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- Table of Contents
CBX5 shows nuclear staining in most tissues by IHC (HPA tissue IHC). This guide helps plan paraffin-section staining with the IHC-validated antibody and select tissue controls using the reported cell-specific staining pattern (datasheet M02780-2; HPA tissue IHC).
Expected localisation, validated protocols, controls and antibodies — the at-a-glance facts below, then the full design guide.
| Expected localisation | Nuclear staining in most tissues (HPA tissue IHC) | |
| Staining pattern | Nuclear staining across varied tissue cell types (HPA tissue IHC) | |
| Antigen retrieval | EDTA pH 8.0 HIER, heat-mediated (datasheet M02780-2) | |
| Positive control | Cerebellum+4 more · see all | |
| Negative control | Heart muscle+4 more · see all |
| Fixation | Keep fixation consistent across sections (standard IHC practice; not target-specific) | |
| Caveat | Cardiomyocytes lack detectable staining (HPA tissue IHC) | |
| Regulation | H3Y41ph excludes chromatin binding (UniProt) | |
| Isoform / epitope | No annotated isoforms; one chain spans aa 1–191 (UniProt) |
Compare the catalog antibody’s IHC-P protocol (datasheet: M02780-2) with published CBX5 chromogenic IHC protocols (PMC3419921; PMC12450695).
| Sample | Paraffin-embedded rat brain tissue; fixative not specified (datasheet M02780-2) |
| Fixation | Image fixative and duration unreported (datasheet M02780-2); 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 M02780-2); 20 min, 95–100 °C (standard) |
| Peroxidase block | 3% H2O2, 10 min, room temperature (standard) |
| Blocking | 10% goat serum (datasheet M02780-2) |
| Primary antibody | Mouse monoclonal (clone 8G6) anti-CBX5, 2μg/ml (datasheet M02780-2) |
| Primary incubation | Overnight at 4 °C (datasheet M02780-2) |
| Detection | Streptavidin-biotin complex (SABC), DAB chromogen (datasheet M02780-2) |
| Counterstain | Hematoxylin, blue, dehydrate and mount (standard) |
| Expected result | CBX5-positive staining in cells in molecular layer of cerebellum (HPA tissue IHC: High). HPA tissue profile: Nuclear expression in most tissues. No signal in the no-primary control. |
CBX5 should appear chiefly in nuclei, consistent with its chromatin and centromere associations and lack of a transmembrane segment (UniProt P45973). In paraffin-section IHC, expect staining in many tissues, including neuronal cells in cerebral cortex and cytotrophoblasts in placenta (HPA tissue IHC: High). HPA describes nuclear expression in most tissues but rates agreement between staining and RNA expression as medium (HPA tissue IHC: Enhanced reliability).
| Distinct nuclear chromogen in cerebral cortex neuronal cells or placental cytotrophoblasts, with limited surrounding color. | This fits CBX5 localization (UniProt P45973: nucleus and chromatin) and the High staining recorded for those specific cells (HPA tissue IHC). Judge cell identity and nuclear placement together; staining elsewhere in the section does not establish that these reference populations stained. |
| Predominantly cytoplasmic or membranous color, while nuclei remain clear. | That compartment conflicts with the expected nuclear pattern (UniProt P45973; HPA tissue IHC: nuclear expression in most tissues). Treat it as a possible staining or interpretation artifact. Examine a known-positive cell population and a no-primary control before calling the cytoplasmic color CBX5. |
| Strong color in cardiomyocytes or skeletal-muscle myocytes. | HPA records CBX5 as Not detected in those named cell types (HPA tissue IHC). Consider cross-reactivity or endogenous detection activity, especially if nuclei are not clearly stained. These are cell-specific observations; they do not declare every cell in heart or skeletal muscle negative. |
| Diffuse color across stroma, lumina, or nuclei and cytoplasm alike, obscuring cell borders. | A uniform haze is difficult to score as CBX5 because the reference distribution is nuclear (HPA tissue IHC; UniProt P45973). Background from detection reagents or inadequate washing is a general IHC possibility; compare no-primary and positive-control sections before assigning a biological pattern. |
| No nuclear signal in the expected cells of a known-positive control section. | Absent staining in cerebral cortex neuronal cells or placental cytotrophoblasts disagrees with their High HPA observations (HPA tissue IHC). First assess section quality, antibody and detection performance, and whether those exact cells are present; a failed control cannot support a negative result in the test section. |
| Nuclear and chromatin association | CBX5 is a heterochromatin component and is reported at centromeric and pericentromeric regions (UniProt P45973). Nuclear staining is therefore the primary compartment check. A paraffin-section chromogenic result need not resolve individual centromeres to be consistent with this localization. |
| Cell-specific reference intensity | HPA reports High staining in cerebellar molecular-layer cells, hippocampal glial cells, gallbladder glandular cells, and parathyroid glandular cells; prostate glandular cells are Low (HPA tissue IHC). Compare the same cell type when choosing controls or interpreting apparent intensity differences. |
| Strength of antibody evidence | HPA lists CAB017548 as IHC Enhanced; HPA016699 has no listed IHC status (HPA antibodies). The tissue profile also has Enhanced reliability, described as medium staining-to-RNA consistency (HPA tissue IHC). Keep those two evidence labels distinct when judging an unexpected pattern. |
| Protein architecture | The supplied record describes a single 1–191 chain, no signal peptide, no transmembrane segment, and no annotated isoforms (UniProt P45973). Those annotations support a nuclear, intracellular interpretation; they provide no basis for predicting a secreted, shed, or membrane staining pattern. |
| IF/ICC Q: Where should signal appear? | A: In the nucleoplasm (HPA subcellular ICC-IF: enhanced main location). UniProt also places CBX5 in the nucleus and on chromosomes, including centromeres (UniProt P45973). This is an IF/ICC localization check, not an additional IHC protocol or a claim that every nucleus must stain equally. |
| Situation | Likely cause | Next action |
|---|---|---|
| Known-positive nuclei are blank. | The run may have failed, or the expected cells may be missing from the examined area; HPA reports those cells as High (HPA tissue IHC). | Locate the named positive cell population, then check antibody preparation, detection reagents, and run controls. Review antigen-retrieval and dilution records as general IHC workflow checks; no CBX5-specific retrieval condition is supplied. |
| Chromogen is mainly outside nuclei. | The compartment disagrees with CBX5's nuclear localization (UniProt P45973; HPA tissue IHC). Off-target staining or background is possible. | Compare a no-primary section and the same run's positive section. Confirm that counterstained nuclei are identifiable before scoring localization; adjust general blocking or washing only if the controls implicate background. |
| Cardiomyocytes stain strongly. | HPA records cardiomyocytes as Not detected (HPA tissue IHC); antibody cross-reactivity or endogenous chromogenic activity is possible. | Check nuclear placement and a no-primary control. If using enzyme detection, evaluate its endogenous-activity control and blocking step as general IHC practice before accepting this as CBX5 staining. |
| Diffuse color masks tissue detail. | A broad haze prevents assessment of the nuclear reference pattern (HPA tissue IHC; UniProt P45973). Detection background is a general IHC possibility. | Inspect no-primary and reagent controls, then review wash and blocking steps. Reassess only where nuclei and cell boundaries can be distinguished. |
| A low-expression reference cell looks negative. | HPA rates prostate glandular cells Low, whereas parathyroid glandular cells are High (HPA tissue IHC). | Use a named high-staining population to verify the run first. Score the low-staining population against its own reference and background; avoid treating every faint nucleus as a technical failure. |
| An unfamiliar tissue shows patchy nuclear staining. | HPA's profile is cell-specific and has medium staining-to-RNA consistency (HPA tissue IHC: Enhanced reliability); the supplied record does not establish the expected intensity for every cell. | Identify and score the stained cell populations separately. Compare them with the supplied HPA cell-level examples, and report unsupported populations as observations rather than assigning a reference intensity. |
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 | Cells in molecular layer | High | Protein (IHC) | HPA → |
| Cerebral cortex | Neuronal cells | High | Protein (IHC) | HPA → |
| Gallbladder | Glandular cells | High | Protein (IHC) | HPA → |
| Hippocampus | Glial cells | High | Protein (IHC) | HPA → |
| Parathyroid gland | Glandular cells | High | Protein (IHC) | HPA → |
| Tissue | Cell type | Level | Evidence | Source |
|---|---|---|---|---|
| Heart muscle | Cardiomyocytes | Not detected | Protein (IHC) | HPA → |
| Liver | Cholangiocytes | Not detected | Protein (IHC) | HPA → |
| Skeletal muscle | Myocytes | Not detected | Protein (IHC) | HPA → |
| Smooth muscle | Smooth muscle cells | Not detected | Protein (IHC) | HPA → |
| Soft tissue | Chondrocytes | Not detected | Protein (IHC) | HPA → |
Troubleshoot CBX5 staining in paraffin sections by checking nuclear localisation, retrieval, detection background and cell type before comparing chromogenic signal across specimens.
Anti-CBX5 antibodies have IHC images from human, mouse, and rat tissues (catalog IHC captions), plus IF images from HeLa and A549 cells (catalog IF captions).
M02780-2 shows IHC in rat brain and human adrenocortical adenoma, ovarian serous adenocarcinoma, and breast cancer; A02780-3 shows IHC in human lung and mammary cancers and mouse intestine (catalog IHC captions). M02780 shows IHC in mouse and rat brain, while M02780-3 shows staining in rat and mouse pancreas and human breast carcinoma (catalog IHC captions).
Which to pick: For human tissue IHC, choose A02780-3: its paraffin-section captions document EDTA pH 8.0 retrieval and 1 μg/ml primary antibody (A02780-3 IHC captions). For IF/ICC, choose M02780-2: its applications include both, and its A549 cell IF caption documents 5 μg/ml primary antibody and DAPI counterstaining (M02780-2 catalog applications; M02780-2 IF caption). For tissue IHC across human, mouse, and rat samples, consider M02780-3: its captions show staining in all three species, but do not report the fixative or section processing (M02780-3 IHC captions).