonglial cells are negative from the reported glial staining alone (HPA: cerebral cortex, glial cells).
Positive control tissue: Cerebral cortex (Glial cells, HPA High)
Negative control tissue: Adipose tissue (HPA Not detected)
ICC-IF cell lines (HPA subcellular resource): HPA carries no ICC-IF cell line for SLITRK1; derive a cell-line control from the positive tissue's cell type (Glial cells) and confirm it by RNA or western blot first.
Technical controls: Include a no-primary, secondary-only control, an isotype control matched to the primary antibody’s host species and clonality, and SLITRK1 knockout tissue if available as a biological negative. For chromogenic brain IHC, block endogenous peroxidase and check whether tissue pigment could be mistaken for staining; for IF, assess autofluorescence with an unstained section.
⚠️Feasibility: A target-specific fixation window or fixation effect is unreported in the supplied evidence, and the selected A07507 human brain IHC caption does not state the fixative (selected-SKU tissue-IHC caption). Antigen retrieval dependency is also unreported, so assess retrieval conditions empirically for paraffin sections. The evidence does not establish whether frozen sections or IF are easier for SLITRK1; brain pigment can complicate interpretation of chromogenic staining.
HPA tissue IHC evidence for SLITRK1
Comprehensive Human Protein Atlas IHC scoring per tissue (reliability: Enhanced — Medium consistency between antibody staining and RNA expression data. At least one protein variant secreted, tissue location of RNA and protein might differ and correlation is complex. Presumed off target binding observed and disregarded. External characterization data supports antibody staining.). 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 | Glial cells | High | Protein (IHC) | HPA → |
| Cerebellum | Purkinje cells | Medium | Protein (IHC) | HPA → |
| Hippocampus | 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 → |
| Adrenal gland | Glandular cells | Not detected | Protein (IHC) | HPA → |
| Appendix | Endocrine cells | Not detected | Protein (IHC) | HPA → |
| Bone marrow | Hematopoietic cells | Not detected | Protein (IHC) | HPA → |
| Breast | Adipocytes | Not detected | Protein (IHC) | HPA → |
Section 3
Advanced SLITRK1 IHC Tips
Troubleshoot SLITRK1 staining in paraffin sections by checking retrieval, cell identity and signal location against the available tissue evidence.
Which retrieval conditions should I try first for weak SLITRK1 staining in paraffin sections?
Start with citrate buffer at pH 6.0 for heat-induced epitope retrieval at 95–98 °C for 20 minutes (page retrieval setting). Allow sections to cool in the retrieval buffer, then keep the antibody dilution, detection reagent and development time constant while assessing the result (standard IHC practice). Test cerebral cortex alongside a negative tissue section, and inspect the relevant cells rather than judging overall slide darkness (HPA tissue IHC: high staining in cerebral-cortex glial cells; standard IHC practice). If staining remains weak, compare a more alkaline retrieval buffer on serial sections as a fallback, recording any increase in background or tissue damage (standard IHC practice).
Could fixation explain weak or uneven SLITRK1 staining?
Target-specific fixation sensitivity is unknown because the supplied SLITRK1 tissue-IHC caption does not state a fixative (A07507 tissue-IHC caption). For paraffin-section IHC, document the fixative, time in fixative, tissue thickness and processing history before comparing staining across specimens (standard IHC practice). A routine starting point is 10% neutral buffered formalin, with fixation time chosen for specimen size and laboratory validation rather than treated as an established SLITRK1 optimum (standard IHC practice). If a run is uneven, compare matched sections with identical citrate pH 6.0 retrieval and detection settings, then assess whether the difference tracks processing history (page retrieval setting; standard IHC practice).
Should SLITRK1 appear at the cell surface or in the cytoplasm?
SLITRK1 has an extracellular region at residues 18–622, a transmembrane segment at 623–643 and a cytoplasmic tail at 644–696 (UniProt Q96PX8 topology). The tissue-IHC reference describes selective cytoplasmic expression in the CNS, including high staining in cerebral-cortex glial cells (HPA tissue IHC). Accordingly, assess cytoplasmic staining in the expected cells while recording any apparent membrane enrichment separately; the expected pattern depends on epitope accessibility and the staining method (HPA tissue IHC; UniProt Q96PX8 topology; standard IHC practice). Use serial sections, a negative control and consistent chromogen development to distinguish cellular signal from diffuse tissue colour before assigning a compartment (standard IHC practice).
How should antibody epitope location affect my interpretation of SLITRK1 IHC?
The supplied record lists 0 isoforms, so an isoform-specific staining claim is unsupported here (UniProt Q96PX8 record). SLITRK1 contains extracellular leucine-rich repeat regions, a transmembrane segment at residues 623–643 and a cytoplasmic tail at 644–696 (UniProt Q96PX8 domains and topology). Check the catalog antibody’s stated immunogen or mapped epitope before using staining location to infer which part of the protein is detected (standard IHC practice). If that information is unavailable, report the observed cellular pattern without assigning it to an extracellular domain, cytoplasmic tail or processed species; compare consistent staining in expected cells with the negative control (UniProt Q96PX8 topology; HPA tissue IHC; standard IHC practice).
How can I compare SLITRK1 IHC with multiplex immunofluorescence?
Treat IF/ICC as a separate assay: the supplied SLITRK1 evidence includes a tissue-IHC image, but no cell-line ICC/IF images (A07507 tissue-IHC caption; HPA subcellular record). In a pilot multiplex experiment, pair SLITRK1 with a validated glial marker for cerebral cortex, where glial staining is reported as high, and include single-stain controls (HPA tissue IHC; standard IF practice). Choose a fluorophore and imaging channel with low tissue autofluorescence, checking an unstained section under the same exposure settings (standard IF practice). Set permeabilisation only after checking whether the antibody recognises the extracellular 18–622 region or cytoplasmic 644–696 tail; access to a cytoplasmic epitope requires membrane permeabilisation (UniProt Q96PX8 topology; standard IF practice).
What should I check when SLITRK1 chromogenic staining is widespread?
First compare a no-primary control and a known low-signal tissue with the test section under identical detection and DAB development conditions (standard IHC practice). Adipocytes in adipose tissue and glandular cells in adrenal gland are reported as not detected, providing useful reference patterns rather than proof that every cell there must be blank (HPA tissue IHC). For chromogenic IHC, verify the peroxidase block, blocking step, washes and antibody titration, and check whether excess DAB development obscures cell boundaries (standard IHC practice). Interpret widespread colour cautiously because the tissue-IHC assessment notes presumed off-target binding, and compare any residual signal with the expected selective CNS pattern (HPA tissue IHC).
How should I quantify SLITRK1 staining across brain sections? ⚠ ANSWER MARKED FOR VERIFICATION
Define the region and cell population before scoring; cerebral-cortex glial cells show high staining, while cerebellar Purkinje cells and hippocampal neuronal cells show medium staining in the tissue reference (HPA tissue IHC). For cell-level chromogenic scoring, record the percentage of positive cells and intensity categories, then calculate an H-score using 0–3 intensity weights if that scale is prespecified (standard IHC practice). Where cell counting is reliable, report positive-cell density per mm² of evaluable tissue and exclude folds, necrosis and cut edges using the same rules across slides (standard IHC practice). Normalise counts to the total number of eligible cells or evaluable area, and compare only sections stained and imaged under matched conditions (standard IHC practice).
How can I distinguish credible SLITRK1 staining from an artefact?
Look for reproducible staining in the expected cells: the tissue-IHC reference reports selective CNS cytoplasmic expression, with high staining in cerebral-cortex glial cells and medium staining in cerebellar Purkinje cells and hippocampal neuronal cells (HPA tissue IHC). A strong nuclear-only pattern or staining concentrated at cut edges, folds or necrotic areas warrants review against adjacent intact tissue and a no-primary control (HPA tissue IHC; standard IHC practice). Check endogenous peroxidase blocking when colour appears independently of the primary antibody, and assess staining at the same DAB development time (standard IHC practice). Because presumed off-target binding was observed in the tissue-IHC assessment, confirm any unexpected cell or compartment pattern with an independent antibody or other orthogonal evidence before calling it SLITRK1 (HPA tissue IHC; standard IHC practice).
Boster reagents
Best SLITRK1 / SLIT and NTRK-like protein 1 IHC Antibodies
A07507 has IHC and IF images from human brain tissue (catalog image captions). Its listed applications include IHC-P and IF, with stated reactivity to human, mouse and rat (catalog applications and reactivity).
Real IHC data
Anti-SLIT and NTRK-like protein 1 Slitrk1 Antibody
Cat # A07507
A07507 will render with a human brain tissue IHC image at 2.5 μg/mL (catalog IHC image caption). Its IF image also shows human brain tissue at 20 μg/mL; the catalog lists human, mouse and rat reactivity (catalog IF image caption; catalog reactivity).
Which to pick: Choose A07507 for tissue IHC because IHC-P is listed, though its IHC caption identifies human brain tissue without reporting the fixative (catalog applications; catalog IHC image caption). For IF, choose A07507 based on its human brain image; confirm performance for ICC separately because the catalog lists IF but provides no ICC image (catalog IF image caption; catalog applications). A07507 is the listed cross-species option for human, mouse and rat, but the supplied images show human tissue only; clonality is unreported (catalog reactivity; catalog image captions; catalog clone field).
Each figure is that product's own IHC / IF validation image from its datasheet.
References
- UniProt Consortium. UniProt entry Q96PX8 (SLIK1_HUMAN, SLIT and NTRK-like protein 1).
- Human Protein Atlas. SLITRK1 tissue IHC expression (reliability: Enhanced).
- Human Protein Atlas. SLITRK1 subcellular location (ICC-IF): Membrane, Secreted.
- Human Protein Atlas. SLITRK1 antibody validation summary (1 antibodies).
- Developmentally regulated and evolutionarily conserved expression of SLITRK1 in brain circuits implicated in Tourette syndrome. The Journal of comparative neurology 2009 — PMC3292218.
- PubMed PMID:11572484 — UniProt-cited evidence.
- PubMed PMID:12975309 — UniProt-cited evidence.
- PubMed PMID:15057823 — UniProt-cited evidence.
Immunohistochemistry protocol sheet for SLITRK1 (SLIT and NTRK-like protein 1). Expected localisation Cytoplasmic staining in CNS cells (HPA tissue IHC). Antigen retrieval: Citrate pH 6.0 HIER, 95–98 °C, 20 min (rule: cytoplasmic / membrane antigen). Validated IHC antibody: A07507 at 2.5 μg/mL (the product's own IHC validation image is shown). Controls (HPA): positive Cerebral cortex (Glial 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 A07507); 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-SLITRK1, 2.5 μg/mL (datasheet A07507); 9. Primary incubation: Overnight at 4 °C (standard). Watch for: Fixation: Keep fixation consistent across paraffin sections. (standard IHC practice; not target-specific); Caveat: A secreted variant may shift protein from RNA-positive cells (HPA tissue IHC); Isoform / epitope: No listed isoforms; extracellular versus cytoplasmic epitope matters (UniProt); Regulation: Predominant expression in frontal cortex (UniProt). Evidence: UniProt Q96PX8, HPA tissue IHC · Enhanced, HPA ICC-IF · Membrane, Secreted, Datasheet A07507, PMC3292218. QR code links to https://www.bosterbio.com/bosterbio-gene-info-cards/SLITRK1/immunohistochemistry-ihc-guide.