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- Table of Contents
Plan chromogenic CDKN2A IHC-P using the catalog antibody’s human colon example (datasheet A00016-1 IHC-P). Expect mainly nuclear tissue staining, with high staining in colon glandular cells, and account for the reported splice/transcript discrepancy (HPA tissue IHC).
Expected localisation, validated protocols, controls and antibodies — the at-a-glance facts below, then the full design guide.
| Expected localisation | Mainly nuclear in tissue (HPA tissue IHC); cytoplasmic location also annotated (UniProt) | |
| Staining pattern | Mainly nuclear staining; high in colon glandular cells (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 were used (datasheet A00016-1 IHC-P) (selected-SKU IHC image A00016-1) | |
| Caveat | Splice/transcript discrepancy complicates interpretation (HPA tissue IHC) | |
| Regulation | Staining intensity varies by cell type and tissue (HPA tissue IHC) | |
| Isoform / epitope | Six isoforms, including ARF; verify which isoform the epitope detects (UniProt) |
Start with the catalog antibody’s IHC-P protocol (datasheet A00016-1), then compare the published melanoma protocol (PMC2948432: methods).
| 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 is a soluble protein with no transmembrane segment and is annotated in the nucleus and cytoplasm (UniProt P42771 topology and subcellular location). In tissue IHC, expect mainly nuclear staining, particularly in appendix and colon glandular cells and testicular elongated or late spermatids (HPA: mainly nuclear; High in these cells). HPA rates its tissue profile Enhanced but reports only medium agreement with RNA data and a splice or transcript discrepancy (HPA: reliability description).
| Distinct nuclear staining in appendix or colon glandular cells, or in testicular elongated or late spermatids. | This fits the reported high-expression cell types and mainly nuclear tissue pattern (HPA: High in these cells; mainly nuclear). Judge staining within the identified cells, since a tissue label alone does not identify which cells carry the signal (HPA: cell-level tissue IHC). |
| Strong staining confined to cell borders, lumens, or extracellular material, with no convincing nuclear signal. | Treat this as a compartment mismatch requiring investigation: CDKN2A has no transmembrane segment, and HPA tissue staining is mainly nuclear (UniProt P42771 topology; HPA: tissue profile). Check morphology and the detection controls before assigning this signal to CDKN2A (general IHC practice). |
| Staining in cells reported as negative, such as skeletal-muscle myocytes or adipocytes. | The pattern conflicts with those HPA observations and may reflect antibody cross-reactivity or endogenous detection activity (HPA: Not detected in skeletal-muscle myocytes and adipocytes; general IHC practice). A negative tissue observation is a comparator, not proof that every stained cell is false positive (HPA: tissue IHC profile). |
| Diffuse color across cells and surrounding tissue, without distinct nuclear boundaries. | This does not reproduce the mainly nuclear profile (HPA: tissue IHC profile). Check background from the detection system and nonspecific binding using an appropriate negative control; score cells only where morphology and nuclear signal can be distinguished (general IHC practice). |
| No nuclear signal in appendix or colon glandular cells on an otherwise interpretable section. | This disagrees with the reported high staining in those cell types (HPA: High in appendix and colon glandular cells). Review the sampled cells, antibody validation and run controls before calling the specimen negative; HPA also reports medium staining–RNA consistency (HPA: reliability description; general IHC practice). |
| Compartment and topology | Use predominantly nuclear tissue staining as the primary interpretation anchor (HPA: mainly nuclear). Cytoplasmic CDKN2A is annotated, so a cytoplasmic component is possible, but a membrane-only pattern lacks support from its topology (UniProt P42771 subcellular location and topology). |
| Cell type and tissue selection | Appendix and colon glandular cells and testicular elongated or late spermatids provide reported high-staining comparators (HPA: High). Skeletal-muscle myocytes and adipocytes are reported as not detected; assess the named cells rather than all cells in either section (HPA: tissue IHC). |
| Transcript and isoform interpretation | Six isoforms are listed, including ARF and smARF; isoform 3 is described as pancreas-specific (UniProt P42771 isoforms and tissue specificity). HPA flags a splice or transcript discrepancy, so tissue RNA abundance alone should not settle an unexpected IHC result (HPA: reliability description). |
| Antibody validation | HPA lists CAB000445 as IHC Enhanced and CAB000093 and CAB018232 as IHC Approved (HPA: antibodies). These are antibody-specific statuses; apply a listed status only to the matching antibody, and use that antibody’s own validation when interpreting discordant staining (HPA: antibodies; general IHC practice). |
| IF/ICC Q: What location should be expected? | A: Mainly nucleoplasm; HPA also lists cytosol and primary-cilium locations as uncertain (HPA: subcellular ICC-IF). Those ICC-IF observations support an imaging interpretation, but do not change the mainly nuclear tissue-IHC expectation (HPA: subcellular ICC-IF; tissue IHC). |
| Situation | Likely cause | Next action |
|---|---|---|
| Expected glandular-cell nuclei are blank in appendix or colon. | The sampled cells may be absent, or the IHC run may have failed; those cells are reported High (HPA: appendix and colon glandular cells; general IHC practice). | Confirm glandular-cell morphology, inspect the run’s positive control, and review the IHC validation of the antibody used before interpreting absence as biological (general IHC practice; HPA: antibody statuses). |
| Only edge, luminal, or extracellular deposits appear. | That distribution does not fit the mainly nuclear tissue pattern or the lack of a transmembrane segment (HPA: tissue profile; UniProt P42771 topology). | Check the negative detection control and compare deposits with intact nuclei on the counterstained section; withhold a CDKN2A-positive call until a cellular pattern is resolved (general IHC practice). |
| A reported negative cell type stains strongly. | Cross-reactivity or endogenous detection activity is possible, especially if the signal occurs in HPA-negative adipocytes or skeletal-muscle myocytes (HPA: Not detected in those cells; general IHC practice). | Repeat with appropriate negative detection controls and confirm the exact stained cell type; compare antibody-specific IHC validation before treating the result as an exception (general IHC practice; HPA: antibody statuses). |
| The whole section looks uniformly colored. | Diffuse detection background or nonspecific binding may obscure the reported mainly nuclear pattern (general IHC practice; HPA: tissue profile). | Inspect a negative control, review blocking and detection steps, and evaluate whether counterstained nuclei remain distinguishable; do not score diffuse color as cellular positivity (general IHC practice). |
| Brain staining seems to conflict with the UniProt tissue note. | UniProt says CDKN2A is not detected in brain, while HPA reports Medium staining in caudate glial cells and cerebellar molecular-layer cells (UniProt P42771 tissue specificity; HPA: caudate and cerebellum). | Record the specific region, cell type, compartment and antibody, then report the source disagreement; HPA flags medium RNA–staining consistency and a transcript discrepancy (HPA: reliability description; general IHC practice). |
| ICC-IF shows a ciliary or cytosolic signal alongside nuclear staining. | HPA supports nucleoplasmic localization but marks cytosol and primary-cilium locations uncertain (HPA: subcellular ICC-IF). | Interpret those additional locations cautiously against the supported nucleoplasmic signal and imaging controls; use the tissue-IHC pattern when scoring paraffin sections (HPA: subcellular ICC-IF; tissue IHC; general IF practice). |
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, cellular localisation, antibody specificity and scoring before interpreting biological differences.
The catalog shows IHC data from human, rat and mouse tissues (catalog IHC captions), plus IF images from human cells and human and rat colon (A00016-1 IF captions).
A00016-1 has paraffin-section IHC images from human and rat colon and IF images from human cells and human and rat colon (A00016-1 image captions). A00016-3 has paraffin-section IHC images from rat, human and mouse tissues; M00016 has a paraffin-section IHC image from human gastric tissue (A00016-3 and M00016 IHC captions).
Which to pick: For tissue IHC, start with A00016-1: its human and rat colon captions report paraffin sections fixed with formaldehyde and stained at 10 μg/mL and 5 μg/mL, respectively (A00016-1 IHC captions). For broader cross-species tissue examples, consider mouse monoclonal A00016-3; its caption shows rat, human and mouse paraffin sections but does not report a fixative (A00016-3 catalog entry and IHC caption). For human IF/ICC, rabbit monoclonal M00016 lists both applications, while A00016-1 offers specific IF images of human cells and colon; M00016’s gastric IHC caption reports paraffin sections but no fixative (M00016 catalog entry and IHC caption; A00016-1 IF captions).