IKZF3 / Zinc finger protein Aiolos · IHC design guide

Design Immunohistochemistry for IKZF3

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).

Evidence assembled Oct 2026 · For research use; verify linked source records and product datasheet before use
Immunohistochemistry protocol sheet for IKZF3 (IHC for IKZF3): expected localisation Nuclear staining in immune-cell subsets (HPA tissue IHC), antibody A01611-2, validated IHC image, and IHC protocol steps
Printable IKZF3 IHC protocol sheet — expected localisation Nuclear staining in immune-cell subsets (HPA tissue IHC), antibody A01611-2, controls and protocol steps. Open the full IKZF3 IHC guide →

IKZF3 Immunohistochemistry Experimental Design Guide

Expected localisation, validated protocols, controls and antibodies — the at-a-glance facts below, then the full design guide.

Must know before staining
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
Important caveats
Reasons your staining may differ from the expected pattern.
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)
Section 1

Recommended IKZF3 IHC & IF Protocols

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).

Recommended immunohistochemistry (IHC-P) protocol parameters
SampleParaffin-embedded human tonsil tissue; fixative not specified (datasheet A01611-2)
FixationImage fixative and duration unreported (datasheet A01611-2); verify before use.
Sectioning4–5 µm sections on charged slides (standard)
DeparaffinisationXylene, graded ethanol series to water (standard)
Antigen retrievalHeat retrieval: EDTA pH 8.0 (datasheet A01611-2); 20 min, 95–100 °C (standard)
Peroxidase block3% H2O2, 10 min, room temperature (standard)
Blocking10% goat serum (datasheet A01611-2)
Primary antibodyRabbit anti-IKZF3, 2-5 μg/ml (datasheet A01611-2)
Primary incubationOvernight at 4 °C (datasheet A01611-2)
DetectionHRP-conjugated secondary, DAB chromogen (datasheet A01611-2)
CounterstainHematoxylin, blue, dehydrate and mount (standard)
Expected resultIKZF3-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.
💡Decision noteStart with EDTA pH 8.0 heat retrieval for the catalog antibody (datasheet A01611-2). The gastric cancer study mentions citrate buffer but gives no retrieval conditions (PMC12900698).
Section 2

What Is the Expected IKZF3 Staining Pattern?

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).

What am I looking at on my slide?
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).
💡Expected IKZF3 appearanceCall positive when discrete nuclear chromogenic staining is visible in the expected immune-cell subset—high in the HPA-listed positive populations—while broad staining of HPA-listed negative cell types is treated as suspect (HPA: tissue IHC).
How each factor affects the staining
Strength of the tissue evidenceHPA 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 tissueAppendix 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 cellsAdipocytes 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 contextUniProt 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.
Why is my staining missing, weak or wrong?
SituationLikely causeNext 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).

Sample controls for IKZF3 IHC & IF

🧪Run tonsil first and score germinal center cells for IKZF3 staining (HPA: High in tonsil germinal center cells). Use adipose tissue adipocytes as the negative comparator (HPA: Not detected in adipocytes); on the tonsil slide, morphologically identified non-lymphoid cells should show counterstain without convincing IKZF3 nuclear signal (UniProt: lymphocyte differentiation function; HPA: High in germinal center cells).
Positive control tissue: Appendix (Non-germinal center cells, HPA High)
Negative control tissue: Adipose tissue (HPA Not detected)
ICC-IF cell lines (HPA subcellular resource): HPA ICC-IF images show IKZF3 in HEL, RT-4, U2OS, with annotated localisation: Nucleoplasm (supported) (HPA subcellular).
Technical controls: Run no-primary (secondary-only), concentration-matched rabbit IgG isotype, and an IKZF3 knockout biological negative where available (caption: rabbit anti-IKZF3). Block endogenous peroxidase and check for residual DAB signal in tonsil with the no-primary control (caption: HRP/DAB detection).
⚠️Feasibility: A target-specific fixation window or fixation effect is unreported, and the selected A01611-2 tonsil caption does not state a fixative (caption: fixative not stated). The caption demonstrates staining after heat retrieval in EDTA at pH 8.0, but provides no comparison without retrieval, so retrieval dependence is unreported (caption: tonsil IHC). The evidence does not establish whether frozen sections or IF are easier; for chromogenic tonsil IHC, endogenous peroxidase can mimic DAB signal and warrants the control above (caption: HRP/DAB detection).

HPA tissue IHC evidence for IKZF3

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.

Positive expression · recommended positive controls

TissueCell typeLevelEvidenceSource
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 →

Undetected expression · recommended negative controls

TissueCell typeLevelEvidenceSource
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 →
Section 3

Advanced IKZF3 IHC Tips

Troubleshoot IKZF3 staining in paraffin sections by checking retrieval, nuclear localisation and immune cell specificity (datasheet A01611-2; HPA tissue IHC).

Which retrieval conditions should I try when IKZF3 nuclear staining is weak?
Start with heat-mediated antigen retrieval in EDTA buffer at pH 8.0 for paraffin sections (datasheet A01611-2). The catalog antibody produced staining in paraffin-embedded human tonsil after this retrieval, followed by 2 μg/ml primary antibody overnight at 4°C (datasheet A01611-2). If nuclear staining remains weak, check heating consistency and section adhesion, then compare a small retrieval-time series while keeping antibody concentration and detection constant (standard IHC practice). Score signal in germinal center cells and inspect surrounding tissue for diffuse staining, because retrieval changes can increase background alongside signal (HPA: High in tonsil germinal center cells; standard IHC practice).
Could fixation explain variable IKZF3 staining between paraffin blocks?
Target-specific fixation sensitivity for IKZF3 is unknown from the supplied evidence; the catalog image identifies paraffin embedding but does not state the fixative (datasheet A01611-2). Record each block’s fixative and fixation duration, and compare sections processed through the same retrieval and detection run before attributing variation to fixation (standard IHC practice). Use a tonsil section as a run control, assessing nuclear staining in germinal center cells under the stated EDTA pH 8.0 retrieval condition (datasheet A01611-2; HPA: High in tonsil germinal center cells). If blocks differ, optimise processing with matched controls; do not infer a particular fixation effect from IKZF3 localisation or phosphorylation annotations (UniProt Q9UKT9; standard IHC practice).
How should I assess predominantly cytoplasmic IKZF3 staining in tissue?
Judge the chromogenic result first against nuclear staining in subsets of immune cells within lymphoid organs (HPA tissue IHC). IKZF3 is annotated in both nucleus and cytoplasm, and nucleoplasm is its supported main location, with cytosol additionally supported in cell imaging (UniProt Q9UKT9; HPA subcellular). Predominantly cytoplasmic DAB without matching nuclear signal therefore warrants review of cell identity, morphology, retrieval and primary-antibody background before assignment to IKZF3 (standard IHC practice). Compare adjacent immune-rich and relatively unstained compartments within the same section, then repeat with a primary-omission control if diffuse cytoplasmic colour persists (HPA tissue IHC; standard IHC practice).
Can this stain distinguish IKZF3 isoforms or altered epitopes?
Do not score a chromogenic nuclear signal as a specific IKZF3 isoform unless the antibody epitope and isoform coverage have been established separately (UniProt Q9UKT9: 16 isoforms; standard IHC practice). The supplied catalog caption documents staining conditions but does not identify the recognised epitope or establish isoform selectivity (datasheet A01611-2). IKZF3 has annotated phosphorylated residues, including positions 22, 42, 326 and 378, but their effect on this antibody’s tissue staining is unknown (UniProt Q9UKT9). When samples disagree, compare nuclear staining under matched retrieval conditions and describe the result as antibody-detected IKZF3 until epitope-specific validation is available (standard IHC practice).
How can I compare IKZF3 immunofluorescence with the chromogenic IHC result?
Treat IF/ICC as a separate validation experiment: the supplied catalog evidence demonstrates paraffin-section chromogenic staining, not a matched fluorescence workflow (datasheet A01611-2). Multiplex IKZF3 with a marker for the expected immune-cell population, and assess nuclear overlap at the single-cell level (HPA tissue IHC; standard IF practice). Choose a fluorophore channel with low tissue autofluorescence and include single-colour and no-primary controls to separate bleed-through from specific signal (standard IF practice). IKZF3 has no annotated transmembrane segment, but its precise antibody epitope is unspecified; validate permeabilisation that gives antibody access to the nuclear antigen without assuming an extracellular epitope (UniProt Q9UKT9; standard IF practice).
What should I check when DAB staining spreads beyond immune-cell nuclei?
Inspect the primary-omission control and the section’s unstained regions before increasing the threshold for a positive IKZF3 call (standard IHC practice). The catalog example used 10% goat serum blocking, 2 μg/ml primary antibody overnight at 4°C, and peroxidase-linked detection with DAB (datasheet A01611-2). If background is widespread, titrate the primary antibody and review washing, blocking and endogenous-peroxidase quenching under otherwise matched conditions (standard IHC practice). Keep the HPA reliability note in view: its tissue profile reports presumed off-target binding, so diffuse staining outside the expected immune-cell nuclei needs independent scrutiny (HPA tissue IHC).
How should I quantify IKZF3-positive cells across sections? ⚠ ANSWER MARKED FOR VERIFICATION
Define the tissue compartment and eligible cell population before scoring, because HPA reports nuclear expression in subsets of immune cells rather than uniform tissue staining (HPA tissue IHC). Report the percentage of eligible nuclei that stain, with a stated intensity scale or H-score, using one threshold across sections processed together (standard IHC practice). For infiltration studies, also report positive-cell density per mm² of analysed tissue and normalise counts to the measured viable area or total eligible immune cells (standard IHC practice). Exclude folds and necrotic regions by a predefined rule, and retain representative images plus control results so differences in cell abundance are distinguishable from staining intensity (standard IHC practice).
When is an apparent IKZF3-positive cell likely an artefact?
A convincing result is nuclear staining in an appropriate immune-cell population, consistent with the HPA tissue profile and IKZF3’s transcription-factor role (HPA tissue IHC; UniProt Q9UKT9). Reconsider an isolated cytoplasmic or nonimmune-cell signal, while recognising that cytosolic localisation is additionally supported and cannot be dismissed solely by compartment (HPA subcellular; standard IHC practice). Check whether colour concentrates at section edges, folds or necrotic areas, and whether it persists in a primary-omission control after endogenous-peroxidase blocking (standard IHC practice). Interpret borderline areas alongside morphology and an on-run tonsil control, since presumed off-target binding was observed in the HPA tissue assessment (HPA tissue IHC; standard IHC practice).
Boster reagents

Best IKZF3 / Zinc finger protein Aiolos IHC Antibodies

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).

Real IHC data IHC analysis of IKZF3 using anti-IKZF3 antibody (A01611-2). IKZF3 was detected in a paraffin-embedded section of human tonsil tissue. Heat mediated antigen retrieval was performed in EDTA buffer (pH 8.0, epitope retrieval solution). The tissue section was blocked with 10% goat serum. The tissue section was then incubated with 2 μg/ml rabbit anti-IKZF3 Antibody (A01611-2) overnight at 4°C. Peroxidase Conjugated Goat Anti-rabbit IgG was used as secondary antibody and incubated for 30 minutes at 37°C. The tissue section was developed using HRP Conjugated Rabbit IgG Super Vision Assay Kit (Catalog # SV0002) with DAB as the chromogen.
Anti-IKZF3 Antibody ®
Cat # A01611-2
Real IHC data Figure 2. IHC analysis of IKZF3 using anti-IKZF3 antibody (M01611-2). IKZF3 was detected in a paraffin-embedded section of human breast cancer tissue. Heat mediated antigen retrieval was performed in EDTA buffer (pH 8.0, epitope retrieval solution). The tissue section was blocked with 10% goat serum. The tissue section was then incubated with a dilution of 1:50 rabbit anti-IKZF3 Antibody (M01611-2) overnight at 4°C. Peroxidase Conjugated Goat Anti-rabbit IgG was used as secondary antibody and incubated for 30 minutes at 37°C. The tissue section was developed using HRP Conjugated Rabbit IgG Super Vision Assay Kit (Catalog # SV0002) with DAB as the chromogen.
Anti-IKZF3 Rabbit Monoclonal Antibody
Cat # M01611-2

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).

Each figure is that product's own IHC / IF validation image from its datasheet.

References

  1. UniProt Consortium. UniProt entry Q9UKT9 (IKZF3_HUMAN, Zinc finger protein Aiolos).
  2. Human Protein Atlas. IKZF3 tissue IHC expression (reliability: Enhanced).
  3. Human Protein Atlas. IKZF3 subcellular location (ICC-IF): Mainly localized to the nucleoplasm. In addition localized to the cytosol..
  4. Human Protein Atlas. IKZF3 antibody validation summary (2 antibodies).
  5. IKZF3 promotes gastric cancer progression via Hedgehog signaling activation and is targetable by SANT-1. Acta biochimica et biophysica Sinica 2025 — PMC12900698.
  6. Phosphoproteomic analysis of lung tissue from patients with pulmonary arterial hypertension. Pulmonary circulation 2021 — PMC8711668.
  7. IRF4/MUM1 expression is associated with poor survival outcomes in patients with peripheral T-cell lymphoma. Journal of Cancer 2017 — PMC5436254.
  8. IKZF3 amplification predicts worse prognosis especially in intestinal-type gastric cancer. Journal of cancer research and clinical oncology 2024 — PMC11272681.
  9. PubMed PMID:10552935 — UniProt-cited evidence.
  10. PubMed PMID:11745366 — UniProt-cited evidence.
  11. PubMed PMID:17646674 — UniProt-cited evidence.