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PPARD / Peroxisome proliferator-activated receptor delta · IHC design guide
Design Immunohistochemistry for PPARD
Plan PPARD paraffin-section IHC around the nuclear staining reported in most tissues (HPA tissue IHC). Compare staining with tissue controls while accounting for the reported low consistency between antibody staining and RNA levels (HPA tissue IHC).
Evidence assembled Oct 2026 · For research use; verify linked source records and product datasheet before use
PPARD 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 | Nuclear staining in most tissues (HPA tissue IHC) | |
| Staining pattern | Nuclear signal in most tissues; high in several glandular cell types (HPA tissue IHC) | |
| Antigen retrieval | Tris-EDTA pH 9.0 HIER, 95–98 °C, 20 min (rule: nuclear antigen) | |
| Positive control | Adrenal gland+4 more · see all | |
| Negative control | Heart muscle+3 more · see all |
Important caveats
Reasons your staining may differ from the expected pattern.
| Fixation | Keep fixation conditions consistent across sections. (standard IHC practice; not target-specific) | |
| Caveat | Antibody staining and RNA levels show low consistency (HPA tissue IHC) | |
| Regulation | Expression regulation unspecified (UniProt) | |
| Isoform / epitope | 4 isoforms; epitope coverage is unresolved (UniProt) |
Section 1
Recommended PPARD IHC & IF Protocols
The catalog antibody IHC-P protocol is accompanied by published PPARD staining methods for bovine corpus luteum and yak tissue sections (PMC7297635; PMC11855600).
| Sample | Paraffin-embedded Mouse Brain tissue; fixative not specified (datasheet M01557) |
| Fixation | Image fixative and duration unreported (datasheet M01557); verify before use. |
| Sectioning | 4–5 µm sections on charged slides (standard) |
| Deparaffinisation | Xylene, graded ethanol series to water (standard) |
| Antigen retrieval | Heat-induced epitope retrieval in Tris-EDTA buffer, pH 9.0, 20 min at 95–98 °C (standard rule: nuclear antigen) |
| Peroxidase block | 3% H2O2, 10 min, room temperature (standard) |
| Blocking | 10% normal serum of the secondary host, 30 min, room temperature (standard) |
| Primary antibody | Mouse monoclonal (clone 2F9) anti-PPARD, 1:100 recommended; image 1:200 (datasheet M01557) |
| 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 | PPARD-positive staining in glandular cells of adrenal gland (HPA tissue IHC: High). HPA tissue profile: Nuclear expression in most tissues. No signal in the no-primary control. |
💡Decision noteStart with Tris-EDTA pH 9.0 HIER at 95–98 °C for 20 min (page retrieval rule: nuclear antigen); compare citrate pH 6.0 if needed (PMC11855600).
Section 2
What Is the Expected PPARD Staining Pattern?
PPARD is a nuclear receptor without a transmembrane segment (UniProt Q03181: subcellular location and topology). In paraffin sections, expect nuclear staining in many tissues, including glandular cells of the colon and breast and squamous epithelial cells of the cervix (HPA: tissue IHC). HPA rates the tissue profile Approved but reports low consistency between antibody staining and RNA expression; interpret any single tissue result with that limitation (HPA: reliability description).
| Distinct nuclear staining in colon glandular cells, with nuclei identifiable against the counterstain. | This fits PPARD's nuclear location and an HPA High staining example (UniProt Q03181: subcellular location; HPA: High in colon glandular cells). Judge the cellular pattern as well as signal strength; a brown deposit alone does not identify a positive nucleus (general IHC practice). |
| Predominantly cytoplasmic staining, especially when nuclei remain unstained. | That distribution conflicts with the reported nuclear location (UniProt Q03181: subcellular location; HPA: nuclear expression in most tissues). Review controls and staining conditions before calling it PPARD; morphology, counterstain and primary omission can help identify misplaced or nonspecific signal (general IHC practice). |
| Strong staining in an unexpected cell population while the expected cells remain pale. | Compare the named cell population, rather than the organ alone, with HPA's observations (HPA: tissue IHC). Cross-reactivity or endogenous chromogen activity is possible; use a primary-omission control and inspect where deposit sits in the section (general IHC practice). |
| Diffuse brown haze across tissue and spaces between cells. | Diffuse deposit lacks the nuclear, cell-associated pattern reported for PPARD (UniProt Q03181: subcellular location; HPA: tissue IHC). Background can arise during blocking, antibody incubation, washing or detection; assess a primary-omission section alongside the stained slide (general IHC practice). |
| No nuclear signal in colon glandular cells or another HPA High cell population. | An absent result in a reported High population calls for checking the assay before inferring absent PPARD (HPA: High in colon glandular cells; general IHC practice). HPA's Approved profile has low antibody–RNA consistency, so its High calls are useful comparators, not guarantees for every specimen (HPA: reliability description). |
💡Expected PPARD appearanceCall a convincing positive result when nuclear chromogen is discernible in an HPA High population such as colon glandular cells; isolated cytoplasmic colour or diffuse deposit is suspect (UniProt Q03181: nucleus; HPA: High in colon glandular cells; general IHC practice).
| Subcellular location | PPARD is reported in the nucleus and has no transmembrane segment; score nuclei within identifiable cells (UniProt Q03181: subcellular location and topology; general IHC practice). |
| Cell-specific tissue contrast | HPA reports High staining in colon glandular cells but Not detected in prostate glandular cells. This is an observed IHC contrast, not a universal absence claim (HPA: tissue IHC). |
| RNA–protein agreement | The tissue profile is Approved despite low consistency between antibody staining and RNA expression. Do not use RNA alone to settle an ambiguous slide (HPA: reliability description; general IHC practice). |
| Antibody evidence | CAB017635 is a mouse monoclonal antibody with Approved IHC status; the payload does not report an Enhanced IHC rating or ICC validation for it (HPA: antibody validation). |
| Isoforms and epitope uncertainty | UniProt lists 4 isoforms and an NR ligand-binding domain at residues 211–439. The supplied evidence does not locate this antibody's epitope or establish isoform coverage (UniProt Q03181: isoforms and domains; HPA: antibody listing). |
| Situation | Likely cause | Next action |
|---|---|---|
| Colon glandular nuclei appear unstained despite a working chromogenic run. | The result differs from HPA's High example; the supplied sources do not identify a PPARD-specific fixation or retrieval failure (HPA: High in colon glandular cells). | Check section integrity, counterstain, detection controls and the catalog antibody's IHC-P instructions; review routine retrieval only within that validated workflow (general IHC practice). |
| Brown signal appears mainly in cytoplasm or along cell edges. | The compartment conflicts with the reported nuclear pattern; morphology or nonspecific deposit may explain it (UniProt Q03181: nucleus; HPA: nuclear expression in most tissues; general IHC practice). | Compare stained and primary-omission sections at the same magnification, confirm intact nuclei, and avoid scoring cytoplasmic colour as nuclear positivity (general IHC practice). |
| A suspected negative control stains strongly. | HPA's Not detected calls describe observed cells, not an absolute absence across specimens; unwanted detection signal is another possibility (HPA: tissue IHC; general IHC practice). | Confirm the exact cell type, assess nuclear localisation, and use a primary-omission control to investigate endogenous detection activity (HPA: tissue IHC; general IHC practice). |
| Skeletal-muscle myocytes lack staining even though UniProt says skeletal-muscle expression is maximal. | These source statements measure different things: UniProt reports tissue specificity, while HPA reports myocyte IHC as Not detected (UniProt Q03181: tissue specificity; HPA: skeletal muscle myocytes). | Record the discrepancy and judge the slide against additional HPA High cell populations and assay controls; do not force a positive myocyte call (HPA: tissue IHC; general IHC practice). |
| Patchy nuclear staining is hard to distinguish from uneven background. | HPA reports nuclear expression in most tissues, but its Approved tissue profile has low antibody–RNA consistency; patchiness alone cannot resolve specificity (HPA: profile and reliability description). | Score only identifiable nuclei in a stated cell population, compare a primary-omission section, and document distribution separately from intensity (general IHC practice). |
| Q: Can this IHC pattern establish the expected IF/ICC result? | HPA provides no ICC-IF images or main subcellular location in this payload, and CAB017635 has no listed ICC validation (HPA: subcellular and antibody records). | A: Use nuclear PPARD localisation as a biological expectation, but assess IF/ICC validation on its own guide page; this IHC evidence does not establish an IF/ICC staining pattern (UniProt Q03181: nucleus; HPA: ICC-IF and antibody records). |
Experiment evidence
IHC & IF images showing PPARD staining
M01557 · IHCImmunohistochemistry validation of PPARD using Anti-PPAR Delta Monoclonal Antibody (M01557). Immunohistochemistry (IHC) analysis of paraffin
M01557 · IHCImmunohistochemistry validation of PPARD using Anti-PPAR Delta Monoclonal Antibody (M01557). Immunohistochemical analysis of human-liver tis
HPA · Cerebral cortexHuman Protein Atlas IHC, Cerebral cortex. Source: https://www.proteinatlas.org/ENSG00000112033-PPARD/tissue/cerebral+cortex#imid_4673112
HPA · ColonHuman Protein Atlas IHC, Colon. Source: https://www.proteinatlas.org/ENSG00000112033-PPARD/tissue/colon#imid_4673054
HPA · LiverHuman Protein Atlas IHC, Liver. Source: https://www.proteinatlas.org/ENSG00000112033-PPARD/tissue/liver#imid_4673047
HPA · KidneyHuman Protein Atlas IHC, Kidney. Source: https://www.proteinatlas.org/ENSG00000112033-PPARD/tissue/kidney#imid_4673040
← swipe / scroll for more images →
Real IHC / IF data behind the staining-pattern expectations in this section.
Sample controls for PPARD IHC & IF
🧪Run colon first and assess staining in glandular cells (HPA: High in colon glandular cells). Use heart muscle cardiomyocytes as the negative tissue (HPA: Not detected in heart muscle cardiomyocytes); on the colon slide, use unstained non-glandular cells as an internal background comparator without assuming they lack PPARD.
Positive control tissue: Adrenal gland (Glandular cells, HPA High)
Negative control tissue: Heart muscle (HPA Not detected)
ICC-IF cell lines (HPA subcellular resource): HPA carries no ICC-IF cell line for PPARD; derive a cell-line control from the positive tissue's cell type (Glandular cells) and confirm it by RNA or western blot first.
Technical controls: Include a no-primary, secondary-only control and a mouse monoclonal isotype-matched control (caption: mouse monoclonal antibody), plus PPARD-knockout tissue as a biological specificity control. Quench endogenous peroxidase and check for residual chromogen background in the colon section (standard chromogenic IHC practice).
⚠️Feasibility: A target-specific fixation window and retrieval requirement are unreported in the supplied evidence; compare standard antigen-retrieval conditions on paraffin sections (standard IHC practice). The selected M01557 mouse-brain paraffin-section caption reports a 1:200 dilution but does not report the fixative (caption: paraffin-embedded mouse brain; 1:200; fixative unreported). The supplied evidence does not establish whether frozen sections or IF would be easier, and colon glandular staining should be distinguished from luminal background (HPA: High in colon glandular cells; standard chromogenic IHC practice).
HPA tissue IHC evidence for PPARD
Comprehensive Human Protein Atlas IHC scoring per tissue (reliability: Approved — Low 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
| Tissue | Cell type | Level | Evidence | Source |
|---|---|---|---|---|
| Adrenal gland | Glandular cells | High | Protein (IHC) | HPA → |
| Breast | Glandular cells | High | Protein (IHC) | HPA → |
| Cervix | Squamous epithelial cells | High | Protein (IHC) | HPA → |
| Colon | Glandular cells | High | Protein (IHC) | HPA → |
| Epididymis | Glandular cells | High | Protein (IHC) | HPA → |
Undetected expression · recommended negative controls
| Tissue | Cell type | Level | Evidence | Source |
|---|---|---|---|---|
| Heart muscle | Cardiomyocytes | Not detected | Protein (IHC) | HPA → |
| Liver | Cholangiocytes | Not detected | Protein (IHC) | HPA → |
| Prostate | Glandular cells | Not detected | Protein (IHC) | HPA → |
| Skeletal muscle | Myocytes | Not detected | Protein (IHC) | HPA → |
Section 3
Advanced PPARD IHC Tips
Troubleshoot PPARD staining by checking nuclear localisation, retrieval, controls and cell-specific scoring alongside the available tissue evidence (UniProt Q03181; HPA tissue IHC).
What should I change if nuclear PPARD staining is weak after retrieval?
Start with Tris-EDTA pH 9.0 heat-induced retrieval at 95–98 °C for 20 min (page retrieval rule: nuclear antigen). Cool sections consistently, then compare nuclear staining and tissue preservation across slides processed in the same run (standard IHC practice). If staining remains weak, test a shorter or longer heating interval on matched sections before trying citrate pH 6.0 as a fallback (standard IHC practice). Judge each condition by nuclear signal in an appropriate control and by background, since PPARD is nuclear and the reported tissue staining has low consistency with RNA expression (UniProt Q03181 subcellular location; HPA tissue IHC reliability).
Can fixation explain weak PPARD staining in paraffin sections?
Target-specific fixation sensitivity is unknown: the catalog image describes paraffin-embedded mouse brain but does not state its fixative (M01557 tissue-IHC caption). Record the fixative, fixation duration and section processing for each specimen, and compare matched samples before attributing a weak result to fixation (standard IHC practice). If staining varies between batches, run the same control tissue through retrieval and detection together to locate the step where performance changes (standard IHC practice). Do not infer a fixation effect from PPARD's nuclear localisation, lack of a transmembrane segment or tissue-expression patterns; those observations do not establish fixation sensitivity (UniProt Q03181 topology and subcellular location; HPA tissue IHC).
How should I assess cytoplasmic staining when PPARD is expected in nuclei?
Treat nuclear staining as the primary localisation criterion because PPARD is annotated as nuclear and HPA reports nuclear expression in most tissues (UniProt Q03181 subcellular location; HPA tissue IHC profile). Check whether the chromogenic deposit overlaps identifiable nuclei after counterstaining, rather than scoring diffuse cytoplasmic colour as PPARD-positive by default (standard IHC practice). PPARD has no transmembrane segment, so a crisp membrane pattern warrants review of antibody specificity and background controls (UniProt Q03181 topology; standard IHC practice). Compare the pattern with a no-primary control and with similarly processed sections, while recognising that HPA reports low consistency between antibody staining and RNA expression (standard IHC practice; HPA tissue IHC reliability).
Could an unmapped epitope make this antibody miss a PPARD isoform?
PPARD has 4 listed isoforms, but the supplied catalog caption does not map the antibody epitope or establish isoform coverage (UniProt Q03181 isoforms; M01557 tissue-IHC caption). The annotated ligand-binding domain spans residues 211–439 of the 441-residue record, which does not by itself show where this antibody binds (UniProt Q03181 domains and length). If expected nuclear staining is absent, seek epitope and isoform documentation before interpreting a negative section as loss of all PPARD forms (standard IHC practice). Compare an independently validated antibody and appropriate tissue controls when available, and report the result as staining with this antibody rather than isoform-specific expression (standard IHC practice).
How can I check a PPARD pattern in multiplex IF?
Plan multiplex IF around nuclear PPARD and a marker that identifies the cell population being scored, such as a validated glandular-cell marker in a glandular specimen (UniProt Q03181 subcellular location; HPA tissue IHC positive-cell entries; standard IF practice). Choose a red or far-red channel after checking tissue autofluorescence and spectral overlap, and include single-stain controls for channel separation (standard IF practice). For access to a nuclear epitope, optimise permeabilisation after fixation; PPARD has no transmembrane segment that defines a membrane-facing epitope (UniProt Q03181 topology; standard IF practice). Verify antibody performance in IF separately, because the supplied M01557 caption documents paraffin-section IHC and the HPA subcellular payload supplies no ICC/IF images (M01557 tissue-IHC caption; HPA subcellular).
What controls help distinguish PPARD signal from chromogenic background?
Run a no-primary control and inspect nuclei, vessel-associated colour, edges and damaged areas before assigning brown deposit to PPARD (standard IHC practice; UniProt Q03181 subcellular location). In a peroxidase-based assay, block endogenous peroxidase before DAB development and keep development time consistent across comparison slides (standard chromogenic IHC practice). Titrate the primary around the caption's 1:200 dilution on matched paraffin sections, assessing nuclear signal against diffuse background rather than increasing concentration automatically (M01557 tissue-IHC caption; standard IHC practice). For the mouse monoclonal antibody shown on mouse brain, include controls that reveal secondary-reagent binding to mouse tissue (M01557 tissue-IHC caption; standard IHC practice).
How should I quantify PPARD-positive nuclei across tissue samples? ⚠ ANSWER MARKED FOR VERIFICATION
Define the cell population and tissue region before scoring, then count nuclei rather than total brown area because PPARD's expected location is nuclear (UniProt Q03181 subcellular location; standard IHC practice). Report the percentage of positive nuclei or an H-score from 0–300, with fixed intensity thresholds and the number of evaluable cells or regions (standard IHC scoring practice). For spatial comparisons, report positive nuclei per mm² and normalise to the viable tissue area or the counted cells in the same compartment (standard IHC practice). Keep retrieval, imaging and scoring settings consistent, and separate cell types because HPA describes different staining levels across tissue cell populations (standard IHC practice; HPA tissue IHC).
When is a PPARD-positive IHC result convincing?
A convincing result shows reproducible nuclear staining in intact cells, with little corresponding colour in no-primary controls (UniProt Q03181 subcellular location; standard IHC practice). Check cell identity: HPA reports high staining in several glandular populations but no detection in skeletal-muscle myocytes, despite UniProt describing maximal tissue levels in skeletal muscle (HPA tissue IHC; UniProt Q03181 tissue specificity). Exclude section-edge staining, necrotic regions and residual endogenous peroxidase colour before calling focal DAB deposits positive (standard chromogenic IHC practice). Interpret a negative result cautiously because HPA rates the tissue staining Approved while reporting low consistency with RNA expression, and the M01557 image documents only its stated paraffin-section context (HPA tissue IHC reliability; M01557 tissue-IHC caption).
Boster reagents
Best PPARD / Peroxisome proliferator-activated receptor delta IHC Antibodies
M01557 has IHC images of paraffin-embedded mouse brain and human liver, lung, and uterus (IHC image captions); IF is listed, but no IF image is supplied (catalog applications; IF image alts).
Real IHC data
Anti-PPAR Delta Monoclonal Antibody
Cat # M01557
M01557 is the only SKU shown, with IHC images of paraffin-embedded mouse brain and human liver, lung, and uterus (IHC image captions). Its listed applications are IHC and IF, and its listed reactivity is Human, Mouse, and Rat (catalog applications; catalog reactivity).
Which to pick: Choose M01557 for tissue IHC: its mouse brain image specifies paraffin-embedded tissue, while its human liver, lung, and uterus captions report IHC without specifying processing; the fixative is unreported (IHC image captions). M01557 is also the IF option because IF is listed, although no IF image or separate ICC validation is supplied (catalog applications; IF image alts). For work across Human, Mouse, and Rat, M01557 is the listed mouse monoclonal option; the supplied IHC images cover Mouse and Human (catalog host and clone; catalog reactivity; IHC image captions).
Each figure is that product's own IHC / IF validation image from its datasheet.
References
- UniProt Consortium. UniProt entry Q03181 (PPARD_HUMAN, Peroxisome proliferator-activated receptor delta).
- Human Protein Atlas. PPARD tissue IHC expression (reliability: Approved).
- Human Protein Atlas. PPARD subcellular location (ICC-IF): Highest expression in SK-MEL-30: 55.8 nTPM.
- Human Protein Atlas. PPARD antibody validation summary (1 antibodies).
- PPARD and Interferon Gamma Promote Transformation of Gastric Progenitor Cells and Tumorigenesis in Mice. Gastroenterology 2019 — PMC6581611.
- Pregnancy-associated changes of peroxisome proliferator-activated receptor delta (PPARD) and cytochrome P450 family 21 subfamily A member 2 (CYP21A2) expression in the bovine corpus luteum. The Journal of reproduction and development 2020 — PMC7297635.
- Nuclear receptors regulate lipid metabolism and oxidative stress markers in chondrocytes. Journal of molecular medicine (Berlin, Germany) 2017 — PMC5357281.
- Insights from Tandem Mass Tag (TMT) Proteomic Analysis on Protein Network Modification in Control of Yak Hair Follicle Cycle. International journal of molecular sciences 2025 — PMC11855600.
- PubMed PMID:1333051 — UniProt-cited evidence.
- PubMed PMID:10851270 — UniProt-cited evidence.
- PubMed PMID:18619963 — UniProt-cited evidence.
Immunohistochemistry protocol sheet for PPARD (Peroxisome proliferator-activated receptor delta). Expected localisation Nuclear staining in most tissues (HPA tissue IHC). Antigen retrieval: Tris-EDTA pH 9.0 HIER, 95–98 °C, 20 min (rule: nuclear antigen). Validated IHC antibody: M01557 at 1:100 recommended; image 1:200 (the product's own IHC validation image is shown). Controls (HPA): positive Adrenal gland (Glandular cells); negative Heart muscle. IHC-P workflow on paraffin sections; fixative unspecified. Protocol steps: 1. Sample: Paraffin-embedded Mouse Brain tissue; fixative not specified (datasheet M01557); 2. Fixation: Image fixative and duration unreported (datasheet M01557); verify before use.; 3. Sectioning: 4–5 µm sections on charged slides (standard); 4. Deparaffinisation: Xylene, graded ethanol series to water (standard); 5. Antigen retrieval: Heat-induced epitope retrieval in Tris-EDTA buffer, pH 9.0 , 20 min at 95–98 °C…; 6. Peroxidase block: 3% H2O2, 10 min , room temperature (standard); 7. Blocking: 10% normal serum of the secondary host, 30 min , room temperature (standard); 8. Primary antibody: Mouse monoclonal (clone 2F9) anti-PPARD, 1:100 recommended; image 1:200 (datasheet M01557); 9. Primary incubation: Overnight at 4 °C (standard). Watch for: Fixation: Keep fixation conditions consistent across sections. (standard IHC practice; not target-specific); Caveat: Antibody staining and RNA levels show low consistency (HPA tissue IHC); Isoform / epitope: 4 isoforms; epitope coverage is unresolved (UniProt); Regulation: Expression regulation unspecified (UniProt). Evidence: UniProt Q03181, HPA tissue IHC · Approved, HPA cell-line RNA · Highest expression in SK-MEL-30: 55.8 nTPM, Datasheet M01557, PMC7297635, PMC11855600. QR code links to https://www.bosterbio.com/bosterbio-gene-info-cards/PPARD/immunohistochemistry-ihc-guide.