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ZNF397 / Zinc finger protein 397 · IHC design guide
Design Immunohistochemistry for ZNF397
Plan chromogenic ZNF397 IHC on paraffin sections with the catalog antibody at 1:100–1:300 (datasheet A13857). Assess cytoplasmic staining (HPA tissue IHC) with controls, and interpret tissue patterns cautiously because staining and RNA expression show low consistency (HPA tissue IHC).
Evidence assembled Oct 2026 · For research use; verify linked source records and product datasheet before use
ZNF397 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 | Mostly cytoplasmic in tissue IHC (HPA tissue IHC); nuclear location annotated (UniProt) | |
| Staining pattern | Cytoplasmic staining in most tissues (HPA tissue IHC) | |
| Antigen retrieval | Tris-EDTA pH 9.0 HIER, heat-mediated (datasheet A13857) | |
| Positive control | Bone marrow+4 more · see all | |
| Negative control | Oral mucosa+1 more · see all |
Important caveats
Reasons your staining may differ from the expected pattern.
| Fixation | Keep fixation consistent across paraffin sections (standard IHC practice; not target-specific); Matched tissue-IHC evidence does not establish the fixation claim. Validate the specimen-specific method before use. (selected-SKU IHC image A13857) | |
| Caveat | Staining and RNA expression show low consistency (HPA tissue IHC) | |
| Regulation | Strongly expressed in testis (UniProt) | |
| Isoform / epitope | Three isoforms; antibody epitope coverage is unspecified (UniProt) |
Section 1
Recommended ZNF397 IHC & IF Protocols
Compare the catalog antibody’s IHC-P protocol (datasheet A13857) with published ZNF397 IHC in mouse xenograft tumors (PMC11285331).
| Sample | Paraffin-embedded human tonsil tissue; fixative not specified (datasheet A13857) |
| Fixation | Image fixative and duration unreported (datasheet A13857); verify before use. |
| Sectioning | 4–5 µm sections on charged slides (standard) |
| Deparaffinisation | Xylene, graded ethanol series to water (standard) |
| Antigen retrieval | Heat retrieval: Tris-EDTA pH 9.0 (datasheet A13857); 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 | Rabbit anti-ZNF397, 1:100-1:300 (datasheet A13857) |
| Primary incubation | Overnight at 4 °C (standard) |
| Detection | HRP-polymer secondary, DAB chromogen 5–10 min (standard) |
| Counterstain | Hematoxylin, blue, dehydrate and mount (standard) |
| Expected result | ZNF397-positive staining in hematopoietic cells of bone marrow (HPA tissue IHC: High). HPA tissue profile: Cytoplasmic expression in most tissues. No signal in the no-primary control. |
💡Decision noteStart with Tris-EDTA pH 9.0 HIER for the catalog antibody (datasheet A13857); use heated sodium citrate to reproduce the published protocol (PMC11285331).
Section 2
What Is the Expected ZNF397 Staining Pattern?
In paraffin-section IHC, ZNF397 is reported mainly as cytoplasmic staining across tissues, with high staining in selected glandular and hematopoietic cells and in cerebral-cortex neuropil (HPA tissue IHC). Nuclear staining is biologically plausible because ZNF397 localizes to both nucleus and cytoplasm (UniProt Q8NF99). It has no transmembrane segment (UniProt Q8NF99 topology). Treat the tissue pattern as provisional: HPA rates its IHC reliability Uncertain because antibody staining and RNA expression have low consistency (HPA tissue IHC).
| Cytoplasmic staining is strong in bone-marrow hematopoietic cells or breast and duodenal glandular cells (HPA: High). | This matches reported positive cell populations and the predominant tissue-IHC compartment (HPA tissue IHC). Compare stained cells with nearby unstained structures; a matching pattern supports interpretation but does not establish specificity because tissue-IHC reliability is Uncertain (HPA tissue IHC). |
| Staining is confined to nuclei, with little cytoplasmic signal in a tissue expected to show cytoplasmic staining (HPA tissue IHC). | This departs from the reported tissue-IHC profile (HPA tissue IHC). Nuclear localization remains possible (UniProt Q8NF99), and nucleoli are an approved ICC-IF location (HPA subcellular). Review controls and morphology before calling nuclear-only IHC either genuine or artefactual. |
| Strong chromogen appears in oral-mucosa squamous epithelium or skeletal-muscle myocytes (HPA: Not detected). | These cell types are reported as unstained in tissue IHC (HPA tissue IHC). Check for cross-reactivity and endogenous detection activity (general IHC practice). HPA's Uncertain reliability prevents treating either reported negative as a definitive biological absence (HPA tissue IHC). |
| Diffuse colour covers cells and extracellular spaces without a readable cellular pattern. | This is background until controls show otherwise (general IHC practice). Reassess blocking, washing, antibody concentration and chromogen development (general IHC practice); diffuse colour cannot establish ZNF397 localization, even where HPA reports positive staining (HPA tissue IHC). |
| A bone-marrow section shows no hematopoietic-cell signal, including with the positive control (HPA: High in hematopoietic cells). | First investigate assay performance and whether the expected cell population is present (general IHC practice). HPA reports high staining there, but its tissue-IHC reliability is Uncertain; one negative section alone cannot resolve ZNF397 expression (HPA tissue IHC). |
💡Expected ZNF397 appearanceCall a plausible positive result when discrete cytoplasmic staining marks the reported positive cells at a visibly strong level (HPA tissue IHC: High); widespread colour without cell boundaries is background (general IHC practice), and the call remains provisional (HPA tissue IHC: Uncertain).
| Compartment and topology | Nucleus and cytoplasm are listed locations, and no transmembrane segment is annotated (UniProt Q8NF99). Tissue IHC is predominantly cytoplasmic, while ICC-IF adds nucleoli, plasma membrane, cytosol and microtubules (HPA tissue IHC; HPA subcellular). Interpret each application against its own observed pattern. |
| Tissue and cell selection | High IHC staining is reported in bone-marrow hematopoietic cells, several glandular populations, endometrial stromal cells and cerebral-cortex neuropil (HPA tissue IHC). Oral-mucosa squamous cells and skeletal-muscle myocytes are reported Not detected (HPA tissue IHC). These are provisional comparison sites because reliability is Uncertain (HPA tissue IHC). |
| Expression and staining discordance | UniProt reports moderate expression in skeletal muscle, whereas HPA reports myocyte IHC as Not detected (UniProt Q8NF99 tissue specificity; HPA tissue IHC). HPA also describes low tissue RNA specificity and low staining–RNA consistency (HPA tissue IHC). Do not infer protein absence or assay specificity from one readout. |
| Antibody evidence | The listed antibody HPA026087 is rated IHC Uncertain and ICC Supported; the overall tissue-IHC profile is also Uncertain (HPA antibodies; HPA tissue IHC). Record which antibody and controls produced a pattern before comparing results. An ICC rating does not upgrade tissue-IHC confidence (HPA antibodies). |
| Isoforms and epitope | Three isoforms are annotated, and the SCAN box spans residues 50–132 (UniProt Q8NF99). No antibody epitope or isoform coverage is supplied here, so staining cannot be assigned to one isoform or explained by differential recognition. Verify those properties from antibody-specific evidence before making an isoform claim. |
| IF/ICC Q: What localization should an IF image show? | A: HPA reports approved nucleolar, plasma-membrane and cytosolic locations, plus microtubules, with images from A-431, U-251MG and U2OS (HPA subcellular). HPA026087 is ICC Supported (HPA antibodies). This observation is context for the separate IF/ICC guide, not a tissue-IHC scoring rule. |
| Situation | Likely cause | Next action |
|---|---|---|
| No cytoplasmic signal in bone-marrow hematopoietic cells (HPA: High). | A failed staining run or an unrepresentative section is possible (general IHC practice); HPA's IHC call is Uncertain (HPA tissue IHC). | Confirm the cells are present, inspect a concurrently stained control, and review retrieval and detection settings (general IHC practice). |
| Strong staining in oral-mucosa squamous cells (HPA: Not detected). | Cross-reactivity or endogenous detection activity is possible (general IHC practice); the HPA negative is provisional (HPA tissue IHC: Uncertain). | Check a no-primary control and the distribution of colour, then compare with a reported positive cell population (general IHC practice; HPA tissue IHC). |
| Nuclear-only staining in a tissue with expected cytoplasmic staining (HPA tissue IHC). | The pattern differs from tissue IHC, although nuclear ZNF397 is annotated (UniProt Q8NF99; HPA tissue IHC). | Inspect morphology and controls; repeat with independently validated evidence before interpreting a nuclear-only tissue pattern (general IHC practice). |
| Diffuse colour obscures cell boundaries. | Excess antibody, insufficient washing or prolonged chromogen development can raise background (general IHC practice). | Review the no-primary control and adjust staining conditions systematically, preserving a readable cellular pattern (general IHC practice). |
| Colour persists when primary antibody is omitted. | Endogenous detection activity or nonspecific detection-reagent binding is possible (general IHC practice). | Address the activity appropriate to the detection chemistry and repeat the no-primary control (general IHC practice). |
| Skeletal-muscle myocytes stain despite the HPA Not detected call (HPA tissue IHC). | The finding conflicts with HPA IHC yet UniProt reports moderate skeletal-muscle expression; neither resolves antibody specificity (UniProt Q8NF99; HPA tissue IHC). | Check cell identification and controls, then seek independent validation before accepting or rejecting the signal (general IHC practice; HPA tissue IHC: Uncertain). |
Experiment evidence
IHC & IF images showing ZNF397 staining
A13857 · IHCImmunohistochemical analysis of paraffin-embedded human tonsil. 1, Tris-EDTA, pH9.0 was used for antigen retrieval. 2 Antibody was diluted a
HPA · Cerebral cortexHuman Protein Atlas IHC, Cerebral cortex. Source: https://www.proteinatlas.org/ENSG00000186812-ZNF397/tissue/cerebral+cortex#imid_6602840
HPA · ColonHuman Protein Atlas IHC, Colon. Source: https://www.proteinatlas.org/ENSG00000186812-ZNF397/tissue/colon#imid_6602774
HPA · LiverHuman Protein Atlas IHC, Liver. Source: https://www.proteinatlas.org/ENSG00000186812-ZNF397/tissue/liver#imid_6602775
HPA · KidneyHuman Protein Atlas IHC, Kidney. Source: https://www.proteinatlas.org/ENSG00000186812-ZNF397/tissue/kidney#imid_6602760
HPA · ICC-IF A-431Human Protein Atlas immunofluorescence, A-431, antibody HPA026087; green = ZNF397, blue = nucleus, red = microtubules.
HPA · ICC-IF A-431Human Protein Atlas immunofluorescence, A-431, antibody HPA026087; green = ZNF397, blue = nucleus, red = microtubules.
← swipe / scroll for more images →
Real IHC / IF data behind the staining-pattern expectations in this section.
Sample controls for ZNF397 IHC & IF
🧪Start with bone marrow; hematopoietic cells should stain (HPA: High in bone-marrow hematopoietic cells). Use oral mucosa squamous epithelial cells as the negative tissue (HPA: Not detected in oral-mucosa squamous epithelial cells); any unstained cells within the bone-marrow section should show background only, but HPA does not identify a validated internal negative cell type there (HPA: bone-marrow hematopoietic cells High).
Positive control tissue: Bone marrow (Hematopoietic cells, HPA High)
Negative control tissue: Oral mucosa (HPA Not detected)
ICC-IF cell lines (HPA subcellular resource): HPA ICC-IF images show ZNF397 in A-431, U-251MG, U2OS, with annotated localisation: Nucleoli (approved), Plasma membrane (approved), Cytosol (approved) (HPA subcellular).
Technical controls: Run a no-primary, secondary-only control and a control immunoglobulin matched to the primary antibody’s host species, isotype, and monoclonal or polyclonal format; assess biological specificity with ZNF397-knockout material or immunizing-peptide competition if available (standard IHC practice). Quench endogenous peroxidase in bone marrow before chromogenic detection and check the control sections for residual signal (standard IHC practice; HPA: bone-marrow hematopoietic cells High).
⚠️Feasibility: A target-specific fixation window or fixation effect is unreported, and the selected paraffin-section tonsil caption does not state the fixative (A13857 tissue-IHC caption: fixative not stated). Tris-EDTA retrieval at pH 9.0 and a 1:200 primary dilution are documented for tonsil, so retrieval needs verification in bone marrow (A13857 tissue-IHC caption). Neither frozen sections nor IF/ICC is established as easier by the supplied evidence; endogenous peroxidase may raise chromogenic background in bone marrow (standard IHC practice).
HPA tissue IHC evidence for ZNF397
Comprehensive Human Protein Atlas IHC scoring per tissue (reliability: Uncertain — Low consistency between antibody staining and RNA expression data. Pending external verification.). Rows are taken directly from the HPA tissue chart — click any row's HPA link to view the source.
Positive expression · recommended positive controls
| Tissue | Cell type | Level | Evidence | Source |
|---|---|---|---|---|
| Bone marrow | Hematopoietic cells | High | Protein (IHC) | HPA → |
| Breast | Glandular cells | High | Protein (IHC) | HPA → |
| Cerebral cortex | Neuropil | High | Protein (IHC) | HPA → |
| Duodenum | Glandular cells | High | Protein (IHC) | HPA → |
| Endometrium | Cells in endometrial stroma | High | Protein (IHC) | HPA → |
Section 3
Advanced ZNF397 IHC Tips
Use matched controls and compartment-specific scoring when assessing ZNF397 in paraffin sections; reported tissue staining has uncertain reliability (HPA tissue IHC).
Which retrieval conditions should I start with for ZNF397 paraffin-section IHC?
Use heat-mediated Tris-EDTA at pH 9.0 for antigen retrieval in paraffin sections (datasheet A13857). The selected tonsil image used this buffer with primary antibody at 1:200, incubated at 4 °C overnight (A13857 caption). Keep heating and cooling conditions consistent across sections, and assess nuclear and cytoplasmic signal separately because both locations are reported (UniProt Q8NF99; standard IHC practice). If staining remains weak, compare lower-pH citrate retrieval on adjacent sections as a fallback, checking for tissue damage and background (standard IHC practice). Treat any alternative as a tested adjustment, rather than a validated condition for this antibody (datasheet A13857; standard IHC practice).
How should I handle fixation when ZNF397 staining varies between paraffin sections?
Target-specific fixation sensitivity for ZNF397 is unknown: the selected paraffin-embedded tonsil caption does not state its fixative (A13857 caption). Record the fixative, fixation duration, and processing history for each specimen before comparing staining intensity (standard IHC practice). When these conditions differ, assess sections in matched processing groups and include a consistently processed control section in each run (standard IHC practice). Use the documented 1:200 primary dilution and 4 °C overnight incubation as a starting point for the catalog antibody (A13857 caption). Do not attribute a staining difference to fixation alone without a controlled comparison (standard IHC practice).
How should I evaluate nuclear, cytoplasmic, and membrane-like ZNF397 staining?
Score nuclear and cytoplasmic staining separately because both are reported locations for ZNF397 (UniProt Q8NF99). Tissue IHC is described as predominantly cytoplasmic, but its reliability is uncertain owing to poor agreement with RNA data (HPA tissue IHC). Cell imaging additionally reports nucleoli, plasma membrane, and cytosol as approved locations, with microtubules as an additional location (HPA subcellular). Because ZNF397 has no transmembrane segment, evaluate membrane-like chromogen against cell boundaries and control sections before assigning it to the target (UniProt Q8NF99 topology; standard IHC practice). Record the stained cell type and compartment alongside intensity so apparent agreement does not mask different patterns (standard IHC practice).
Could ZNF397 isoforms or epitope accessibility explain uneven IHC staining?
ZNF397 has 3 listed isoforms, and the supplied evidence does not map the catalog antibody’s epitope to any of them (UniProt Q8NF99; A13857 caption). Isoforms 1 and 3 can associate, while isoform 1 association depends on the SCAN domain (UniProt Q8NF99). The SCAN box spans residues 50–132, and phosphoserine is reported at residue 31; neither fact establishes antibody recognition (UniProt Q8NF99). Obtain epitope or immunogen mapping before interpreting different staining patterns as isoform-specific (standard IHC practice). Compare retrieval conditions on matched sections if accessibility is suspected, while retaining identical detection and scoring conditions (standard IHC practice).
How can IF help assess a puzzling ZNF397 IHC pattern?
Use IF as an orthogonal localisation check; HPA lists ICC/IF images and reports nucleoli, plasma membrane, and cytosol as approved locations (HPA subcellular). Multiplex ZNF397 with a validated marker for the cell population being assessed, such as a glandular-cell marker when examining glandular staining (HPA tissue IHC; standard IF practice). Choose fluorophores whose emission can be distinguished from the specimen’s autofluorescence, and include single-label controls for channel separation (standard IF practice). The antibody epitope’s membrane side is unspecified, so assess detergent permeabilisation for intracellular signal and compare with a nonpermeabilised condition when evaluating surface signal (A13857 caption; standard IF practice). Interpret IF against the IHC compartment and cell type, rather than intensity alone (standard IHC/IF practice).
What should I check when ZNF397 chromogenic staining is diffuse or widespread?
First compare stained sections with no-primary controls to identify signal from detection reagents or endogenous tissue components (standard IHC practice). Apply a peroxidase block before chromogenic peroxidase detection, and assess whether DAB develops in the control section (standard IHC practice). Check blocking, washing, and primary concentration while retaining the caption’s 1:200 dilution as the documented reference condition (A13857 caption; standard IHC practice). Widespread cytoplasmic staining alone is weak evidence of specificity because HPA describes that pattern but rates its tissue IHC reliability uncertain (HPA tissue IHC). Inspect section edges, damaged areas, and pigment before scoring cellular ZNF397 signal (standard IHC practice).
How should I quantify ZNF397 staining across paraffin sections? ⚠ ANSWER MARKED FOR VERIFICATION
Define the cell population and score nuclear and cytoplasmic chromogen separately, since both compartments are reported for ZNF397 (UniProt Q8NF99). For each compartment, record the percentage of positive eligible cells and an H-score from 0–300 using intensity grades 0–3 (standard IHC practice). When positive cells form discrete populations, also report their density per mm² of viable evaluated tissue (standard IHC practice). Normalise cell counts to the eligible cell population or viable tissue area, and apply the same thresholds across sections (standard IHC practice). Report control-section performance alongside scores because the published tissue IHC profile has uncertain reliability (HPA tissue IHC).
When does a ZNF397-positive IHC result merit further validation?
Treat staining as more credible when it is cellular, reproducible, and supported by appropriate control sections and a plausible compartment (UniProt Q8NF99; standard IHC practice). Check whether the stained cells match the population being assessed: HPA reports high staining in bone-marrow hematopoietic cells but no detection in oral-mucosa squamous cells (HPA tissue IHC). Do not use these patterns as definitive controls, because HPA rates its ZNF397 tissue staining uncertain (HPA tissue IHC). Review sharp edge staining, necrotic regions, pigment, and endogenous peroxidase signal before calling chromogen target-positive (standard IHC practice). Investigate isolated membrane-like staining particularly carefully because ZNF397 lacks a transmembrane segment, despite reported membrane localisation in cell imaging (UniProt Q8NF99 topology; HPA subcellular).
Boster reagents
Best ZNF397 / Zinc finger protein 397 IHC Antibodies
A13857 is a human-reactive anti-ZNF397 antibody with paraffin-section IHC data (catalog; IHC figure caption). IF is listed as an application, but no IF figure is supplied (catalog).
Real IHC data
Anti-Zinc finger protein 397 ZNF397 Antibody
Cat # A13857
A13857 is listed for human IHC and IF (catalog: applications and reactivity). Its IHC figure shows paraffin-embedded human tonsil; the catalog supplies no IF figure (IHC figure caption; catalog).
Which to pick: For tissue IHC, choose A13857: its own figure documents paraffin-embedded human tonsil, Tris-EDTA retrieval at pH 9.0, and a 1:200 primary dilution; the fixative is unreported (A13857 IHC figure caption). For IF/ICC, A13857 lists IF at 1:200–1:1000, but the payload provides no IF figure or ICC validation (A13857 catalog). No cross-species option is documented because A13857 lists human reactivity only (A13857 catalog).
Each figure is that product's own IHC / IF validation image from its datasheet.
References
- UniProt Consortium. UniProt entry Q8NF99 (ZN397_HUMAN, Zinc finger protein 397).
- Human Protein Atlas. ZNF397 tissue IHC expression (reliability: Uncertain).
- Human Protein Atlas. ZNF397 subcellular location (ICC-IF): Mainly localized to the nucleoli, plasma membrane and cytosol. In addition localized to the microtubules..
- Human Protein Atlas. ZNF397 antibody validation summary (1 antibodies).
- ZNF397 Deficiency Triggers TET2-Driven Lineage Plasticity and AR-Targeted Therapy Resistance in Prostate Cancer. Cancer discovery 2024 — PMC11285331.
- PubMed PMID:12801647 — UniProt-cited evidence.
- PubMed PMID:15489334 — UniProt-cited evidence.
- PubMed PMID:23186163 — UniProt-cited evidence.
Immunohistochemistry protocol sheet for ZNF397 (Zinc finger protein 397). Expected localisation Mostly cytoplasmic in tissue IHC (HPA tissue IHC); nuclear location annotated (UniProt). Antigen retrieval: Tris-EDTA pH 9.0 HIER, heat-mediated (datasheet A13857). Validated IHC antibody: A13857 at 1:100-1:300 (the product's own IHC validation image is shown). Controls (HPA): positive Bone marrow (Hematopoietic cells); negative Oral mucosa. IHC workflow; specimen preparation unspecified. Protocol steps: 1. Sample: Paraffin-embedded human tonsil tissue; fixative not specified (datasheet A13857); 2. Fixation: Image fixative and duration unreported (datasheet A13857); verify before use.; 3. Sectioning: 4–5 µm sections on charged slides (standard); 4. Deparaffinisation: Xylene, graded ethanol series to water (standard); 5. Antigen retrieval: Heat retrieval: Tris-EDTA pH 9.0 (datasheet A13857); 20 min, 95–100 °C (standard); 6. Peroxidase block: 3% H2O2, 10 min , room temperature (standard); 7. Blocking: 10% normal serum of the secondary host, 30 min , room temperature (standard); 8. Primary antibody: Rabbit anti-ZNF397, 1:100-1:300 (datasheet A13857); 9. Primary incubation: Overnight at 4 °C (standard). Watch for: Fixation: Keep fixation consistent across paraffin sections (standard IHC practice; not target-specific); Matched tissue-IHC evidence does not establish the fixation claim. Validate the specimen-specific method before use. (selected-SKU IHC image A13857); Caveat: Staining and RNA expression show low consistency (HPA tissue IHC); Isoform / epitope: Three isoforms; antibody epitope coverage is unspecified (UniProt); Regulation: Strongly expressed in testis (UniProt). Evidence: UniProt Q8NF99, HPA tissue IHC · Uncertain, HPA ICC-IF · Mainly localized to the nucleoli, plasma membrane and cytosol. In…, Datasheet A13857, PMC11285331. QR code links to https://www.bosterbio.com/bosterbio-gene-info-cards/ZNF397/immunohistochemistry-ihc-guide.