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- Table of Contents
Plan HDAC5 paraffin IHC with appendix or colon glandular cells as high-staining references (HPA tissue IHC). Score cytoplasmic and nuclear staining separately, since both occur across tissues (HPA tissue IHC).
Expected localisation, validated protocols, controls and antibodies — the at-a-glance facts below, then the full design guide.
| Expected localisation | Cytoplasmic in most tissues; nuclear in several (HPA tissue IHC) | |
| Staining pattern | Glandular cells can stain strongly; cytoplasmic, sometimes nuclear (HPA tissue IHC) | |
| Antigen retrieval | EDTA pH 8.0 HIER, heat-mediated (datasheet A01230-6) | |
| Positive control | Appendix+4 more · see all | |
| Negative control | None in HPA (detected in all 44 tissues); use no-primary + isotype controls |
| Fixation | Keep fixation consistent across sections. (standard IHC practice; not target-specific) | |
| Caveat | Phosphorylation-driven shuttling may change compartmental staining (UniProt) | |
| Regulation | Differentiation shifts nuclear signal (UniProt) | |
| Isoform / epitope | Three isoforms; epitope coverage is unspecified (UniProt) |
Compare the catalog antibody’s IHC-P protocol (datasheet A01230-6) with two published HDAC5 staining protocols (PMC7791055; PMC9576526).
| Sample | Paraffin-embedded mouse small intestine tissue; fixative not specified (datasheet A01230-6) |
| Fixation | Image fixative and duration unreported (datasheet A01230-6); 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 A01230-6); 20 min, 95–100 °C (standard) |
| Peroxidase block | 3% H2O2, 10 min, room temperature (standard) |
| Blocking | 10% goat serum (datasheet A01230-6) |
| Primary antibody | Rabbit anti-HDAC5, 2-5μg/ml (datasheet A01230-6) |
| Primary incubation | Overnight at 4 °C (datasheet A01230-6) |
| Detection | Streptavidin-biotin complex (SABC), DAB chromogen (datasheet A01230-6) |
| Counterstain | Hematoxylin, blue, dehydrate and mount (standard) |
| Expected result | HDAC5-positive staining in glandular cells of appendix (HPA tissue IHC: High). HPA tissue profile: Cytoplasmic expression in most tissues. Additional nuclear expression in several tissues. No signal in the no-primary control. |
HDAC5 can occupy the nucleus and cytoplasm and shuttle between them (UniProt Q9UQL6: subcellular location). In tissue IHC, expect predominantly cytoplasmic staining, with additional nuclear staining in some tissues (HPA tissue IHC: expression profile). High staining is reported in several glandular cell populations, bone marrow hematopoietic cells, skin Langerhans cells, and tonsil germinal center cells (HPA tissue IHC: high). HPA rates the tissue pattern Approved, with medium consistency between staining and RNA data (HPA tissue IHC: reliability).
| Clear cytoplasmic signal in colon glandular cells, with or without nuclear signal in the section. | This fits the reported tissue pattern: colon glandular cells stain at a high level, and cytoplasmic expression predominates across tissues (HPA tissue IHC: colon; expression profile). Nuclear staining can also be credible because HDAC5 shuttles between compartments (UniProt Q9UQL6: subcellular location). |
| A sharp plasma membrane rim or extracellular deposit is the dominant signal. | This does not fit the reported nuclear and cytoplasmic locations (UniProt Q9UQL6: subcellular location) or the tissue IHC profile (HPA tissue IHC: expression profile). Check morphology and controls before calling it HDAC5; no transmembrane segment or signal peptide is annotated (UniProt Q9UQL6: topology; processing). |
| The strongest deposit lies in an unexpected cell population while the expected cells remain faint. | Compare cell identity with the HPA images and reported levels; for example, colon glandular cells are high, whereas skeletal myocytes are low (HPA tissue IHC: colon; skeletal muscle). Unexpected staining can reflect cross-reactivity or endogenous chromogen activity (general IHC practice), but a single field cannot establish either cause. |
| Color spreads across stroma, lumina, and cells without readable intracellular boundaries. | That distribution cannot support a compartment call against the expected cellular pattern (HPA tissue IHC: expression profile). Diffuse deposit can arise from nonspecific binding, endogenous detection activity, or overdevelopment (general IHC practice); evaluate the negative control and detection chemistry. |
| A known high-staining tissue has no cellular signal. | First confirm that the expected cell population is present: appendix, colon, duodenum, salivary gland, and thyroid glandular cells are reported high (HPA tissue IHC: high). A blank positive control suggests an assay failure, though HPA's Approved rating and medium RNA agreement do not guarantee every specimen will stain (HPA tissue IHC: reliability). |
| Choice of comparison tissue | Use a reported high population to assess whether the run worked; colon glandular cells and bone marrow hematopoietic cells are examples (HPA tissue IHC: high). Heart cardiomyocytes and skeletal myocytes are reported low, so weak staining there alone is less informative (HPA tissue IHC: low). |
| Compartment and cell state | HDAC5 shuttles between nucleus and cytoplasm; during myocyte differentiation it moves into the cytoplasm (UniProt Q9UQL6: subcellular location). Interpret either cellular compartment in context, while using the tissue IHC profile as the primary guide for paraffin sections (HPA tissue IHC: expression profile). |
| Antibody evidence | Three listed antibodies have Approved IHC status: HPA030991, HPA076420, and CAB019400 (HPA antibodies: IHC). The tissue profile has medium consistency with RNA data (HPA tissue IHC: reliability); an unusual pattern therefore needs controls and review, rather than an automatic positive call. |
| Protein forms and processing | UniProt lists 3 isoforms and a full-length chain, with no annotated signal peptide or propeptide (UniProt Q9UQL6: isoforms; processing). These facts support caution when comparing antibody results, but the payload gives no epitope map or isoform-specific staining prediction. |
| IF/ICC Q: must nuclear speckles appear in IHC? | No. HPA reports nuclear speckles as the main supported ICC-IF location, with cytosol supported and Golgi approved (HPA subcellular: ICC-IF). Its tissue IHC summary instead reports mostly cytoplasmic staining plus nuclear staining in several tissues (HPA tissue IHC: expression profile); do not require a speckle pattern in chromogenic sections. |
| Situation | Likely cause | Next action |
|---|---|---|
| No signal in the expected cells of a high-staining control. | The staining run or control selection may have failed (general IHC practice); the expected high level is tissue and cell specific (HPA tissue IHC: high). | Confirm the named cells are present, then review the catalog antibody's IHC-P instructions, retrieval, dilution, and detection controls (general IHC practice). Do not infer HDAC5-specific fixation sensitivity from the HPA profile. |
| All structures, including stroma or empty spaces, carry chromogen. | Nonspecific binding, endogenous detection activity, or excessive development is possible (general IHC practice). | Inspect a no-primary control; check blocking, washes, endogenous-activity control, and development time (general IHC practice). Score cellular staining only after diffuse background is resolved. |
| Only a bright membrane outline appears in otherwise identifiable cells. | A membrane-dominant pattern conflicts with reported nuclear and cytoplasmic localization (UniProt Q9UQL6: subcellular location; topology). | Compare with a known high-staining tissue and a no-primary control; assess whether the outline follows tissue edges or detection deposits (general IHC practice). |
| A nuclear-only pattern appears where cytoplasm was expected. | Nuclear HDAC5 is biologically plausible (UniProt Q9UQL6: subcellular location), and HPA reports additional nuclear expression in several tissues (HPA tissue IHC: expression profile). | Confirm nuclear boundaries with the counterstain and compare the same cell type with HPA tissue images; avoid rejecting the run solely because nuclei stain (general IHC practice; HPA tissue IHC: expression profile). |
| Unexpected cells stain more strongly than the named high-staining population. | Cell identification, cross-reactivity, or endogenous chromogen activity may explain the discrepancy (general IHC practice); HPA levels refer to specified cell populations (HPA tissue IHC: high). | Recheck morphology and the no-primary control, then compare with HPA's tissue and cell labels before assigning HDAC5 positivity (general IHC practice; HPA tissue IHC: high). |
| A muscle section gives only weak signal. | Low staining is reported for cardiomyocytes and skeletal myocytes (HPA tissue IHC: low). | Run a reported high-staining population alongside it, such as colon glandular cells, before changing assay settings (HPA tissue IHC: colon; general IHC practice). |
Comprehensive Human Protein Atlas IHC scoring per tissue (reliability: Approved — 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 → |
| Colon | Glandular cells | High | Protein (IHC) | HPA → |
| Duodenum | Glandular cells | High | Protein (IHC) | HPA → |
| Salivary gland | Glandular cells | High | Protein (IHC) | HPA → |
| Tissue | Cell type | Level | Evidence | Source |
|---|---|---|---|---|
| None in HPA: HDAC5 is detected in all 44 scored tissues. Use a no-primary (secondary-only) and an isotype control instead. | ||||
Use compartment-aware controls and matched processing to troubleshoot HDAC5 staining in paraffin-section chromogenic IHC (UniProt Q9UQL6 localisation; general IHC practice).
Anti-HDAC5 antibodies have paraffin-section IHC images from human, mouse, and rat tissues (IHC captions) and IF/ICC images from human A431 and U20S cells (IF captions).
A01230-5 has IHC images from human placenta and mouse and rat small intestine (A01230-5 IHC captions). A01230-6 has IHC images from mouse small intestine and human placenta, esophageal squamous carcinoma, and lung cancer, plus IF/ICC images from A431 and U20S cells (A01230-6 IHC and IF captions).
Which to pick: For paraffin-section IHC, choose A01230-5 for citrate retrieval at pH 6 and 0.5–1 μg/ml, or A01230-6 for EDTA retrieval at pH 8 and 2–5 μg/ml (respective IHC captions; catalog dilutions). For IF/ICC, choose A01230-6: its application list includes both, and its IF captions show human cell staining at 5 μg/ml (catalog; A01230-6 IF captions). For IHC across human, mouse, and rat tissues, A01230-5 has images from all three species; A01230-6 has human and mouse IHC images, while its broader reactivity list also includes rat (respective IHC captions; catalog reactivity). The IHC captions do not report a fixative (respective IHC captions).