This website uses cookies to ensure you get the best experience on our website.
- Table of Contents
BTF3L4 / Transcription factor BTF3 homolog 4 · IHC design guide
Design Immunohistochemistry for BTF3L4
Plan BTF3L4 staining in paraffin sections using the catalog antibody at 1:100–1:300 (datasheet). Compare cytoplasmic staining in cerebral cortex neurons and skeletal muscle myocytes, both reported as high (HPA tissue IHC).
Evidence assembled Oct 2026 · For research use; verify linked source records and product datasheet before use
BTF3L4 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 | Cytoplasmic tissue staining (HPA tissue IHC) | |
| Staining pattern | Cytoplasmic staining in neurons and myocytes (HPA tissue IHC) | |
| Antigen retrieval | Citrate pH 6.0 HIER, 95–98 °C, 20 min (rule: cytoplasmic / membrane antigen) | |
| Positive control | Cerebral cortex+4 more · see all | |
| Negative control | Bone marrow+1 more · see all |
Important caveats
Reasons your staining may differ from the expected pattern.
| Fixation | Keep fixation conditions consistent across sections. (standard IHC practice; not target-specific) | |
| Caveat | Staining has medium consistency with RNA data (HPA tissue IHC) | |
| Regulation | Expression regulation unannotated (UniProt) | |
| Isoform / epitope | 3 isoforms; epitope coverage is unspecified (UniProt) |
Section 1
Recommended BTF3L4 IHC & IF Protocols
Compare the catalog antibody’s IHC-P protocol (datasheet) with the published BTF3L4 liver-section workflow (PMC10899873).
| Sample | Paraffin-embedded human brain tissue; fixative not specified (datasheet A15784) |
| Fixation | Image fixative and duration unreported (datasheet A15784); verify before use. |
| Sectioning | 4–5 µm sections on charged slides (standard) |
| Deparaffinisation | Xylene, graded ethanol series to water (standard) |
| Antigen retrieval | Heat-induced epitope retrieval in citrate buffer, pH 6.0, 20 min at 95–98 °C (standard rule: cytoplasmic / membrane antigen) |
| 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-BTF3L4, 1:100 - 1:300 (datasheet A15784) |
| 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 | BTF3L4-positive staining in neuronal cells of cerebral cortex (HPA tissue IHC: High). HPA tissue profile: General cytoplasmic expression. No signal in the no-primary control. |
💡Decision noteStart with citrate pH 6.0 retrieval at 95–98 °C for 20 min (page antigen retrieval); the article does not specify retrieval conditions (PMC10899873).
Section 2
What Is the Expected BTF3L4 Staining Pattern?
In paraffin section IHC, expect mainly cytoplasmic BTF3L4 staining in neuronal cells and skeletal myocytes, with staining also reported in several epithelial and glandular cell types (HPA tissue IHC). The IHC profile is Approved, with medium agreement between staining and RNA data and external verification pending (HPA tissue IHC). UniProt does not annotate a subcellular location or transmembrane segment (UniProt Q96K17).
| Clear cytoplasmic signal in cerebral cortex neurons or skeletal myocytes. | This fits the reported High staining in those cells and the general cytoplasmic IHC profile (HPA tissue IHC). Judge the signal in the named cells, rather than treating every stained cell in the section as an equivalent positive. |
| Predominantly nuclear staining in a paraffin section, with little cytoplasmic signal. | This differs from the general cytoplasmic tissue IHC profile (HPA tissue IHC). Review cell boundaries, counterstain and detection controls before accepting the pattern. Nucleoplasmic signal has been reported by a separate ICC-IF assay, so nuclear staining alone does not establish an IHC artefact (HPA subcellular). |
| Strong signal in bone marrow hematopoietic cells or soft tissue fibroblasts. | Those cells were reported as Not detected in tissue IHC (HPA tissue IHC). Recheck cell identity and controls for cross-reactivity or endogenous detection activity. Treat the mismatch as a reason to investigate, not proof that the antibody is nonspecific. |
| Broad, hazy colour across cells and surrounding tissue, without clear cell boundaries. | The result cannot be confidently scored as the reported cellular pattern (HPA tissue IHC). In general IHC practice, nonspecific binding, incomplete blocking or detection background can create this appearance; inspect a control section processed without primary antibody. |
| No signal in cerebral cortex neurons or skeletal myocytes. | This conflicts with the reported High staining in those cells (HPA tissue IHC). Confirm that the expected cells are present, then check the staining run with an appropriate positive control. One negative section does not by itself establish absent BTF3L4 expression. |
💡Expected BTF3L4 appearanceCall a paraffin section positive when cytoplasmic staining is clear in the expected cells, especially High signal in cerebral cortex neurons or skeletal myocytes; broad haze or strong staining confined to reported negative cell types warrants investigation (HPA tissue IHC).
| Tissue and cell selection | Cerebral cortex neurons and skeletal myocytes are reported High; several glandular and epithelial cell types are Medium, while bone marrow hematopoietic cells and soft tissue fibroblasts are Not detected (HPA tissue IHC). Choose controls by cell type within the section. |
| IHC versus IF/ICC: what compartment should I expect? | Paraffin section IHC has a general cytoplasmic profile (HPA tissue IHC). ICC-IF reports approved nucleoplasm and cytosol locations (HPA subcellular). Assess each assay against its own observed pattern; the IF result does not establish a nuclear IHC requirement. |
| Antibody validation | The tissue IHC profile is Approved, with medium staining-to-RNA consistency and external verification pending (HPA tissue IHC). HPA067026 is IHC Approved; HPA074056 has no listed IHC status (HPA antibodies). These labels do not guarantee that every stained structure is BTF3L4. |
| Isoforms and protein architecture | UniProt lists 3 isoforms, one chain spanning residues 1–158, and no signal peptide, propeptide or transmembrane segment (UniProt Q96K17). The payload does not map antibody epitopes to isoforms, so it cannot predict isoform-specific IHC staining. |
| Situation | Likely cause | Next action |
|---|---|---|
| Expected positive cells show no visible chromogen. | The result conflicts with reported High staining in cerebral cortex neurons or skeletal myocytes (HPA tissue IHC); the failed step is unknown. | In general IHC practice, verify tissue identity, positive-control performance, primary antibody application and detection reagents. Review retrieval and antibody dilution against the validated assay instructions before changing conditions. |
| The entire section has diffuse brown background. | General IHC possibilities include nonspecific binding or endogenous detection activity; this appearance cannot be assigned to the reported cellular pattern (HPA tissue IHC). | Run a section without primary antibody and inspect the pattern. In general IHC practice, check blocking, washes and detection chemistry, then reassess whether signal resolves into identifiable cells. |
| Bone marrow hematopoietic cells stain strongly. | These cells are listed as Not detected (HPA tissue IHC). Cell misidentification, cross-reactivity or endogenous detection activity remain possible explanations. | Confirm the cell population and compare a section without primary antibody. Review the same run's expected positive tissue before interpreting the unexpected stain as BTF3L4. |
| Soft tissue fibroblasts appear strongly positive. | Fibroblasts in soft tissue are listed as Not detected (HPA tissue IHC); an unexpected signal needs verification. | Check morphology and staining controls, then compare intensity and distribution with an expected positive cell type. Record the discrepancy instead of using fibroblasts as an established positive control. |
| Staining is chiefly nuclear in IHC. | The distribution differs from the general cytoplasmic tissue IHC profile (HPA tissue IHC), although nucleoplasm is an approved ICC-IF location (HPA subcellular). | Check counterstain, cellular outlines and a section without primary antibody. Score the paraffin section against IHC evidence; seek independent confirmation before assigning a new IHC compartment. |
| A low-staining tissue gives a faint or variable result. | Parathyroid glandular cells, liver cholangiocytes, ovarian stroma cells and adipocytes are listed as Low (HPA tissue IHC). Faint staining alone is therefore hard to interpret. | Compare the run with reported High positive cells and a detection control (HPA tissue IHC; general IHC practice). Keep cell identity and background in view when scoring weak signal. |
Experiment evidence
IHC & IF images showing BTF3L4 staining
A15784 · IHCImmunohistochemistry analysis of paraffin-embedded human brain tissue, using BTF3L4 Antibody. The picture on the right is blocked with the s
HPA · Cerebral cortexHuman Protein Atlas IHC, Cerebral cortex. Source: https://www.proteinatlas.org/ENSG00000134717-BTF3L4/tissue/cerebral+cortex#imid_18236111
HPA · ColonHuman Protein Atlas IHC, Colon. Source: https://www.proteinatlas.org/ENSG00000134717-BTF3L4/tissue/colon#imid_18236037
HPA · LiverHuman Protein Atlas IHC, Liver. Source: https://www.proteinatlas.org/ENSG00000134717-BTF3L4/tissue/liver#imid_18236054
HPA · KidneyHuman Protein Atlas IHC, Kidney. Source: https://www.proteinatlas.org/ENSG00000134717-BTF3L4/tissue/kidney#imid_18236047
HPA · ICC-IF SH-SY5YHuman Protein Atlas immunofluorescence, SH-SY5Y, antibody HPA067026; green = BTF3L4, blue = nucleus, red = microtubules.
HPA · ICC-IF SH-SY5YHuman Protein Atlas immunofluorescence, SH-SY5Y, antibody HPA067026; green = BTF3L4, blue = nucleus, red = microtubules.
← swipe / scroll for more images →
Real IHC / IF data behind the staining-pattern expectations in this section.
Sample controls for BTF3L4 IHC & IF
🧪Run cerebral cortex first and look for staining in neuronal cells (HPA: High in cerebral cortex neuronal cells). Use bone marrow hematopoietic cells as the negative tissue (HPA: Not detected); on the cortex slide, treat morphologically identified cells without signal as internal background references, without assuming every non-neuronal cell is negative.
Positive control tissue: Cerebral cortex (Neuronal cells, HPA High)
Negative control tissue: Bone marrow (HPA Not detected)
ICC-IF cell lines (HPA subcellular resource): HPA ICC-IF images show BTF3L4 in SH-SY5Y, U-251MG, U2OS, HBEC3-KT, with annotated localisation: Nucleoplasm (approved), Cytosol (approved) (HPA subcellular).
Technical controls: Include no-primary (secondary-only) and host- and clonality-appropriate isotype or nonimmune IgG controls, plus a BTF3L4 knockout specimen or peptide-block control; the selected antibody caption shows peptide blocking in paraffin-embedded human brain tissue (A15784 caption: peptide block). Quench endogenous peroxidase and check for pigment or other background before scoring cortical staining (standard chromogenic IHC practice).
⚠️Feasibility: The selected tissue-IHC caption reports paraffin-embedded human brain but does not state the fixative; a BTF3L4-specific fixation window is unreported (A15784 caption: fixative not stated). Retrieval dependence is unreported, so compare retrieved and unretrieved sections during optimization; the supplied evidence does not establish that frozen sections or IF are easier (A15784 caption: paraffin tissue IHC; HPA: ICC-IF images). In cortex, distinguish chromogen from endogenous pigment when scoring neuronal cells (standard brain IHC practice).
HPA tissue IHC evidence for BTF3L4
Comprehensive Human Protein Atlas IHC scoring per tissue (reliability: Approved — Medium 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 |
|---|---|---|---|---|
| Cerebral cortex | Neuronal cells | High | Protein (IHC) | HPA → |
| Skeletal muscle | Myocytes | High | Protein (IHC) | HPA → |
| Adrenal gland | Glandular cells | Medium | Protein (IHC) | HPA → |
| Appendix | Glandular cells | Medium | Protein (IHC) | HPA → |
| Breast | Glandular cells | Medium | Protein (IHC) | HPA → |
Section 3
Advanced BTF3L4 IHC Tips
Troubleshoot BTF3L4 staining in paraffin section IHC using the page retrieval setting, the catalog antibody image, and compartment specific reference patterns.
How should I adjust retrieval if BTF3L4 staining is weak or uneven?
Start with citrate pH 6.0 heat induced antigen retrieval at 95–98 °C for 20 min (page retrieval setting). If staining is weak, first check that sections reached the intended temperature and remained immersed throughout, then compare an adjacent section with a modestly longer retrieval time while keeping detection conditions constant (standard IHC practice). Include a known positive section, such as cerebral cortex with neuronal staining, to distinguish retrieval failure from a low expressing specimen (HPA tissue IHC: High in cerebral cortex neuronal cells). Record tissue damage and background alongside signal intensity, since harsher retrieval can reduce the interpretability of chromogenic staining (standard IHC practice).
Could fixation explain weak staining in my paraffin sections?
The selected antibody image identifies paraffin embedded human brain tissue but does not state its fixative, so BTF3L4 specific fixation sensitivity is unknown (A15784 tissue IHC caption). Record the fixative, fixation duration, processing schedule, section age, and retrieval run for each specimen before attributing a weak result to fixation (standard IHC practice). Compare sections processed under matched conditions and stain them in the same run, using cerebral cortex neuronal cells as a reference when available (HPA tissue IHC: High in cerebral cortex neuronal cells). If signal remains weak, assess antibody concentration and detection controls systematically; staining patterns alone cannot establish a fixation effect (standard IHC practice).
Should BTF3L4 stain nuclei, cytoplasm, or both in IHC?
Expect cytoplasmic tissue staining as the principal IHC reference pattern (HPA tissue IHC: General cytoplasmic expression). Nucleoplasmic and cytosolic localisation are both reported from cell based imaging, so carefully resolved nuclear signal can be plausible, but it should not replace examination of cell identity and tissue morphology (HPA subcellular: Nucleoplasm and cytosol, approved). UniProt supplies no subcellular annotation and reports no transmembrane segment, so a sharply membranous pattern lacks support from this record (UniProt Q96K17: subcellular location unannotated; topology without a transmembrane segment). Compare nuclear and cytoplasmic staining separately across matched sections, and inspect counterstained cells at high magnification before assigning a compartment (standard IHC practice).
How can isoforms or epitope masking affect this IHC result?
BTF3L4 has 3 annotated isoforms, but the supplied evidence does not map this antibody’s epitope to a shared or isoform specific sequence (UniProt Q96K17: isoforms 1, 2, and 3; A15784 caption: epitope not specified). Its NAC-A/B domain spans residues 33–98, with reported modifications at lysine 5 and threonine 111; none establishes which feature this antibody recognises (UniProt Q96K17: domain and modified residues). If staining differs between specimens, compare matched retrieval runs and consult an epitope map before proposing isoform selectivity (standard IHC practice). The peptide blocked brain image supports competition under that image’s conditions, but does not identify the recognised isoform or explain every tissue pattern (A15784 tissue IHC caption).
How should I check BTF3L4 localisation with multiplex IF?
Use a neuronal cell marker when examining cerebral cortex, where neuronal BTF3L4 staining is reported as High, and inspect the BTF3L4 channel against the cell marker and nuclear counterstain (HPA tissue IHC: Cerebral cortex neuronal cells, High; standard IF practice). Choose fluorophores after checking unstained tissue for autofluorescence, and favour a spectrally separated channel with low background for the weaker target signal (standard IF practice). For cytosolic and nucleoplasmic access, test gentle permeabilisation after fixation while preserving morphology; no transmembrane segment or membrane sided epitope is annotated (HPA subcellular: Nucleoplasm and cytosol; UniProt Q96K17 topology). Optimise IF fixation and antibody conditions independently, since the selected paraffin brain caption does not report an IF method (A15784 tissue IHC caption).
How do I separate weak BTF3L4 staining from chromogenic background?
Run a section without primary antibody, review an unstained section, and compare background in the same cell compartments used for scoring (standard chromogenic IHC practice). Apply a peroxidase block before peroxidase based detection and control DAB development time across sections; these are general workflow steps rather than BTF3L4 specific validation (standard chromogenic IHC practice). Bone marrow hematopoietic cells and soft tissue fibroblasts were reported as Not detected, but should serve as contextual references rather than absolute negative controls across assays (HPA tissue IHC: Bone marrow and soft tissue, Not detected). Reassess diffuse precipitate, tissue edges, and endogenous pigment under the counterstain before increasing antibody concentration (standard IHC practice).
What should I score when comparing BTF3L4 IHC sections? ⚠ ANSWER MARKED FOR VERIFICATION
Define the compartment and cell population before scoring: cytoplasmic staining is the tissue IHC reference, while cell based imaging also reports nucleoplasmic localisation (HPA tissue IHC: General cytoplasmic expression; HPA subcellular: Nucleoplasm and cytosol). For a defined population, report percent positive cells and an H-score using the same intensity categories and threshold across slides; report positive cell density per mm² when cell counts are the endpoint (standard IHC quantification practice). Normalise counts to the analysed tissue area or eligible cell number, and exclude folds, necrosis, and section edges consistently (standard IHC quantification practice). Compare similarly processed sections and document counterstain, detection time, and region selection so apparent group differences remain interpretable (standard IHC practice).
When is a BTF3L4 positive IHC pattern convincing?
Look for reproducible staining in intact cells with the expected morphology and distribution, using cytoplasmic tissue staining as the initial reference (HPA tissue IHC: General cytoplasmic expression; standard IHC practice). Cerebral cortex neuronal cells and skeletal muscle myocytes were reported as High, whereas bone marrow hematopoietic cells and soft tissue fibroblasts were Not detected in the reference tissue survey (HPA tissue IHC: named cell populations and levels). Treat exclusively membranous staining cautiously because no transmembrane segment is annotated, while allowing well resolved nuclear staining to be assessed alongside the reported nucleoplasmic location (UniProt Q96K17 topology; HPA subcellular: Nucleoplasm). Check edge effects, necrosis, endogenous peroxidase, and no primary controls before calling a discrepant pattern biological (standard chromogenic IHC practice).
Boster reagents
Best BTF3L4 / Transcription factor BTF3 homolog 4 IHC Antibodies
A15784 is listed for IHC and IF in human and mouse (catalog: applications and reactivity); its IHC image shows paraffin-embedded human brain tissue (A15784 image caption).
Real IHC data
Anti-BTF3L4 Antibody
Cat # A15784
A15784 is the only listed SKU; its IHC image shows paraffin-embedded human brain tissue alongside a peptide-blocked image (A15784 image caption). IF and ICC are listed applications for human and mouse, but no IF image is supplied (catalog: applications, reactivity and image captions).
Which to pick: For tissue IHC, choose A15784: its image documents paraffin-embedded human brain tissue, with an IHC dilution of 1:100–1:300 (A15784 image caption; catalog: IHC dilution). For IF/ICC or human and mouse studies, A15784 is the listed rabbit polyclonal option, with IF at 1:50; IF/ICC use and mouse reactivity come from the application and reactivity listings rather than an IF image (catalog: host, clonality, applications, reactivity and IF dilution). The IHC caption does not report the fixative (A15784 image caption).
Each figure is that product's own IHC / IF validation image from its datasheet.
References
- UniProt Consortium. UniProt entry Q96K17 (BT3L4_HUMAN, Transcription factor BTF3 homolog 4).
- Human Protein Atlas. BTF3L4 tissue IHC expression (reliability: Approved).
- Human Protein Atlas. BTF3L4 subcellular location (ICC-IF): Mainly localized to the nucleoplasm and cytosol..
- Human Protein Atlas. BTF3L4 antibody validation summary (2 antibodies).
- BTF3L4 Overexpression Mediates APAP-induced Liver Injury in Mouse and Cellular Models. Journal of clinical and translational hepatology 2024 — PMC10899873.
- Multi-omics analysis of BTF3L4 as a prognostic and immune biomarker in hepatocellular carcinoma. Translational cancer research 2026 — PMC12971597.
- PubMed PMID:14702039 — UniProt-cited evidence.
- PubMed PMID:16710414 — UniProt-cited evidence.
- PubMed PMID:15489334 — UniProt-cited evidence.
Immunohistochemistry protocol sheet for BTF3L4 (Transcription factor BTF3 homolog 4). Expected localisation Cytoplasmic tissue staining (HPA tissue IHC). Antigen retrieval: Citrate pH 6.0 HIER, 95–98 °C, 20 min (rule: cytoplasmic / membrane antigen). Validated IHC antibody: A15784 at 1:100 - 1:300 (the product's own IHC validation image is shown). Controls (HPA): positive Cerebral cortex (Neuronal cells); negative Bone marrow. IHC-P workflow on paraffin sections; fixative unspecified. Protocol steps: 1. Sample: Paraffin-embedded human brain tissue; fixative not specified (datasheet A15784); 2. Fixation: Image fixative and duration unreported (datasheet A15784); 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-induced epitope retrieval in citrate buffer, pH 6.0 , 20 min at 95–98 °C…; 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-BTF3L4, 1:100 - 1:300 (datasheet A15784); 9. Primary incubation: Overnight at 4 °C (standard). Watch for: Fixation: Keep fixation conditions consistent across sections. (standard IHC practice; not target-specific); Caveat: Staining has medium consistency with RNA data (HPA tissue IHC); Isoform / epitope: 3 isoforms; epitope coverage is unspecified (UniProt); Regulation: Expression regulation unannotated (UniProt). Evidence: UniProt Q96K17, HPA tissue IHC · Approved, HPA ICC-IF · Mainly localized to the nucleoplasm and cytosol., Datasheet A15784, PMC10899873. QR code links to https://www.bosterbio.com/bosterbio-gene-info-cards/BTF3L4/immunohistochemistry-ihc-guide.