IKZF1 / DNA-binding protein Ikaros · IHC design guide

Design Immunohistochemistry for IKZF1

IKZF1 paraffin IHC shows nuclear staining in immune cells, especially in lymphoid tissue (HPA tissue IHC). This guide covers fixation consistency, the catalog antibody’s 0.5–1 μg/ml IHC dilution (datasheet PB9643), and interpretation across 8 isoforms (UniProt).

Evidence assembled Oct 2026 · For research use; verify linked source records and product datasheet before use
Immunohistochemistry protocol sheet for IKZF1 (IHC for IKZF1): expected localisation Nuclear staining in immune cells (HPA tissue IHC), antibody PB9643, validated IHC image, and IHC protocol steps
Printable IKZF1 IHC protocol sheet — expected localisation Nuclear staining in immune cells (HPA tissue IHC), antibody PB9643, controls and protocol steps. Open the full IKZF1 IHC guide →

IKZF1 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 cells (HPA tissue IHC)
Staining pattern Immune-cell nuclei in most tissues; abundant in lymphoid tissue (HPA tissue IHC)
Antigen retrieval EDTA pH 8.0 HIER, heat-mediated (datasheet PB9643)
Positive control ⓘ Bone marrow+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 Immune-cell nuclei can confound tissue-cell scoring (HPA tissue IHC)
Regulation Most abundant in lymphoid tissue (HPA tissue IHC)
Isoform / epitope 8 isoforms; map the antibody epitope across them (UniProt)
Section 1

Recommended IKZF1 IHC & IF Protocols

The catalog antibody’s IHC-P protocol is paired with published IKZF1 staining protocols for salivary gland, human tissue, and follicular lymphoma specimens (PMC10545362; PMC10333745; PMC10539171).

Recommended immunohistochemistry (IHC-P) protocol parameters
SampleParaffin-embedded human tonsil tissue; fixative not specified (datasheet PB9643)
FixationImage fixative and duration unreported (datasheet PB9643); 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 PB9643); 20 min, 95–100 °C (standard)
Peroxidase block3% H2O2, 10 min, room temperature (standard)
Blocking10% goat serum (datasheet PB9643)
Primary antibodyRabbit anti-IKZF1, 0.5-1μg/ml (datasheet PB9643)
Primary incubationOvernight at 4 °C (datasheet PB9643)
DetectionStreptavidin-biotin complex (SABC), DAB chromogen (datasheet PB9643)
CounterstainHematoxylin, blue, dehydrate and mount (standard)
Expected resultIKZF1-positive staining in hematopoietic cells of bone marrow (HPA tissue IHC: Medium). HPA tissue profile: Nuclear expression of immune cells in most tissues, most abundant in lymphoid tissues. No signal in the no-primary control.
💡Decision noteStart with EDTA pH 8.0 heat retrieval (datasheet: PB9643); the salivary gland protocol also used EDTA pH 8.0 (PMC10545362).
Section 2

What Is the Expected IKZF1 Staining Pattern?

IKZF1 should appear chiefly in nuclei of immune cells, with the most abundant tissue staining in lymphoid sites (HPA tissue IHC: Enhanced). Resting lymphocytes may show diffuse nuclear distribution; proliferating cells may show pericentromeric heterochromatin localization (UniProt Q13422). IKZF1 has no transmembrane segment (UniProt Q13422 topology). HPA also reports cytoplasmic localization, but its ICC-IF evidence rates cytosol as uncertain (HPA subcellular).

What am I looking at on my slide?
Immune-cell nuclei stain in lymphoid tissue; germinal center cells in lymph node or tonsil show medium staining (HPA tissue IHC).This fits the expected compartment and cell distribution (HPA tissue IHC; UniProt Q13422). Score the cells that stain, not the whole section: mixed tissue can contain both positive immune cells and unstained neighboring cells (standard IHC practice).
Predominantly cytoplasmic staining appears while nuclei remain unstained.Treat this as discordant with the main nuclear pattern (HPA tissue IHC; HPA subcellular: supported nucleoplasm). UniProt lists cytoplasm, but HPA rates cytosol uncertain in ICC-IF; cytoplasmic color alone is weak evidence of a specific IHC result (UniProt Q13422; HPA subcellular).
Adipocytes or bronchial respiratory epithelial cells stain strongly.These cell types were not detected in the supplied HPA tissue IHC observations (HPA tissue IHC). Investigate antibody cross-reactivity or endogenous chromogenic detection activity (standard IHC practice). Do not label every nonimmune cell positive as erroneous: placental cytotrophoblasts showed medium staining (HPA tissue IHC).
Color spreads across cells, stroma, or the entire section without a clear nuclear pattern.Diffuse background cannot establish IKZF1 localization (standard IHC interpretation; HPA tissue IHC: nuclear immune-cell profile). Check background with an appropriate detection-only control, then judge whether signal remains restricted to expected cells and nuclei (standard IHC practice).
No nuclear signal appears in an otherwise interpretable lymph node or tonsil section.Germinal center cells showed medium staining in both tissues (HPA tissue IHC), so inspect antibody and detection controls before calling the sample negative (standard IHC practice). A negative field alone cannot distinguish a true absence from a failed run (standard IHC interpretation).
💡Expected IKZF1 appearanceCall a result positive when immune-cell nuclei are clearly stained, with medium germinal center staining expected in lymph node or tonsil (HPA tissue IHC); isolated cytoplasmic color or strong staining of HPA-negative cell types warrants investigation (HPA subcellular; HPA tissue IHC).
How each factor affects the staining
Cell population and tissue context (HPA tissue IHC)HPA describes nuclear immune-cell expression across most tissues and the greatest abundance in lymphoid tissues; bone marrow hematopoietic cells, splenic red-pulp cells, and placental cytotrophoblasts each showed medium staining (HPA tissue IHC). Compare named cell populations rather than treating an entire tissue as uniformly positive or negative (standard IHC interpretation).
Nuclear distribution and cell state (UniProt Q13422)Resting lymphocytes can show diffuse nuclear IKZF1; proliferating cells can show pericentromeric heterochromatin localization, dependent on DNA binding regulated by phosphorylation and dephosphorylation (UniProt Q13422). Different nuclear textures may therefore fit the record; this does not establish a target-specific effect of fixation or retrieval.
Isoforms and antibody recognition (UniProt Q13422)UniProt lists 8 IKZF1 isoforms and says isoform composition modulates transcription regulator activity (UniProt Q13422). The payload gives no antibody epitopes, so it cannot establish which isoforms any IHC-validated antibody detects; avoid assigning a staining difference to one isoform without further evidence.
Confidence in the tissue pattern (HPA tissue IHC; HPA antibodies)The tissue profile is rated Enhanced, with high consistency between antibody staining and RNA expression data (HPA tissue IHC). HPA also lists Enhanced IHC status for HPA035221, HPA035222, and CAB009247 (HPA antibodies). These ratings support the reported pattern, but do not resolve a questionable field on their own.
IF/ICC localization Q&A (HPA subcellular)Where should IKZF1 appear in IF/ICC? Mainly in the nucleoplasm, which HPA marks supported; additional cytosol is marked uncertain (HPA subcellular). The listed ICC-IF image cell lines are HDLM-2, JURKAT, and REH (HPA subcellular). This localization comparison does not supply an IF/ICC protocol.
Why is my staining missing, weak or wrong?
SituationLikely causeNext action
Nuclei are negative in a lymph node or tonsil control (HPA tissue IHC).A failed staining or detection run is possible when expected medium germinal center signal is absent (HPA tissue IHC; standard IHC practice).Confirm the control contains germinal center cells, then review antibody dilution, retrieval conditions, and detection reagents against the validated IHC-P procedure (standard IHC practice). The supplied evidence gives no target-specific optimal settings.
Signal is mainly cytoplasmic, with little nuclear staining.The pattern conflicts with HPA's supported nucleoplasmic localization; HPA rates cytosol uncertain in ICC-IF (HPA subcellular).Compare a known-positive immune-cell control and assess nuclear counterstaining and background before accepting the cytoplasmic signal (standard IHC practice).
Adipocytes or bronchial respiratory epithelial cells stain (HPA tissue IHC: not detected).Cross-reactivity or endogenous detection activity may produce staining outside the reported cell pattern (standard IHC practice).Use an appropriate detection-only control and compare cell identity with the HPA tissue profile (standard IHC practice; HPA tissue IHC). Account for HPA's placental cytotrophoblast staining before generalizing to all nonimmune cells (HPA tissue IHC).
The section has widespread diffuse color that obscures nuclei.Nonspecific background or endogenous chromogenic activity can complicate interpretation (standard IHC practice).Check background controls and review blocking, washes, and detection conditions in the IHC workflow; score IKZF1 only where nuclear signal is distinguishable (standard IHC practice; HPA tissue IHC: nuclear profile).
Only a few cells stain in an otherwise low-signal field.The sampled cell mix may differ from a named HPA-positive population; HPA reports low expression in appendix lymphoid tissue but medium staining in several listed populations (HPA tissue IHC).Identify the stained cells and compare like-for-like tissue compartments; include a separate known-positive section when the sample offers few expected positive cells (standard IHC practice; HPA tissue IHC).
IF/ICC shows cytosolic fluorescence without convincing nucleoplasmic signal.HPA supports nucleoplasm as the main ICC-IF location and marks cytosol uncertain (HPA subcellular).Treat the result as unresolved, compare localization with the HPA ICC-IF record, and use the separate IF/ICC guide for method choices (HPA subcellular).

Sample controls for IKZF1 IHC & IF

🧪Run tonsil first and look for IKZF1 staining in germinal center cells (HPA: Medium in tonsil germinal center cells). Use adipose tissue as the negative tissue, where adipocytes are listed as not detected; on the tonsil slide, internal negative cells should lack specific nuclear staining, but do not assume every cell outside germinal centers is negative (HPA: Not detected in adipocytes; HPA: Medium in tonsil germinal center cells; UniProt Q13422: nucleus).
Positive control tissue: Bone marrow (Hematopoietic cells, HPA Medium)
Negative control tissue: Adipose tissue (HPA Not detected)
ICC-IF cell lines (HPA subcellular resource): HPA ICC-IF images show IKZF1 in HDLM-2, JURKAT, REH, with annotated localisation: Nucleoplasm (supported) (HPA subcellular).
Technical controls: Include a no-primary, secondary-only control, a concentration-matched rabbit IgG isotype control, and verified IKZF1 knockout material or an immunizing-peptide block if the peptide is available (selected PB9643 caption: rabbit primary antibody; standard IHC practice). For the caption’s SABC/DAB detection on tonsil, check endogenous peroxidase and biotin background (selected PB9643 caption: SABC with DAB; standard IHC practice).
⚠️Feasibility: A target-specific fixation window or fixation effect is unreported, and the selected PB9643 paraffin-section caption does not state the fixative (selected PB9643 caption). The demonstrated IHC workflow uses heat retrieval in EDTA at pH 8.0; the supplied evidence does not establish whether frozen sections or IF are easier (selected PB9643 caption). Dense germinal center nuclei can complicate cell-by-cell scoring, so assess nuclear signal against the counterstain (HPA: Medium in tonsil germinal center cells; UniProt Q13422: nucleus; standard IHC practice).

HPA tissue IHC evidence for IKZF1

Comprehensive Human Protein Atlas IHC scoring per tissue (reliability: Enhanced — High consistency between antibody staining and RNA expression data.). 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
Bone marrow Hematopoietic cells Medium Protein (IHC) HPA →
Lymph node Germinal center cells Medium Protein (IHC) HPA →
Placenta Cytotrophoblasts Medium Protein (IHC) HPA →
Spleen Cells in red pulp Medium Protein (IHC) HPA →
Tonsil Germinal center cells Medium 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 IKZF1 IHC Tips

Troubleshoot IKZF1 staining in paraffin sections by checking retrieval, nuclear localisation, cell identity and background before scoring chromogenic signal.

How should I adjust retrieval when IKZF1 nuclear staining is weak?
Start with heat-mediated retrieval in EDTA pH 8.0 (datasheet PB9643). The catalog antibody detected IKZF1 in a paraffin-embedded human tonsil section after this retrieval, followed by 1 μg/ml primary antibody overnight at 4°C (datasheet PB9643). If staining is weak, check that sections remained covered during heating, cooled consistently and were processed alongside a tonsil control; these handling checks help distinguish retrieval variation from a failed stain. Change one retrieval variable at a time, because excessive heating can damage morphology and make nuclear scoring unreliable. The caption does not state the fixative, so its result cannot establish performance across fixation conditions (datasheet PB9643).
Could fixation explain loss of IKZF1 staining in my paraffin sections?
Target-specific fixation sensitivity for IKZF1 is unknown from the supplied evidence: the catalog tonsil image describes a paraffin-embedded section but does not state its fixative (datasheet PB9643). Record each specimen’s fixative, fixation duration and processing history, then compare sections processed together using the same EDTA pH 8.0 retrieval and 1 μg/ml primary concentration (datasheet PB9643). Include a positive tonsil section in the run, since germinal center cells show IKZF1 staining (HPA: Medium in tonsil germinal center cells). If the control stains and the specimen does not, review preservation and cell composition before changing antibody concentration. Neither tissue staining patterns nor IKZF1 phosphorylation sites establish a particular fixation effect (HPA: tissue IHC; UniProt Q13422: modified residues).
What IKZF1 staining pattern should I expect within positive cells?
Evaluate nuclear staining first: IKZF1 is a nuclear protein, and tissue IHC shows nuclear expression of immune cells, especially in lymphoid tissues (UniProt Q13422: subcellular location; HPA: tissue IHC profile). Resting lymphocytes may show diffuse nuclear distribution, whereas proliferating cells may show pericentromeric heterochromatin localisation that depends on regulated DNA binding (UniProt Q13422: subcellular location). Compare nuclear signal with the counterstain and inspect individual cells at sufficient magnification before assigning a punctate pattern. Cytoplasmic signal deserves separate review because UniProt also lists cytoplasm, while the HPA cytosol assignment is uncertain (UniProt Q13422: subcellular location; HPA: subcellular location). Check a tonsil control for the expected cell-associated nuclear pattern (HPA: Medium in tonsil germinal center cells).
Can a negative stain exclude every IKZF1 isoform?
No: IKZF1 has 8 listed isoforms, and their functions can differ (UniProt Q13422: isoforms and function). The supplied catalog caption establishes staining in a paraffin-embedded tonsil section but gives no antibody epitope or isoform coverage (datasheet PB9643). Consult the antibody’s documented immunogen or epitope before interpreting a negative section as absence of all isoforms, and use an orthogonal assay if isoform identity matters. Assess nuclear distribution carefully because DNA binding and phosphorylation state regulate localisation to pericentromeric heterochromatin (UniProt Q13422: subcellular location). Keep scoring criteria consistent across specimens; differences in staining pattern alone cannot identify which isoform is present.
How can IF help investigate an ambiguous IKZF1 IHC pattern?
Use IF as a separate investigation of cell identity and compartment when chromogenic staining is ambiguous. Multiplex IKZF1 with a validated marker of the expected immune cell population, and inspect nuclear overlap with a DNA counterstain; tissue IHC predominantly places IKZF1 in immune-cell nuclei (HPA: tissue IHC profile). Select fluorophores after checking the specimen’s autofluorescence in unstained controls, favouring a spectrally separated channel where background is lower. Use permeabilisation compatible with a nuclear epitope, since IKZF1 has no transmembrane segment and is mainly nuclear (UniProt Q13422: topology and subcellular location). Validate IF fixation and antibody conditions independently; the paraffin-section caption supplies no IF protocol or fixative (datasheet PB9643).
How do I reduce diffuse brown background without losing nuclear signal?
First compare the stained section with a no-primary control to locate background from detection reagents, tissue pigment or endogenous peroxidase. For a peroxidase and DAB workflow, include a peroxidase block and avoid overdevelopment; these are general chromogenic IHC controls. The catalog tonsil example used 10% goat serum block, 1 μg/ml primary overnight at 4°C, and DAB detection (datasheet PB9643). If diffuse staining persists, check wash quality and titrate the primary around the documented condition while keeping retrieval at EDTA pH 8.0 (datasheet PB9643). Judge improvement by clearer nuclei in germinal center cells and cleaner adjacent tissue, not by overall darkness (HPA: Medium in tonsil germinal center cells).
What should I score when comparing IKZF1 across tissue sections? ⚠ ANSWER MARKED FOR VERIFICATION
Define the cell population and region before scoring, then measure the percentage of nuclei with convincing signal or use an H-score combining nuclear intensity and percentage, on a 0–300 scale. If cell abundance itself is the endpoint, count IKZF1-positive nuclei per mm² and report the tissue area analysed. Normalise positive-cell measures to all eligible nuclei within the same compartment, because IKZF1 expression is concentrated in immune cells across many tissues (HPA: tissue IHC profile). Exclude folds, necrosis and section edges using the same rules for every slide. Keep retrieval and DAB development consistent, and use a tonsil control to monitor run variation (datasheet PB9643; HPA: Medium in tonsil germinal center cells).
How can I distinguish true IKZF1 staining from artefact?
A credible result places signal in identifiable nuclei of the expected cells; tissue IHC reports nuclear staining in immune cells, with germinal center cells positive in tonsil (HPA: tissue IHC profile; HPA: Medium in tonsil germinal center cells). Compare the section with a no-primary control and a concurrently processed positive control before interpreting faint brown deposits. Treat staining confined to edges, folds or necrotic areas cautiously, and check whether diffuse brown signal persists after a general peroxidase block. Strong cytoplasmic staining without convincing nuclei needs further validation: cytoplasm is listed by UniProt, but HPA labels its cytosol localisation uncertain (UniProt Q13422: subcellular location; HPA: subcellular location). Record cell identity, compartment and artefact exclusions with the score.
Boster reagents

Best IKZF1 / DNA-binding protein Ikaros IHC Antibodies

PB9643 has IHC images from human tonsil and mouse and rat spleen paraffin sections, plus IF in MCF-7 cells (catalog image captions). Both antibodies list human, mouse and rat reactivity (catalog).

Real IHC data IHC analysis of Ikaros using anti-Ikaros antibody (PB9643). Ikaros 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 1 μg/ml rabbit anti-Ikaros Antibody (PB9643) overnight at 4°C. Biotinylated goat anti-rabbit IgG was used as secondary antibody and incubated for 30 minutes at 37°C. The tissue section was developed using Strepavidin-Biotin-Complex (SABC) (Catalog # SA1022) with DAB as the chromogen.
Anti-Ikaros/IKZF1 Antibody ®
Cat # PB9643

M00531-1 lists IHC and human, mouse and rat reactivity, but has no supplied IHC image or specimen (catalog applications, reactivity and image captions). PB9643 has IHC images of human tonsil and mouse and rat spleen paraffin sections, plus an IF image of MCF-7 cells (catalog image captions).

Which to pick: Choose PB9643 for tissue IHC: its own captions document paraffin sections from all three species, EDTA pH 8.0 retrieval and 1 μg/ml primary antibody; the fixative is unreported (PB9643 IHC image captions). Choose PB9643 for IF/ICC because both applications are listed and its IF image shows MCF-7 cells at 5 μg/ml (catalog applications; PB9643 IF image caption). For cross-species IHC, PB9643 has images from human, mouse and rat tissue; M00531-1 offers a rabbit monoclonal, clone AEFA-9, with IHC and all three species listed, but no supplied IHC image (catalog applications, reactivity and image captions).

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

References

  1. UniProt Consortium. UniProt entry Q13422 (IKZF1_HUMAN, DNA-binding protein Ikaros).
  2. Human Protein Atlas. IKZF1 tissue IHC expression (reliability: Enhanced).
  3. Human Protein Atlas. IKZF1 subcellular location (ICC-IF): Mainly localized to the nucleoplasm. In addition localized to the cytosol..
  4. Human Protein Atlas. IKZF1 antibody validation summary (3 antibodies).
  5. Identification of key genes in salivary gland in Sjögren's syndrome complicated with Hashimoto thyroiditis: Common pathogenesis and potential diagnostic markers. Medicine 2023 — PMC10545362.
  6. IKZF1 as a potential therapeutic target for dendritic cell-mediated immunotherapy in IgA nephropathy. Cell communication and signaling : CCS 2025 — PMC12057048.
  7. Dual targeting of protein translation and nuclear protein export results in enhanced antimyeloma effects. Blood advances 2023 — PMC10333745.
  8. Novel insights into the pathogenesis of follicular lymphoma by molecular profiling of localized and systemic disease forms. Leukemia 2023 — PMC10539171.
  9. PubMed PMID:8964602 — UniProt-cited evidence.
  10. PubMed PMID:8543809 — UniProt-cited evidence.
  11. PubMed PMID:14702039 — UniProt-cited evidence.