This website uses cookies to ensure you get the best experience on our website.
- Table of Contents
FOXJ1 / Forkhead box protein J1 · IHC design guide
Design Immunohistochemistry for FOXJ1
Plan FOXJ1 chromogenic IHC in paraffin sections around nuclear staining in cells with motile cilia (HPA tissue IHC). Use the catalog antibody’s IHC protocol and tissue controls to assess staining, bearing in mind presumed off-target binding (datasheet A04942-3; HPA tissue IHC).
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 may occur (HPA tissue IHC) | |
| Regulation | Staining tracks motile-ciliated cells (HPA tissue IHC) | |
| Isoform / epitope | Full-length chain; no annotated isoforms or processing (UniProt) |
Section 1
Recommended FOXJ1 IHC & IF Protocols
The catalog antibody’s IHC-P protocol is paired with 3 published FOXJ1 chromogenic IHC protocols (datasheet: A04942-3; 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 retrieval at pH 8.0 for the catalog antibody (datasheet: A04942-3). Use the article’s stated retrieval when reproducing a published protocol.
Section 2
What Is the Expected FOXJ1 Staining Pattern?
FOXJ1 is a nuclear transcription factor with no transmembrane segment (UniProt Q92949: location and topology). In paraffin-section IHC, expect staining in the nuclei of cells with motile cilia (HPA: tissue IHC profile). HPA rates the tissue pattern Enhanced for consistency with RNA expression, while noting that presumed off-target staining was observed and disregarded (HPA: tissue IHC reliability).
| Strong nuclear staining in bronchial or fallopian-tube ciliated cells, with neighboring cells less prominent. | This fits the expected cell type and compartment: HPA reports High staining in those ciliated cell populations and describes nuclear expression in cells with motile cilia (HPA: tissue IHC); FOXJ1 is nuclear (UniProt Q92949: location). |
| Prominent staining along the ciliary border or throughout the cytoplasm, without a convincing nuclear signal. | The dominant compartment conflicts with the reference pattern (HPA: nuclear expression; UniProt Q92949: nucleus). Review morphology, counterstain and detection background before scoring it as FOXJ1; the supplied sources do not establish a ciliary-border or diffuse cytoplasmic IHC pattern. |
| Strong staining in adipocytes or adrenal glandular cells, especially when their nuclei are highlighted. | HPA reports FOXJ1 as Not detected in those specified cells (HPA: adipose tissue and adrenal gland IHC). Consider antibody cross-reactivity or endogenous detection activity; check controls and the exact stained cell type before treating this as target-specific signal (general IHC practice). |
| A pale, diffuse chromogen haze covers ciliated and nonciliated areas alike. | A field-wide haze does not reproduce the cell-restricted nuclear pattern (HPA: tissue IHC profile). Assess background with a reagent or primary-omission control and review blocking, washing and chromogen development (general IHC practice); the pattern alone cannot identify its cause. |
| No nuclear staining appears in morphologically ciliated bronchial epithelium. | Bronchial ciliated cells are a High-staining reference population (HPA: bronchus IHC). First verify that the sampled section contains those cells, then compare a known-positive section processed in the same run; absent signal alone does not identify which IHC step failed (general IHC practice). |
💡Expected FOXJ1 appearanceCall positive when ciliated epithelial cells show strong nuclear staining in bronchus or fallopian tube (HPA: High in ciliated cells; nuclear profile); predominant ciliary-border, diffuse cytoplasmic or widespread nonciliated-cell color is discordant with that reference pattern (HPA: tissue IHC profile; UniProt Q92949: nucleus).
| Cell selection and scoring | Score the nuclei of identifiable ciliated cells, rather than the whole epithelium (HPA: nuclear expression in cells with motile cilia). HPA reports High staining in bronchus, endometrium and fallopian tube; Medium in efferent ducts and nasopharynx (HPA: tissue IHC). |
| Reference tissue limits | HPA reports Low staining in choroid-plexus ependymal cells and testis Leydig cells (HPA: tissue IHC). These are weaker visual references than the listed High-staining ciliated populations; a negative result there is less useful for checking whether an IHC run worked (general IHC practice). |
| Evidence and antibody choice | HPA assigns Enhanced tissue reliability based on agreement with RNA data, notes presumed off-target binding that was disregarded, and lists HPA005714 as IHC Enhanced (HPA: tissue IHC; antibody validation). Use the expected cell type and nuclear location when interpreting any positive stain (HPA: tissue IHC profile). |
| Intracellular target | FOXJ1 has no annotated signal peptide, propeptide, transmembrane segment or glycosylation sites; its annotated chain spans residues 1–421 (UniProt Q92949: processing, topology and glycosylation). These annotations support a nuclear target interpretation, but provide no antigen-retrieval setting or evidence of fixation sensitivity. |
| IF/ICC? | FOXJ1's reference location is nuclear (UniProt Q92949: location), but HPA supplies no ICC-IF images or main subcellular location for this record (HPA: subcellular). For IF/ICC design and controls, use its dedicated guide; this IHC pattern cannot establish an IF/ICC staining result. |
| Situation | Likely cause | Next action |
|---|---|---|
| Known-positive bronchus has no convincing nuclear signal. | The target cell population may be absent from the section, or the IHC run may have lost detectable signal (HPA: High in bronchial ciliated cells; general IHC practice). | Confirm ciliated-cell morphology, then compare a known-positive section in the same run; review primary-antibody use, retrieval, detection and counterstain records (general IHC practice). No FOXJ1-specific retrieval condition is supplied. |
| Nuclei look positive in many nonciliated cells. | That distribution exceeds HPA's cell-restricted reference pattern and may reflect cross-reactivity or nonspecific detection (HPA: nuclear expression in cells with motile cilia; general IHC practice). | Compare with the relevant HPA tissue and cell reference, inspect a primary-omission control, and verify the antibody's IHC validation before assigning cell identities (HPA: tissue IHC and antibody validation; general IHC practice). |
| Color concentrates at the apical ciliary border. | Border-dominant color conflicts with the reported nuclear location (HPA: tissue IHC profile; UniProt Q92949: location); its cause cannot be assigned from appearance alone. | Check a nuclear counterstain and examine whether nuclei in the same ciliated cells are labeled; assess a detection control for surface or edge background (general IHC practice). |
| Diffuse background makes nuclei hard to judge. | A broadly distributed signal obscures the restricted nuclear pattern (HPA: tissue IHC profile). Residual detection activity or insufficient blocking or washing are possible general IHC causes (general IHC practice). | Compare a primary-omission control, review blocking and wash steps, and check whether chromogen development obscured cellular detail (general IHC practice); rescore only where cell boundaries and nuclei remain interpretable. |
| A low-staining tissue appears negative while the positive control works. | HPA lists Low staining in choroid-plexus ependymal cells and testis Leydig cells (HPA: tissue IHC); a blank field there gives limited evidence of an assay failure. | Interpret the exact cell type and section morphology, then use a High-staining bronchus or fallopian-tube reference to assess run performance (HPA: tissue IHC; general IHC practice). |
| An IF/ICC image is being used to validate the paraffin IHC result. | HPA provides no ICC-IF images or main-location assessment for this FOXJ1 record (HPA: subcellular), so it supplies no observed IF/ICC pattern for comparison. | Judge paraffin IHC against HPA's tissue IHC cell pattern and the nuclear UniProt location (HPA: tissue IHC; UniProt Q92949: location). Address IF/ICC staining and its controls in the separate guide. |
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 expect staining in ciliated cells (cell body) (HPA: High in bronchus ciliated cells). Use adipose tissue as the negative tissue (HPA: Not detected in adipocytes); on the bronchus slide, adjacent nonciliated cells should lack specific nuclear staining (HPA: 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; a host- and class-matched rabbit IgG isotype control for the catalog antibody; and FOXJ1-knockout material as a biological negative (selected tissue-IHC caption: rabbit primary; standard IHC practice). For chromogenic detection in bronchus, block endogenous peroxidase and assess endogenous biotin background when using the caption’s biotin–streptavidin system (selected tissue-IHC caption: SABC/DAB; standard IHC practice).
⚠️Feasibility: A target-specific fixation window and fixation effect are unreported, and the selected A04942-3 paraffin-section caption does not state a fixative (selected tissue-IHC caption). The caption used heat retrieval in EDTA at pH 8.0, but does not establish whether retrieval is required under other conditions (selected tissue-IHC caption). The supplied evidence does not establish that frozen sections or IF are easier; in bronchus, check that any background from endogenous peroxidase or biotin does not obscure the expected ciliated-cell signal (HPA: High in bronchus ciliated cells; selected tissue-IHC caption: SABC/DAB; standard IHC practice).
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
Troubleshoot FOXJ1 staining by checking nuclear localisation, ciliated cell identity, tissue processing and assay controls before scoring chromogenic IHC.
How should I adjust retrieval when FOXJ1 nuclear staining is weak?
Start with heat-mediated EDTA retrieval at pH 8.0 for paraffin sections (datasheet A04942-3). Because the caption does not report heating time or temperature, record those settings and change one at a time while comparing adjacent sections (datasheet A04942-3; standard IHC practice). After retrieval, the documented workflow used 10% goat serum and 2 µg/mL primary antibody overnight at 4°C (datasheet A04942-3). If nuclear signal remains weak, compare a modestly longer heat exposure with the starting condition, checking that tissue morphology and background remain acceptable (standard IHC practice). Score nuclei in ciliated epithelial cells rather than diffuse surface staining (HPA tissue IHC; UniProt Q92949 localisation).
Can fixation explain inconsistent FOXJ1 staining across paraffin sections?
Target-specific FOXJ1 fixation sensitivity is unknown because the selected paraffin-section caption does not state a fixative (datasheet A04942-3). Record each specimen’s fixative, fixation duration and processing history before comparing staining intensity across cases (standard IHC practice). Keep section thickness, EDTA retrieval at pH 8.0 and the documented 2 µg/mL overnight primary incubation constant while testing processing differences (datasheet A04942-3; standard IHC practice). Examine nuclear staining and tissue morphology together, since uneven preservation can complicate interpretation of a nuclear target (UniProt Q92949 localisation; standard IHC practice). Avoid assigning a FOXJ1-specific fixation effect to a weak section until comparable material and controls support it (standard IHC practice).
Where should FOXJ1 staining appear, and what if the signal is apical?
Interpret FOXJ1 primarily as a nuclear signal: it is annotated as nuclear, and HPA describes nuclear expression in cells with motile cilia (UniProt Q92949 localisation; HPA tissue IHC). In bronchus and fallopian tube, ciliated cells are reported as high expression examples for comparison (HPA tissue IHC). FOXJ1 has no annotated transmembrane segment, so an isolated apical rim should prompt inspection for surface deposit or detection background (UniProt Q92949 topology; standard IHC practice). Compare nuclear staining with the cell’s morphology and with a no-primary control on a nearby section (standard IHC practice). Do not count apical DAB alone as a positive nucleus when estimating the fraction of FOXJ1-positive cells (UniProt Q92949 localisation; standard IHC practice).
How can I assess epitope-related failure without a mapped antibody epitope?
The supplied record lists 0 isoforms and a single 1–421 chain, but it does not locate the catalog antibody’s epitope (UniProt Q92949 record). It also annotates 0 glycosylation sites and 0 modified residues; those annotations do not establish how fixation affects antibody binding (UniProt Q92949 record; standard IHC practice). Start with the documented EDTA retrieval at pH 8.0 and compare adjacent sections under controlled detection conditions (datasheet A04942-3; standard IHC practice). If signal is absent, check antibody handling and a suitable positive tissue before attributing failure to an isoform or blocked epitope (HPA tissue IHC; standard IHC practice). Document any retrieval change alongside nuclear specificity and morphology (UniProt Q92949 localisation; standard IHC practice).
How should I adapt the FOXJ1 question for multiplex IF?
Use IF as a separately optimised assay; the selected antibody caption documents chromogenic staining of a paraffin section, not an IF result (datasheet A04942-3). Pair nuclear FOXJ1 with a marker identifying the expected ciliated cell population, and include single-label controls to assess channel bleed-through (HPA tissue IHC; standard IF practice). Select fluorophores after checking tissue autofluorescence in unstained sections, placing the weaker signal in the cleaner channel where practical (standard IF practice). FOXJ1 is nuclear and has no transmembrane segment, so test permeabilisation that permits antibody access to nuclear epitopes while preserving morphology (UniProt Q92949 localisation and topology; standard IF practice). Assess nuclear colocalisation with a counterstain before transferring IF observations into IHC interpretation (standard IF and IHC practice).
What should I check when DAB obscures FOXJ1-positive nuclei?
First compare a no-primary section with the test section to locate signal arising from detection reagents or tissue rather than primary-antibody binding (standard IHC practice). The selected workflow uses a biotinylated secondary, a streptavidin–biotin complex and DAB, so include a control appropriate to that detection chain when background persists (datasheet A04942-3; standard IHC practice). Apply a peroxidase block and check endogenous biotin background as general precautions for this chromogenic workflow (standard IHC practice). If background remains diffuse, review blocking, washes, the documented 2 µg/mL primary concentration and DAB development time one variable at a time (datasheet A04942-3; standard IHC practice). Retain only convincing nuclear signal in expected cells for scoring (UniProt Q92949 localisation; HPA tissue IHC).
How should I score heterogeneous FOXJ1 staining in ciliated epithelium? ⚠ ANSWER MARKED FOR VERIFICATION
Define the region of interest and eligible epithelial cells before scoring, then report the percentage of cells with FOXJ1-positive nuclei (UniProt Q92949 localisation; HPA tissue IHC; standard IHC practice). For intensity variation, an H-score sums each intensity category’s percentage times its 0–3 intensity grade, yielding 0–300 (standard IHC practice). Alternatively, report positive nuclei per mm² when area is the relevant denominator (standard IHC practice). Normalise cell-based results to the number of evaluable ciliated epithelial cells, and state how denuded or damaged areas were excluded (HPA tissue IHC; standard IHC practice). Keep thresholds and DAB development consistent across sections, and report biological replicates separately (standard IHC practice).
How do I distinguish true FOXJ1 positivity from a staining artefact?
A convincing FOXJ1-positive cell has nuclear staining in an expected motile-ciliated population, consistent with its nuclear annotation and HPA tissue pattern (UniProt Q92949 localisation; HPA tissue IHC). HPA reports high expression in bronchial and fallopian-tube ciliated cells, providing tissue and cell-type references (HPA tissue IHC). Treat isolated cytoplasmic or apical DAB, section-edge enhancement and necrotic areas cautiously, and compare them with intact interior tissue (UniProt Q92949 localisation; standard IHC practice). Use no-primary and detection-system controls to investigate endogenous peroxidase or biotin-related signal before assigning it to FOXJ1 (datasheet A04942-3 detection method; standard IHC practice). HPA’s enhanced rating still notes presumed off-target binding, so corroborate unexpected patterns independently (HPA tissue IHC).
Boster reagents
Best FOXJ1 / Forkhead box protein J1 IHC Antibodies
A04942-3 has IHC data from rat ovary paraffin sections (IHC image caption) and IF/ICC data from CACO-2 cells (IF image caption); listed reactivity is human and rat (catalog).
Real IHC data
Anti-FOXJ1 Antibody ®
Cat # A04942-3
A04942-3 will render with its own IHC figure showing rat ovary paraffin sections (IHC image caption). Its IF caption shows CACO-2 cells, and its application list includes IHC, ICC and IF (IF image caption; catalog applications).
Which to pick: For tissue IHC, choose A04942-3: its rat ovary paraffin-section image used EDTA retrieval at pH 8.0 and 2 μg/mL primary antibody; the fixative is unreported (IHC image caption). For IF/ICC, the same SKU has a CACO-2 cell image using 5 μg/mL primary antibody (IF image caption). For human and rat work, A04942-3 lists both species, although the supplied IHC image shows rat tissue; clonality is unreported (catalog reactivity; IHC image caption; catalog clone field).
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 may occur (HPA tissue IHC); Isoform / epitope: Full-length chain; no annotated isoforms or processing (UniProt); Regulation: Staining tracks motile-ciliated cells (HPA tissue IHC). 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.