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- Table of Contents
Plan chromogenic SMARCA4 IHC around a nuclear staining readout (HPA tissue IHC). Compare defined cell populations and start with the catalog antibody at 1:50 (datasheet M00223).
Expected localisation, validated protocols, controls and antibodies — the at-a-glance facts below, then the full design guide.
| Expected localisation | Nuclei across tissues (HPA tissue IHC) | |
| Staining pattern | Broad nuclear staining in glandular, glial and other cells (HPA tissue IHC) | |
| Antigen retrieval | EDTA pH 8.0 HIER, heat-mediated (datasheet M00223) | |
| Positive control | Adrenal gland+4 more · see all | |
| Negative control | None in HPA (detected in all 44 tissues); use no-primary + isotype controls |
| Fixation | Keep fixation consistent across sections. (standard IHC practice; not target-specific) | |
| Caveat | Many cell types stain; score nuclei by cell population (HPA tissue IHC) | |
| Regulation | Low tissue specificity (HPA tissue RNA) | |
| Isoform / epitope | 5 isoforms; check antibody epitope coverage (UniProt) |
The catalog antibody’s IHC-P protocol specifies EDTA pH 8.0 retrieval (datasheet M00223). Two published paraffin-section protocols provide additional conditions (PMC4752399; PMC9391575).
| Sample | Paraffin-embedded human colon cancer tissue; fixative not specified (datasheet M00223) |
| Fixation | Image fixative and duration unreported (datasheet M00223); 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 M00223); 20 min, 95–100 °C (standard) |
| Peroxidase block | 3% H2O2, 10 min, room temperature (standard) |
| Blocking | 10% goat serum (datasheet M00223) |
| Primary antibody | Rabbit monoclonal (clone GFB-19) anti-SMARCA4, 1:50 (datasheet M00223) |
| Primary incubation | Overnight at 4 °C (datasheet M00223) |
| Detection | HRP-conjugated secondary, DAB chromogen (datasheet M00223) |
| Counterstain | Hematoxylin, blue, dehydrate and mount (standard) |
| Expected result | SMARCA4-positive staining in glandular cells of adrenal gland (HPA tissue IHC: High). HPA tissue profile: Ubiquitous nuclear expression. No signal in the no-primary control. |
SMARCA4 is a nuclear chromatin-remodeling protein with no transmembrane segment (UniProt P51532: subcellular location and topology). In paraffin-section IHC, expect nuclear staining across many cell types; HPA describes ubiquitous nuclear expression with low tissue specificity and rates its tissue pattern Supported, based on consistency between antibody staining and RNA expression (HPA: tissue IHC).
| Nuclear staining in glandular cells, hematopoietic cells or glia. | This fits the expected compartment (UniProt P51532: nucleus). HPA reports High staining in adrenal and appendix glandular cells, bone-marrow hematopoietic cells, and caudate and cerebral-cortex glia (HPA: tissue IHC). Judge each cell against its nuclear counterstain. |
| Predominantly cytoplasmic or membranous staining with little nuclear signal. | This conflicts with the expected nuclear IHC pattern (UniProt P51532: nucleus; HPA: ubiquitous nuclear expression). Review antibody specificity, detection background and whether the nuclei themselves stained before interpreting it as SMARCA4. |
| Strong staining confined to an unexpected cell population while nearby nuclei remain blank. | Check for cross-reactivity or endogenous detection activity (general IHC practice). HPA describes a broad nuclear pattern, so an unexpected cell type alone does not establish a false positive; the compartment and appropriate controls matter (HPA: tissue IHC). |
| Diffuse color over nuclei, cytoplasm and tissue spaces. | A widespread deposit obscures whether staining is nuclear (general chromogenic IHC practice). Review background controls and detection conditions; diffuse color alone cannot establish SMARCA4 expression (UniProt P51532: nucleus). |
| No nuclear staining in a section expected to be positive. | HPA reports High staining in several tissue and cell combinations, including bronchial respiratory epithelial cells and breast adipocytes (HPA: tissue IHC). If the tested section contains a documented positive cell population, investigate the assay before scoring it negative. |
| Tissue and cell selection | HPA reports ubiquitous nuclear expression and low tissue specificity, with High staining in selected cell populations (HPA: tissue IHC). Use a listed population as an assay check; do not treat every unlisted tissue as negative. |
| Antibody evidence | CAB004208 has Supported IHC status, while HPA048340 has no IHC status in the supplied antibody list (HPA: antibody validation). A tissue-level Supported rating does not validate every antibody or every staining result. |
| Isoforms and epitope | UniProt lists 5 SMARCA4 isoforms (UniProt P51532: isoforms). The supplied record gives no antibody epitope, so it cannot establish which isoforms a particular IHC antibody detects. |
| Processing and topology | UniProt reports no signal peptide, propeptide or transmembrane segment and describes one chain spanning residues 1–1647 (UniProt P51532: processing and topology). These facts support a nuclear interpretation; they do not specify an antigen-retrieval condition. |
| IF/ICC Q&A: What location should I expect? | HPA reports mainly nucleoplasm, nucleoli fibrillar center and nucleoli rim in ICC-IF, with cytosol listed as an additional location (HPA: subcellular). This is an IF observation, not a paraffin-IHC protocol or a reason to score cytoplasmic-only IHC as positive. |
| Situation | Likely cause | Next action |
|---|---|---|
| No signal in an HPA-listed High population. | The IHC run may have failed; the supplied sources do not identify a SMARCA4-specific fixation sensitivity (HPA: tissue IHC). | Confirm that the expected cells are present and review the positive control, primary-antibody conditions, retrieval and detection steps (general IHC practice). Do not infer tissue absence from one failed run. |
| Signal lies mainly outside nuclei. | The pattern disagrees with UniProt nuclear localization and HPA tissue IHC (UniProt P51532: nucleus; HPA: tissue IHC). | Compare with the nuclear counterstain and a primary-omission control; assess whether the signal is nonspecific or comes from detection reagents (general IHC practice). |
| Only one unexpected cell population stains. | The broad HPA profile does not make an unlisted population inherently negative (HPA: ubiquitous nuclear expression). Cross-reactivity or endogenous activity remains possible (general IHC practice). | Check whether staining is nuclear, then compare the population with controls and a documented positive population before assigning a cell-specific interpretation. |
| Diffuse chromogen obscures cell boundaries. | Excess background or endogenous enzyme activity can interfere with chromogenic IHC interpretation (general IHC practice). | Inspect primary-omission and detection controls; review blocking, washing, antibody dilution and chromogen development against the assay instructions (general IHC practice). |
| A tested antibody gives a different pattern from the tissue reference. | HPA's tissue pattern does not establish IHC performance for every antibody; the supplied list marks CAB004208 Supported for IHC and gives HPA048340 no IHC status (HPA: antibody validation). | Check the chosen antibody's IHC validation and controls. Avoid transferring the Supported designation or a staining conclusion between antibodies. |
| Nucleolar or cytosolic IF detail seems inconsistent with the IHC slide. | HPA's finer subcellular locations come from ICC-IF, while its tissue IHC profile is described as nuclear (HPA: subcellular; HPA: tissue IHC). | Score the paraffin IHC slide for interpretable nuclear staining. Consult the separate IF/ICC guide for that application's localisation and controls. |
Comprehensive Human Protein Atlas IHC scoring per tissue (reliability: Supported — High 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.
| Tissue | Cell type | Level | Evidence | Source |
|---|---|---|---|---|
| Adrenal gland | Glandular cells | High | Protein (IHC) | HPA → |
| Appendix | Glandular cells | High | Protein (IHC) | HPA → |
| Bone marrow | Hematopoietic cells | High | Protein (IHC) | HPA → |
| Breast | Adipocytes | High | Protein (IHC) | HPA → |
| Bronchus | Respiratory epithelial cells | High | Protein (IHC) | HPA → |
| Tissue | Cell type | Level | Evidence | Source |
|---|---|---|---|---|
| None in HPA: SMARCA4 is detected in all 44 scored tissues. Use a no-primary (secondary-only) and an isotype control instead. | ||||
Troubleshoot SMARCA4 chromogenic IHC in paraffin sections by checking retrieval, nuclear localisation, antibody specificity, controls and scoring before interpreting apparent loss.
Catalog antibodies have IHC images from human, mouse and rat tissues, plus IF images from mouse testis and cultured cells (catalog image captions).
M00223 shows IHC in human colon cancer, A00223-1 in human intestinal cancer, and M00223-1 in human lung cancer, all in paraffin sections (each SKU’s IHC image caption). A00223 shows IHC in rat brain and mouse testis, while M00223-3 shows staining in rat stomach (each SKU’s IHC image caption).
Which to pick: For human tissue IHC, M00223 is a rabbit monoclonal with a paraffin-section image using EDTA retrieval and 1:50 primary antibody (M00223 catalog entry; M00223 IHC image caption); the fixative is unreported (M00223 IHC image caption). For IF/ICC, A00223-1 has a cultured-cell IF image at 2 μg/mL and lists both applications (A00223-1 IF image caption; A00223-1 catalog entry). For IHC across human, mouse and rat samples, A00223-1 has paraffin-section images from all three species with citrate retrieval, and its listed IHC range is 0.5–1 μg/mL; the fixative is unreported (A00223-1 IHC image captions; A00223-1 catalog entry).