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- Table of Contents
This guide covers PDK3 staining in paraffin sections using the catalog antibody's IHC conditions (datasheet A05658-1). Compare stained hepatocytes or lung macrophages with adipocytes reported as not detected, and interpret results cautiously because staining and RNA data show low consistency (HPA tissue IHC).
Expected localisation, validated protocols, controls and antibodies — the at-a-glance facts below, then the full design guide.
| Expected localisation | Cytoplasmic tissue staining (HPA tissue IHC); mitochondrial matrix annotation (UniProt) | |
| Staining pattern | Cytoplasmic staining in lung macrophages (HPA tissue IHC) | |
| Antigen retrieval | EDTA pH 8.0 HIER, heat-mediated (datasheet A05658-1) | |
| Positive control | Cerebral cortex+4 more · see all | |
| Negative control | Adipose tissue+4 more · see all |
| Fixation | Keep fixation consistent across sections (standard IHC practice; not target-specific) | |
| Caveat | Staining shows low consistency with RNA data (HPA tissue IHC) | |
| Regulation | Expression regulation not specified (UniProt) | |
| Isoform / epitope | 2 isoforms; epitope coverage unspecified (UniProt) |
The catalog antibody has a datasheet IHC-P protocol (datasheet: A05658-1); the published options below report PDK3 staining in urothelial and prostate cancer samples (PMC8473833; PMC9174590).
| Sample | Paraffin-embedded human meningioma tissue; fixative not specified (datasheet A05658-1) |
| Fixation | Image fixative and duration unreported (datasheet A05658-1); 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 A05658-1); 20 min, 95–100 °C (standard) |
| Peroxidase block | 3% H2O2, 10 min, room temperature (standard) |
| Blocking | 10% goat serum (datasheet A05658-1) |
| Primary antibody | Rabbit anti-PDK3, 2-5 μg/ml (datasheet A05658-1) |
| Primary incubation | Overnight at 4 °C (datasheet A05658-1) |
| Detection | HRP-conjugated secondary, DAB chromogen (datasheet A05658-1) |
| Counterstain | Hematoxylin, blue, dehydrate and mount (standard) |
| Expected result | PDK3-positive staining in neuronal cells of cerebral cortex (HPA tissue IHC: Medium). HPA tissue profile: Cytoplasmic expression in several tissues. No signal in the no-primary control. |
PDK3 is a mitochondrial matrix protein with no transmembrane segment (UniProt Q15120 topology). In paraffin IHC, expect cytoplasmic staining in selected cells, including cortical and hippocampal neurons, hepatocytes, and lung macrophages (HPA tissue IHC: Medium). HPA rates tissue staining Approved but reports low agreement with RNA expression and pending external verification (HPA tissue IHC: reliability). Interpret individual tissues with that limitation in mind.
| Cytoplasmic staining in cortical or hippocampal neurons, hepatocytes, or lung macrophages (HPA tissue IHC: Medium). | This matches the reported cell distribution (HPA tissue IHC). A chromogenic cytoplasmic signal is compatible with mitochondrial PDK3, but ordinary IHC cannot by itself resolve the mitochondrial matrix (UniProt Q15120: matrix; general IHC practice). |
| Predominantly nuclear or membrane staining, with little cytoplasmic signal. | Recheck specificity and detection controls: these are not the expected dominant IHC compartments (UniProt Q15120: mitochondrial matrix; HPA tissue IHC: cytoplasmic). HPA also reports uncertain nucleolar localization by ICC-IF, so isolated nucleolar signal is not proof of either specificity or artefact (HPA subcellular). |
| Strong signal in a cell population reported as undetected, such as adipocytes or cardiomyocytes (HPA tissue IHC: Not detected). | Consider cross-reactivity or endogenous detection activity and compare controls (general IHC practice). HPA's low staining–RNA agreement limits how confidently an apparent mismatch can be called false (HPA tissue IHC: reliability); UniProt reports expression in heart (UniProt Q15120: tissue specificity). |
| Diffuse staining across cells and tissue spaces, with poor separation between cells. | Treat this as background until controls clarify it; excessive antibody or incomplete blocking can produce nonspecific staining (general IHC practice). A broad haze does not establish the cell-specific cytoplasmic pattern reported by HPA (HPA tissue IHC: profile). |
| No signal in a matched liver or cerebral cortex section, including the expected cell population (HPA tissue IHC: Medium). | Check whether the assay detects its positive control before interpreting an experimental negative (general IHC practice). HPA reports medium staining in hepatocytes or cortical neurons, but its Approved rating has low agreement with RNA data (HPA tissue IHC: reliability). |
| Compartment and topology (UniProt Q15120: mitochondrial matrix; no transmembrane segment). | A cytoplasmic IHC pattern is biologically plausible; matrix-level localization requires finer-resolution evidence than routine chromogenic sections provide (HPA tissue IHC: cytoplasmic; general IHC practice). Do not score membrane staining as the expected pattern (UniProt Q15120 topology). |
| Tissue choice and evidence strength (HPA tissue IHC: reliability Approved). | HPA reports Medium staining in neuronal cells, hepatocytes, macrophages, and several glandular populations, but low staining–RNA agreement and pending external verification limit extrapolation (HPA tissue IHC). Its Not detected entries describe observed IHC results, not proven protein absence (HPA tissue IHC). |
| Antibody evidence (HPA antibodies: HPA046583 IHC Approved; HPA072492 ICC Supported). | The supplied validation applies to different antibodies and applications (HPA antibodies). It does not establish that an ICC-IF pattern will be reproduced by the IHC antibody, or that either antibody has IHC Enhanced validation (HPA antibodies). |
| IF/ICC Q: Where should PDK3 appear? A: Mainly in mitochondria (HPA subcellular: supported). | HPA additionally lists nucleoli with uncertain support and images from A-431, MCF-7, and RT-4 (HPA subcellular). Treat that nucleolar observation cautiously; this IHC section supplies no IF/ICC protocol option (HPA subcellular). |
| Target-specific fixation effects are not established by the supplied assay evidence. Verify with a matched IHC source before attributing a result to fixation. | No target-specific fixation effect is reported in the supplied HPA or UniProt evidence. Choose and document retrieval conditions empirically for the IHC assay (general IHC practice); do not infer a PDK3-specific retrieval requirement from staining level or topology (HPA tissue IHC; UniProt Q15120). |
| Situation | Likely cause | Next action |
|---|---|---|
| Expected hepatocyte or cortical neuronal signal is absent (HPA tissue IHC: Medium). | Assay detection, primary-antibody concentration, or retrieval conditions may need optimization (general IHC practice); the supplied sources give no PDK3-specific cause. | Run a matched reported-positive section with detection controls; titrate the IHC-validated antibody and compare documented retrieval conditions (HPA tissue IHC: Medium; general IHC practice). |
| Signal remains in a no-primary control. | Endogenous detection activity or nonspecific secondary/detection chemistry can produce signal (general IHC practice). | Address the detection system's endogenous activity and blocking steps, then repeat the control beside the test section (general IHC practice). |
| Haze obscures cytoplasmic cell boundaries. | Excess primary reagent, inadequate blocking, or incomplete washing can raise background (general IHC practice). | Titrate the IHC-validated antibody and optimize blocking and washes; retain the reported-positive tissue for comparison (HPA tissue IHC: Medium; general IHC practice). |
| Dominant membrane or nuclear staining appears. | A compartment mismatch raises concern about nonspecific staining; nucleolar localization remains uncertain by ICC-IF (UniProt Q15120 topology; HPA subcellular). | Compare no-primary and reported-positive sections before scoring; require a discernible cytoplasmic component consistent with tissue IHC (HPA tissue IHC: cytoplasmic; general IHC practice). |
| Cardiomyocytes stain despite HPA's Not detected IHC result (HPA tissue IHC). | Cross-reactivity is possible, but UniProt reports heart expression and HPA reports low staining–RNA agreement (general IHC practice; UniProt Q15120; HPA tissue IHC). | Check controls and repeat with independent specificity evidence before calling either the staining or HPA observation definitive (general IHC practice; HPA tissue IHC: reliability). |
| Cells outside the expected population stain strongly within a reported-positive tissue (HPA tissue IHC: cell-specific entries). | Cross-reactivity or endogenous detection activity may mimic a new cell distribution (general IHC practice). | Compare morphology and counterstain, review no-primary controls, and report the departure from HPA's specified cell pattern rather than assigning it to PDK3 alone (HPA tissue IHC; general IHC practice). |
Comprehensive Human Protein Atlas IHC scoring per tissue (reliability: Approved — Low consistency between antibody staining and RNA expression data. Pending external verification.). 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 |
|---|---|---|---|---|
| Cerebral cortex | Neuronal cells | Medium | Protein (IHC) | HPA → |
| Duodenum | Glandular cells | Medium | Protein (IHC) | HPA → |
| Endometrium | Glandular cells | Medium | Protein (IHC) | HPA → |
| Hippocampus | Neuronal cells | Medium | Protein (IHC) | HPA → |
| Liver | Hepatocytes | Medium | Protein (IHC) | HPA → |
| Tissue | Cell type | Level | Evidence | Source |
|---|---|---|---|---|
| Adipose tissue | Adipocytes | Not detected | Protein (IHC) | HPA → |
| Adrenal gland | Glandular cells | Not detected | Protein (IHC) | HPA → |
| Bronchus | Basal cells | Not detected | Protein (IHC) | HPA → |
| Cerebellum | Cells in granular layer | Not detected | Protein (IHC) | HPA → |
| Colon | Endothelial cells | Not detected | Protein (IHC) | HPA → |
Troubleshoot chromogenic PDK3 staining by checking retrieval, cellular context, and mitochondrial localisation; the catalog antibody has a paraffin-section IHC example (datasheet A05658-1).
The IHC-validated anti-PDK3 antibody has paraffin-section images from human meningioma and rectum adenocarcinoma, plus mouse and rat testis; IF data come from HeLa cells (catalog image captions).
A05658-1 is listed for IHC and shows PDK3 staining in paraffin sections of human meningioma and rectum adenocarcinoma, mouse testis, and rat testis (catalog applications; A05658-1 IHC captions). A05658-1 is also listed for IF/ICC, with an IF image from HeLa cells (catalog applications; A05658-1 IF caption).
Which to pick: Choose A05658-1 for paraffin-section tissue IHC: its own captions document EDTA retrieval at pH 8.0, primary antibody at 2 μg/ml, and HRP/DAB detection (A05658-1 IHC captions). For IF/ICC, its HeLa image documents 5 μg/ml; for cross-species tissue IHC, its images cover human, mouse, and rat (A05658-1 IF caption; A05658-1 IHC captions). Clonality and tissue fixative are unreported.