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FOXJ1 / Forkhead box protein J1 · IHC design guide
Design Immunohistochemistry for FOXJ1
Plan FOXJ1 staining in paraffin sections using nuclear signal in motile-ciliated cells as the expected pattern (HPA tissue IHC). This guide covers fixation consistency, staining controls and interpretation alongside the IHC-validated antibody's protocol.
Evidence assembled Oct 2026 · For research use; verify linked source records and product datasheet before use
FOXJ1 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 | Nuclei of motile-ciliated cells (HPA tissue IHC) | |
| Staining pattern | Nuclear staining in cells with motile cilia (HPA tissue IHC) | |
| Antigen retrieval | EDTA pH 8.0 HIER, heat-mediated (datasheet A04942-3) | |
| Positive control | Bronchus+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 was observed and disregarded (HPA tissue IHC) | |
| Regulation | Expression regulation unreported (UniProt) | |
| Isoform / epitope | No annotated isoforms or processing; epitope map unknown (UniProt) |
Section 1
Recommended FOXJ1 IHC & IF Protocols
The catalog antibody’s IHC-P protocol is followed by 3 published FOXJ1 chromogenic IHC protocols (PMC5442446; PMC5364032; PMC5774442).
| Sample | Paraffin-embedded rat ovary tissue; fixative not specified (datasheet A04942-3) |
| Fixation | Image fixative and duration unreported (datasheet A04942-3); 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 A04942-3); 20 min, 95–100 °C (standard) |
| Peroxidase block | 3% H2O2, 10 min, room temperature (standard) |
| Blocking | 10% goat serum (datasheet A04942-3) |
| Primary antibody | Rabbit anti-FOXJ1, 2-5μg/ml (datasheet A04942-3) |
| Primary incubation | Overnight at 4 °C (datasheet A04942-3) |
| Detection | Streptavidin-biotin complex (SABC), DAB chromogen (datasheet A04942-3) |
| Counterstain | Hematoxylin, blue, dehydrate and mount (standard) |
| Expected result | FOXJ1-positive staining in ciliated cells (cell body) of bronchus (HPA tissue IHC: High). HPA tissue profile: Nuclear expression in cells with motile cilia. No signal in the no-primary control. |
💡Decision noteStart with heat-mediated EDTA pH 8.0 for the catalog antibody (datasheet: A04942-3). The published protocols provide pressure-cooker alternatives (PMC5442446; PMC5364032; PMC5774442).
Section 2
What Is the Expected FOXJ1 Staining Pattern?
FOXJ1 is a nuclear transcription factor with no transmembrane segment (UniProt Q92949: location, function and topology). In paraffin-section IHC, expect nuclear staining in cells with motile cilia (HPA: tissue IHC profile). HPA reports high staining in bronchial, endometrial and fallopian-tube ciliated cells, and rates the tissue pattern Enhanced, while noting presumed off-target binding that was disregarded (HPA: tissue IHC).
| Distinct nuclear staining in ciliated epithelial cells of bronchus, endometrium or fallopian tube. | This fits the expected FOXJ1 compartment and cell population (UniProt Q92949: nucleus; HPA: nuclear expression in cells with motile cilia). HPA rates staining in these listed cell populations High (HPA: tissue IHC); use neighboring cells and the section's background to judge whether the signal is selective (general IHC practice). |
| Strong staining confined to cytoplasm, the apical surface or cilia, with no convincing nuclear signal. | This does not match the reported nuclear pattern (UniProt Q92949: nucleus; HPA: tissue IHC profile). Treat it as an unresolved staining artefact or nonspecific signal, then reassess localization with a nuclear counterstain and appropriate detection controls (general IHC practice). |
| Prominent staining in adipocytes, adrenal glandular cells or bone-marrow hematopoietic cells. | HPA reports FOXJ1 as Not detected in those specific cell populations (HPA: tissue IHC). Check antibody specificity and, for chromogenic IHC, endogenous detection activity before assigning the signal to FOXJ1 (general IHC practice). HPA also notes that presumed off-target binding was observed and disregarded in its tissue assessment (HPA: tissue IHC reliability description). |
| Broad, diffuse staining obscures nuclei across multiple cell types. | A diffuse field cannot establish the selective nuclear pattern reported for FOXJ1 (HPA: tissue IHC profile). Examine the no-primary control and the detection system, and optimize washing, blocking or antibody concentration as appropriate (general IHC practice). The diffuse appearance alone does not identify its cause (general IHC practice). |
| No nuclear signal in ciliated cells of a well-preserved bronchus or fallopian-tube section. | That result conflicts with HPA's High staining in the specified ciliated cells (HPA: tissue IHC). First verify that the expected cells are present; then review the IHC workflow and a run control before interpreting the sample as biologically negative (general IHC practice). |
💡Expected FOXJ1 appearanceCall a result positive when discrete nuclear chromogen marks ciliated epithelial cells, typically strongly in HPA-listed High populations; isolated cytoplasmic or widespread non-ciliated-cell staining is suspect (UniProt Q92949: nucleus; HPA: tissue IHC profile and High cell populations).
| Cell population and tissue choice | HPA reports High staining in bronchial, endometrial and fallopian-tube ciliated cells; Medium in efferent-duct and nasopharyngeal ciliated cells; and Low in choroid-plexus ependymal and testicular Leydig cells (HPA: tissue IHC). Compare like cell populations when judging signal strength. |
| Intracellular location and protein annotation | FOXJ1 is nuclear, has no transmembrane segment or signal peptide, and is annotated as a single 1–421 chain (UniProt Q92949: location, topology and processing). These annotations support nuclear interpretation; they do not specify an antibody epitope or predict retrieval performance. |
| Strength and limit of tissue evidence | HPA rates its tissue IHC profile Enhanced for agreement between staining and RNA expression, while explicitly reporting presumed off-target binding that was disregarded (HPA: tissue IHC reliability description). Its positive pattern supports tissue selection but does not make every stained cell specific. |
| Antibody and IF evidence | HPA lists HPA005714 as IHC Enhanced (HPA: antibody validation). Its supplied ICC-IF record gives no main location and no cell lines with ICC-IF images (HPA: subcellular record), so it cannot independently confirm an IF staining pattern or supply an IF protocol. |
| Situation | Likely cause | Next action |
|---|---|---|
| No staining in the expected ciliated cells of bronchus or fallopian tube. | The expected cells may be absent from the examined field, or an IHC step may have failed (general IHC practice); HPA reports High staining in those specified cell populations (HPA: tissue IHC). | Confirm cell identity and section quality, then inspect the run control, primary-antibody step, retrieval conditions and detection reagents (general IHC practice). Do not infer FOXJ1 absence from a failed control. |
| Only cytoplasmic or apical staining is visible. | The compartment disagrees with nuclear FOXJ1 localization (UniProt Q92949: nucleus; HPA: tissue IHC profile). The image alone cannot establish whether the cause is nonspecific binding or another workflow issue (general IHC practice). | Use the counterstain to resolve nuclei, inspect a no-primary control, and reassess antibody and detection conditions (general IHC practice). Score nuclear signal separately from the misplaced staining. |
| Many cell types stain, including an HPA-listed negative population. | For example, HPA reports adipocytes as Not detected (HPA: tissue IHC). Broad signal could reflect cross-reactivity or endogenous chromogenic detection activity (general IHC practice); HPA reports presumed off-target binding in its tissue assessment (HPA: reliability description). | Compare with a no-primary control and review the blocking and detection steps (general IHC practice). Require the expected nuclear pattern in ciliated cells before assigning FOXJ1 positivity (HPA: tissue IHC profile). |
| The whole section has diffuse chromogen or patchy haze. | Diffuse background can obscure whether ciliated-cell nuclei are selectively stained (general IHC practice; HPA: nuclear tissue IHC profile). Its appearance does not identify a FOXJ1-specific mechanism. | Review no-primary and run controls, washing, blocking and antibody concentration within the chosen IHC workflow (general IHC practice). Reassess the section only when nuclei can be distinguished from background. |
| Signal in efferent ducts or nasopharynx looks weaker than in bronchus. | HPA grades ciliated cells in efferent ducts and nasopharynx Medium, versus High in bronchus (HPA: tissue IHC). A weaker result in these listed populations can therefore agree with the reported pattern. | Compare nuclear localization and cell selectivity before treating intensity alone as a failure (HPA: tissue IHC profile; general IHC practice). Keep tissue and cell population attached to any intensity score. |
| Can the HPA ICC-IF record confirm the expected IF pattern? | The supplied HPA subcellular record has no reported main location or cell lines with ICC-IF images (HPA: subcellular record). It provides no image-based IF confirmation. | Use the nuclear expectation as a starting interpretation (UniProt Q92949: nucleus; HPA: tissue IHC profile), and establish IF performance with controls in the separate IF/ICC guide (general IF practice). |
Experiment evidence
IHC & IF images showing FOXJ1 staining
A04942-3 · IHCIHC analysis of FOXJ1 using anti-FOXJ1 antibody (A04942-3). FOXJ1 was detected in paraffin-embedded section of rat ovary tissue. Heat mediat
A04942-3 · IFIF analysis of FOXJ1 using anti-FOXJ1 antibody (A04942-3). FOXJ1 was detected in immunocytochemical section of CACO-2 cells. Enzyme antigen
HPA · Cerebral cortexHuman Protein Atlas IHC, Cerebral cortex. Source: https://www.proteinatlas.org/ENSG00000129654-FOXJ1/tissue/cerebral+cortex#imid_18960342
HPA · ColonHuman Protein Atlas IHC, Colon. Source: https://www.proteinatlas.org/ENSG00000129654-FOXJ1/tissue/colon#imid_18960260
HPA · LiverHuman Protein Atlas IHC, Liver. Source: https://www.proteinatlas.org/ENSG00000129654-FOXJ1/tissue/liver#imid_18960269
HPA · KidneyHuman Protein Atlas IHC, Kidney. Source: https://www.proteinatlas.org/ENSG00000129654-FOXJ1/tissue/kidney#imid_18960262
← swipe / scroll for more images →
Real IHC / IF data behind the staining-pattern expectations in this section.
Sample controls for FOXJ1 IHC & IF
🧪Run bronchus first and look for FOXJ1 staining in ciliated cells (HPA: High in bronchial ciliated cells; UniProt Q92949: nucleus). Use adipose tissue as the negative tissue (HPA: Not detected in adipocytes); nonciliated cells on the bronchus slide should serve as internal negative cells and lack nuclear staining (HPA: bronchial staining in ciliated cells; UniProt Q92949: nucleus).
Positive control tissue: Bronchus (Ciliated cells (cell body), HPA High)
Negative control tissue: Adipose tissue (HPA Not detected)
ICC-IF cell lines (HPA subcellular resource): HPA carries no ICC-IF cell line for FOXJ1; derive a cell-line control from the positive tissue's cell type (Ciliated cells (cell body)) and confirm it by RNA or western blot first.
Technical controls: Include a no-primary, secondary-only control and an isotype control matched to the rabbit primary antibody’s clonality (selected-SKU IHC caption: rabbit anti-FOXJ1; standard IHC practice), plus FOXJ1 knockout tissue or peptide competition if the immunizing peptide is available (standard IHC specificity controls). In bronchus, block endogenous peroxidase and check for endogenous biotin background when using the caption’s biotin-based DAB detection (selected-SKU IHC caption: biotinylated secondary, SABC and DAB; standard IHC practice).
⚠️Feasibility: A target-specific fixation window or fixation effect is unreported, and the selected-SKU paraffin-section caption does not state a fixative (selected-SKU IHC caption: fixative unreported). The caption uses heat-mediated retrieval in EDTA at pH 8.0, but it does not establish that retrieval is required; the supplied evidence does not establish whether frozen sections or IF are easier (selected-SKU IHC caption: paraffin section and EDTA retrieval; HPA subcellular: no ICC-IF images). In bronchus, do not score staining on mucus or the ciliary edge as FOXJ1 nuclear signal (HPA: bronchial ciliated cells; UniProt Q92949: nucleus; standard IHC interpretation).
HPA tissue IHC evidence for FOXJ1
Comprehensive Human Protein Atlas IHC scoring per tissue (reliability: Enhanced — High consistency between antibody staining and RNA expression data. Presumed off target binding observed and disregarded. Protein expression in respiratory epithelia can be correlated with lung RNA-seq 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
| Tissue | Cell type | Level | Evidence | Source |
|---|---|---|---|---|
| Bronchus | Ciliated cells (cell body) | High | Protein (IHC) | HPA → |
| Endometrium | Ciliated epithelial cells | High | Protein (IHC) | HPA → |
| Fallopian tube | Ciliated cells (cell body) | High | Protein (IHC) | HPA → |
| Efferent ducts | Ciliated cells | Medium | Protein (IHC) | HPA → |
| Nasopharynx | Ciliated cells (cell body) | Medium | Protein (IHC) | HPA → |
Undetected expression · recommended negative controls
| Tissue | Cell type | Level | Evidence | Source |
|---|---|---|---|---|
| Adipose tissue | Adipocytes | Not detected | Protein (IHC) | HPA → |
| Adrenal gland | Glandular cells | Not detected | Protein (IHC) | HPA → |
| Appendix | Glandular cells | Not detected | Protein (IHC) | HPA → |
| Bone marrow | Hematopoietic cells | Not detected | Protein (IHC) | HPA → |
| Breast | Adipocytes | Not detected | Protein (IHC) | HPA → |
Section 3
Advanced FOXJ1 IHC Tips
Use nuclear staining in ciliated cells as the main readout for FOXJ1 in paraffin section IHC (UniProt Q92949; HPA tissue IHC).
Which retrieval conditions should I try first for weak FOXJ1 staining?
Start with heat mediated antigen retrieval in EDTA, pH 8.0, for paraffin sections (datasheet A04942-3). The selected image used this retrieval before 2 μg/mL primary antibody overnight at 4°C, so keep those conditions together when reproducing it (datasheet A04942-3). If nuclear signal remains weak, check deparaffinisation, section adhesion and whether the heated buffer covered the sections before changing retrieval conditions (general IHC practice). Compare any adjusted heating time against a concurrently processed positive control containing ciliated cells (HPA tissue IHC; general IHC practice). Judge improvement by nuclear staining with limited signal outside the nuclei, the expected FOXJ1 location (UniProt Q92949; HPA tissue IHC).
Could fixation explain absent nuclear FOXJ1 staining?
Target specific fixation sensitivity is unknown: the selected paraffin section caption does not state a fixative (datasheet A04942-3). Record the fixation and processing history for each block, then compare similarly processed sections before attributing a weak result to the antibody (general IHC practice). Include a ciliated epithelium control in the same staining run; bronchial and fallopian tube ciliated cells show high FOXJ1 staining in the tissue atlas (HPA tissue IHC). If a known positive control also fails, inspect retrieval, primary incubation and detection alongside fixation history (general IHC practice). Do not infer a fixation effect from FOXJ1’s nuclear location or lack of annotated glycosylation (UniProt Q92949).
How should I assess FOXJ1 staining outside the nucleus?
Score convincing FOXJ1 signal in nuclei of cells with motile cilia, consistent with its transcription factor role and reported location (UniProt Q92949; HPA tissue IHC). The atlas reports high staining in bronchial and fallopian tube ciliated cells and endometrial ciliated epithelial cells (HPA tissue IHC). Inspect a counterstained section at sufficient magnification to distinguish nuclear chromogen from pigment or deposits over the cell body (general IHC practice). If cytoplasmic staining predominates, compare the pattern with an omission control and a positive tissue processed in the same run (general IHC practice). Document any discordant pattern separately from the nuclear positive cell count (general IHC practice).
Could isoforms or epitope position explain inconsistent FOXJ1 IHC?
The supplied record lists a 421 amino acid FOXJ1 chain and no annotated isoforms, but does not identify the catalog antibody’s epitope (UniProt Q92949; datasheet A04942-3). It also reports no transmembrane segment, signal peptide, glycosylation sites or modified residues (UniProt Q92949). Those annotations cannot establish whether a particular epitope survives tissue processing, so compare staining across sections processed with the same retrieval and incubation conditions (general IHC practice). If results differ between blocks, check processing records and the nuclear pattern in a positive control before proposing an isoform explanation (general IHC practice; HPA tissue IHC). Report the epitope as unspecified unless separately documented (datasheet A04942-3).
How can I compare FOXJ1 IF with this chromogenic IHC result?
For IF, pair nuclear FOXJ1 signal with a separately validated marker of ciliated epithelial cells, and check whether the signals identify the same cells (HPA tissue IHC; general IF practice). Choose fluorophores and filters after examining unstained tissue for autofluorescence, especially in the channel assigned to the weaker signal (general IF practice). Because FOXJ1 is nuclear and has no transmembrane segment, use permeabilisation appropriate for access to an intracellular nuclear epitope and validate it in the IF preparation (UniProt Q92949; general IF practice). Include single stain controls to assess channel bleed through and a no primary control for nonspecific fluorescence (general IF practice). The paraffin IHC caption does not establish IF fixation or antibody performance (datasheet A04942-3).
What should I check when FOXJ1 DAB staining is diffuse?
The selected paraffin section used 10% goat serum blocking, a biotinylated secondary antibody, a streptavidin biotin complex and DAB development (datasheet A04942-3). For diffuse DAB, compare a no primary control and review secondary binding, washing and chromogen development under matched conditions (general IHC practice). Include a peroxidase block in the chromogenic workflow and assess endogenous biotin if background persists with this biotin based detection method (general IHC practice; datasheet A04942-3). Inspect whether colour lies in nuclei of ciliated cells or spreads across tissue without cell specificity (HPA tissue IHC; general IHC practice). Adjust blocking or detection conditions using controls while retaining the documented primary concentration as a reference (datasheet A04942-3; general IHC practice).
How should I quantify FOXJ1 positive cells across sections? ⚠ ANSWER MARKED FOR VERIFICATION
Define a positive cell by nuclear DAB staining and apply the same intensity threshold to all sections in a comparison (UniProt Q92949; general IHC practice). Report the percentage of positive nuclei among morphologically identified ciliated epithelial cells, with the number of eligible cells examined for each section (HPA tissue IHC; general IHC practice). If intensity matters, an H score combines the percentages at each intensity grade; keep its scoring rules fixed and report the underlying counts (general IHC practice). For uneven sampling, positive nuclei per mm² of eligible epithelium can supplement the percentage (general IHC practice). Exclude damaged regions using rules set before scoring (general IHC practice).
How can I distinguish true FOXJ1 staining from artefact?
A credible positive result has nuclear staining in cells with motile cilia, matching FOXJ1’s location and the tissue atlas pattern (UniProt Q92949; HPA tissue IHC). High staining is reported in bronchial and fallopian tube ciliated cells, whereas adrenal glandular cells and adipose tissue adipocytes are reported as not detected (HPA tissue IHC). Treat staining confined to section edges, necrotic areas or the wrong cell compartment as suspect and inspect a neighbouring intact region (general IHC practice; UniProt Q92949). A no primary control helps reveal detection background, including endogenous enzyme signal in a DAB workflow (general IHC practice). Interpret a negative result only after an appropriate positive control shows the expected nuclear pattern in the same run (HPA tissue IHC; general IHC practice).
Boster reagents
Best FOXJ1 / Forkhead box protein J1 IHC Antibodies
A04942-3 has IHC data from rat ovary paraffin sections and IF data from CACO-2 cells (catalog image captions); its listed reactivity covers human and rat (catalog reactivity).
Real IHC data
Anti-FOXJ1 Antibody ®
Cat # A04942-3
A04942-3 is listed for IHC and IF/ICC with human and rat reactivity (catalog applications/reactivity). Its IHC image shows rat ovary paraffin sections, and its IF image shows CACO-2 cells (catalog image captions).
Which to pick: For tissue IHC, choose A04942-3: its image documents rat ovary paraffin sections with heat retrieval in EDTA at pH 8.0 and DAB detection; the fixative is unreported (A04942-3 IHC caption). For IF/ICC, A04942-3 has an IF image of CACO-2 cells (A04942-3 IF caption); see the separate IF/ICC guide. For work across human and rat samples, A04942-3 lists reactivity with both species and IHC/IF/ICC applications, although its IHC image documents rat tissue only; its host is rabbit and clonality is unreported (catalog reactivity/applications/host/clone; A04942-3 IHC caption).
Each figure is that product's own IHC / IF validation image from its datasheet.
References
- UniProt Consortium. UniProt entry Q92949 (FOXJ1_HUMAN, Forkhead box protein J1).
- Human Protein Atlas. FOXJ1 tissue IHC expression (reliability: Enhanced).
- Human Protein Atlas. FOXJ1 subcellular location (ICC-IF): Highest expression in Hep-G2: 4.3 nTPM.
- Human Protein Atlas. FOXJ1 antibody validation summary (1 antibodies).
- Unveiling the prevalence and impact of silent rhinovirus infection in chronic rhinosinusitis with nasal polyps. Annals of allergy, asthma & immunology : official publication of the American College of Allergy, Asthma, & Immunology 2025 — PMC11972899.
- Distinct patterns of primary and motile cilia in Rathke's cleft cysts and craniopharyngioma subtypes. Modern pathology : an official journal of the United States and Canadian Academy of Pathology, Inc 2016 — PMC5442446.
- Decreased FOXJ1 expression and its ciliogenesis programme in aggressive ependymoma and choroid plexus tumours. The Journal of pathology 2016 — PMC5364032.
- The link between FOXJ1 expression level in bladder carcinoma and tumor recurrence. Oncology letters 2018 — PMC5774442.
- PubMed PMID:9530170 — UniProt-cited evidence.
- PubMed PMID:9073514 — UniProt-cited evidence.
- PubMed PMID:15489334 — UniProt-cited evidence.
Immunohistochemistry protocol sheet for FOXJ1 (Forkhead box protein J1). Expected localisation Nuclei of motile-ciliated cells (HPA tissue IHC). Antigen retrieval: EDTA pH 8.0 HIER, heat-mediated (datasheet A04942-3). Validated IHC antibody: A04942-3 at 2-5μg/ml (the product's own IHC validation image is shown). Controls (HPA): positive Bronchus (Ciliated cells (cell body)); negative Adipose tissue. IHC-P workflow on paraffin sections; fixative unspecified. Protocol steps: 1. Sample: Paraffin-embedded rat ovary tissue; fixative not specified (datasheet A04942-3); 2. Fixation: Image fixative and duration unreported (datasheet A04942-3); 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: EDTA pH 8.0 (datasheet A04942-3); 20 min, 95–100 °C (standard); 6. Peroxidase block: 3% H2O2, 10 min , room temperature (standard); 7. Blocking: 10% goat serum (datasheet A04942-3); 8. Primary antibody: Rabbit anti-FOXJ1, 2-5μg/ml (datasheet A04942-3); 9. Primary incubation: Overnight at 4 °C (datasheet A04942-3). Watch for: Fixation: Keep fixation consistent across sections (standard IHC practice; not target-specific); Caveat: Presumed off-target staining was observed and disregarded (HPA tissue IHC); Isoform / epitope: No annotated isoforms or processing; epitope map unknown (UniProt); Regulation: Expression regulation unreported (UniProt). Evidence: UniProt Q92949, HPA tissue IHC · Enhanced, HPA cell-line RNA · Highest expression in Hep-G2: 4.3 nTPM, Datasheet A04942-3, PMC5442446, PMC5364032. QR code links to https://www.bosterbio.com/bosterbio-gene-info-cards/FOXJ1/immunohistochemistry-ihc-guide.