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- Table of Contents
Plan PAX6 IHC in paraffin sections around nuclear staining in retinal ganglion cells and the cerebellar granular layer (HPA tissue IHC). This guide covers fixation, antigen retrieval, antibody dilution, chromogenic detection and cell-level scoring.
Expected localisation, validated protocols, controls and antibodies — the at-a-glance facts below, then the full design guide.
| Expected localisation | Nuclear in retina and cerebellar granular layer (HPA tissue IHC) | |
| Staining pattern | Retinal ganglion and cerebellar granular cell nuclei (HPA tissue IHC) | |
| Antigen retrieval | EDTA pH 8.0 HIER, heat-mediated (datasheet PB9768) | |
| Positive control | Appendix+4 more · see all | |
| Negative control | Adipose tissue+4 more · see all |
| Fixation | Keep fixation consistent across paraffin sections. (standard IHC practice; not target-specific) | |
| Caveat | Pancreatic endocrine cells show low staining (HPA tissue IHC) | |
| Regulation | TRIM11-linked turnover (by similarity) (UniProt) | |
| Isoform / epitope | Three isoforms (1, 5a, 3); epitope coverage is unknown (UniProt) |
Compare the catalog antibody’s EDTA pH 8.0 IHC-P protocol (datasheet PB9768) with four published PAX6 IHC protocols (PMC9606524; PMC7695321; PMC2699344; PMC5023747).
| Sample | Paraffin-embedded mouse pancreas tissue; fixative not specified (datasheet PB9768) |
| Fixation | Image fixative and duration unreported (datasheet PB9768); 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 PB9768); 20 min, 95–100 °C (standard) |
| Peroxidase block | 3% H2O2, 10 min, room temperature (standard) |
| Blocking | 10% goat serum (datasheet PB9768) |
| Primary antibody | Rabbit anti-PAX6, 0.5-1μg/ml (datasheet PB9768) |
| Primary incubation | Overnight at 4 °C (datasheet PB9768) |
| Detection | Streptavidin-biotin complex (SABC), DAB chromogen (datasheet PB9768) |
| Counterstain | Hematoxylin, blue, dehydrate and mount (standard) |
| Expected result | PAX6-positive staining in endocrine cells of appendix (HPA tissue IHC: High). HPA tissue profile: Distinct nuclear expression mainly in retina and cerebellar granular layer. No signal in the no-primary control. |
PAX6 is a nuclear transcription factor with no transmembrane segment (UniProt P26367). In paraffin-section IHC, expect nuclear staining chiefly in retinal ganglion cells and cerebellar granular cells, with staining also reported in intestinal endocrine cells (HPA tissue IHC). HPA rates the tissue pattern Enhanced, while reporting medium consistency between antibody staining and RNA expression; interpret individual sections in that context (HPA tissue IHC).
| Nuclear chromogen in retinal ganglion cells or the cerebellar granular layer, with limited staining in surrounding cells. | This matches the reported PAX6 compartment and prominent tissue pattern (UniProt P26367; HPA tissue IHC). Judge the named cell population and its nuclei; a positive section does not imply that every cell should stain (HPA tissue IHC). |
| Predominantly cytoplasmic or membrane-like staining, with little nuclear signal. | That distribution conflicts with the nuclear localization reported by UniProt and the nucleoplasmic localization seen by HPA ICC-IF (UniProt P26367; HPA subcellular). Treat it as suspect staining and review morphology and detection controls before scoring it as PAX6. |
| Strong staining in cells listed as undetected, such as adipocytes or bronchial respiratory epithelial cells. | HPA reports no detection in those specified cells (HPA tissue IHC). Cross-reactivity or endogenous chromogenic activity is a possible assay explanation, not an established cause; confirm the cell identity and examine a detection-only control (standard IHC practice). |
| Diffuse chromogen across tissue, including spaces between cells, without a discernible nuclear pattern. | A diffuse field cannot support a PAX6-positive call based on its expected nuclear localization (UniProt P26367). General IHC causes include excess background from detection reagents or insufficient blocking or washing; assess those with appropriate controls (standard IHC practice). |
| No nuclear staining in a section containing identifiable retinal ganglion cells or cerebellar granular cells. | Those are reported high-staining populations, so an entirely blank result warrants an assay check (HPA tissue IHC). Verify that the expected cells are present and assess section handling, retrieval and detection controls before interpreting absence as biology (standard IHC practice). |
| Compartment: nucleus without a transmembrane segment (UniProt P26367). | Score staining in nuclei. Membrane-like staining lacks support from the supplied localization and topology; nuclear counterstaining helps distinguish chromogen in a nucleus from signal in adjacent cytoplasm (UniProt P26367; standard IHC practice). |
| Cell distribution varies within and between tissues (HPA tissue IHC). | HPA reports high levels in retinal ganglion cells, cerebellar granular cells and several intestinal endocrine populations, but low levels in pancreatic endocrine cells (HPA tissue IHC). Select and read controls by cell population, rather than treating a whole tissue as uniformly positive. |
| Tissue evidence is Enhanced, with medium antibody-to-RNA consistency (HPA tissue IHC). | HPA lists HPA030775 and CAB034143 as Enhanced for IHC; this supports the reported pattern but does not validate every unexpected stained cell (HPA antibodies; HPA tissue IHC). Use localization, morphology and assay controls when interpreting a discordant field. |
| Three isoforms are listed: 1, 5a and 3 (UniProt P26367). | The supplied record gives no antibody epitope or isoform coverage. An IHC result therefore cannot establish which isoform contributed to the stain, and a negative result cannot establish that every isoform is absent (UniProt P26367; supplied antibody evidence). |
| No signal peptide, propeptide or annotated cleavage is listed (UniProt P26367). | The supplied processing record offers no basis to expect a shed or secreted staining pattern (UniProt P26367). It also gives no target-specific fixation or retrieval sensitivity; choose and evaluate those conditions as general IHC workflow variables (standard IHC practice). |
| Situation | Likely cause | Next action |
|---|---|---|
| Expected positive nuclei are blank in retina or cerebellum. | The expected cell population may be absent from the section, or the IHC workflow may have failed; HPA reports high staining in the named populations (HPA tissue IHC). | Confirm the cells on the counterstained slide, then check a working positive control and the retrieval and detection steps (standard IHC practice). Avoid calling the tissue negative from an unverified blank field. |
| Staining is mainly cytoplasmic or outlines cell borders. | That compartment differs from the reported nuclear and nucleoplasmic locations (UniProt P26367; HPA subcellular). Background or nonspecific antibody binding remains possible (standard IHC practice). | Compare chromogen with nuclear counterstain and a detection-only control. Score PAX6 only where cell identity and nuclear localization are clear (UniProt P26367; standard IHC practice). |
| Many HPA-listed negative cells stain strongly. | The result conflicts with the specified negative cell populations; cross-reactivity or endogenous detection activity are possible explanations (HPA tissue IHC; standard IHC practice). | Verify morphology and run appropriate detection-only and endogenous-activity controls for the chromogenic system (standard IHC practice). Reassess any residual, cell-specific nuclear staining against HPA's cell-level pattern. |
| The section has broad, hazy chromogenic background. | Background can obscure the nuclear pattern expected for PAX6 (UniProt P26367). In general IHC, blocking, washing or detection-reagent conditions can contribute (standard IHC practice). | Inspect control sections and optimize those general workflow conditions; read only discrete nuclear signal after background is controlled (standard IHC practice; UniProt P26367). |
| Pancreatic endocrine cells look weaker than retinal ganglion cells. | HPA lists pancreatic endocrine cells as Low and retinal ganglion cells as High; equal staining is not the expected comparison (HPA tissue IHC). | Interpret each identified cell population against its own reported level, with an appropriate positive section in the same run (HPA tissue IHC; standard IHC practice). |
| Does an IF/ICC image need to match this paraffin-section IHC result? | HPA ICC-IF reports mainly nucleoplasmic PAX6, but it is a different application from tissue IHC (HPA subcellular; HPA tissue IHC). | Use the IF/ICC guide for that assay. Here, compare only the supported localization expectation; do not infer an IF/ICC protocol or tissue staining level from its images (HPA subcellular). |
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 |
|---|---|---|---|---|
| Appendix | Endocrine cells | High | Protein (IHC) | HPA → |
| Cerebellum | Granular cells - nucleus | High | Protein (IHC) | HPA → |
| Colon | Endocrine cells | High | Protein (IHC) | HPA → |
| Duodenum | Endocrine cells | High | Protein (IHC) | HPA → |
| Rectum | Endocrine cells | High | Protein (IHC) | HPA → |
| Tissue | Cell type | Level | Evidence | Source |
|---|---|---|---|---|
| Adipose tissue | Adipocytes | Not detected | Protein (IHC) | HPA → |
| Adrenal gland | Glandular cells | Not detected | Protein (IHC) | HPA → |
| Bone marrow | Hematopoietic cells | Not detected | Protein (IHC) | HPA → |
| Breast | Adipocytes | Not detected | Protein (IHC) | HPA → |
| Bronchus | Respiratory epithelial cells | Not detected | Protein (IHC) | HPA → |
Troubleshoot PAX6 staining by checking retrieval, nuclear localisation, cell identity and assay controls before comparing signal across sections (UniProt P26367; HPA tissue IHC).
PAX6 antibodies have IHC images from human brain, human pancreatic cancer, mouse brain and pancreas, and rat brain and pancreas (catalog image captions); IF is illustrated in HeLa cells (A00273-1 image caption).
PB9768 has paraffin-section IHC images from mouse and rat pancreas and human pancreatic cancer (PB9768 image captions); M00273-3 has paraffin-section IHC images from mouse and rat brain (M00273-3 image captions). A00273-1 has an IHC image from formalin-fixed, paraffin-embedded human brain and an IF image from HeLa cells (A00273-1 image captions); M00273-5 has a mouse-brain staining image, with processing unreported (M00273-5 image caption).
Which to pick: For tissue IHC, choose PB9768 for pancreas at 0.5–1 μg/ml (PB9768 datasheet; PB9768 image captions) or M00273-3 for brain at 1:50 (M00273-3 catalog dilution; M00273-3 image captions); both captions show paraffin sections but do not report the fixative (PB9768 and M00273-3 image captions). For IF/ICC, choose M00273-3 for its listed ICC/IF application across human, mouse and rat (M00273-3 catalog), or A00273-1 for its illustrated human-cell IF application (A00273-1 catalog and IF image caption). For cross-species tissue IHC, PB9768 and M00273-3 list human, mouse and rat reactivity (PB9768 and M00273-3 catalogs); M00273-3 is monoclonal (M00273-3 catalog), while PB9768 has no clone specified (PB9768 catalog).