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SNX6 / Sorting nexin-6 · IHC design guide
Design Immunohistochemistry for SNX6
Plan SNX6 IHC on paraffin sections using the catalog antibody at 2–5 μg/ml (datasheet A06545). Assess cytoplasmic staining in glandular cells and kidney tubules, bearing in mind the low consistency between antibody staining and RNA expression (HPA tissue IHC).
Evidence assembled Oct 2026 · For research use; verify linked source records and product datasheet before use
SNX6 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 several tissues (HPA tissue IHC) | |
| Staining pattern | Cytoplasmic staining in glandular and kidney tubule cells (HPA tissue IHC) | |
| Antigen retrieval | EDTA pH 8.0 HIER, heat-mediated (datasheet A06545) | |
| Positive control | Breast+4 more · see all | |
| Negative control | Adipose tissue+4 more · see all |
Important caveats
Reasons your staining may differ from the expected pattern.
| Fixation | Matched tissue-IHC evidence does not establish the fixation claim. Validate the specimen-specific method before use. (selected-SKU IHC image A06545); target-specific effects are unknown. | |
| Caveat | IHC staining has low consistency with tissue RNA expression (HPA tissue IHC) | |
| Regulation | Tissue expression regulation is not annotated (UniProt) | |
| Isoform / epitope | 2 isoforms; residue 1 is absent in a processed chain; epitope unknown (UniProt) |
Section 1
Recommended SNX6 IHC & IF Protocols
The catalog antibody provides the IHC-P starting protocol (datasheet A06545); the published option below describes SNX6 staining in mouse brain sections (PMC5323044).
| Sample | Paraffin-embedded human ovarian cancer tissue; fixative not specified (datasheet A06545) |
| Fixation | Image fixative and duration unreported (datasheet A06545); verify before use. |
| Sectioning | 4–5 µm sections on charged slides (standard) |
| Deparaffinisation | Xylene, graded ethanol series to water (standard) |
| Antigen retrieval | Heat retrieval: EDTA pH 8.0 (datasheet A06545); 20 min, 95–100 °C (standard) |
| Peroxidase block | 3% H2O2, 10 min, room temperature (standard) |
| Blocking | 10% goat serum (datasheet A06545) |
| Primary antibody | Rabbit anti-SNX6, 2-5 μg/ml (datasheet A06545) |
| Primary incubation | Overnight at 4 °C (datasheet A06545) |
| Detection | HRP-conjugated secondary, DAB chromogen (datasheet A06545) |
| Counterstain | Hematoxylin, blue, dehydrate and mount (standard) |
| Expected result | SNX6-positive staining in glandular cells of breast (HPA tissue IHC: Medium). HPA tissue profile: Cytoplasmic expression in several tissues. No signal in the no-primary control. |
💡Decision noteFor paraffin sections, start with heat-mediated EDTA retrieval at pH 8.0 (datasheet A06545). The published mouse brain protocol used citrate at pH 6.0 (PMC5323044).
Section 2
What Is the Expected SNX6 Staining Pattern?
SNX6 should give mainly cytoplasmic staining in several tissues (HPA: tissue IHC). Early endosomes, their membranes and cytoplasmic vesicles are expected sites; SNX6 has no transmembrane segment, and only a minor proportion is nuclear (UniProt Q9UNH7: localization and topology). Medium staining is reported in breast, colon, stomach and small-intestine glandular cells, kidney tubule cells and skeletal-muscle myocytes (HPA: tissue IHC). The tissue profile is Approved, with low consistency between antibody staining and RNA expression (HPA: tissue IHC).
| Cytoplasmic chromogen in the expected cells, with discrete granular or punctate areas. | This fits the reported IHC profile and endosomal or vesicular localization (HPA: tissue IHC; UniProt Q9UNH7). Granules may be hard to resolve in a paraffin section; score the cellular compartment and the appropriate cell population together. |
| Staining is predominantly nuclear, uniformly surface-membranous, or confined to extracellular material. | Reassess specificity and slide interpretation: only a minor nuclear pool is reported, and SNX6 has no transmembrane segment (UniProt Q9UNH7: localization and topology). A little nuclear staining alone is therefore less concerning than nuclear dominance. |
| Strong staining appears in an HPA-listed undetected cell population. | For example, adipocytes are reported as not detected (HPA: tissue IHC). Check cell identity, antibody specificity and endogenous chromogenic activity before calling the signal SNX6. An HPA negative is a comparator, not proof that every specimen must be negative. |
| Color spreads across tissue structures or appears where no cell is identifiable. | Treat this as background until controls and cellular localization support a specific result. Excess detection signal, insufficient blocking or residual endogenous activity are general IHC possibilities; diffuse color alone does not match the reported cytoplasmic profile (HPA: tissue IHC). |
| No cytoplasmic signal is visible in a selected HPA medium-staining population. | A failed run, inadequate detection or unsuitable staining conditions are possible. Recheck the assay with the listed cell population and controls before interpreting absence of SNX6; HPA reports medium staining in several such populations, with low staining-to-RNA consistency (HPA: tissue IHC). |
💡Expected SNX6 appearanceCall a convincing positive when chromogen is mainly cytoplasmic in an HPA medium-staining cell population, with at most minor nuclear signal (HPA: tissue IHC; UniProt Q9UNH7: localization); dominant nuclear, extracellular or widespread cell-independent color warrants review.
| Tissue and cell selection | Breast, colon, stomach and small-intestine glandular cells, kidney tubule cells and skeletal-muscle myocytes are medium examples (HPA: tissue IHC). Lung macrophages are low, so they offer a less clear visual comparator (HPA: tissue IHC). |
| Localization at section resolution | SNX6 is associated with early endosomes, their membranes and cytoplasmic vesicles (UniProt Q9UNH7). HPA describes tissue staining as cytoplasmic (HPA: tissue IHC). Do not require individual endosomes to be resolved in chromogenic IHC. |
| Antibody evidence and limits | HPA049374 is Approved for IHC (HPA: antibodies). The tissue profile is also Approved but has low consistency between antibody staining and RNA expression (HPA: tissue IHC). Use compartment, cell type and controls together when interpreting a result. |
| Isoforms and epitope coverage | Two isoforms and an N-terminally processed chain beginning at residue 2 are recorded (UniProt Q9UNH7). No antibody epitope is supplied, so this record cannot establish which forms contribute to the observed stain or predict an epitope-specific processing effect. |
| IF/ICC Q&A: What pattern is expected? | Supported endosomal and lysosomal localization is reported in ICC-IF (HPA: subcellular). HPA049374 is Supported for ICC (HPA: antibodies). This answers the localization question; the primary application here is tissue IHC. |
| Fixation sensitivity | Target-specific fixation sensitivity is unreported in the supplied UniProt and HPA records. Antigen-retrieval choices are general IHC assay decisions; these records do not show that a particular retrieval condition changes SNX6 staining. |
| Situation | Likely cause | Next action |
|---|---|---|
| A listed medium-staining population has no visible signal. | The run or detection may have failed, or the tested section may differ from the HPA example; medium staining is reported for the listed populations (HPA: tissue IHC). | Check a run control, tissue integrity and reagent steps; repeat with an HPA-listed medium-staining cell population before concluding that SNX6 is absent. |
| Color is diffuse across cells and surrounding tissue. | Nonspecific detection, excess chromogen or inadequate blocking are general IHC possibilities. The reported tissue profile is cytoplasmic (HPA: tissue IHC). | Review a no-primary control, blocking and detection conditions; score only cell-associated staining with a plausible cytoplasmic distribution. |
| Nuclei dominate the stain. | A minor nuclear proportion is documented, but nuclear dominance is not the expected distribution (UniProt Q9UNH7: localization). | Compare with the cytoplasmic signal and controls; review antibody concentration and detection conditions before accepting the nuclear result. |
| Unexpected cells stain strongly, including an HPA-listed undetected population. | Cross-reactivity or endogenous chromogenic activity is possible; HPA reports adipocytes as not detected (HPA: tissue IHC). | Verify cell identity and examine a no-primary control; compare an expected medium-staining population in the same run before assigning specificity. |
| Only weak staining appears in a proposed positive comparator. | The chosen population may normally stain weakly: lung macrophages are Low, whereas several glandular populations are Medium (HPA: tissue IHC). | Use an HPA-listed medium-staining population as the visual comparator and confirm that the weak signal is cellular and cytoplasmic. |
| A membrane rim is scored as the sole positive pattern. | SNX6 associates with early-endosome membranes but has no transmembrane segment (UniProt Q9UNH7: localization and topology). A surface rim alone does not establish the reported cytoplasmic tissue pattern (HPA: tissue IHC). | Inspect cell borders and cytoplasm at higher magnification, then compare controls and an expected positive population before accepting the rim as specific. |
Experiment evidence
IHC & IF images showing SNX6 staining
A06545 · IHCIHC analysis of SNX6 using anti-SNX6 antibody (A06545). SNX6 was detected in a paraffin-embedded section of human ovarian cancer tissue. Hea
A06545 · IFIF analysis of SNX6 using anti-SNX6 antibody (A06545). SNX6 was detected in an immunocytochemical section of U20S cells. Enzyme antigen retr
HPA · Cerebral cortexHuman Protein Atlas IHC, Cerebral cortex. Source: https://www.proteinatlas.org/ENSG00000129515-SNX6/tissue/cerebral+cortex#imid_13677407
HPA · ColonHuman Protein Atlas IHC, Colon. Source: https://www.proteinatlas.org/ENSG00000129515-SNX6/tissue/colon#imid_13672185
HPA · LiverHuman Protein Atlas IHC, Liver. Source: https://www.proteinatlas.org/ENSG00000129515-SNX6/tissue/liver#imid_13672186
HPA · KidneyHuman Protein Atlas IHC, Kidney. Source: https://www.proteinatlas.org/ENSG00000129515-SNX6/tissue/kidney#imid_13672171
HPA · ICC-IF A-431Human Protein Atlas immunofluorescence, A-431, antibody HPA049374; green = SNX6, blue = nucleus, red = microtubules.
HPA · ICC-IF A-431Human Protein Atlas immunofluorescence, A-431, antibody HPA049374; green = SNX6, blue = nucleus, red = microtubules.
← swipe / scroll for more images →
Real IHC / IF data behind the staining-pattern expectations in this section.
Sample controls for SNX6 IHC & IF
🧪Run kidney first: tubular cells should stain (HPA: Medium in kidney tubule cells). Use adipose tissue as the negative tissue, where adipocytes are listed as not detected (HPA: Not detected in adipocytes); on the kidney slide, cells that remain unstained should show counterstain without specific chromogen deposit, but the supplied evidence does not identify a verified negative kidney cell type.
Positive control tissue: Breast (Glandular cells, HPA Medium)
Negative control tissue: Adipose tissue (HPA Not detected)
ICC-IF cell lines (HPA subcellular resource): HPA ICC-IF images show SNX6 in A-431, MCF-7, U2OS, NIH 3T3, with annotated localisation: Endosomes (supported), Lysosomes (supported) (HPA subcellular).
Technical controls: Include no-primary (secondary-only) and concentration-matched rabbit IgG isotype controls (caption: rabbit anti-SNX6 primary), plus SNX6-knockout tissue or cells as a biological negative. For kidney IHC, quench endogenous peroxidase before HRP detection and block endogenous biotin if using avidin–biotin detection (standard IHC practice).
⚠️Feasibility: The selected A06545 paraffin-section caption reports heat retrieval in EDTA at pH 8.0, but its fixative is unreported; no target-specific fixation window or fixation effect is supplied (A06545 caption). Paraffin IHC has a directly described workflow (A06545 caption), while HPA documents ICC-IF images and supported endosomal and lysosomal localization; the evidence does not establish that frozen sections or IF are easier (HPA: subcellular localization). Kidney sections may show endogenous biotin background with avidin–biotin detection (standard IHC practice).
HPA tissue IHC evidence for SNX6
Comprehensive Human Protein Atlas IHC scoring per tissue (reliability: Approved — Low 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 |
|---|---|---|---|---|
| Breast | Glandular cells | Medium | Protein (IHC) | HPA → |
| Colon | Glandular cells | Medium | Protein (IHC) | HPA → |
| Kidney | Cells in tubules | Medium | Protein (IHC) | HPA → |
| Skeletal muscle | Myocytes | Medium | Protein (IHC) | HPA → |
| Small intestine | Glandular 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 → |
| Bone marrow | Hematopoietic cells | Not detected | Protein (IHC) | HPA → |
| Bronchus | Basal cells | Not detected | Protein (IHC) | HPA → |
| Caudate | Glial cells | Not detected | Protein (IHC) | HPA → |
Section 3
Advanced SNX6 IHC Tips
Use the paraffin-section staining evidence for A06545 as the starting point, then judge signal against SNX6 localisation and tissue-level controls.
Which retrieval conditions should I try first for SNX6 in paraffin sections?
Start with heat-mediated antigen retrieval in EDTA at pH 8.0 for paraffin sections (datasheet A06545). The selected tissue-IHC image used this condition with 2 μg/ml primary antibody overnight at 4°C, so keep those variables fixed while judging retrieval (datasheet A06545). Compare retrieved and no-retrieval sections from the same block, assessing cytoplasmic signal in viable cells and background at tissue edges; the no-retrieval section tests the effect of heating (standard IHC practice; HPA: cytoplasmic expression). If signal remains weak, vary heating duration on adjacent sections before trying another retrieval buffer, and record whether added signal retains the expected cytoplasmic distribution (standard IHC practice; UniProt Q9UNH7 localisation).
Could fixation explain weak or uneven SNX6 staining?
Target-specific sensitivity of SNX6 to fixation is unknown: the selected paraffin-section caption does not state the fixative (datasheet A06545). Record each specimen’s fixative, fixation duration, processing history, and section age before comparing intensity, because these variables can change antigen accessibility in IHC (standard IHC practice). Run sections from differently processed blocks together with the same EDTA pH 8.0 retrieval and 2 μg/ml primary concentration to identify a processing-associated difference without changing several steps at once (datasheet A06545; standard IHC practice). Do not infer fixation tolerance from the SNX6 tissue staining profile or its lack of a transmembrane segment; neither establishes fixation sensitivity (HPA: tissue IHC; UniProt Q9UNH7 topology).
What SNX6 staining pattern is plausible, and when is nuclear signal suspicious?
Expect predominantly cytoplasmic staining, potentially with punctate endosomal enrichment, because SNX6 associates with early endosome membranes and cytoplasmic vesicles (UniProt Q9UNH7 localisation; HPA: cytoplasmic tissue expression). Supported endosome and lysosome localisation in cell imaging provides a useful compartment comparison, although puncta may be harder to resolve with chromogenic tissue IHC (HPA: subcellular localisation; standard IHC practice). A minor nuclear pool is reported, so isolated weak nuclear staining is possible, but uniform strong nuclear staining should prompt scrutiny of controls and counterstain (UniProt Q9UNH7 localisation; standard IHC practice). Compare viable interior cells with section edges and omit-primary controls before assigning diffuse nuclear DAB to SNX6 (standard IHC practice).
Can this antibody distinguish SNX6 isoforms or an altered epitope?
SNX6 has 2 annotated isoforms, but the supplied tissue-IHC caption does not map this antibody’s epitope or establish isoform selectivity (UniProt Q9UNH7 isoforms; datasheet A06545). The protein contains a PX domain at residues 26–173 and a BAR domain at 203–406; those boundaries do not identify which region A06545 recognizes (UniProt Q9UNH7 domains; datasheet A06545). N-terminal processing and phosphorylation at serines 116 and 194 are annotated, yet no supplied staining evidence links them to epitope accessibility (UniProt Q9UNH7 processing and modified residues). Treat a changed IHC pattern as an assay observation until epitope mapping or an independent antibody supports a molecular explanation (standard IHC practice).
How should I assess SNX6 by multiplex IF after reviewing the IHC result?
For a separate IF assay, pair SNX6 with a marker identifying the expected cell type, such as glandular cells in breast or colon tissue, and assess compartment overlap within those cells (HPA: medium staining in breast and colon glandular cells; standard IF practice). Include an endosome or lysosome marker when testing punctate localisation, since those locations are supported by cell imaging (HPA: subcellular localisation). Choose a fluorophore channel that separates signal from measured tissue autofluorescence, and check single-stain controls for spectral bleed-through (standard IF practice). SNX6 lacks a transmembrane segment, but this antibody’s epitope side is unmapped; optimise permeabilisation for access to its cytoplasmic and endosomal pools rather than assuming a membrane-facing epitope (UniProt Q9UNH7 topology and localisation; datasheet A06545; standard IF practice).
How can I reduce diffuse DAB background without losing SNX6 signal?
Use the selected paraffin-section method as a comparison point: 10% goat serum block, 2 μg/ml primary overnight at 4°C, and peroxidase-linked secondary for 30 minutes at 37°C (datasheet A06545). Include a no-primary section to reveal secondary or detection-system background, and block endogenous peroxidase before DAB development as a general chromogenic IHC step (standard IHC practice). If staining is widespread, titrate the primary and shorten DAB development on adjacent sections while checking that cytoplasmic staining persists in viable cells (standard IHC practice; HPA: cytoplasmic expression). Keep retrieval at EDTA pH 8.0 during that comparison so a background change can be attributed more clearly to detection conditions (datasheet A06545; standard IHC practice).
How should I score SNX6 staining across heterogeneous tissue sections? ⚠ ANSWER MARKED FOR VERIFICATION
Define the scored cell population and exclude necrosis, folds, and damaged edges before measuring cytoplasmic DAB signal (standard IHC practice; HPA: cytoplasmic expression). For each viable compartment, report the percentage of positive cells and an H-score based on staining intensity; record nuclear staining separately if it is present (standard IHC practice; UniProt Q9UNH7 localisation). If the endpoint is puncta or positive-cell counts per area, report density per mm² of viable tissue and normalise to the area of the same annotated compartment across sections (standard IHC practice). Apply one threshold and development setting to the comparison set, and interpret small tissue differences cautiously because antibody staining and RNA data showed low consistency in HPA tissue assessment (standard IHC practice; HPA: Approved, low consistency).
What distinguishes convincing SNX6 staining from a tissue artefact?
A convincing result places signal mainly in the cytoplasm of viable cells, with possible endosomal puncta; only a minor SNX6 proportion is reported in the nucleus (HPA: cytoplasmic tissue expression; UniProt Q9UNH7 localisation). Check whether the stained cell population is plausible: HPA reports medium staining in breast glandular cells and kidney tubule cells, while adipocytes were not detected (HPA: tissue IHC). Treat staining concentrated at cut edges, over necrosis, or across many nuclei as suspect until adjacent sections and a no-primary control are reviewed (standard IHC practice). Endogenous peroxidase can also produce DAB signal, so compare a peroxidase-blocked section and avoid calling signal specific solely from its brown colour (standard IHC practice).
Boster reagents
Best SNX6 / Sorting nexin-6 IHC Antibodies
The IHC-validated antibody A06545 has IHC data from human paraffin-embedded ovarian cancer tissue and IF/ICC data from U20S cells (catalog IHC/IF captions).
Real IHC data
Anti-SNX6 Antibody ®
Cat # A06545
A06545 will render with an IHC figure from a human paraffin-embedded ovarian cancer section (catalog IHC caption). It also has an IF/ICC figure from U20S cells; the catalog lists human, mouse, and rat reactivity (catalog IF caption; catalog reactivity).
Which to pick: Choose A06545 for paraffin-section IHC: its IHC caption shows EDTA pH 8.0 retrieval and 2 μg/ml primary antibody in human ovarian cancer tissue; the fixative is unreported (catalog IHC caption). The same SKU is listed for IF/ICC and has a U20S-cell IF figure (catalog applications; catalog IF caption). For mouse or rat samples, A06545 is the listed option based on reactivity, but those species are not shown in its IHC or IF captions; clonality is unreported (catalog reactivity; catalog IHC/IF captions; catalog clone field).
Each figure is that product's own IHC / IF validation image from its datasheet.
References
- UniProt Consortium. UniProt entry Q9UNH7 (SNX6_HUMAN, Sorting nexin-6).
- Human Protein Atlas. SNX6 tissue IHC expression (reliability: Approved).
- Human Protein Atlas. SNX6 subcellular location (ICC-IF): Localized to the endosomes and lysosomes..
- Human Protein Atlas. SNX6 antibody validation summary (1 antibodies).
- Ablation of SNX6 leads to defects in synaptic function of CA1 pyramidal neurons and spatial memory. eLife 2017 — PMC5323044.
- PubMed PMID:11485546 — UniProt-cited evidence.
- PubMed PMID:12508121 — UniProt-cited evidence.
- PubMed PMID:15489334 — UniProt-cited evidence.
Immunohistochemistry protocol sheet for SNX6 (Sorting nexin-6). Expected localisation Cytoplasmic staining in several tissues (HPA tissue IHC). Antigen retrieval: EDTA pH 8.0 HIER, heat-mediated (datasheet A06545). Validated IHC antibody: A06545 at 2-5 μg/ml (the product's own IHC validation image is shown). Controls (HPA): positive Breast (Glandular cells); negative Adipose tissue. IHC-P workflow on paraffin sections; fixative unspecified. Protocol steps: 1. Sample: Paraffin-embedded human ovarian cancer tissue; fixative not specified (datasheet A06545); 2. Fixation: Image fixative and duration unreported (datasheet A06545); 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 retrieval: EDTA pH 8.0 (datasheet A06545); 20 min, 95–100 °C (standard); 6. Peroxidase block: 3% H2O2, 10 min , room temperature (standard); 7. Blocking: 10% goat serum (datasheet A06545); 8. Primary antibody: Rabbit anti-SNX6, 2-5 μg/ml (datasheet A06545); 9. Primary incubation: Overnight at 4 °C (datasheet A06545). Watch for: Fixation: Matched tissue-IHC evidence does not establish the fixation claim. Validate the specimen-specific method before use. (selected-SKU IHC image A06545); target-specific effects are unknown.; Caveat: IHC staining has low consistency with tissue RNA expression (HPA tissue IHC); Isoform / epitope: 2 isoforms; residue 1 is absent in a processed chain; epitope unknown (UniProt); Regulation: Tissue expression regulation is not annotated (UniProt). Evidence: UniProt Q9UNH7, HPA tissue IHC · Approved, HPA ICC-IF · endosomes and lysosomes., Datasheet A06545, PMC5323044. QR code links to https://www.bosterbio.com/bosterbio-gene-info-cards/SNX6/immunohistochemistry-ihc-guide.