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- Table of Contents
Plan paraffin-section YY1 IHC around the ubiquitous nuclear staining pattern reported in tissue (HPA tissue IHC). Use high-staining follicle cells or cytotrophoblasts as reference populations, and interpret staining with the reported cross-gene targeting caution (HPA tissue IHC).
Expected localisation, validated protocols, controls and antibodies — the at-a-glance facts below, then the full design guide.
| Expected localisation | Ubiquitous nuclear staining in tissue (HPA tissue IHC) | |
| Staining pattern | Nuclear staining across tissue cell types (HPA tissue IHC) | |
| Antigen retrieval | EDTA pH 8.0 HIER, heat-mediated (datasheet M00833-3) | |
| Positive control | Ovary+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 may reflect proteins from more than one gene (HPA tissue IHC) | |
| Regulation | No staining-linked induction annotated (UniProt) | |
| Isoform / epitope | No annotated isoforms; one full-length chain (UniProt) |
The catalog antibody’s IHC-P protocol is accompanied by three published YY1 IHC protocols for gastric and esophageal cancer tissues (PMC12754092; PMC3986816; PMC4196789).
| Sample | Paraffin-embedded human thyroid cancer tissue; fixative not specified (datasheet M00833-3) |
| Fixation | Image fixative and duration unreported (datasheet M00833-3); 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 M00833-3); 20 min, 95–100 °C (standard) |
| Peroxidase block | 3% H2O2, 10 min, room temperature (standard) |
| Blocking | 10% goat serum (datasheet M00833-3) |
| Primary antibody | Mouse monoclonal (clone 3F3E7) anti-YY1, 2 μg/ml (datasheet M00833-3) |
| Primary incubation | Overnight at 4 °C (datasheet M00833-3) |
| Detection | HRP-conjugated secondary, DAB chromogen (datasheet M00833-3) |
| Counterstain | Hematoxylin, blue, dehydrate and mount (standard) |
| Expected result | YY1-positive staining in follicle cells of ovary (HPA tissue IHC: High). HPA tissue profile: Ubiquitous nuclear expression. No signal in the no-primary control. |
YY1 should appear mainly as nuclear staining in paraffin sections: UniProt places it at the nuclear matrix, and HPA reports ubiquitous nuclear expression with low tissue specificity (UniProt P25490 subcellular location; HPA tissue IHC). HPA rates its tissue pattern Supported, while cautioning that the staining antibody targets protein from more than one gene (HPA tissue IHC). Expect stronger signal in some cell populations than others (HPA tissue IHC).
| Nuclear chromogen in follicle cells, cytotrophoblasts, peritubular cells or urothelial cells. | This matches HPA's High staining in those populations and its ubiquitous nuclear profile (HPA tissue IHC). Judge each population against its own morphology and counterstain; a uniformly dark section alone does not establish cell-specific YY1 staining (standard IHC practice). |
| Predominantly cytoplasmic or surface staining, with little nuclear signal. | This conflicts with the reported nuclear matrix location and nuclear tissue pattern (UniProt P25490 subcellular location; HPA tissue IHC). Review compartment assignment against the counterstain and controls; nonspecific antibody binding or detection background is possible, but appearance alone cannot identify the cause (standard IHC practice). |
| Strong signal confined to an unexpected cell population while the expected nuclei are weak. | Check the tissue's HPA cell-level pattern before calling a mismatch: YY1 expression is broadly nuclear, and the supplied HPA list contains Low, not negative, populations (HPA tissue IHC). Persistent discordance may reflect cross-reactivity or endogenous detection activity; the image alone cannot distinguish them (standard IHC practice). |
| Haze or chromogen over nuclei, cytoplasm and surrounding section without clear cellular boundaries. | Diffuse staining prevents confident nuclear scoring (standard IHC practice). Assess a no-primary control for endogenous or reagent background, then review blocking, antibody dilution, washes and chromogen development as general IHC variables (standard IHC practice); HPA does not assign a YY1-specific cause (HPA tissue IHC). |
| No nuclear signal in an otherwise intact known-positive control section. | Target-specific fixation effects are not established by the supplied assay evidence. Verify with a matched IHC source before attributing a result to fixation. |
| Tissue and cell context | HPA reports High staining in ovarian follicle cells, placental cytotrophoblasts, testicular peritubular cells and bladder urothelial cells; neuronal cells in cerebral cortex and hepatocytes are Low, not negative (HPA tissue IHC). Compare like cell populations when judging intensity. |
| Antibody evidence and specificity | The HPA tissue profile is Supported but cautions that the staining antibody targets protein from more than one gene (HPA tissue IHC). HPA lists IHC as Supported for HPA001119 and CAB009392; that status supports their reported patterns without proving every stained nucleus is YY1 (HPA antibodies; HPA tissue IHC). |
| Cellular location and topology | UniProt associates YY1 with the nuclear matrix and records no transmembrane segment or signal peptide (UniProt P25490). Nuclear staining is therefore the primary compartment check; these annotations do not predict an antigen retrieval setting or a fixation response. |
| IF/ICC Q: What pattern is expected? | A: HPA reports mainly nucleoplasmic YY1, with additional signal at nucleoli fibrillar centers and nuclear bodies; its main and additional locations are Supported (HPA subcellular ICC-IF). This observation aids compartment comparison, but it is from ICC-IF, not paraffin-section IHC. |
| Situation | Likely cause | Next action |
|---|---|---|
| Positive-control tissue has no nuclear stain. | The control may lack the intended High cell population, or an IHC run step may have failed (HPA tissue IHC; standard IHC practice). | Confirm the relevant cells are present; check the antibody used, retrieval record and detection reagents with run controls before interpreting study sections (standard IHC practice). |
| Chromogen dominates the cytoplasm or cell edges. | That distribution conflicts with YY1's nuclear location; nonspecific binding or detection background is possible (UniProt P25490 subcellular location; standard IHC practice). | Compare stained cells with the nuclear counterstain and a no-primary control; review blocking, washes and detection conditions (standard IHC practice). |
| The entire section has diffuse color. | Background can obscure nuclear boundaries; the supplied HPA data do not establish a YY1-specific mechanism (HPA tissue IHC; standard IHC practice). | Inspect the no-primary control and review blocking, dilution, washes and chromogen development as general IHC checks (standard IHC practice). |
| A Low population stains faintly. | Low staining is reported for several populations, including hepatocytes and cortical neuronal cells; Low does not mean absent (HPA tissue IHC). | Assess nuclear localization and compare with a High population within the validated staining context; avoid treating faint signal alone as failure (HPA tissue IHC; standard IHC practice). |
| Unexpected cells show strong nuclear stain. | YY1 has a ubiquitous nuclear profile, but HPA cautions that the tissue-staining antibody targets protein from more than one gene (HPA tissue IHC). | Verify cell identity and compare the distribution with HPA's cell-level observations; use an independent specificity control before assigning unexpected staining to YY1 (HPA tissue IHC; standard IHC practice). |
| IF/ICC puncta are used to judge a chromogenic section. | HPA's supported nucleoli fibrillar center and nuclear-body observations come from ICC-IF images (HPA subcellular ICC-IF). | Use nuclear staining as the primary IHC compartment criterion; evaluate any finer pattern within the limits of the section and chromogenic readout (HPA tissue IHC; standard IHC practice). |
Comprehensive Human Protein Atlas IHC scoring per tissue (reliability: Supported — High 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 |
|---|---|---|---|---|
| Ovary | Follicle cells | High | Protein (IHC) | HPA → |
| Placenta | Cytotrophoblasts | High | Protein (IHC) | HPA → |
| Testis | Peritubular cells | High | Protein (IHC) | HPA → |
| Urinary bladder | Urothelial cells | High | Protein (IHC) | HPA → |
| Adrenal gland | Glandular cells | Medium | Protein (IHC) | HPA → |
| Tissue | Cell type | Level | Evidence | Source |
|---|---|---|---|---|
| None in HPA: YY1 is detected in all 45 scored tissues. Use a no-primary (secondary-only) and an isotype control instead. | ||||
Troubleshoot YY1 staining in paraffin sections by checking nuclear localisation, specimen processing and controls before comparing staining intensity.
Anti-YY1 antibodies have images from human paraffin-section IHC and A431-cell IF (catalog image captions); catalog reactivity fields list human, mouse and rat.
M00833-3 and M00833-2 show IHC in human thyroid cancer paraffin sections (respective IHC captions); M00833-1 shows IHC in a human laryngeal squamous cell carcinoma paraffin section (M00833-1 IHC caption). M00833 shows IHC in paraffin-embedded human bladder (M00833 IHC caption); PB9909 shows IF in A431 cells (PB9909 IF caption).
Which to pick: For tissue IHC, choose mouse monoclonal M00833-2: its captions document human paraffin sections from four tissue types with EDTA pH 8 retrieval (M00833-2 catalog and IHC captions); the fixative is unreported (M00833-2 IHC captions). For IF/ICC, choose PB9909, which has an A431-cell IF image and listed IF/ICC applications (PB9909 IF caption and application list). For cross-species planning, rabbit monoclonal M00833 lists human, mouse and rat reactivity plus IHC/ICC/IF applications (M00833 catalog); its paraffin-embedded bladder image documents human tissue only, and the fixative is unreported (M00833 IHC caption).