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- Table of Contents
Plan SIGMAR1 paraffin section IHC around the cytoplasmic staining reported in most tissues, with high staining in hepatocytes (HPA tissue IHC). This guide covers fixation consistency, antibody concentration, chromogenic detection and interpretation of its ER and nuclear envelope localisation (UniProt).
Expected localisation, validated protocols, controls and antibodies — the at-a-glance facts below, then the full design guide.
| Expected localisation | Cytoplasmic staining (HPA tissue IHC); ER and nuclear envelope localisation (UniProt) | |
| Staining pattern | Cytoplasmic in most tissues; high in hepatocytes (HPA tissue IHC) | |
| Antigen retrieval | EDTA pH 8.0 HIER, heat-mediated (datasheet A02493-2) | |
| Positive control | Cerebellum+4 more · see all | |
| Negative control | Adipose tissue+2 more · see all |
| Fixation | Keep fixation consistent across sections. (standard IHC practice; not target-specific) | |
| Caveat | Ligand binding can alter localisation (UniProt) | |
| Regulation | Expression regulation is not established (UniProt) | |
| Isoform / epitope | 5 isoforms; map the epitope to each; residues 31–223 are cytoplasmic (UniProt) |
Compare the catalog antibody’s IHC-P protocol (datasheet A02493-2) with four published SIGMAR1 paraffin-section protocols (PMC11858467; PMC10083329; PMC11089145; PMC11351121).
| Sample | Paraffin-embedded rat colon tissue; fixative not specified (datasheet A02493-2) |
| Fixation | Image fixative and duration unreported (datasheet A02493-2); 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 A02493-2); 20 min, 95–100 °C (standard) |
| Peroxidase block | 3% H2O2, 10 min, room temperature (standard) |
| Blocking | 10% goat serum (datasheet A02493-2) |
| Primary antibody | Rabbit anti-SIGMAR1, 2-5 μg/ml (datasheet A02493-2) |
| Primary incubation | Overnight at 4 °C (datasheet A02493-2) |
| Detection | HRP-conjugated secondary, DAB chromogen (datasheet A02493-2) |
| Counterstain | Hematoxylin, blue, dehydrate and mount (standard) |
| Expected result | SIGMAR1-positive staining in purkinje cells of cerebellum (HPA tissue IHC: High). HPA tissue profile: Cytoplasmic expression in most tissues. No signal in the no-primary control. |
SIGMAR1 is a membrane protein with 1 transmembrane segment and a cytoplasmic region spanning residues 31–223 (UniProt Q99720 topology). In paraffin IHC, expect predominantly cytoplasmic staining in many tissues (HPA: tissue IHC profile), especially Purkinje cells, hepatocytes, and trophoblastic cells (HPA: High). HPA rates the tissue staining evidence Enhanced, with medium consistency between staining and RNA expression (HPA: reliability description).
| Cytoplasmic staining in hepatocytes, trophoblastic cells, or cerebellar Purkinje cells. | This fits the observed tissue pattern: each cell population is rated High (HPA: tissue IHC). An ER-associated or nuclear-envelope distribution is biologically plausible (UniProt Q99720 subcellular location), but routine chromogenic IHC may not resolve those membranes individually (general IHC practice). Judge the result against cell identity and background as well as intensity. |
| Predominantly filled-nuclear staining, with little cytoplasmic signal, in an expected-positive population. | This departs from HPA’s predominantly cytoplasmic tissue profile (HPA: tissue IHC). UniProt reports nuclear-envelope membranes, which can appear close to the nucleus; it does not establish diffuse nucleoplasmic staining (UniProt Q99720 subcellular location). Check morphology and a control section before assigning a nuclear pattern (general IHC practice). |
| Strong signal in adipocytes, marrow hematopoietic cells, or soft-tissue fibroblasts. | These populations are listed as Not detected in the sampled HPA tissue IHC images (HPA: tissue IHC). Unexpected staining may reflect nonspecific antibody binding or endogenous detection activity (general IHC practice). The HPA entries are reference observations, so investigate the discrepancy without treating them as proof that every specimen must be negative. |
| Diffuse color across tissue, stroma, and spaces without recognizable cellular boundaries. | An even deposit obscures the cell-associated pattern reported by HPA (HPA: cytoplasmic expression in most tissues). Excess primary antibody, inadequate blocking or washing, and chromogen or endogenous-enzyme background are possible general IHC causes (general IHC practice). Such a slide cannot establish a SIGMAR1-positive compartment. |
| No detectable stain in a hepatocyte-rich liver section run as a positive control. | HPA rates hepatocytes High (HPA: liver tissue IHC), making a blank control a reason to check the assay before interpreting test sections. Confirm that the section contains preserved hepatocytes, the IHC-validated antibody and detection reagents were applied, and the run controls worked (general IHC practice). A blank result alone does not identify the failed step. |
| Membrane topology and apparent compartment | SIGMAR1 has 1 transmembrane segment at residues 10–30, followed by a cytoplasmic region (UniProt Q99720 topology). UniProt places it at the ER and nuclear-envelope membranes during interphase (UniProt Q99720 subcellular location). This supports a cytoplasmic or perinuclear appearance, but the slide cannot by itself distinguish those closely spaced membranes (general IHC practice). |
| Tissue and cell selection | HPA reports High staining in hepatocytes, trophoblastic cells, and Purkinje cells; Medium staining in several epithelial or neuronal populations; and Low staining in kidney tubules, prostate glands, and cardiomyocytes (HPA: tissue IHC). Choose a documented High population for a positive control. A Low population is a less decisive test of assay sensitivity (general IHC practice). |
| Strength and limits of the IHC evidence | HPA labels its tissue IHC evidence Enhanced while describing medium consistency with RNA expression (HPA: reliability description). Two listed antibodies have Enhanced IHC status and one has Approved IHC status (HPA: antibody validation). Those ratings support the reference pattern; they do not validate an unlisted catalog antibody or prove that every tissue section will match it. |
| Isoforms and protein processing | UniProt lists 5 SIGMAR1 isoforms, no annotated signal peptide or propeptide, and no annotated glycosylation sites (UniProt Q99720 isoforms and processing). The payload gives no antibody epitope or isoform coverage. Do not infer that an unexpected compartment represents a particular isoform, cleavage product, or glycosylated form from this IHC result. |
| IF/ICC: what pattern can this section support? | The HPA subcellular summary says Membrane, but provides no main location or ICC-IF image-bearing cell lines (HPA: subcellular ICC-IF). UniProt supports ER and nuclear-envelope membrane localization (UniProt Q99720 subcellular location). These facts give a localization expectation, not an IF/ICC validation result; the separate IF/ICC guide should address that application. |
| Situation | Likely cause | Next action |
|---|---|---|
| The liver positive control is blank. | An assay or section problem is possible despite High hepatocyte staining in HPA (HPA: liver tissue IHC). The observation alone does not identify a SIGMAR1-specific cause. | Check hepatocyte preservation, reagent application, detection chemistry, and run controls; then optimize retrieval and antibody dilution as general paraffin-IHC variables (general IHC practice). No SIGMAR1-specific retrieval or fixation sensitivity is established here. |
| The whole section has brown haze or diffuse color. | Broad background can result from excess primary antibody, incomplete washing or blocking, or endogenous detection activity (general IHC practice). It obscures HPA’s cell-associated cytoplasmic profile (HPA: tissue IHC). | Compare a no-primary control, review blocking and wash steps, and titrate the primary and chromogen development under the assay’s general IHC controls (general IHC practice). Score cells only after background permits compartment assessment. |
| The strongest signal fills nuclei. | HPA describes cytoplasmic tissue staining, while UniProt specifies nuclear-envelope membranes rather than a general nucleoplasmic pool (HPA: tissue IHC; UniProt Q99720 subcellular location). | Recheck counterstained cell outlines and compare an expected-positive tissue with a no-primary control (general IHC practice). Record a true nuclear-only pattern as discordant instead of reclassifying it as nuclear-envelope staining. |
| Adipocytes, marrow cells, or fibroblasts stain strongly. | Those sampled populations are Not detected in HPA tissue IHC (HPA: tissue IHC). Nonspecific binding or endogenous detection activity is possible (general IHC practice). | Inspect the matching no-primary control and tissue morphology; adjust general blocking or detection steps if background persists (general IHC practice). Confirm the unexpected cell pattern independently before attributing it to SIGMAR1. |
| A Low reference tissue stains weakly or inconsistently. | HPA rates kidney tubules, prostate glandular cells, and cardiomyocytes Low (HPA: tissue IHC). Their faint staining offers limited assurance that a negative run is technically sound (general IHC practice). | Include a documented High population, such as hepatocytes, in the same run when feasible (HPA: tissue IHC). Interpret weak target staining only after checking that control and the section’s cellular morphology (general IHC practice). |
| A perinuclear rim is hard to distinguish from diffuse cytoplasm. | UniProt reports ER and nuclear-envelope membrane localization, and HPA reports a broad cytoplasmic tissue pattern (UniProt Q99720 subcellular location; HPA: tissue IHC). Chromogenic light microscopy has limited resolution for these adjacent structures (general IHC practice). | Report the observable cytoplasmic or perinuclear pattern and the identified cell type; avoid assigning a precise membrane from this section alone (general IHC practice). Use the separate IF/ICC guide if subcellular resolution is the study goal. |
Comprehensive Human Protein Atlas IHC scoring per tissue (reliability: Enhanced — Medium 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 |
|---|---|---|---|---|
| Cerebellum | Purkinje cells | High | Protein (IHC) | HPA → |
| Liver | Hepatocytes | High | Protein (IHC) | HPA → |
| Placenta | Trophoblastic cells | High | Protein (IHC) | HPA → |
| Adrenal gland | Glandular cells | Medium | Protein (IHC) | HPA → |
| Appendix | Glandular cells | Medium | Protein (IHC) | HPA → |
Use the catalog antibody’s paraffin-section evidence as a starting point, then interpret staining against SIGMAR1 topology and tissue patterns.
The IHC-validated anti-SIGMAR1 antibody has real paraffin-section data from rat and mouse colon, human colon adenocarcinoma, and human stomach cancer (catalog IHC image captions).
A02493-2 has IHC images from rat and mouse colon, human colon adenocarcinoma, and human stomach cancer, all in paraffin sections (A02493-2 IHC image captions). Its listed reactivity includes Human, Monkey, Mouse, and Rat; the IHC images cover Human, Mouse, and Rat (catalog reactivity; A02493-2 IHC image captions).
Which to pick: Choose A02493-2 for paraffin-section tissue IHC; its rat and mouse colon captions report 2 μg/ml primary antibody and EDTA retrieval at pH 8.0, while the fixative is unreported (A02493-2 IHC image captions). For cross-species IHC, A02493-2 lists Human, Monkey, Mouse, and Rat reactivity, with IHC images for Human, Mouse, and Rat (catalog reactivity; A02493-2 IHC image captions). No SKU here is documented for IF/ICC: A02493-2 has no listed IF/ICC application, IF dilution, or IF image (catalog applications; IF dilution and image fields).