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- Table of Contents
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).
Expected localisation, validated protocols, controls and antibodies — the at-a-glance facts below, then the full design guide.
| 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 |
| 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) |
The catalog antibody’s IHC-P protocol is accompanied by one published automated PPARA IHC method (PMC10763066: Immunohistochemistry).
| Sample | Paraffin-embedded H. skeletal muscle tissue; fixative not specified (datasheet M00600) |
| Fixation | Image fixative and duration unreported (datasheet M00600); 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 1331CT894.186.143) anti-PPARA, 1:25 (datasheet M00600) |
| 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 | PPARA-positive staining in adipocytes of adipose tissue (HPA tissue IHC: High). HPA tissue profile: General nuclear expression. No signal in the no-primary control. |
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.
| 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). |
| Reference tissue and cell selection | HPA 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 strength | The 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 validation | The 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 features | PPARA 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. |
| Situation | Likely cause | Next 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. |
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.
| Tissue | Cell type | Level | Evidence | Source |
|---|---|---|---|---|
| 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 → |
| Tissue | Cell type | Level | Evidence | Source |
|---|---|---|---|---|
| None in HPA: PPARA is detected in all 45 scored tissues. Use a no-primary (secondary-only) and an isotype control instead. | ||||
Troubleshoot PPARA staining in paraffin sections by checking retrieval, nuclear localisation, background and cell-specific scoring before interpreting the chromogenic signal.
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).
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).