HDAC5 / Histone deacetylase 5 · IHC design guide

Design Immunohistochemistry for HDAC5

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).

Evidence assembled Oct 2026 · For research use; verify linked source records and product datasheet before use
Immunohistochemistry protocol sheet for HDAC5 (IHC for HDAC5): expected localisation Cytoplasmic in most tissues; nuclear in several (HPA tissue IHC), antibody A01230-6, validated IHC image, and IHC protocol steps
Printable HDAC5 IHC protocol sheet — expected localisation Cytoplasmic in most tissues; nuclear in several (HPA tissue IHC), antibody A01230-6, controls and protocol steps. Open the full HDAC5 IHC guide →

HDAC5 Immunohistochemistry Experimental Design Guide

Expected localisation, validated protocols, controls and antibodies — the at-a-glance facts below, then the full design guide.

Must know before staining
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
Important caveats
Reasons your staining may differ from the expected pattern.
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)
Section 1

Recommended HDAC5 IHC & IF Protocols

Compare the catalog antibody’s IHC-P protocol (datasheet A01230-6) with two published HDAC5 staining protocols (PMC7791055; PMC9576526).

Recommended immunohistochemistry (IHC-P) protocol parameters
SampleParaffin-embedded mouse small intestine tissue; fixative not specified (datasheet A01230-6)
FixationImage fixative and duration unreported (datasheet A01230-6); verify before use.
Sectioning4–5 µm sections on charged slides (standard)
DeparaffinisationXylene, graded ethanol series to water (standard)
Antigen retrievalHeat retrieval: EDTA pH 8.0 (datasheet A01230-6); 20 min, 95–100 °C (standard)
Peroxidase block3% H2O2, 10 min, room temperature (standard)
Blocking10% goat serum (datasheet A01230-6)
Primary antibodyRabbit anti-HDAC5, 2-5μg/ml (datasheet A01230-6)
Primary incubationOvernight at 4 °C (datasheet A01230-6)
DetectionStreptavidin-biotin complex (SABC), DAB chromogen (datasheet A01230-6)
CounterstainHematoxylin, blue, dehydrate and mount (standard)
Expected resultHDAC5-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.
💡Decision noteStart with EDTA pH 8.0 heat retrieval (datasheet A01230-6). The pressure-cooker protocol does not specify a retrieval buffer (PMC7791055).
Section 2

What Is the Expected HDAC5 Staining Pattern?

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).

What am I looking at on my slide?
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).
💡Expected HDAC5 appearanceCall a positive result when identifiable cells show predominantly cytoplasmic HDAC5 staining, sometimes with nuclear staining, with high signal in an HPA high-staining population such as colon glandular cells; isolated extracellular or membrane-like deposit is suspect (HPA tissue IHC: expression profile; colon; UniProt Q9UQL6: subcellular location; topology).
How each factor affects the staining
Choice of comparison tissueUse 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 stateHDAC5 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 evidenceThree 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 processingUniProt 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.
Why is my staining missing, weak or wrong?
SituationLikely causeNext 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).

Sample controls for HDAC5 IHC & IF

🧪Run duodenum first and expect glandular cells to stain strongly (HPA: High in duodenal glandular cells). HPA detects HDAC5 in all 44 scored tissues, so there is no supported negative tissue; use no-primary and isotype controls, and treat cells on the positive slide with little or no staining as a within-slide comparison rather than a proven biological negative (HPA: no negative tissue rows; detected in all 44 scored tissues).
Positive control tissue: Appendix (Glandular cells, HPA High)
Negative control tissue: None in HPA: HDAC5 is detected in all 44 scored tissues. Use a no-primary (secondary-only) and an isotype control instead.
ICC-IF cell lines (HPA subcellular resource): HPA ICC-IF images show HDAC5 in A-431, U-251MG, U2OS, with annotated localisation: Nuclear speckles (supported) (HPA subcellular).
Technical controls: Include a no-primary, secondary-only section, a concentration-matched rabbit IgG isotype control, and HDAC5-knockout tissue or a peptide-block control if available (caption: rabbit primary antibody; standard IHC practice). For duodenum with chromogenic detection, block endogenous peroxidase and check endogenous biotin background before using the caption’s biotin-based detection system (caption: biotinylated secondary and streptavidin-biotin complex with DAB; standard IHC practice).
⚠️Feasibility: A target-specific fixation window or fixation effect is unreported, and the selected A01230-6 paraffin-section caption does not state a fixative (selected-SKU caption: fixative not stated). Heat retrieval in EDTA at pH 8.0 is a documented starting condition, but the supplied evidence does not establish that retrieval is required (selected-SKU caption: heat retrieval in EDTA, pH 8.0). The evidence does not establish whether frozen sections or IF are easier; in duodenum, assess glandular background alongside specific staining, especially with biotin-based chromogenic detection (HPA: High in duodenal glandular cells; caption: biotin-based DAB detection; standard IHC practice).

HPA tissue IHC evidence for HDAC5

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.

Positive expression · recommended positive controls

TissueCell typeLevelEvidenceSource
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 →

Undetected expression · recommended negative controls

TissueCell typeLevelEvidenceSource
None in HPA: HDAC5 is detected in all 44 scored tissues. Use a no-primary (secondary-only) and an isotype control instead.
Section 3

Advanced HDAC5 IHC Tips

Use compartment-aware controls and matched processing to troubleshoot HDAC5 staining in paraffin-section chromogenic IHC (UniProt Q9UQL6 localisation; general IHC practice).

How should I optimize retrieval when HDAC5 staining is weak?
Start with heat-mediated retrieval in EDTA pH 8.0 for paraffin sections (datasheet A01230-6). The selected image used that retrieval before overnight incubation at 4°C with 2 μg/mL antibody (datasheet A01230-6). If staining is weak, vary heating time in small steps while keeping section thickness, cooling, antibody concentration, and detection constant (general IHC practice). Compare each condition on adjacent sections with a no-primary control, recording nuclear and cytoplasmic staining separately because HDAC5 can occupy both compartments (UniProt Q9UQL6 localisation; general IHC practice). Increased DAB intensity alone does not establish improved antigen detection if background rises with it (general IHC practice).
Could fixation explain inconsistent HDAC5 staining between paraffin-section batches?
The selected tissue-IHC caption identifies paraffin embedding but does not report the fixative, so target-specific HDAC5 fixation sensitivity is unknown (datasheet A01230-6). Record fixative, fixation duration, tissue size, processing schedule, and section age for each batch before attributing differences to the antigen (general IHC practice). Compare matched sections using the same EDTA pH 8.0 retrieval and 2 μg/mL primary incubation to reduce processing variables (datasheet A01230-6; general IHC practice). Include a similarly processed positive tissue and no-primary section in each run (general IHC practice). Treat altered nuclear-to-cytoplasmic staining as a finding requiring matched controls, since HDAC5 shuttles between those compartments (UniProt Q9UQL6 localisation).
Is cytoplasmic HDAC5 staining credible when nuclear staining is faint?
Yes: HDAC5 is reported in both nucleus and cytoplasm, with phosphorylation-linked export involving Ser-259 and Ser-498 (UniProt Q9UQL6 localisation). Tissue IHC shows cytoplasmic expression in most tissues and additional nuclear expression in several tissues, although its staining-to-RNA consistency is medium (HPA tissue IHC). Score nuclear and cytoplasmic DAB separately within the same defined cell population, using the counterstain to set nuclear boundaries (general IHC practice). Confirm that the signal survives changes in detection intensity and is absent from the no-primary control before interpreting a compartment shift (general IHC practice). Avoid calling faint nuclei negative solely because cytoplasmic staining is stronger (general IHC practice).
Can this stain distinguish HDAC5 isoforms or phosphorylation states?
HDAC5 has 3 annotated isoforms and multiple modified residues, including phosphorylated Ser-259 and Ser-498 (UniProt Q9UQL6 isoforms and modified residues). The supplied tissue-IHC caption does not identify the antibody epitope or demonstrate isoform or phosphosite selectivity (datasheet A01230-6). Therefore, report staining as antibody-reactive HDAC5 unless epitope mapping and appropriate specificity controls establish a narrower interpretation (general IHC practice). Compare serial sections processed with identical retrieval and detection when testing a biological condition, and record nuclear and cytoplasmic scores separately (general IHC practice; UniProt Q9UQL6 localisation). A change in compartmental staining cannot by itself identify the responsible phosphosite (UniProt Q9UQL6 localisation; general IHC practice).
How can IF help check the cell type and compartment seen by IHC?
Use IF on a separate, appropriately validated preparation to compare HDAC5 with a validated marker of the expected cell type; HPA reports high tissue-IHC staining in several glandular cell populations (HPA tissue IHC; general IF practice). Choose spectrally separated fluorophores and consider a far-red HDAC5 channel when tissue autofluorescence obscures shorter wavelengths (general IF practice). Because HDAC5 has no transmembrane segment and occupies nuclear and cytoplasmic compartments, permeabilize sufficiently for intracellular epitope access, then compare with a matched omission control (UniProt Q9UQL6 topology and localisation; general IF practice). Include a nuclear counterstain and acquire single-channel controls before interpreting overlap (general IF practice). IF colocalisation does not establish antibody specificity in chromogenic paraffin-section IHC (general IHC/IF practice).
What should I change if DAB background obscures HDAC5 staining?
The selected IHC image used 10% goat-serum block, 2 μg/mL rabbit primary overnight at 4°C, biotinylated secondary, and streptavidin-biotin/DAB detection (datasheet A01230-6). Run no-primary and secondary-only sections to locate background arising before or after primary incubation (general IHC practice). Check peroxidase blocking, wash stringency, DAB development time, and endogenous biotin interference when using biotin-based detection (general IHC practice; datasheet A01230-6 detection). Titrate primary concentration against a matched positive section while keeping retrieval and development fixed (general IHC practice). Accept a setting only when cell-associated nuclear or cytoplasmic signal remains distinguishable from diffuse deposit and tissue-edge staining (UniProt Q9UQL6 localisation; general IHC practice).
How should I quantify HDAC5 across differently cellular tissue regions? ⚠ ANSWER MARKED FOR VERIFICATION
Define the tissue region and cell population before scoring, then report nuclear and cytoplasmic HDAC5 separately because both compartments are documented (UniProt Q9UQL6 localisation; general IHC practice). For each compartment, use percent positive cells or an H-score combining percent positive with intensity grades 0–3 (general IHC practice). Normalize counts to eligible nucleated cells, and report positive-cell density per mm² of viable tissue when region size varies (general IHC practice). Keep retrieval, staining batch, DAB development, illumination, and threshold rules consistent across comparisons (general IHC practice). Record excluded necrotic, folded, and edge regions so differences in usable tissue do not masquerade as HDAC5 changes (general IHC practice).
How do I distinguish convincing HDAC5 staining from artefact?
Assess crisp cell-associated nuclear or cytoplasmic staining, since HDAC5 is reported in both compartments and HPA observes cytoplasmic staining in most tissues (UniProt Q9UQL6 localisation; HPA tissue IHC). Compare the stained cells with the expected population: HPA reports high staining in colon glandular cells but low staining in skeletal-muscle myocytes (HPA tissue IHC). Distrust signal limited to section edges, folds, necrotic areas, or pigment-like deposits, and check a no-primary section for endogenous enzyme or detection background (general IHC practice). Use matched retrieval and detection across specimens before assigning a biological difference (general IHC practice). HPA rates tissue staining as approved with medium staining-to-RNA consistency, so corroborate unexpected patterns independently (HPA tissue IHC; general IHC practice).
Boster reagents

Best HDAC5 / Histone deacetylase 5 IHC Antibodies

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).

Real IHC data IHC analysis of HDAC5 using anti-HDAC5 antibody (A01230-6). HDAC5 was detected in paraffin-embedded section of mouse small intestine tissue. Heat mediated antigen retrieval was performed in EDTA buffer (pH8.0, epitope retrieval solution). The tissue section was blocked with 10% goat serum. The tissue section was then incubated with 2μg/ml rabbit anti-HDAC5 Antibody (A01230-6) overnight at 4°C. Biotinylated goat anti-rabbit IgG was used as secondary antibody and incubated for 30 minutes at 37°C. The tissue section was developed using Strepavidin-Biotin-Complex (SABC) (Catalog # SA1022) with DAB as the chromogen.
Anti-HDAC5 Antibody ®
Cat # A01230-6
Real IHC data IHC analysis of HDAC5 using anti-HDAC5 antibody (A01230-5). HDAC5 was detected in paraffin-embedded section of human placenta tissue. Heat mediated antigen retrieval was performed in citrate buffer (pH6, epitope retrieval solution) for 20 mins. The tissue section was blocked with 10% goat serum. The tissue section was then incubated with 1μg/ml rabbit anti-HDAC5 Antibody (A01230-5) overnight at 4°C. Biotinylated goat anti-rabbit IgG was used as secondary antibody and incubated for 30 minutes at 37°C. The tissue section was developed using Strepavidin-Biotin-Complex (SABC)(Catalog # SA1022) with DAB as the chromogen.
Anti-HDAC5 Antibody ®
Cat # A01230-5

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).

Each figure is that product's own IHC / IF validation image from its datasheet.

References

  1. UniProt Consortium. UniProt entry Q9UQL6 (HDAC5_HUMAN, Histone deacetylase 5).
  2. Human Protein Atlas. HDAC5 tissue IHC expression (reliability: Approved).
  3. Human Protein Atlas. HDAC5 subcellular location (ICC-IF): Mainly localized to the nuclear speckles. In addition localized to the Golgi apparatus and cytosol..
  4. Human Protein Atlas. HDAC5 antibody validation summary (3 antibodies).
  5. METTL14-regulated PI3K/Akt signaling pathway via PTEN affects HDAC5-mediated epithelial-mesenchymal transition of renal tubular cells in diabetic kidney disease. Cell death & disease 2021 — PMC7791055.
  6. HDAC5-mediated Smad7 silencing through MEF2A is critical for fibroblast activation and hypertrophic scar formation. International journal of biological sciences 2022 — PMC9576526.
  7. Gene Co-expression Analysis Identifies Histone Deacetylase 5 and 9 Expression in Midbrain Dopamine Neurons and as Regulators of Neurite Growth via Bone Morphogenetic Protein Signaling. Frontiers in cell and developmental biology 2019 — PMC6753186.
  8. Role of Dorsal Striatum Histone Deacetylase 5 in Incubation of Methamphetamine Craving. Biological psychiatry 2018 — PMC6026084.
  9. PubMed PMID:10220385 — UniProt-cited evidence.
  10. PubMed PMID:9628581 — UniProt-cited evidence.
  11. PubMed PMID:12168954 — UniProt-cited evidence.