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- Table of Contents
Plan paraffin-section IKZF3 staining around nuclear signal in subsets of lymphoid immune cells (HPA tissue IHC), using the catalog antibody at 2–5 μg/mL (datasheet A01611-2). Use tonsil or spleen as positive tissue (HPA tissue IHC), and score nuclear staining by cell population while accounting for presumed off-target binding (HPA tissue IHC).
Expected localisation, validated protocols, controls and antibodies — the at-a-glance facts below, then the full design guide.
| Expected localisation | Nuclear staining in immune-cell subsets (HPA tissue IHC) | |
| Staining pattern | Nuclear staining in subsets of lymphoid immune cells (HPA tissue IHC) | |
| Antigen retrieval | EDTA pH 8.0 HIER, heat-mediated (datasheet A01611-2) | |
| Positive control | Appendix+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 | Presumed off-target staining may confound scoring (HPA tissue IHC) | |
| Regulation | Intensity regulation unreported (UniProt) | |
| Isoform / epitope | 16 isoforms; epitope coverage is unknown (UniProt) |
The catalog antibody protocol uses EDTA pH 8.0 heat retrieval (datasheet A01611-2). The published IHC examples below cover gastric cancer and peripheral T-cell lymphoma (PMC12900698; PMC5436254; PMC11272681).
| Sample | Paraffin-embedded human tonsil tissue; fixative not specified (datasheet A01611-2) |
| Fixation | Image fixative and duration unreported (datasheet A01611-2); 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 A01611-2); 20 min, 95–100 °C (standard) |
| Peroxidase block | 3% H2O2, 10 min, room temperature (standard) |
| Blocking | 10% goat serum (datasheet A01611-2) |
| Primary antibody | Rabbit anti-IKZF3, 2-5 μg/ml (datasheet A01611-2) |
| Primary incubation | Overnight at 4 °C (datasheet A01611-2) |
| Detection | HRP-conjugated secondary, DAB chromogen (datasheet A01611-2) |
| Counterstain | Hematoxylin, blue, dehydrate and mount (standard) |
| Expected result | IKZF3-positive staining in non-germinal center cells of appendix (HPA tissue IHC: High). HPA tissue profile: Nuclear expression in subsets of immune cells in lymphoid organs. No signal in the no-primary control. |
IKZF3 should appear mainly in nuclei of subsets of immune cells in lymphoid organs (HPA: tissue IHC profile). Cytoplasmic localisation is also reported, but the expected tissue IHC pattern is nuclear (UniProt Q9UKT9: nucleus and cytoplasm; HPA: tissue IHC profile). IKZF3 has no transmembrane segment (UniProt Q9UKT9: topology). HPA rates tissue staining Enhanced, while reporting medium consistency with RNA expression and presumed off-target binding that was disregarded (HPA: tissue IHC reliability).
| Distinct nuclear staining in subsets of lymphoid cells, with unstained neighbouring cells. | This fits the cell-restricted pattern: high staining occurs in spleen white-pulp cells, tonsil germinal-center cells, and lymph-node non-germinal-center cells (HPA: tissue IHC). Score the identified cell population rather than assigning one intensity to the whole section (standard IHC practice). |
| Predominantly cytoplasmic staining, with little or no nuclear signal in the expected cells. | Recheck localisation and controls before calling the slide positive: tissue IHC describes nuclear expression, although UniProt also lists cytoplasm and ICC-IF supports cytosol (HPA: tissue IHC and subcellular; UniProt Q9UKT9: subcellular location). Cytoplasmic signal alone does not establish the expected tissue IHC pattern. |
| Strong staining in adipocytes or respiratory epithelial cells instead of the expected immune-cell subsets. | Treat this as suspect staining: HPA reports IKZF3 not detected in adipocytes of adipose tissue and respiratory epithelial cells of bronchus (HPA: tissue IHC). Investigate antibody cross-reactivity or endogenous chromogenic activity before interpreting it as IKZF3 (standard IHC practice). |
| Haze or colour spread across cells and surrounding tissue, obscuring nuclear boundaries. | A diffuse deposit cannot be scored as the reported cell-specific nuclear pattern (HPA: tissue IHC profile). Review blocking, washes, detection chemistry, and counterstain so individual nuclei can be assessed (standard IHC practice). |
| No convincing nuclear signal in a section containing a documented positive cell population. | A blank expected-positive compartment makes the result inconclusive: HPA reports high staining in spleen white-pulp cells and medium staining in bone-marrow hematopoietic cells (HPA: tissue IHC). Verify the relevant cells are present, then review assay controls and staining conditions (standard IHC practice). |
| Strength of the tissue evidence | HPA labels the tissue IHC evidence Enhanced, but notes medium consistency with RNA and presumed off-target binding that was disregarded (HPA: tissue IHC reliability). Read an unexpected pattern cautiously and compare compartment, cell identity, and controls. |
| Choice of positive tissue | Appendix non-germinal-center cells, endometrial lymphocytes, lymph-node non-germinal-center cells, spleen white-pulp cells, and tonsil germinal-center cells are rated High; bone-marrow hematopoietic cells are Medium (HPA: tissue IHC). Identify the listed cells before judging a section negative. |
| Choice of comparison cells | Adipocytes in adipose tissue and bronchial respiratory epithelial cells are listed as Not detected; lung alveolar cells are Low (HPA: tissue IHC). These are cell-specific comparisons, not claims that every cell in those tissues lacks IKZF3. |
| Molecular context | UniProt lists 16 isoforms, four example phosphorylated residues, no signal peptide, and no transmembrane segment (UniProt Q9UKT9: isoforms, modified residues, processing, topology). The supplied evidence gives no antibody epitope or isoform coverage, so it cannot predict which variants the IHC assay detects. |
| IF/ICC Q: Where should signal appear? | A: Mainly in nucleoplasm, with additional supported cytosol localisation in ICC-IF images from HEL, RT-4, and U2OS (HPA: subcellular). This supports an IF localisation check; it does not establish an IHC-positive tissue result or an IF protocol. |
| Situation | Likely cause | Next action |
|---|---|---|
| Expected-positive spleen white pulp lacks nuclear staining. | The assessed cells may be absent from the field, or the IHC run may have failed; HPA rates white-pulp cells High (HPA: tissue IHC; standard IHC practice). | Confirm white-pulp cells on the section and inspect run controls, detection, and counterstain before reporting a negative result (standard IHC practice). |
| Only cytoplasmic colour appears in lymphoid cells. | Tissue IHC reports nuclear expression; cytoplasm is also a reported IKZF3 location, so localisation alone cannot identify the source of the colour (HPA: tissue IHC; UniProt Q9UKT9: subcellular location). | Check nuclear boundaries and compare a documented positive cell population and detection controls; withhold a tissue-IHC positive call if nuclear staining remains absent (HPA: tissue IHC; standard IHC practice). |
| Adipocytes stain strongly. | Adipocytes in adipose tissue are listed as Not detected, making this pattern unexpected; cross-reactivity or endogenous detection activity is possible (HPA: tissue IHC; standard IHC practice). | Inspect a detection control and assess the stain's cellular distribution before attributing adipocyte colour to IKZF3 (standard IHC practice). |
| Colour covers much of the section without clear nuclear edges. | Diffuse background can arise from nonspecific binding, incomplete washing, or detection background (standard IHC practice). It obscures the nuclear immune-cell pattern reported by HPA (HPA: tissue IHC profile). | Review blocking and washes, and inspect a detection control; reassess only where individual cells and nuclei remain interpretable (standard IHC practice). |
| A lymphoid section has mixed positive and negative cells. | HPA describes expression in subsets, including different named populations across lymphoid organs (HPA: tissue IHC profile and positive cells). Mixed staining can therefore be expected. | Identify the relevant compartment and score its cells separately; compare intensity with the tissue and cell labels supplied by HPA (HPA: tissue IHC; standard IHC practice). |
| A negative comparison tissue shows occasional stained cells. | HPA's Not detected labels apply to specified cell types, such as bronchial respiratory epithelial cells, rather than every cell in a tissue (HPA: tissue IHC). | Identify the stained cell type before calling the comparison failed; investigate staining of the HPA-listed negative cell type with controls (HPA: tissue IHC; standard IHC practice). |
Comprehensive Human Protein Atlas IHC scoring per tissue (reliability: Enhanced — Medium consistency between antibody staining and RNA expression data. Presumed off target binding observed and disregarded.). 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 |
|---|---|---|---|---|
| Appendix | Non-germinal center cells | High | Protein (IHC) | HPA → |
| Endometrium | Lymphocytes | High | Protein (IHC) | HPA → |
| Lymph node | Non-germinal center cells | High | Protein (IHC) | HPA → |
| Spleen | Cells in white pulp | High | Protein (IHC) | HPA → |
| Tonsil | Germinal center cells | High | 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 → |
| Breast | Adipocytes | Not detected | Protein (IHC) | HPA → |
| Bronchus | Respiratory epithelial cells | Not detected | Protein (IHC) | HPA → |
| Caudate | Glial cells | Not detected | Protein (IHC) | HPA → |
Troubleshoot IKZF3 staining in paraffin sections by checking retrieval, nuclear localisation and immune cell specificity (datasheet A01611-2; HPA tissue IHC).
Anti-IKZF3 IHC images cover human tonsil and breast cancer, rat thymus, and mouse spleen; an IF/ICC image covers SIHA cells (catalog image captions).
A01611-2 has paraffin-section IHC images from human tonsil, rat thymus, and mouse spleen, plus an IF/ICC image from SIHA cells (A01611-2 image captions). M01611-2 has a paraffin-section IHC image from human breast cancer tissue and lists IF/ICC as an application, without an IF/ICC image in the payload (M01611-2 image captions; catalog applications).
Which to pick: Choose A01611-2 for cross-species paraffin-section IHC because its own captions show human, rat, and mouse tissue stained after EDTA retrieval at pH 8.0; the fixative is unreported (A01611-2 IHC image captions). Choose monoclonal M01611-2 for human breast cancer paraffin-section IHC at 1:50, with EDTA retrieval at pH 8.0 shown in its own caption; the fixative is unreported (M01611-2 catalog entry; M01611-2 IHC image caption). For IF/ICC, choose A01611-2 when an imaged example matters: its SIHA-cell caption uses 5 μg/ml, while M01611-2 lists IF/ICC without an image in the payload (A01611-2 IF image caption; M01611-2 catalog entry).