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SIN3B / Paired amphipathic helix protein Sin3b · IHC design guide
Design Immunohistochemistry for SIN3B
Plan chromogenic SIN3B IHC in paraffin sections using the catalog antibody’s 2–5 μg/ml range (datasheet A06424-2). Compare nuclear staining in smooth muscle and stomach glandular cells while accounting for uncertain staining reliability (HPA tissue IHC).
Evidence assembled Oct 2026 · For research use; verify linked source records and product datasheet before use
SIN3B 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 staining in several tissues (HPA tissue IHC) | |
| Staining pattern | Nuclear staining in smooth muscle and stomach glandular cells (HPA tissue IHC) | |
| Antigen retrieval | EDTA pH 8.0 HIER, heat-mediated (datasheet A06424-2) | |
| Positive control | Smooth muscle+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 | Presumed off-target binding; reliability uncertain (HPA tissue IHC) | |
| Regulation | No expression regulator annotated (UniProt) | |
| Isoform / epitope | 3 isoforms; no membrane sidedness; epitope coverage unknown (UniProt) |
Section 1
Recommended SIN3B IHC & IF Protocols
The catalog antibody has an IHC-P protocol (datasheet A06424-2). The published mouse prostate protocol below provides a paraffin-section example (PMC5626631).
| Sample | Paraffin-embedded human bladder cancer tissue; fixative not specified (datasheet A06424-2) |
| Fixation | Image fixative and duration unreported (datasheet A06424-2); 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 A06424-2); 20 min, 95–100 °C (standard) |
| Peroxidase block | 3% H2O2, 10 min, room temperature (standard) |
| Blocking | 10% goat serum (datasheet A06424-2) |
| Primary antibody | Rabbit anti-SIN3B, 2-5 μg/ml (datasheet A06424-2) |
| Primary incubation | Overnight at 4 °C (datasheet A06424-2) |
| Detection | HRP-conjugated secondary, DAB chromogen (datasheet A06424-2) |
| Counterstain | Hematoxylin, blue, dehydrate and mount (standard) |
| Expected result | SIN3B-positive staining in smooth muscle cells of smooth muscle (HPA tissue IHC: High). HPA tissue profile: Nuclear expression in several tissues. No signal in the no-primary control. |
💡Decision noteStart with heat-mediated EDTA pH 8.0 retrieval for the catalog antibody (datasheet A06424-2); the published mouse prostate method used citrate pH 6.0 (PMC5626631).
Section 2
What Is the Expected SIN3B Staining Pattern?
SIN3B is a nuclear transcriptional corepressor with no transmembrane segment (UniProt O75182: nucleus, function, topology). For IHC, look for nuclear staining in smooth muscle cells and stomach glandular cells, which HPA reports as high; several other cell types show medium staining (HPA: tissue IHC). Treat this as a provisional pattern: HPA rates tissue IHC reliability uncertain, citing low agreement with RNA data and presumed off-target binding (HPA: tissue IHC).
| Nuclear chromogen in smooth muscle cells or stomach glandular cells, with identifiable unstained surrounding structures. | This fits the reported high-staining cell types and expected nuclear location (HPA: high in smooth muscle cells and stomach glandular cells; UniProt O75182: nucleus). Score the named cells and their nuclei, not the whole tissue uniformly. The fit supports interpretation but does not resolve HPA’s uncertain tissue IHC reliability (HPA: tissue IHC). |
| Signal is mainly diffuse cytoplasmic, while nuclei are faint or clear. | That distribution conflicts with UniProt’s nuclear assignment and HPA’s nuclear tissue profile (UniProt O75182: nucleus; HPA: tissue IHC). Inspect the no-primary and detection controls, then reassess background and staining conditions (standard IHC practice). Do not classify cytoplasmic color alone as SIN3B-positive. |
| Strong staining appears in a cell population HPA lists as not detected, such as adipocytes. | HPA reports SIN3B as not detected in adipocytes, so strong staining there is a specificity warning, not proof that SIN3B is absent from every adipose tissue cell (HPA: adipocytes not detected; tissue IHC uncertain). Cross-reactivity or endogenous detection activity are possible explanations; compare controls before assigning either cause (standard IHC practice). |
| Broad, low-contrast color covers nuclei, cytoplasm, and tissue spaces. | This is difficult to score as cell-specific nuclear staining against HPA’s tissue profile (HPA: nuclear expression in several tissues). Check the no-primary control, wash steps, blocking, and chromogen development for general background (standard IHC practice). Background alone cannot establish a SIN3B distribution. |
| No nuclear signal is visible in smooth muscle cells or stomach glandular cells. | Those are HPA’s high-staining examples, so an absent signal calls for a run-level check (HPA: high in smooth muscle cells and stomach glandular cells). Review tissue integrity, retrieval, antibody and detection steps, and counterstain visibility (standard IHC practice). HPA’s uncertain IHC rating limits how strongly one negative section can be interpreted (HPA: tissue IHC). |
💡Expected SIN3B appearanceA plausible IHC positive is clear nuclear staining in smooth muscle cells or stomach glandular cells at HPA’s reported high level; widespread extranuclear color or strong staining of HPA-listed undetected cell types warrants control-based review (HPA: tissue IHC; UniProt O75182: nucleus).
| Compartment and assay | UniProt places SIN3B in the nucleus, and HPA describes nuclear tissue IHC (UniProt O75182: nucleus; HPA: tissue IHC). HPA’s ICC-IF record also approves a plasma membrane location; that separate imaging result should not be imposed as the expected chromogenic IHC pattern (HPA: subcellular ICC-IF). |
| Cell type selection | HPA reports high staining in smooth muscle cells and stomach glandular cells, medium staining in several neuronal and epithelial populations, and no detection in specified other cell types (HPA: tissue IHC). Interpret each listed level for its named cell population, with the HPA reliability caveat. |
| Antibody evidence | The HPA050329 antibody is rated uncertain for IHC and approved for ICC-IF; HPA also flags presumed off-target tissue staining (HPA: antibody validation; tissue IHC). An ICC-IF approval does not independently validate every IHC-positive cell population. |
| Isoforms and target-specific conditions | UniProt lists three SIN3B isoforms, but the supplied sources give no antibody epitope or isoform-specific IHC pattern (UniProt O75182: isoforms; HPA: antibody validation). Target-specific fixation sensitivity is unreported here; retrieval conditions must be evaluated as general IHC workflow conditions, not as a proven SIN3B effect. |
| Situation | Likely cause | Next action |
|---|---|---|
| Expected high-staining cells show no nuclear chromogen. | A failed staining run is possible, but a single negative result does not identify the failed step (HPA: high in smooth muscle cells and stomach glandular cells; tissue IHC uncertain). | Confirm the named cells are present, then review the IHC-validated antibody, retrieval, detection reagents, and a run control together (standard IHC practice). Record the actual tissue and cell type before interpreting absence. |
| Nuclear staining appears, but no-primary sections also develop color. | Signal can arise from the detection system or endogenous tissue activity rather than primary-antibody binding (standard chromogenic IHC practice). | Use the no-primary result to assess detection background; check appropriate blocking and detection controls, then repeat scoring only where control background is acceptably low (standard IHC practice). |
| Strong signal occurs in an HPA-listed undetected cell type. | The discrepancy raises concern about specificity, especially given HPA’s uncertain tissue IHC rating and presumed off-target binding (HPA: tissue IHC). It does not by itself identify the molecular cause. | Verify cell identity and nuclear localization, compare no-primary staining, and seek an independent specificity check before calling that population SIN3B-positive (standard IHC practice; HPA: tissue IHC uncertain). |
| Most of the section has diffuse color that obscures nuclei. | General background can prevent reliable nuclear scoring; it is not a documented SIN3B-specific fixation effect (standard IHC practice; HPA: nuclear tissue profile). | Check blocking, washes, chromogen development, and control sections; assess whether counterstained nuclei remain distinguishable before scoring (standard IHC practice). |
| Signal is predominantly cytoplasmic or membranous in IHC. | That pattern does not match HPA’s nuclear tissue IHC summary or UniProt’s nuclear assignment (HPA: tissue IHC; UniProt O75182: nucleus). HPA’s approved additional plasma membrane location comes from ICC-IF (HPA: subcellular ICC-IF). | Document the compartment and compare staining controls; avoid treating the ICC-IF membrane observation as validation of a membranous chromogenic IHC result (HPA: subcellular ICC-IF; standard IHC practice). |
| What should an IF/ICC image show? | IF/ICC has separate localization evidence and is a different assay from paraffin-section IHC (HPA: subcellular ICC-IF; tissue IHC). | Look primarily for nucleoplasmic signal; HPA also approves an additional plasma membrane location in ICC-IF images from HEK293, U-251MG, and U2OS (HPA: subcellular ICC-IF). Interpret that image evidence within an IF/ICC guide. |
Experiment evidence
IHC & IF images showing SIN3B staining
A06424-2 · IHCIHC analysis of SIN3B using anti-SIN3B antibody (A06424-2). SIN3B was detected in a paraffin-embedded section of human bladder cancer tissue
A06424-2 · IHCIHC analysis of SIN3B using anti-SIN3B antibody (A06424-2). SIN3B was detected in a paraffin-embedded section of human colon cancer tissue.
A06424-2 · IFIF analysis of SIN3B using anti-SIN3B antibody (A06424-2) and anti-Beta Tubulin antibody (M01857-3). SIN3B was detected in an immunocytochem
HPA · Cerebral cortexHuman Protein Atlas IHC, Cerebral cortex. Source: https://www.proteinatlas.org/ENSG00000127511-SIN3B/tissue/cerebral+cortex#imid_13912400
HPA · ColonHuman Protein Atlas IHC, Colon. Source: https://www.proteinatlas.org/ENSG00000127511-SIN3B/tissue/colon#imid_13919662
HPA · LiverHuman Protein Atlas IHC, Liver. Source: https://www.proteinatlas.org/ENSG00000127511-SIN3B/tissue/liver#imid_13919671
HPA · KidneyHuman Protein Atlas IHC, Kidney. Source: https://www.proteinatlas.org/ENSG00000127511-SIN3B/tissue/kidney#imid_13919672
HPA · ICC-IF HEK293Human Protein Atlas immunofluorescence, HEK293, antibody HPA050329; green = SIN3B, blue = nucleus, red = microtubules.
HPA · ICC-IF HEK293Human Protein Atlas immunofluorescence, HEK293, antibody HPA050329; green = SIN3B, blue = nucleus, red = microtubules.
← swipe / scroll for more images →
Real IHC / IF data behind the staining-pattern expectations in this section.
Sample controls for SIN3B IHC & IF
🧪Run smooth muscle first: smooth muscle cells should show SIN3B staining (HPA: High in smooth muscle cells). Use adipose tissue as the comparison tissue (HPA: Not detected in adipocytes); HPA does not identify an internal negative cell type in smooth muscle, so only cells independently verified as SIN3B-negative should be expected to lack specific nuclear staining (UniProt O75182: nucleus).
Positive control tissue: Smooth muscle (Smooth muscle cells, HPA High)
Negative control tissue: Adipose tissue (HPA Not detected)
ICC-IF cell lines (HPA subcellular resource): HPA ICC-IF images show SIN3B in HEK293, U-251MG, U2OS, with annotated localisation: Nucleoplasm (approved) (HPA subcellular).
Technical controls: Include a no-primary, secondary-only control and a rabbit IgG control matched to the primary antibody’s isotype and clonality (selected-SKU caption: rabbit anti-SIN3B); use SIN3B-knockout material, if available, as a biological negative. Quench endogenous peroxidase and check background in the smooth muscle section when using HRP–DAB detection (selected-SKU caption: HRP–DAB).
⚠️Feasibility: A target-specific fixation window or fixation effect is unreported, and the selected-SKU paraffin-section caption does not state a fixative. The caption uses heat retrieval in EDTA at pH 8.0, but does not establish that retrieval is required or that frozen sections or IF are easier (selected-SKU tissue-IHC caption). Assess endogenous peroxidase background in the smooth muscle section during HRP–DAB scoring (selected-SKU caption: HRP–DAB).
HPA tissue IHC evidence for SIN3B
Comprehensive Human Protein Atlas IHC scoring per tissue (reliability: Uncertain — Low consistency between antibody staining and RNA expression data. Presumed off target binding observed and disregarded.). 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 |
|---|---|---|---|---|
| Smooth muscle | Smooth muscle cells | High | Protein (IHC) | HPA → |
| Stomach | Glandular cells | High | Protein (IHC) | HPA → |
| Caudate | Neuronal cells | Medium | Protein (IHC) | HPA → |
| Cerebellum | Purkinje cells | Medium | Protein (IHC) | HPA → |
| Cerebral cortex | 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 → |
| Bone marrow | Hematopoietic cells | Not detected | Protein (IHC) | HPA → |
| Duodenum | Glandular cells | Not detected | Protein (IHC) | HPA → |
| Liver | Cholangiocytes | Not detected | Protein (IHC) | HPA → |
Section 3
Advanced SIN3B IHC Tips
Troubleshoot SIN3B staining by checking retrieval, nuclear localisation, controls and scoring against the available tissue evidence.
Which retrieval conditions should I start with for weak SIN3B staining?
Start with heat mediated retrieval in EDTA at pH 8.0 (datasheet A06424-2). The selected paraffin section example then used 2 μg/ml primary antibody overnight at 4°C, so compare weak staining against that documented starting point (datasheet A06424-2). Keep section thickness, heating time and detection conditions matched while varying retrieval duration on adjacent sections (standard IHC practice). If staining remains weak, test another retrieval buffer or pH as a fallback, with a matched no primary control to reveal added background (standard IHC practice). Judge improvement by nuclear signal and tissue preservation, not by stronger DAB alone (UniProt O75182 localisation; standard IHC practice).
Could fixation explain weak nuclear SIN3B staining?
Target specific fixation sensitivity is unknown: the selected paraffin section caption does not state its fixative (datasheet A06424-2). Record the fixative and fixation duration for each specimen, then compare similarly processed sections before changing antibody concentration (standard IHC practice). Excessive fixation can mask epitopes in IHC generally, while poor fixation can compromise morphology and make nuclear scoring unreliable (standard IHC practice). Begin the comparison with EDTA retrieval at pH 8.0 and 2 μg/ml primary antibody, as documented for this antibody (datasheet A06424-2). Evaluate nuclear staining alongside tissue morphology and a no primary control; do not assign a SIN3B specific fixation effect from tissue patterns (UniProt O75182 localisation; standard IHC practice).
How should I assess nuclear versus membrane SIN3B staining?
Score nuclei first because SIN3B is annotated as nuclear, and tissue IHC reports nuclear expression in several tissues (UniProt O75182 localisation; HPA tissue IHC). Nucleoplasmic localisation is also reported in cell images, alongside an additional plasma membrane location (HPA subcellular). Since SIN3B has no transmembrane segment, membrane staining in paraffin sections needs independent validation before being treated as specific (UniProt O75182 topology; standard IHC practice). Compare nuclear and membrane patterns separately across matched sections and include a no primary control to assess detection background (standard IHC practice). Record the cell compartment explicitly, because pooled DAB intensity could obscure a weak nuclear signal beneath surface staining (standard IHC practice).
Could isoforms or epitope accessibility change the IHC pattern?
SIN3B has 3 annotated isoforms, but the supplied antibody caption does not identify the recognized epitope (UniProt O75182 isoforms; datasheet A06424-2). Map the immunogen or epitope against each isoform before claiming that a negative section lacks all SIN3B forms (standard IHC practice). The protein contains PAH domains at residues 37–107, 153–238 and 292–369, plus reported phosphoserines at 709 and 712 (UniProt O75182 domains and modified residues). These annotations alone do not establish which structures this antibody recognizes after paraffin processing (standard IHC practice). Compare retrieval conditions on adjacent sections and seek an independent epitope or orthogonal assay when isoform specific interpretation matters (standard IHC practice).
How can IF clarify a questionable SIN3B IHC pattern?
Use IF as a separate validation experiment, since this page’s documented antibody example is chromogenic IHC on a paraffin section (datasheet A06424-2). Multiplex SIN3B with a smooth muscle cell marker where that population is being evaluated, while treating the reported high smooth muscle staining cautiously because tissue IHC reliability is uncertain (HPA tissue IHC). Choose spectrally separated fluorophores and inspect an unstained section to place the SIN3B signal away from tissue autofluorescence (standard IF practice). For the expected nuclear epitope, permeabilise the plasma and nuclear barriers after fixation, then compare with a mild or omitted permeabilisation condition if surface signal is suspected (UniProt O75182 localisation and topology; standard IF practice). Include single stain and no primary controls before interpreting colocalisation (standard IF practice).
What should I check when DAB obscures SIN3B nuclei?
The documented section used 10% goat serum blocking, a peroxidase conjugated secondary and DAB detection (datasheet A06424-2). Include a no primary control, block endogenous peroxidase and inspect whether residual DAB follows vessels, damaged tissue or section edges (standard IHC practice). Titrate the primary around the documented 2 μg/ml condition and keep development time matched across comparison sections (datasheet A06424-2; standard IHC practice). Review the secondary reagent against the rabbit primary and check whether blocking and washes reduce diffuse signal without losing nuclear contrast (datasheet A06424-2; standard IHC practice). Because presumed off target binding was observed in tissue IHC, a darker section alone is insufficient evidence of specificity (HPA tissue IHC).
How should I quantify SIN3B staining across paraffin sections? ⚠ ANSWER MARKED FOR VERIFICATION
Define the cell population and count only interpretable nuclei, consistent with the reported nuclear tissue pattern (HPA tissue IHC; standard IHC practice). Report the percentage of positive nuclei plus an H-score from intensity categories, using identical thresholds and imaging settings across sections (standard IHC practice). Normalise positive counts to total eligible nuclei in the same region; if reporting positive cell density per mm², also report the analysed tissue area (standard IHC practice). Exclude folds, necrosis and section edges using rules set before scoring, and assess background with a no primary control (standard IHC practice). Keep membrane staining separate because an additional plasma membrane location has been reported in cell images (HPA subcellular).
When is a SIN3B positive IHC result convincing?
A convincing result shows reproducible nuclear staining in intact cells, matching the annotated localisation and reported tissue pattern (UniProt O75182 localisation; HPA tissue IHC). Compare cell identity and compartment with controls: smooth muscle cells and stomach glandular cells were reported high, while adipocytes were not detected (HPA tissue IHC). Treat those comparisons as provisional because tissue staining had low consistency with RNA and presumed off target binding (HPA tissue IHC reliability). Discount staining confined to edges, necrosis or an endogenous enzyme pattern, and check a no primary section for detection artefact (standard IHC practice). Investigate dominant cytoplasmic or membrane only DAB staining with an independent assay before assigning it to SIN3B (UniProt O75182 localisation; standard IHC practice).
Boster reagents
Best SIN3B / Paired amphipathic helix protein Sin3b IHC Antibodies
A06424-2 has IHC images from paraffin-embedded human bladder cancer, colon cancer and rat testis, plus IF images from HeLa cells and human and rat tissue sections (catalog image captions).
Real IHC data
Anti-SIN3B Antibody ®
Cat # A06424-2
A06424-2 is listed for IHC, IF and ICC, with human, mouse and rat reactivity (catalog applications and reactivity). Its IHC captions show human bladder cancer, human colon cancer and rat testis paraffin sections; its IF captions show HeLa cells and human bladder cancer and rat testis sections (A06424-2 image captions).
Which to pick: For tissue IHC, choose A06424-2: its paraffin-section captions use EDTA retrieval at pH 8.0 and 2 μg/ml primary antibody; the fixative is unreported (A06424-2 IHC image captions). For IF/ICC, A06424-2 is listed for both applications and has IF images from cells and paraffin sections (catalog applications; A06424-2 IF image captions). For cross-species work, A06424-2 lists human, mouse and rat reactivity, with IHC images from human and rat samples; mouse IHC imaging and clonality are unreported (catalog reactivity and clone field; A06424-2 IHC image captions).
Each figure is that product's own IHC / IF validation image from its datasheet.
References
- UniProt Consortium. UniProt entry O75182 (SIN3B_HUMAN, Paired amphipathic helix protein Sin3b).
- Human Protein Atlas. SIN3B tissue IHC expression (reliability: Uncertain).
- Human Protein Atlas. SIN3B subcellular location (ICC-IF): Mainly localized to the nucleoplasm. In addition localized to the plasma membrane..
- Human Protein Atlas. SIN3B antibody validation summary (1 antibodies).
- Chromatin-Associated Protein SIN3B Prevents Prostate Cancer Progression by Inducing Senescence. Cancer research 2017 — PMC5626631.
- PubMed PMID:9734811 — UniProt-cited evidence.
- PubMed PMID:15489334 — UniProt-cited evidence.
- PubMed PMID:12670868 — UniProt-cited evidence.
Immunohistochemistry protocol sheet for SIN3B (Paired amphipathic helix protein Sin3b). Expected localisation Nuclear staining in several tissues (HPA tissue IHC). Antigen retrieval: EDTA pH 8.0 HIER, heat-mediated (datasheet A06424-2). Validated IHC antibody: A06424-2 at 2-5 μg/ml (the product's own IHC validation image is shown). Controls (HPA): positive Smooth muscle (Smooth muscle cells); negative Adipose tissue. IHC-P workflow on paraffin sections; fixative unspecified. Protocol steps: 1. Sample: Paraffin-embedded human bladder cancer tissue; fixative not specified (datasheet A06424-2); 2. Fixation: Image fixative and duration unreported (datasheet A06424-2); 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 A06424-2); 20 min, 95–100 °C (standard); 6. Peroxidase block: 3% H2O2, 10 min , room temperature (standard); 7. Blocking: 10% goat serum (datasheet A06424-2); 8. Primary antibody: Rabbit anti-SIN3B, 2-5 μg/ml (datasheet A06424-2); 9. Primary incubation: Overnight at 4 °C (datasheet A06424-2). Watch for: Fixation: Keep fixation consistent across sections (standard IHC practice; not target-specific); Caveat: Presumed off-target binding; reliability uncertain (HPA tissue IHC); Isoform / epitope: 3 isoforms; no membrane sidedness; epitope coverage unknown (UniProt); Regulation: No expression regulator annotated (UniProt). Evidence: UniProt O75182, HPA tissue IHC · Uncertain, HPA ICC-IF · Mainly localized to the nucleoplasm. In addition localized to the…, Datasheet A06424-2, PMC5626631. QR code links to https://www.bosterbio.com/bosterbio-gene-info-cards/SIN3B/immunohistochemistry-ihc-guide.