This website uses cookies to ensure you get the best experience on our website.
- Table of Contents
Plan CDKN2A IHC-P around mainly nuclear staining in tissue (HPA tissue IHC). A formaldehyde-fixed human colon example uses the catalog antibody at 10 μg/mL (datasheet A00016-1 IHC-P).
Expected localisation, validated protocols, controls and antibodies — the at-a-glance facts below, then the full design guide.
| Expected localisation | Mainly nuclear tissue staining (HPA tissue IHC) | |
| Staining pattern | Mainly nuclear staining in most tissues (HPA tissue IHC) | |
| Antigen retrieval | Citrate pH 6 HIER, heat-mediated (datasheet A00016-1) | |
| Positive control | Appendix+4 more · see all | |
| Negative control | Adipose tissue+4 more · see all |
| Fixation | Formaldehyde-fixed sections shown (selected-SKU IHC image A00016-1); Matched tissue-IHC evidence does not establish the fixation claim. Validate the specimen-specific method before use. (selected-SKU IHC image A00016-1) | |
| Caveat | Splice/transcript discrepancies may complicate interpretation (HPA tissue IHC) | |
| Regulation | RNA enhanced: choroid plexus, pituitary (HPA RNA) | |
| Isoform / epitope | Six isoforms; antibody epitope coverage unspecified (UniProt) |
Compare the catalog antibody’s IHC-P protocol (datasheet A00016-1) with a published primary melanoma IHC protocol (PMC2948432).
| Sample | Formaldehyde-fixed, paraffin-embedded Human Colon tissue (datasheet A00016-1) |
| Fixation | Image formalin-fixed; duration unreported (datasheet A00016-1); 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 (datasheet A00016-1); 20 min, 95–100 °C (standard) |
| Peroxidase block | 3% H2O2, 10 min, room temperature (standard) |
| Blocking | 10% serum (datasheet A00016-1) |
| Primary antibody | Rabbit anti-CDKN2A, 5 - 10 μg/mL (datasheet A00016-1) |
| Primary incubation | Overnight at 4 °C (standard) |
| Detection | HRP-polymer secondary, DAB chromogen 5–10 min (standard) |
| Counterstain | Hematoxylin, blue, dehydrate and mount (standard) |
| Expected result | CDKN2A-positive staining in glandular cells of appendix (HPA tissue IHC: High). HPA tissue profile: Mainly nuclear expression in most tissues. No signal in the no-primary control. |
CDKN2A staining is expected mainly in nuclei, with possible cytoplasmic signal (HPA tissue IHC: mainly nuclear; UniProt P42771: nucleus and cytoplasm). Glandular cells in appendix and colon and elongated or late spermatids in testis are high-staining reference populations (HPA tissue IHC: High). CDKN2A has no transmembrane segment or signal peptide, so a membrane-restricted pattern is unexpected (UniProt P42771 topology). HPA rates the tissue profile Enhanced, while noting medium staining–RNA consistency and a splice or transcript discrepancy (HPA tissue IHC).
| Strong nuclear staining in appendix or colon glandular cells, or testis late spermatids. | This fits the reported high-staining cell populations and mainly nuclear tissue pattern (HPA tissue IHC: High; mainly nuclear). Judge staining in the named cells, not by whole-section darkness; other cells in the section are not established positive controls by these data. |
| Membrane-restricted staining, or cytoplasmic staining with no convincing nuclear signal in a known-positive population. | Recheck specificity and localization: CDKN2A is reported in the nucleus and cytoplasm, with no transmembrane segment (UniProt P42771); HPA tissue staining is mainly nuclear (HPA tissue IHC). Cytoplasmic signal alone is not proof of artifact, but a membrane-only result conflicts with the supplied localization evidence. |
| Strong staining in a cell population reported as not detected, such as adipocytes or skeletal-muscle myocytes. | Treat this as a possible specificity or detection-system problem and verify with controls; HPA reports these named populations as Not detected (HPA tissue IHC). A discrepant stain cannot by itself establish cross-reactivity, because staining patterns can vary with the antibody and assay. |
| Broad, diffuse chromogen deposits obscure nuclei and tissue structure. | Interpretability is limited: a haze lacks the mainly nuclear, cell-specific pattern reported for tissue CDKN2A (HPA tissue IHC). Consider nonspecific binding or endogenous detection activity as general IHC possibilities; the supplied sources do not identify a CDKN2A-specific cause. |
| No staining in appendix or colon glandular cells included as a positive reference. | The result conflicts with HPA's High staining for those populations (HPA tissue IHC: appendix and colon glandular cells, High). Check tissue identity and assay controls before calling the specimen negative; HPA also notes medium staining–RNA consistency and a splice or transcript discrepancy (HPA tissue IHC). |
| Reference tissue and cell population | HPA reports High staining in appendix and colon glandular cells and elongated or late spermatids in testis; adipocytes and skeletal-muscle myocytes are Not detected (HPA tissue IHC). Select and score the stated cell population, since a tissue label alone does not define every cell's expected result. |
| Antibody and transcript context | The tissue profile is Enhanced but has medium agreement with RNA and a splice or transcript discrepancy (HPA tissue IHC). CAB000445 has Enhanced IHC validation; CAB000093 and CAB018232 are Approved for IHC (HPA antibodies). CDKN2A has six annotated isoforms, including ARF (UniProt P42771); an antibody's exact isoform coverage is not supplied. |
| Compartment and processing | UniProt reports nuclear and cytoplasmic localization, no signal peptide, no propeptide and no transmembrane segment (UniProt P42771). HPA tissue staining is mainly nuclear (HPA tissue IHC). These records support checking the compartment, but do not establish any CDKN2A-specific antigen-retrieval or fixation response. |
| IF/ICC Q: What localization can corroborate IHC? | A: Nucleoplasm is supported in HPA ICC-IF; cytosol and primary-cilium locations are uncertain (HPA subcellular). Use this as a localization cross-check only: the tissue IHC profile is mainly nuclear (HPA tissue IHC), and the supplied ICC-IF record does not define an IHC protocol. |
| Situation | Likely cause | Next action |
|---|---|---|
| No signal in a high-staining reference population. | The run may have failed, the selected cell population may be absent, or antibody coverage may differ across isoforms (general IHC practice; UniProt P42771: six isoforms). | Confirm appendix or colon glandular cells are present and review positive controls, antibody documentation and detection steps (HPA tissue IHC: High in those cells; general IHC practice). Do not infer a CDKN2A-specific fixation effect from this result. |
| Only membrane outlines stain. | The pattern is inconsistent with reported nucleus/cytoplasm localization and absence of a transmembrane segment (UniProt P42771 topology). | Compare with a known-positive nuclear reference and appropriate reagent controls; reassess antibody specificity and chromogen deposits (HPA tissue IHC: mainly nuclear; general IHC practice). |
| Reported negative cells stain strongly. | Nonspecific antibody binding or endogenous detection activity is possible (general IHC practice); HPA reports adipocytes and skeletal-muscle myocytes as Not detected (HPA tissue IHC). | Check no-primary and detection controls, then score the exact cell population rather than the entire tissue (general IHC practice; HPA tissue IHC: cell-level annotations). |
| Diffuse background masks cell boundaries. | Nonspecific binding, insufficient washing or endogenous detection activity can produce background in chromogenic IHC (general IHC practice). | Review blocking, washes and detection controls, then reassess whether nuclei remain distinguishable (general IHC practice; HPA tissue IHC: mainly nuclear pattern). |
| Cytoplasmic signal accompanies nuclear staining. | Cytoplasmic localization is recorded by UniProt, while HPA describes tissue staining as mainly nuclear (UniProt P42771; HPA tissue IHC). | Record nuclear and cytoplasmic staining separately; compare cell-specific distribution with the reference tissue before labeling the cytoplasmic component nonspecific (HPA tissue IHC: mainly nuclear; general IHC practice). |
| Brain staining conflicts with an expected negative result. | UniProt says CDKN2A is not detected in brain, whereas HPA reports Medium staining in caudate glial cells and cerebellar molecular-layer cells (UniProt P42771 tissue specificity; HPA tissue IHC). | Document the cell type and antibody used; interpret the discrepancy cautiously in light of HPA's medium staining–RNA consistency and splice or transcript warning (HPA tissue IHC). |
Comprehensive Human Protein Atlas IHC scoring per tissue (reliability: Enhanced — Medium consistency between antibody staining and RNA expression data. Caution, Splice and/or transcript discrepancy exists.). 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 → |
| Colon | Glandular cells | High | Protein (IHC) | HPA → |
| Testis | Elongated or late spermatids | High | Protein (IHC) | HPA → |
| Adrenal gland | Glandular cells | Medium | Protein (IHC) | HPA → |
| Breast | Glandular cells | Medium | Protein (IHC) | HPA → |
| Tissue | Cell type | Level | Evidence | Source |
|---|---|---|---|---|
| Adipose tissue | Adipocytes | Not detected | Protein (IHC) | HPA → |
| Fallopian tube | Ciliated cells (cell body) | Not detected | Protein (IHC) | HPA → |
| Skeletal muscle | Myocytes | Not detected | Protein (IHC) | HPA → |
| Soft tissue | Fibroblasts | Not detected | Protein (IHC) | HPA → |
| Vagina | Squamous epithelial cells | Not detected | Protein (IHC) | HPA → |
Troubleshoot CDKN2A staining in paraffin section IHC by checking retrieval, compartment, cell type, antibody epitope, and controls before interpreting chromogenic signal.
IHC figures cover human and rat colon, rat liver, mouse brain, and human gastric tissue (catalog IHC captions); IF figures cover human cells and human or rat colon tissue (A00016-1 IF captions).
A00016-1 shows paraffin-section IHC in human and rat colon and IF in HeLa, A431, and human and rat colon (A00016-1 IHC/IF captions); A00016-3 shows paraffin-section IHC in rat liver, human brain tumor, breast cancer, esophageal epithelium, mouse brain, and stomach tissue (A00016-3 IHC caption). M00016 shows paraffin-section IHC in human gastric tissue (M00016 IHC caption) and lists human IF/ICC applications, although its IF captions do not identify the specimens (M00016 applications, reactivity, IF captions).
Which to pick: For tissue IHC, choose A00016-1: its human and rat colon paraffin-section examples report formaldehyde fixation and citrate retrieval at pH 6 (A00016-1 IHC captions). For human IF/ICC, M00016 is a rabbit monoclonal listing both applications; its IHC example uses paraffin-embedded human gastric tissue, with the fixative unreported (M00016 catalog clone, applications, reactivity, IHC caption). For cross-species paraffin-section IHC, A00016-3 is a mouse monoclonal with rat liver, mouse brain, and human tissue examples; its caption does not report the fixative (A00016-3 catalog clone, IHC caption).