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- Table of Contents
Plan SMN1 IHC in paraffin sections using the reported nuclear and cytoplasmic tissue pattern (HPA tissue IHC). Compare staining by cell type and account for antibodies that target SMN1/2 (HPA tissue IHC; catalog antibody records).
Expected localisation, validated protocols, controls and antibodies — the at-a-glance facts below, then the full design guide.
| Expected localisation | Nuclear and cytoplasmic tissue staining (HPA tissue IHC) | |
| Staining pattern | Widespread nuclear and cytoplasmic staining across cell types (HPA tissue IHC) | |
| Antigen retrieval | Citrate pH 6 HIER, heat-mediated (datasheet M03420-1) | |
| Positive control | Bone marrow+4 more · see all | |
| Negative control | Adipose tissue+3 more · see all |
| Fixation | Keep fixation consistent across samples. (standard IHC practice; not target-specific) | |
| Caveat | SMN1/2 antibodies may detect both proteins (HPA tissue IHC; catalog antibody records) | |
| Regulation | Staining varies by cell type (HPA tissue IHC) | |
| Isoform / epitope | 4 isoforms; check antibody epitope coverage (UniProt) |
The catalog antibody protocol uses citrate pH 6 heat retrieval (datasheet M03420-1). The published mouse liver IHC protocol below reports sample and primary incubation details (PMC13049938).
| Sample | Paraffin-embedded human mammary cancer tissue; fixative not specified (datasheet M03420-1) |
| Fixation | Image fixative and duration unreported (datasheet M03420-1); verify before use. |
| Sectioning | 4–5 µm sections on charged slides (standard) |
| Deparaffinisation | Xylene, graded ethanol series to water (standard) |
| Antigen retrieval | Heat retrieval: Citrate pH 6, 20 min (datasheet M03420-1) |
| Peroxidase block | 3% H2O2, 10 min, room temperature (standard) |
| Blocking | 10% goat serum (datasheet M03420-1) |
| Primary antibody | Mouse monoclonal (clone 2B10) anti-SMN1, 1μg/ml (datasheet M03420-1) |
| Primary incubation | Overnight at 4 °C (datasheet M03420-1) |
| Detection | Streptavidin-biotin complex (SABC), DAB chromogen (datasheet M03420-1) |
| Counterstain | Hematoxylin, blue, dehydrate and mount (standard) |
| Expected result | SMN1-positive staining in hematopoietic cells of bone marrow (HPA tissue IHC: High). HPA tissue profile: Ubiquitous nuclear and cytoplasmic expression. No signal in the no-primary control. |
SMN1 is found in the nucleus, including gems and Cajal bodies, and in the cytoplasm; it has no transmembrane segment (UniProt Q16637). In paraffin sections, expect nuclear and cytoplasmic staining across many cell types, with stronger staining in selected populations such as caudate neuronal cells (HPA: ubiquitous nuclear and cytoplasmic expression; High in caudate neuronal cells). HPA rates tissue IHC reliability as Supported, with medium consistency between staining and RNA data (HPA: Supported).
| Nuclear and cytoplasmic staining in hematopoietic cells of bone marrow or neuronal cells of caudate. | This fits the reported distribution and provides a useful positive reference: both populations stain at High levels (HPA: High in bone marrow hematopoietic cells; High in caudate neuronal cells). Score the identified cells and their compartments, since an apparently strong whole-section result may obscure which cells carry the signal (general IHC practice). |
| Crisp staining restricted to cell membranes, with no convincing nuclear or cytoplasmic signal. | Treat this as a compartment mismatch and investigate an artefact: SMN1 has no transmembrane segment, while the reported pattern is nuclear and cytoplasmic (UniProt Q16637 topology; HPA: ubiquitous nuclear and cytoplasmic expression). Review morphology and the control slide before assigning such staining to the target (general IHC practice). |
| Strong staining in adipocytes, despite little signal in the expected positive cells on the same run. | Consider cross-reactivity or endogenous detection activity, because adipocytes are reported as Not detected, whereas selected positive populations stain High (HPA: Not detected in adipocytes; High in bone marrow hematopoietic cells). That comparison is cell specific: it does not label every cell in adipose tissue as negative (HPA: adipocyte observation). |
| Diffuse colour covers nuclei, cytoplasm, and surrounding tissue without clear cell boundaries. | This does not resolve the reported intracellular pattern (HPA: ubiquitous nuclear and cytoplasmic expression). Non-specific antibody binding, incomplete washing, or detection background can produce diffuse chromogenic staining (general IHC practice). Check the negative detection control and repeat with controlled washing and reagent concentrations (general IHC practice). |
| No convincing signal in caudate neuronal cells or bone marrow hematopoietic cells. | A negative result in these reported High populations calls the run into question before a test specimen is scored negative (HPA: High in caudate neuronal cells; High in bone marrow hematopoietic cells). Check that the positive-control cells are present, then review retrieval, primary-antibody conditions, and detection reagents as general IHC checks (general IHC practice). |
| Which cells provide a positive or negative reference? | Caudate neuronal cells and bone marrow hematopoietic cells are reported High; adipocytes and ovarian stroma cells are Not detected (HPA: tissue IHC). These are cell-level observations, so use morphology to locate the named population before comparing slides (general IHC practice). |
| Does every positive cell need a nuclear punctum? | No. UniProt places SMN1 in gems and Cajal bodies as well as cytoplasm, while HPA tissue IHC reports broader nuclear and cytoplasmic expression (UniProt Q16637 subcellular location; HPA: tissue IHC profile). Evaluate the full compartment pattern; a distinct punctum is not the sole criterion for a positive paraffin section. |
| Can this staining identify SMN1 alone? | Do not claim gene-specific identification from the tissue pattern: HPA cautions that its target protein comes from more than one gene and rates IHC reliability Supported with medium staining–RNA consistency (HPA: reliability description). The reported pattern supports interpretation of staining, but does not establish which gene supplied it. |
| Does the protein's topology predict surface staining? | No transmembrane segment or signal peptide is reported, and the listed locations are intracellular (UniProt Q16637 topology, processing, subcellular location). A membrane-only result therefore needs control review before interpretation; topology alone does not diagnose the source of the artefact (general IHC practice). |
| Do isoforms change the expected tissue pattern? | Four isoforms are listed—SMN, SMN-delta5, SMN-delta7, and SMN-delta57—but this payload gives no antibody epitope or isoform-specific IHC result (UniProt Q16637 isoforms; HPA: tissue IHC). Do not infer which isoform generated a stain or prescribe an isoform-specific retrieval condition from these data. |
| What should an IF/ICC result look like? | HPA reports supported nuclear-body and cytosolic localisation in ICC-IF; UniProt also lists nuclear gems and Cajal bodies (HPA: subcellular ICC-IF; UniProt Q16637 subcellular location). IF/ICC interpretation belongs in its separate guide; these location data do not supply an IF/ICC protocol option. |
| Situation | Likely cause | Next action |
|---|---|---|
| The positive-control section appears blank. | The expected High population may be absent from the section, or an IHC workflow step may have failed (HPA: High in caudate neuronal cells and bone marrow hematopoietic cells; general IHC practice). | First identify the named cells on the counterstained section. Then check retrieval, primary incubation, and chromogenic detection against the run controls (general IHC practice). No SMN1-specific fixation sensitivity is reported in the supplied sources. |
| Colour is widespread and cell boundaries are hard to read. | Non-specific binding, excess detection signal, or inadequate washing may obscure intracellular detail (general IHC practice). | Compare a negative detection control, review blocking and washes, and adjust reagent conditions using the antibody's IHC instructions (general IHC practice). Reassess whether nuclear and cytoplasmic staining can be resolved (HPA: tissue IHC profile). |
| Only cell outlines or membranes stain. | The observed compartment conflicts with the intracellular locations and lack of a transmembrane segment (HPA: tissue IHC profile; UniProt Q16637 topology). | Inspect the control slide and tissue morphology, then review antibody and detection background (general IHC practice). Do not score a membrane-only pattern as the expected result. |
| Adipocytes stain strongly while expected positive cells do not. | Cross-reactivity or endogenous detection activity is possible; adipocytes are reported Not detected (HPA: adipocytes). | Compare the positive-control population and a negative detection control; review blocking and the detection chemistry (HPA: High in caudate neuronal cells; general IHC practice). Limit conclusions to the identified adipocytes. |
| A low-signal tissue is treated as proof that the antibody failed. | HPA reports Low staining in lung alveolar cells, seminal-vesicle glandular cells, and splenic red-pulp cells (HPA: tissue IHC). | Use an identified High population to judge run performance, then score the low-signal cell population in its own tissue context (HPA: High in caudate neuronal cells; Low in lung alveolar cells; general IHC practice). |
| A clean stain is reported as SMN1-specific. | HPA cautions that the target protein comes from more than one gene; a matching location cannot resolve gene origin (HPA: reliability description; UniProt Q16637 subcellular location). | Report the observed cells, compartments, and controls, and retain the gene-specificity caveat (HPA: tissue IHC profile and reliability description). |
Comprehensive Human Protein Atlas IHC scoring per tissue (reliability: Supported — Medium consistency between antibody staining and RNA expression data. Caution, targets protein from more than one gene.). 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 |
|---|---|---|---|---|
| Bone marrow | Hematopoietic cells | High | Protein (IHC) | HPA → |
| Bronchus | Respiratory epithelial cells | High | Protein (IHC) | HPA → |
| Caudate | Neuronal cells | High | Protein (IHC) | HPA → |
| Cerebellum | Cells in molecular layer | High | Protein (IHC) | HPA → |
| Cerebral cortex | Glial cells | High | Protein (IHC) | HPA → |
| Tissue | Cell type | Level | Evidence | Source |
|---|---|---|---|---|
| Adipose tissue | Adipocytes | Not detected | Protein (IHC) | HPA → |
| Liver | Cholangiocytes | Not detected | Protein (IHC) | HPA → |
| Ovary | Ovarian stroma cells | Not detected | Protein (IHC) | HPA → |
| Soft tissue | Fibroblasts | Not detected | Protein (IHC) | HPA → |
Troubleshoot SMN1/2 chromogenic staining in paraffin sections by checking retrieval, compartment-specific signal, and cell-level controls (datasheet M03420-1; UniProt Q16637 localisation).
IHC images show SMN1/2 staining in human mammary cancer sections and mouse and rat brain sections; an IF image shows staining in U20S cells (catalog image captions).
M03420-1 has an IHC image from a paraffin-embedded human mammary cancer section (M03420-1 IHC caption). PB9398 has IHC images from mouse and rat brain and human mammary cancer tissue, plus an IF image from U20S cells (PB9398 image captions).
Which to pick: For paraffin-section IHC, M03420-1 offers a mouse monoclonal clone with a documented human tissue procedure using citrate retrieval and chromogenic detection; its fixative is unreported (M03420-1 catalog and IHC caption). For IF/ICC, choose PB9398 because its application list includes both and its IF caption documents staining in U20S cells (PB9398 catalog and IF caption). For human, mouse, or rat tissue IHC, PB9398 has images from all three species; M03420-1 lists reactivity with all three but its IHC image shows human tissue only (PB9398 IHC captions; M03420-1 catalog and IHC caption).