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- Table of Contents
Plan SUB1 IHC on paraffin sections around widespread nuclear staining (HPA tissue IHC) and a catalog antibody starting range of 2–5 μg/ml (datasheet: M02698-3). Use liver hepatocytes as a positive reference (HPA tissue IHC) and a no-primary control to assess background (standard IHC practice).
Expected localisation, validated protocols, controls and antibodies — the at-a-glance facts below, then the full design guide.
| Expected localisation | Nuclear staining across tissues (HPA tissue IHC) | |
| Staining pattern | Widespread nuclear staining across cell types (HPA tissue IHC) | |
| Antigen retrieval | EDTA pH 8.0 HIER, heat-mediated (datasheet M02698-3) | |
| Positive control | Appendix+4 more · see all | |
| Negative control | None in HPA (detected in all 45 tissues); use no-primary + isotype controls |
| Fixation | Keep fixation consistent across sections (standard IHC practice; not target-specific) | |
| Caveat | Ubiquitous nuclear signal limits negative-cell controls (HPA tissue IHC) | |
| Regulation | Low tissue specificity (HPA tissue RNA) | |
| Isoform / epitope | No isoforms; mature chain aa 2–127; no TM segment (UniProt) |
The catalog antibody’s IHC-P protocol is accompanied by one published SUB1 IHC protocol using prostate tissues (PMC5140777).
| Sample | Paraffin-embedded human colorectal adenocarcinoma tissue; fixative not specified (datasheet M02698-3) |
| Fixation | Image fixative and duration unreported (datasheet M02698-3); 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 M02698-3); 20 min, 95–100 °C (standard) |
| Peroxidase block | 3% H2O2, 10 min, room temperature (standard) |
| Blocking | 10% goat serum (datasheet M02698-3) |
| Primary antibody | Mouse monoclonal (clone 8D9D1) anti-SUB1, 2-5 μg/ml (datasheet M02698-3) |
| Primary incubation | Overnight at 4 °C (datasheet M02698-3) |
| Detection | HRP-conjugated secondary, DAB chromogen (datasheet M02698-3) |
| Counterstain | Hematoxylin, blue, dehydrate and mount (standard) |
| Expected result | SUB1-positive staining in glandular cells of appendix (HPA tissue IHC: High). HPA tissue profile: Ubiquitous nuclear expression. No signal in the no-primary control. |
SUB1 should appear chiefly in nuclei across many cell types (UniProt P53999: nucleus; HPA tissue IHC: ubiquitous nuclear expression). In HPA tissue sections, high staining is reported in several glandular populations, hepatocytes and bone marrow hematopoietic cells; some muscle, follicle and fibroblast populations show low staining (HPA tissue IHC). HPA rates the tissue staining evidence Supported, with medium consistency between antibody staining and RNA expression (HPA tissue IHC).
| Nuclear staining in glandular cells of colon, breast or appendix, with recognizable tissue structure. | This fits the reported high staining in those cell populations and the ubiquitous nuclear profile (HPA tissue IHC). Score the fraction and intensity of stained nuclei within each identified population; do not treat all cells in a section as equally positive (general IHC practice). |
| Predominantly cytoplasmic or membrane staining, with little nuclear signal. | The compartment conflicts with the nuclear tissue pattern and UniProt localization (HPA tissue IHC; UniProt P53999: nucleus). SUB1 has no annotated transmembrane segment or signal sequence (UniProt P53999 topology). Consider nonspecific staining or a detection artefact before calling this SUB1 positive. |
| Strong staining in cells expected to be low, such as skeletal myocytes or smooth muscle cells. | HPA reports low staining in these cells, but supplies no negative tissue population (HPA tissue IHC). Recheck cell identity and nuclear localization. A strong, misplaced signal may reflect cross-reactivity or endogenous detection activity (general IHC practice); intensity alone cannot establish either cause. |
| Diffuse color across tissue, including spaces between cells, obscures nuclear boundaries. | This cannot be scored confidently as the reported nuclear pattern (HPA tissue IHC). Uneven reagent removal, excess primary antibody or detection background are possible general IHC causes (general IHC practice). Compare a control without primary antibody and inspect whether color follows identifiable nuclei. |
| No convincing nuclear signal in a section chosen for a reported high-staining population. | A negative result in colon glandular cells, liver hepatocytes or bone marrow hematopoietic cells conflicts with the reported high staining (HPA tissue IHC). It does not by itself establish absent SUB1: check tissue identity, assay controls and retrieval and detection performance (general IHC practice). |
| Which compartment should drive the IHC score? | Nuclear staining: UniProt places SUB1 in the nucleus, and HPA describes ubiquitous nuclear tissue expression (UniProt P53999; HPA tissue IHC). HPA ICC-IF further supports nucleoplasmic and nucleolar localization (HPA subcellular). Use a nuclear counterstain and intact cell morphology to judge compartment (general IHC practice). |
| Which tissue comparisons are informative? | HPA reports high staining in colon glandular cells and liver hepatocytes, and low staining in skeletal myocytes and soft-tissue fibroblasts (HPA tissue IHC). These are relative pattern checks, not absolute positive and negative controls: the HPA record lists no negative populations (HPA tissue IHC). |
| How strong is the antibody evidence? | Two listed rabbit polyclonal antibodies, HPA001311 and CAB015351, each have Supported IHC status (HPA antibodies). Overall tissue staining reliability is Supported, with medium staining–RNA consistency (HPA tissue IHC). These summaries support pattern comparison but do not establish that every staining difference reflects SUB1 abundance. |
| What does IF/ICC add here? | It offers a localization cross-check: HPA reports supported nucleoplasmic and nucleolar staining, with images from A-431, U-251MG and U2OS cells (HPA subcellular). Those ICC-IF observations do not define an IHC paraffin-section protocol or prove that nucleoli must be distinguishable in every chromogenic section. |
| Is target-specific fixation sensitivity known? | No target-specific fixation effect is supplied by UniProt or HPA here (UniProt P53999; HPA tissue IHC). If retrieval conditions are compared, interpret the outcome as an assay optimization result rather than a documented SUB1-specific fixation response (general IHC practice). |
| Situation | Likely cause | Next action |
|---|---|---|
| High-staining reference tissue shows no nuclear signal. | Tissue selection, retrieval or detection may have failed; the chosen cell population is reported as high by HPA (HPA tissue IHC; general IHC practice). | Confirm the population on the section, check assay controls, then compare validated retrieval and detection settings within the IHC workflow (general IHC practice). |
| Only cytoplasm or cell outlines stain. | That distribution conflicts with the nuclear localization and lack of a transmembrane segment (UniProt P53999; HPA tissue IHC). Nonspecific primary or detection binding is possible (general IHC practice). | Inspect a control without primary antibody; reassess primary dilution and blocking, then score only identifiable nuclear signal (general IHC practice). |
| Every area develops diffuse chromogen. | Detection background or incomplete washing can obscure the nuclear pattern (general IHC practice; HPA tissue IHC: ubiquitous nuclear expression). | Compare a control without primary antibody, improve washing and titrate the primary or detection reagents as appropriate (general IHC practice). |
| Low-staining muscle appears as strong as a high-staining reference population. | HPA reports low staining in skeletal and smooth muscle cells, so the relative pattern warrants review (HPA tissue IHC). Cell misidentification or assay background is possible (general IHC practice). | Identify cells on the counterstained section, compare nuclear intensity across matched runs and examine a control without primary antibody (general IHC practice). |
| Only some nuclei stain within an expected positive region. | HPA reports population-level staining, not a required positive fraction for every section or nucleus (HPA tissue IHC). Section quality and cell identity can affect interpretation (general IHC practice). | Record intensity and positive fraction by cell population; inspect morphology and compare a reported high-staining tissue in the same run (HPA tissue IHC; general IHC practice). |
| A candidate pattern differs between antibody preparations. | The two HPA-listed antibodies are Supported for IHC, while overall staining–RNA consistency is medium (HPA antibodies; HPA tissue IHC). Discordance needs assessment rather than automatic acceptance of either pattern. | Compare nuclear localization, tissue distribution and controls for each preparation; treat unsupported compartment staining cautiously (UniProt P53999; HPA tissue IHC; general IHC practice). |
Comprehensive Human Protein Atlas IHC scoring per tissue (reliability: Supported — 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 |
|---|---|---|---|---|
| Appendix | Glandular cells | High | Protein (IHC) | HPA → |
| Bone marrow | Hematopoietic cells | High | Protein (IHC) | HPA → |
| Breast | Glandular cells | High | Protein (IHC) | HPA → |
| Cerebellum | Cells in molecular layer | High | Protein (IHC) | HPA → |
| Cervix | Glandular cells | High | Protein (IHC) | HPA → |
| Tissue | Cell type | Level | Evidence | Source |
|---|---|---|---|---|
| None in HPA: SUB1 is detected in all 45 scored tissues. Use a no-primary (secondary-only) and an isotype control instead. | ||||
Use nuclear staining, matched controls and the documented retrieval conditions to troubleshoot SUB1 in chromogenic paraffin-section IHC (UniProt P53999: nucleus; datasheet M02698-3).
Four anti-SUB1 antibodies have human paraffin-section IHC images (catalog IHC captions); three also have human paraffin-section IF images (catalog IF captions). All list human, mouse, and rat reactivity (catalog reactivity).
M02698-3 was imaged by IHC in human colorectal adenocarcinoma, and M02698-2 in human colonic adenoma (respective catalog IHC captions). A02698-1 was imaged by IHC in human bladder epithelial carcinoma, and PB10098 in human esophageal squamous carcinoma (respective catalog IHC captions).
Which to pick: For tissue IHC, choose monoclonal M02698-2 for its human paraffin-section example using EDTA retrieval at pH 8.0 and 2 μg/ml primary antibody; the fixative is unreported (M02698-2 catalog IHC caption; catalog clone). For IF/ICC planning, M02698-3 lists IF and has a human paraffin-section IF image at 5 μg/ml; ICC validation is unreported (M02698-3 catalog applications and IF caption). For cross-species IHC, M02698-3 lists IHC testing in human, mouse, and rat at 2–5 μg/ml, while its pictured paraffin-section IHC example is human and does not report the fixative (M02698-3 catalog dilution data and IHC caption).