PPARA / Peroxisome proliferator-activated receptor alpha · IHC design guide

Design Immunohistochemistry for PPARA

Plan PPARA IHC on paraffin sections with the catalog antibody at 1:25 and DAB detection (datasheet: M00600 IHC-P). Assess nuclear staining across cell types, using the demonstrated skeletal muscle or kidney sections as references (HPA tissue IHC; datasheet: M00600 IHC-P).

Evidence assembled Oct 2026 · For research use; verify linked source records and product datasheet before use
Immunohistochemistry protocol sheet for PPARA (IHC for PPARA): expected localisation Nuclear staining (HPA tissue IHC), antibody M00600, validated IHC image, and IHC protocol steps
Printable PPARA IHC protocol sheet — expected localisation Nuclear staining (HPA tissue IHC), antibody M00600, controls and protocol steps. Open the full PPARA IHC guide →

PPARA 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 (HPA tissue IHC)
Staining pattern General nuclear staining across cell types (HPA tissue IHC)
Antigen retrieval Tris-EDTA pH 9.0 HIER, 95–98 °C, 20 min (rule: nuclear antigen)
Positive control ⓘ Adipose tissue+4 more · see all
Negative control ⓘ None in HPA (detected in all 45 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 Staining and RNA show medium consistency (HPA tissue IHC)
Regulation Ligand-activated; intensity effect unknown (UniProt)
Isoform / epitope 2 isoforms; isoform-specific epitope coverage unknown (UniProt; datasheet)
Section 1

Recommended PPARA IHC & IF Protocols

The catalog antibody’s IHC-P protocol is accompanied by one published automated PPARA IHC method (PMC10763066: Immunohistochemistry).

Recommended immunohistochemistry (IHC-P) protocol parameters
SampleParaffin-embedded H. skeletal muscle tissue; fixative not specified (datasheet M00600)
FixationImage fixative and duration unreported (datasheet M00600); verify before use.
Sectioning4–5 µm sections on charged slides (standard)
DeparaffinisationXylene, graded ethanol series to water (standard)
Antigen retrievalHeat-induced epitope retrieval in Tris-EDTA buffer, pH 9.0, 20 min at 95–98 °C (standard rule: nuclear antigen)
Peroxidase block3% H2O2, 10 min, room temperature (standard)
Blocking10% normal serum of the secondary host, 30 min, room temperature (standard)
Primary antibodyMouse monoclonal (clone 1331CT894.186.143) anti-PPARA, 1:25 (datasheet M00600)
Primary incubationOvernight at 4 °C (standard)
DetectionHRP-polymer secondary, DAB chromogen 5–10 min (standard)
CounterstainHematoxylin, blue, dehydrate and mount (standard)
Expected resultPPARA-positive staining in adipocytes of adipose tissue (HPA tissue IHC: High). HPA tissue profile: General nuclear expression. No signal in the no-primary control.
💡Decision noteStart with Tris-EDTA pH 9.0 retrieval at 95–98 °C for 20 min for this nuclear target (page retrieval rule; UniProt Q07869: nucleus).
Section 2

What Is the Expected PPARA Staining Pattern?

PPARA is a nuclear receptor with no transmembrane segment (UniProt Q07869: localization and topology). In paraffin-section IHC, expect predominantly nuclear staining; HPA describes a general nuclear pattern and high staining in several cell populations, including adipocytes and bronchial respiratory epithelial cells (HPA tissue IHC: Supported, with medium consistency against RNA data). Treat those observations as reference patterns, not a guarantee that every cell in those tissues will stain.

What am I looking at on my slide?
Defined nuclear staining in adipocytes or bronchial respiratory epithelial cells.This fits the expected compartment (UniProt Q07869: nucleus) and observed high-staining cell populations (HPA tissue IHC: adipocytes and respiratory epithelial cells, High). Compare cells with nearby unstained areas and the counterstain so that a dark nucleus is recognizable as signal rather than dense hematoxylin. HPA rates the tissue pattern Supported, with medium consistency against RNA expression (HPA tissue IHC).
Predominantly cytoplasmic, membrane-like, or extracellular color with little nuclear signal.This conflicts with the main IHC localization (HPA tissue IHC: general nuclear expression; UniProt Q07869: nucleus, no transmembrane segment). Review morphology, detection background, and antibody specificity before scoring it as PPARA. A nonnuclear IHC pattern alone does not establish a new PPARA compartment, particularly because the supplied IHC evidence describes nuclei at tissue level (HPA tissue IHC).
Strong color in an unexpected cell population, especially with a weak nuclear pattern.Possible explanations include cross-reactivity or endogenous detection activity; neither can be diagnosed from color alone (general IHC practice). Check whether signal follows cell nuclei and compare the detection-only control. HPA lists specific high-staining populations but supplies no negative tissue or cell population, so an unlisted cell type is a reason to investigate, not proof of false positivity (HPA tissue IHC).
Diffuse color across tissue, blank spaces, or many cell compartments.A widespread haze makes nuclear scoring unreliable even where PPARA could be present (UniProt Q07869: nucleus; general IHC practice). Consider nonspecific reagent binding, incomplete blocking, or detection background as workflow possibilities, then compare a control lacking primary antibody. Do not infer PPARA abundance from the intensity of a diffuse deposit (general IHC practice).
No nuclear signal in a section expected to show high staining.For example, adipocytes and hematopoietic cells are listed as High in HPA tissue IHC (HPA tissue IHC: High). Confirm that the relevant cells are actually present and recognizable before troubleshooting the stain. A negative run may reflect workflow performance or the tested antibody; HPA's Supported rating and medium RNA agreement do not guarantee every specimen or preparation will be positive (HPA tissue IHC).
💡Expected PPARA appearanceA convincing positive is distinct, predominantly nuclear chromogen in an HPA high-staining cell population, such as adipocytes or bronchial respiratory epithelial cells (HPA tissue IHC: High; UniProt Q07869: nucleus); broad cytoplasmic color or tissue-wide haze without nuclear definition should be treated as suspect (general IHC practice).
How each factor affects the staining
Reference tissue and cell selectionHPA reports High staining in adipocytes, hematopoietic cells, respiratory epithelial cells, cerebellar granular-layer cells, and selected endothelial or epithelial cells (HPA tissue IHC: High). Choose a reference section containing an identifiable listed population. HPA provides no negative entries here, so it cannot supply a validated PPARA-negative tissue control (HPA tissue IHC: negative list empty).
Interpretation strengthThe tissue IHC pattern is Supported, with medium consistency between staining and RNA expression (HPA tissue IHC). That supports use as an observed reference while leaving room for specimen and antibody differences. The listed High values refer to particular cell populations, not to uniform staining of an entire organ (HPA tissue IHC: cell-specific High entries).
Antibody validationThe supplied antibody records assign IHC Supported to CAB075701 and no IHC status to HPA066941 (HPA antibodies). Do not transfer an IHC validation label between antibodies. When comparing images or selecting a reference, track the antibody identifier and its application-specific status (HPA antibodies).
Molecular featuresPPARA is a 468-residue chain with no signal peptide, propeptide, transmembrane segment, or annotated glycosylation sites in this record (UniProt Q07869: processing, topology, glycosylation). These facts are consistent with a nuclear interpretation but do not identify the tested antibody's epitope or predict antigen-retrieval behavior. Two isoforms are listed without isoform-specific staining evidence (UniProt Q07869: isoforms).
IF/ICC Q&A: Should ciliary signal redefine the paraffin IHC call?No. HPA ICC-IF lists a primary-cilium main location as uncertain and nucleolar fibrillar-center and nuclear-body locations as supported (HPA subcellular). Those are application-specific observations; the tissue IHC profile remains general nuclear expression (HPA tissue IHC). Assess any IF/ICC image within its own validation context rather than using it to override the paraffin-section IHC pattern.
Why is my staining missing, weak or wrong?
SituationLikely causeNext action
Expected nuclei are faint or absent.The relevant cells may be missing, or the staining run may have insufficient detectable signal (general IHC practice).First verify cell identity on the counterstain; then compare a listed High population processed in the same run (HPA tissue IHC: cell-specific High entries). Review the antibody's IHC validation and the run's retrieval, primary-antibody, and detection records without assuming a PPARA-specific fixation effect (HPA antibodies; general IHC practice).
Nuclei look positive even when primary antibody is omitted.The detection system or tissue can contribute signal without target binding (general IHC practice).Use the primary-omission result to assess background, then review blocking and chromogen development for that run (general IHC practice). Do not score the matching signal as PPARA solely because it falls over nuclei (UniProt Q07869: nucleus; general IHC practice).
Cytoplasmic color overwhelms any nuclear pattern.Nonspecific antibody binding or detection background is possible; compartment mismatch alone does not identify which (general IHC practice).Compare the detection-only control, inspect intact cell boundaries, and reassess the IHC status of the antibody used (general IHC practice; HPA antibodies). Require a discernible nuclear component before calling the result consistent with the reported tissue pattern (HPA tissue IHC: general nuclear expression).
Every area has a light brown haze.Diffuse background may result from reagent binding, blocking, washing, or chromogen development (general IHC practice).Check a primary-omission section and run records; adjust background-control steps according to the detection system (general IHC practice). Re-evaluate only after nuclei can be distinguished from surrounding tissue. HPA's High tissue entries do not justify scoring a uniform haze as positive (HPA tissue IHC: cell-specific High entries).
An unlisted cell type stains strongly.The result could be genuine, cross-reactive, or due to endogenous detection activity; this payload cannot decide among them (HPA tissue IHC: selected positive entries, no negative entries; general IHC practice).Record the cell identity, compartment, and control results. Compare it with the reported nuclear pattern and, where available, an independently validated IHC antibody (HPA tissue IHC: general nuclear expression; general IHC practice). Do not label the cell type PPARA-negative merely because HPA does not list it.
IHC and an ICC-IF image appear to show different compartments.The supplied records describe general nuclear tissue IHC and a partly uncertain ICC-IF localization profile (HPA tissue IHC; HPA subcellular).Keep the applications and validation records separate: score paraffin IHC against its nuclear tissue pattern, and interpret ICC-IF with its location confidence and antibody status (HPA tissue IHC; HPA subcellular; HPA antibodies). Do not change the IHC call solely because an ICC-IF image shows ciliary signal.

Sample controls for PPARA IHC & IF

🧪Start with adipose tissue: adipocytes should stain (HPA: High in adipocytes). HPA detects PPARA in all 45 scored tissues, so there is no supported negative tissue; use no-primary and isotype controls, and treat cells without visible target staining on the positive slide as internal background references without assigning them a negative cell identity (HPA: no negative tissue rows).
Positive control tissue: Adipose tissue (Adipocytes, HPA High)
Negative control tissue: None in HPA: PPARA is detected in all 45 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 PPARA in HEK293, Rh30, ASC52telo, RPTEC/TERT1, hTERT-RPE1 (serum starved), with annotated localisation: Primary cilium (uncertain) (HPA subcellular).
Technical controls: Run a no-primary, secondary-only control and a concentration-matched isotype control appropriate to the primary antibody’s host species and clonality; confirm specificity with PPARA knockout material or a validated peptide-block experiment (standard IHC practice). In adipose sections, check endogenous peroxidase background for chromogenic IHC and tissue autofluorescence if using IF (standard IHC/IF practice).
⚠️Feasibility: No target-specific fixation window or fixation effect is reported in the supplied evidence; the M00600 paraffin-section caption does not state a fixative (M00600 caption: fixative unreported). Retrieval dependence is likewise unreported, so optimize antigen retrieval empirically for the chosen antibody (standard IHC practice). The evidence does not establish that frozen sections or IF are easier; paraffin processing can leave lipid-extraction spaces in adipose tissue that complicate interpretation (standard histology practice).

HPA tissue IHC evidence for PPARA

Comprehensive Human Protein Atlas IHC scoring per tissue (reliability: Supported — 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
Adipose tissue Adipocytes High Protein (IHC) HPA →
Bone marrow Hematopoietic cells High Protein (IHC) HPA →
Bronchus Respiratory epithelial cells High Protein (IHC) HPA →
Cerebellum Cells in granular layer High Protein (IHC) HPA →
Cerebral cortex Endothelial cells High Protein (IHC) HPA →

Undetected expression · recommended negative controls

TissueCell typeLevelEvidenceSource
None in HPA: PPARA is detected in all 45 scored tissues. Use a no-primary (secondary-only) and an isotype control instead.
Section 3

Advanced PPARA IHC Tips

Troubleshoot PPARA staining in paraffin sections by checking retrieval, nuclear localisation, background and cell-specific scoring before interpreting the chromogenic signal.

How should I retrieve PPARA in paraffin sections with weak nuclear staining?
Use Tris-EDTA pH 9.0 heat-induced retrieval at 95–98 °C for 20 min (page setting: nuclear-antigen rule). Allow sections to cool consistently, then compare staining with a matched control section before changing antibody concentration (standard IHC practice). The selected M00600 skeletal-muscle caption reports paraffin sections and 1:25 primary dilution, but gives no retrieval conditions or fixative (M00600 tissue-IHC caption). If nuclear signal remains weak, test a shorter heating interval on adjacent sections while holding detection conditions constant (standard IHC practice). Score nuclear signal separately from diffuse cytoplasmic colour because PPARA is annotated as nuclear (UniProt Q07869).
Could fixation be hiding the PPARA epitope?
Target-specific fixation sensitivity is unknown here: the selected paraffin-section caption does not report a fixative (M00600 tissue-IHC caption). Record the actual fixative and fixation interval for each specimen, and compare sections processed together before attributing weak staining to fixation (standard IHC practice). Use the page’s Tris-EDTA pH 9.0, 95–98 °C for 20 min retrieval as the starting condition (page setting: nuclear-antigen rule). If archived blocks differ in processing history, assess morphology and nuclear signal in matched control tissue alongside the study sections (standard IHC practice). Neither tissue-expression patterns nor sequence annotations establish a PPARA-specific fixation effect (HPA tissue IHC; UniProt Q07869).
What should I make of PPARA colour outside nuclei?
Prioritise interpretable nuclear staining when assessing chromogenic PPARA IHC, because UniProt places PPARA in the nucleus and HPA reports general nuclear tissue expression (UniProt Q07869; HPA tissue IHC). Compare the colour with a nuclear counterstain and inspect whether it sits inside intact cells rather than over extracellular material (standard IHC practice). HPA’s separate ICC/IF profile also lists a primary-cilium location with uncertain support and supported nucleolar fibrillar-centre and nuclear-body locations; those observations do not validate an extranuclear DAB pattern in paraffin sections (HPA subcellular). Recheck conspicuous cytoplasmic or peripheral colour against a no-primary control and adjacent morphology (standard IHC practice). Report mixed patterns by compartment instead of combining them into one positive score (standard IHC practice).
Can this stain distinguish PPARA isoforms or epitope loss?
PPARA has 2 annotated isoforms, but the supplied M00600 caption does not identify the antibody epitope or establish isoform-specific staining (UniProt Q07869; M00600 tissue-IHC caption). Its annotated ligand-binding domain spans residues 239–466; that domain location alone cannot identify which isoform the antibody detects (UniProt Q07869). Treat a negative nucleus as an IHC result, not proof that either isoform is absent, until the epitope and assay controls are established (standard IHC interpretation). Compare serial sections with the same retrieval and detection conditions before investigating an apparent loss of signal (standard IHC practice). If isoform identity matters, obtain epitope documentation and use an independently validated isoform-specific approach (standard assay validation practice).
How can I check an IHC pattern by multiplex IF?
Use IF as a separate validation experiment and retain the paraffin IHC result as the comparison point; the selected M00600 caption documents chromogenic DAB IHC, not IF performance (M00600 tissue-IHC caption). Pair PPARA with a marker for the expected cell population and a nuclear stain, then inspect signal within individual cells (standard multiplex IF practice; HPA tissue IHC). Choose spectrally separated fluorophores after checking tissue autofluorescence, favouring a longer-wavelength channel for a weak target when background is stronger at shorter wavelengths (standard IF practice). PPARA has no transmembrane segment and is annotated as nuclear, so use controlled permeabilisation to allow antibody access to intracellular epitopes (UniProt Q07869; standard IF practice). Include single-colour and no-primary controls to assess bleed-through and nonspecific fluorescence (standard IF practice).
How do I reduce diffuse DAB background without losing nuclear signal?
Check a no-primary section first to identify colour arising from the detection system or tissue rather than primary-antibody binding (standard chromogenic IHC practice). Block endogenous peroxidase before DAB development and keep the development time consistent across comparison sections (standard chromogenic IHC practice). The selected M00600 image used a 1:25 primary dilution, a 1:400 peroxidase-conjugated secondary and DAB; those numbers describe that image, not an established optimum for every specimen (M00600 tissue-IHC caption). If background persists, adjust blocking, washing and primary concentration one variable at a time against a positive control (standard IHC practice). Preserve nuclear contrast during optimisation because general nuclear expression is reported for PPARA tissue IHC (HPA tissue IHC).
How should I score PPARA staining across different cell populations? ⚠ ANSWER MARKED FOR VERIFICATION
Define the cell population and nuclear-positive threshold before scoring, using the same counterstain and imaging settings for all sections (standard quantitative IHC practice). Report the percentage of positive nuclei and, when intensity is reproducible, an H-score calculated as the sum of percentage at each intensity multiplied by its 0–3 intensity grade (standard IHC scoring practice). Normalise positive-cell counts to the number of evaluable cells in that population; for spatial counts, report positive cells per mm² of evaluable tissue (standard quantitative IHC practice). Keep cell populations separate because HPA reports high PPARA staining in several distinct tissue cell types (HPA tissue IHC). Exclude folds, edges and necrotic regions using prespecified morphology criteria (standard quantitative IHC practice).
When is apparent PPARA positivity likely to be an artefact?
A credible chromogenic result places signal in intact nuclei of a defined cell population and reproduces across comparable sections (UniProt Q07869; HPA tissue IHC; standard IHC practice). Check the expected cell population against the section’s morphology; HPA reports high staining in adipocytes, hematopoietic cells and several epithelial or endothelial populations, depending on tissue (HPA tissue IHC). Treat dominant extracellular or diffuse cytoplasmic colour, staining confined to section edges, and colour over necrosis as reasons to investigate artefact (standard IHC practice). A no-primary control helps reveal residual endogenous peroxidase or detection-related DAB colour (standard chromogenic IHC practice). Interpret discrepancies cautiously because HPA rates tissue staining as supported with medium consistency against RNA expression (HPA tissue IHC).
Boster reagents

Best PPARA / Peroxisome proliferator-activated receptor alpha IHC Antibodies

M00600 has IHC images from paraffin-embedded human skeletal muscle and kidney and an IF image from HeLa cells (M00600 image captions); its listed reactivity is Human and Mouse (catalog).

Real IHC data Immunohistochemical analysis of paraffin-embedded H. skeletal muscle section using PPARA Antibody. M00600 was diluted at 1:25 dilution. A peroxidase-conjugated goat anti-mouse IgG at 1:400 dilution was used as the secondary antibody, followed by DAB staining.
Anti-PPARA Antibody
Cat # M00600

M00600 is listed for IHC-P and IF, with IHC images from paraffin-embedded human skeletal muscle and kidney (catalog applications; M00600 IHC captions). Its IF image shows stained HeLa cells (M00600 IF caption).

Which to pick: Choose M00600 for paraffin-section IHC: its images show human skeletal muscle and kidney sections stained at 1:25 (M00600 IHC captions). For cultured-cell IF, M00600 has a HeLa image at 1:25; ICC is not separately listed (M00600 IF caption; catalog applications). M00600 is a mouse monoclonal listed as reactive with Human and Mouse, but the supplied images show human samples only; the IHC captions do not report the fixative (catalog host, clone and reactivity; M00600 image captions).

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

References

  1. UniProt Consortium. UniProt entry Q07869 (PPARA_HUMAN, Peroxisome proliferator-activated receptor alpha).
  2. Human Protein Atlas. PPARA tissue IHC expression (reliability: Supported).
  3. Human Protein Atlas. PPARA subcellular location (ICC-IF): Mainly localized to the primary cilium. In addition localized to the nucleoli fibrillar center, nuclear bodies, centriolar satellites and basal body..
  4. Human Protein Atlas. PPARA antibody validation summary (2 antibodies).
  5. PPARα-ACOT12 axis is responsible for maintaining cartilage homeostasis through modulating de novo lipogenesis. Nature communications 2022 — PMC8733009.
  6. Loss of Dec1 inhibits alcohol-induced hepatic lipid accumulation and circadian rhythm disorder. BMC molecular and cell biology 2024 — PMC10763066.
  7. Conditional overexpression of PPARα in intestinal epithelium diminishes GIP enteroendocrine cells and circulating hormone levels. Molecular metabolism 2026 — PMC13542957.
  8. Disruption of peroxisome proliferator-activated receptor α in hepatocytes protects against acetaminophen-induced liver injury by activating the IL-6/STAT3 pathway. International journal of biological sciences 2022 — PMC8990472.
  9. PubMed PMID:7684926 — UniProt-cited evidence.
  10. PubMed PMID:7981125 — UniProt-cited evidence.
  11. PubMed PMID:8993548 — UniProt-cited evidence.