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- Table of Contents
Plan PGK1 staining in paraffin sections using kidney glomerular cells as a high-staining reference and smooth muscle cells as a low-staining comparison (HPA tissue IHC). The IHC-validated antibody M01449-1 has a reported primary dilution of 1:25 (datasheet M01449-1).
Expected localisation, validated protocols, controls and antibodies — the at-a-glance facts below, then the full design guide.
| Expected localisation | Cytoplasmic and nuclear tissue staining (HPA tissue IHC) | |
| Staining pattern | Widespread cytoplasmic and nuclear staining (HPA tissue IHC) | |
| Antigen retrieval | Citrate pH 6 HIER, heat-mediated (datasheet M01449-1) | |
| Positive control | Breast+4 more · see all | |
| Negative control | Smooth muscle |
| Fixation | Use formaldehyde-fixed paraffin sections (selected-SKU IHC image M01449-1); keep fixation consistent. (standard IHC practice; not target-specific) | |
| Caveat | Staining may reflect protein from more than one gene (HPA tissue IHC) | |
| Regulation | Testis expression decreases in elderly men (UniProt) | |
| Isoform / epitope | 2 isoforms; epitope coverage is unspecified (UniProt) |
Compare the catalog antibody’s citrate pH 6 heat retrieval protocol (datasheet M01449-1) with published PGK1 IHC protocols for neuroblastoma (PMC3869792) and endometrial tissue (PMC5787500).
| Sample | Formaldehyde-fixed, paraffin-embedded human kidney tissue (datasheet M01449-1) |
| Fixation | Image formalin-fixed; duration unreported (datasheet M01449-1); verify before use. |
| Sectioning | 4–5 µm sections on charged slides (standard) |
| Deparaffinisation | Xylene, graded ethanol series to water (standard) |
| Antigen retrieval | Heat retrieval: Citrate pH 6 (datasheet M01449-1); 20 min, 95–100 °C (standard) |
| 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 1086CT10.2.1) anti-PGK1, 1:25 (datasheet M01449-1) |
| Primary incubation | 1 hours at 37°C (datasheet M01449-1) |
| Detection | HRP-polymer secondary, DAB chromogen 5–10 min (standard) |
| Counterstain | Hematoxylin, blue, dehydrate and mount (standard) |
| Expected result | PGK1-positive staining in glandular cells of breast (HPA tissue IHC: High). HPA tissue profile: Ubiquitous cytoplasmic and nuclear expression. No signal in the no-primary control. |
PGK1 is a soluble protein with cytosolic and mitochondrial matrix localization and no transmembrane segment (UniProt P00558: subcellular location and topology). In paraffin sections, expect broad cytoplasmic staining, with nuclear staining also reported by HPA (HPA: ubiquitous cytoplasmic and nuclear expression). HPA records high staining in several glandular populations, kidney glomerular cells, lymph node non-germinal center cells, and late spermatids (HPA: tissue IHC). Its tissue IHC reliability is Approved, with medium consistency against RNA data and a multi-gene targeting caution (HPA: reliability).
| Cytoplasmic stain in breast or cervix glandular cells, with possible nuclear stain. | This fits the reported distribution (HPA: High in breast and cervix glandular cells; ubiquitous cytoplasmic and nuclear expression). Judge intensity against cells on the same section; the HPA High label describes its observed staining level, not a universal exposure or scoring threshold. |
| A crisp membrane rim dominates while cytoplasm is clear. | Membrane-only staining conflicts with the reported cytosolic and mitochondrial matrix locations and lack of a transmembrane segment (UniProt P00558: location and topology). Check whether the rim also appears in controls before assigning it to PGK1; HPA's nuclear observation remains compatible (HPA: tissue IHC profile). |
| Strong signal appears in smooth muscle cells while an expected positive population is clear. | HPA lists smooth muscle cells as Not detected and several glandular populations as High (HPA: tissue IHC). Investigate nonspecific antibody binding or endogenous chromogen activity as possibilities; the pattern alone cannot establish cross-reactivity, particularly because HPA cautions that staining may include proteins from more than one gene (HPA: reliability). |
| Color spreads across tissue, empty spaces, or the entire section without cell boundaries. | This is diffuse background rather than an interpretable cellular pattern. Compare a primary-antibody omission control and a known-positive tissue; those are general IHC controls. PGK1's reported cytoplasmic and nuclear expression does not justify treating uniform extracellular deposit as specific staining (HPA: tissue IHC profile). |
| No cellular signal appears in breast glandular cells or kidney glomerular cells. | Both are reported High by HPA (HPA: breast glandular cells; kidney cells in glomeruli). An entirely blank result therefore needs a technical check before a biological interpretation. HPA's Approved rating has medium RNA–staining consistency, so one negative section does not resolve true PGK1 abundance (HPA: reliability). |
| Compartment and tissue context | UniProt places PGK1 in cytosol and mitochondrial matrix (UniProt P00558: location), while HPA reports cytoplasmic and nuclear tissue staining (HPA: tissue IHC profile). Interpret nuclear color with that source difference in view; neither source supplies a fixed nuclear-to-cytoplasmic ratio. |
| Antibody evidence | Four listed antibodies have Approved IHC status (HPA: HPA045385, HPA073644, HPA073656, CAB010065). HPA also flags multi-gene targeting and medium RNA–staining consistency (HPA: reliability); an Approved label alone cannot identify the source of every stained cell. |
| Isoforms and epitope coverage | Two PGK1 isoforms are recorded (UniProt P00558: isoforms 1 and 2). Their presence does not show whether an antibody distinguishes them; no epitope position or isoform-specific IHC result is supplied. Treat a difference between antibodies as unresolved until their epitopes and validation are known. |
| Antigen retrieval in paraffin sections | Retrieval conditions can affect IHC staining as a general workflow matter. No PGK1-specific fixation sensitivity or retrieval condition is supplied by UniProt or HPA; optimize with a known-positive section and compare staining alongside background, without attributing changes to a demonstrated PGK1 epitope effect. |
| IF/ICC: what should a sperm image show? | HPA approves localization to the mid piece, principal piece, and end piece, while cautioning that the antibodies target proteins from multiple genes (HPA: ICC-IF subcellular). This IF/ICC observation supports a spatial comparison; it is not an IHC-P protocol or proof that each segment's signal is PGK1 alone. |
| Situation | Likely cause | Next action |
|---|---|---|
| Known-positive glandular cells are blank. | Primary binding, retrieval, or detection may have failed; the slide alone cannot identify which step. These cells are reported High (HPA: breast and cervix glandular cells). | Run a known-positive section through the same IHC workflow; check reagent order, antibody use, detection, and counterstain. Adjust retrieval or dilution only with a concurrent control, since PGK1-specific fixation sensitivity is unreported. |
| Smooth muscle cells stain strongly. | HPA reports them as Not detected (HPA: smooth muscle cells). Nonspecific binding or endogenous detection activity is possible; HPA also cautions that antibodies may target proteins from more than one gene (HPA: reliability). | Compare a primary-antibody omission control and an appropriate endogenous-activity control. Recheck the named cell type on the counterstain; do not assign the smooth muscle signal to PGK1 solely from its color. |
| All compartments show a uniform brown haze. | Diffuse deposit may reflect excess reagent, inadequate washing, or endogenous chromogen activity in a general IHC workflow; it does not match a defined cellular pattern (HPA: cytoplasmic and nuclear profile). | Review omission controls, blocking, washing, and detection development. Reassess cell boundaries after background falls; avoid raising a positivity score merely because the entire section darkens. |
| Only cell borders stain. | A membrane-only pattern conflicts with PGK1's reported cytosolic and mitochondrial matrix localization and absence of a transmembrane segment (UniProt P00558: location and topology). | Compare an HPA High population on the same run and inspect omission controls. Review detection artifacts and antibody specificity before interpreting a border-only signal as a new PGK1 location. |
| Two antibodies give different nuclear staining. | HPA reports nuclear tissue staining, but its antibody evidence carries a multi-gene caution (HPA: tissue IHC profile and reliability). The supplied record gives no epitope mapping or antibody-specific nuclear comparison. | Score cytoplasmic and nuclear compartments separately, document antibody identity, and compare matched sections. Treat the discordance as unresolved; do not infer an isoform, processing event, or fixation effect from this comparison alone. |
| A weak section is treated as a definitive negative. | HPA records Low staining in several populations, including small-intestine glandular cells, while breast glandular cells are High (HPA: tissue IHC). Weak color can therefore have different meaning across sampled cell types. | Identify the cell population and compare it with a concurrent HPA High control. Score localized cellular signal separately from background, and report an uncertain result when the control or cell identity is unclear. |
Comprehensive Human Protein Atlas IHC scoring per tissue (reliability: Approved — Medium consistency between antibody staining and RNA expression data. Caution, targets protein from more than one gene.). 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 |
|---|---|---|---|---|
| Breast | Glandular cells | High | Protein (IHC) | HPA → |
| Cervix | Glandular cells | High | Protein (IHC) | HPA → |
| Fallopian tube | Glandular cells | High | Protein (IHC) | HPA → |
| Gallbladder | Glandular cells | High | Protein (IHC) | HPA → |
| Kidney | Cells in glomeruli | High | Protein (IHC) | HPA → |
| Tissue | Cell type | Level | Evidence | Source |
|---|---|---|---|---|
| Smooth muscle | Smooth muscle cells | Not detected | Protein (IHC) | HPA → |
Troubleshoot PGK1 staining in paraffin sections by checking retrieval, cellular distribution, controls and scoring before interpreting changes in signal.
Anti-PGK1 antibodies have IHC images from human kidney, liver and lung cancer paraffin sections, plus IF/ICC images from HepG2 and U87 cells (catalog figure captions).
M01449-1 has IHC images from human kidney and liver sections (M01449-1 figure captions); PA2045 has an IHC image from a human lung cancer section (PA2045 figure caption). A01449 has an ICC image from HepG2 cells (A01449 figure caption); PB9774 has an IF image from U87 cells (PB9774 figure caption).
Which to pick: For tissue IHC, choose M01449-1 for formaldehyde-fixed, paraffin-embedded sections (M01449-1 figure caption: human kidney; catalog: mouse monoclonal, IHC-P) or PA2045 for paraffin sections with a different retrieval example (PA2045 figure caption: EDTA pH 8.0; fixative unreported). For IF/ICC, choose A01449 or PB9774 based on their cell images and listed IF/ICC applications (A01449 figure caption: HepG2; PB9774 figure caption: U87; catalog applications). For planned human, mouse or rat work, PA2045 is the IHC choice and A01449 or PB9774 are IF/ICC choices based on listed reactivity; the cited images show individual samples, not validation in every listed species (catalog reactivity; figure captions).