This website uses cookies to ensure you get the best experience on our website.
- Table of Contents
BCL9L / B-cell CLL/lymphoma 9-like protein · IHC design guide
Design Immunohistochemistry for BCL9L
Plan BCL9L paraffin IHC using high-staining squamous epithelium or kidney tubules as candidate controls (HPA tissue IHC). Interpret nuclear and cytoplasmic staining cautiously because antibody staining shows low consistency with RNA expression (HPA tissue IHC).
Evidence assembled Oct 2026 · For research use; verify linked source records and product datasheet before use
BCL9L Immunohistochemistry Experimental Design Guide
Expected localisation, validated protocols, controls and antibodies — the at-a-glance facts below, then the full design guide.
Must know before staining
| Expected localisation | Nuclear and cytoplasmic in several tissues (HPA tissue IHC) | |
| Staining pattern | High squamous epithelial staining; nuclear/cytoplasmic overall (HPA tissue IHC) | |
| Antigen retrieval | Tris-EDTA pH 9.0 HIER, 95–98 °C, 20 min (rule: nuclear antigen) | |
| Positive control | Adrenal gland+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 | Low staining–RNA concordance limits interpretation (HPA tissue IHC) | |
| Regulation | Expression regulators unspecified (UniProt) | |
| Isoform / epitope | 4 isoforms; verify epitope coverage (UniProt) |
Section 1
Recommended BCL9L IHC & IF Protocols
The catalog antibody’s IHC-P protocol is accompanied by published BCL9L IHC methods for osteosarcoma (PMC7575756), bladder cancer (PMC9141496), and pancreatic cancer (PMC5342010).
| Sample | Tissue sections; selected-image fixative not specified (standard IHC workflow) |
| Fixation | Image fixative and duration unreported (datasheet A05905-1); 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 Tris-EDTA buffer, pH 9.0, 20 min at 95–98 °C (standard rule: nuclear 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-BCL9L, 5 μg/mL (datasheet A05905-1) |
| 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 | BCL9L-positive staining in glandular cells of adrenal gland (HPA tissue IHC: High). HPA tissue profile: Nuclear and cytoplasmic expression in several tissues. No signal in the no-primary control. |
💡Decision noteStart with Tris-EDTA pH 9.0 at 95–98 °C for 20 min (page retrieval; PMC9141496). Citrate pH 6.5 is a published alternative (PMC5342010).
Section 2
What Is the Expected BCL9L Staining Pattern?
BCL9L is a nuclear protein with no transmembrane segment (UniProt Q86UU0). In tissue IHC, HPA reports nuclear and cytoplasmic staining in several tissues, including high staining in squamous epithelial cells, skin keratinocytes and kidney tubular cells (HPA tissue IHC). Interpret that pattern cautiously: HPA rates its tissue IHC reliability Uncertain because antibody staining has low consistency with RNA expression (HPA tissue IHC).
| Distinct nuclear staining in squamous epithelial cells or skin keratinocytes, with some cytoplasmic staining (HPA tissue IHC). | This fits the reported tissue pattern: these cell groups score High, and HPA describes both nuclear and cytoplasmic expression (HPA tissue IHC). Score nuclei and cytoplasm separately; the tissue IHC reliability remains Uncertain (HPA tissue IHC). |
| Membrane-only, extracellular or predominantly granular staining without a discernible nuclear component. | That pattern conflicts with the nuclear location and absence of a transmembrane segment (UniProt Q86UU0). Treat it as suspect, check morphology and detection controls, and seek independent confirmation before assigning it to BCL9L; the tissue IHC assessment is Uncertain (HPA tissue IHC). |
| Strong staining in adipocytes or bone-marrow hematopoietic cells, where HPA reports Not detected (HPA tissue IHC). | The cell identity conflicts with those HPA observations and warrants checks for cross-reactivity or endogenous chromogen-generating activity. It is not proof of either cause: HPA reports low consistency between antibody staining and RNA expression (HPA tissue IHC). |
| Broad chromogen haze across nuclei, cytoplasm and tissue-free areas, obscuring cell boundaries. | A field-wide deposit cannot be scored as cell-specific BCL9L. In a general chromogenic IHC workflow, inspect the no-primary control, background blocking, washes and detection chemistry; compare only interpretable cells with the reported nuclear and cytoplasmic pattern (HPA tissue IHC). |
| No discernible staining in adrenal glandular cells or kidney tubular cells, both scored High by HPA (HPA tissue IHC). | A failed run or limited assay sensitivity is possible. First verify tissue identity and the detection system with controls, then review the antibody's validated IHC-P conditions. HPA's Uncertain reliability means one negative section does not settle BCL9L expression (HPA tissue IHC). |
💡Expected BCL9L appearanceCall a result consistent with the reported pattern when identifiable squamous epithelial cells, keratinocytes or kidney tubular cells show clear nuclear staining, with possible cytoplasmic staining and locally high intensity (HPA tissue IHC); compartment-free haze or staining confined to membranes is suspect given the nuclear location and lack of a transmembrane segment (UniProt Q86UU0).
| Tissue and cell selection | HPA scores squamous epithelial cells in cervix, esophagus, oral mucosa, tonsil and vagina High, as well as skin keratinocytes and kidney tubular cells (HPA tissue IHC). Select and score the named cell population, because a tissue-wide average can hide a cell-specific result. |
| Interpretive confidence | HPA rates tissue IHC Uncertain due to low consistency between antibody staining and RNA expression; HPA049370 is IHC Uncertain (HPA tissue IHC; HPA antibody validation). Use the pattern as a comparison, and require corroboration for a consequential localization claim. |
| Isoforms and processing | UniProt lists four BCL9L isoforms and a full-length chain, with no signal peptide or propeptide (UniProt Q86UU0). The supplied record gives no antibody epitope, so it cannot establish which isoforms an IHC signal represents. |
| IF/ICC Q: what location should an image show? | A: HPA reports mainly nucleoplasmic signal, with additional nucleoli fibrillar-center localization; its listed ICC assessments are Supported (HPA subcellular; HPA antibody validation). That supports an IF/ICC localization comparison, while the separate tissue IHC assessment remains Uncertain (HPA tissue IHC). |
| Situation | Likely cause | Next action |
|---|---|---|
| A High-scoring HPA cell population is blank (HPA tissue IHC). | The run may lack sensitivity, or the sampled section may not contain the intended cells; tissue IHC reliability is Uncertain (HPA tissue IHC). | Confirm morphology, include a positive control and check chromogenic detection. As general IHC practice, review the IHC-P antibody instructions and retrieval conditions before changing them. |
| Signal is cytoplasmic only, with no clear nuclear staining. | Cytoplasmic staining is reported, but a purely cytoplasmic result does not show the nuclear location reported for BCL9L (HPA tissue IHC; UniProt Q86UU0). | Check nuclear counterstaining and focus through the section; score compartments separately. If the pattern persists, seek independent antibody or orthogonal evidence because HPA tissue IHC is Uncertain (HPA tissue IHC). |
| Cells scored Not detected by HPA stain strongly (HPA tissue IHC). | Cross-reactivity or endogenous detection activity is possible; an HPA Not detected call is an observation, not an absolute absence claim (HPA tissue IHC). | Identify the stained cells, run a no-primary detection control and review blocking. Compare the same cell type across sections before interpreting the result. |
| Diffuse brown background prevents cell-level scoring. | General chromogenic IHC causes include nonspecific antibody binding, residual detection activity or inadequate washing. | Inspect a no-primary control, refresh blocking and wash steps, and optimize antibody concentration within the antibody's validated IHC-P guidance. Score only signal with identifiable cellular boundaries. |
| Staining is concentrated at tissue edges or varies across one section. | Uneven reagent coverage or local processing variation can produce this general IHC artifact; the supplied sources establish no BCL9L-specific fixation effect. | Repeat with even reagent coverage and matched processing, then compare intact regions containing the same cell population. Do not infer a BCL9L-specific fixation mechanism from this pattern. |
| IHC and ICC/IF appear to disagree. | HPA supports nucleoplasmic ICC localization, while its tissue IHC assessment is Uncertain (HPA subcellular; HPA tissue IHC). The assays also show different preparations. | Compare the nuclear compartment and cell identity in each assay, verify each assay's controls, and report the disagreement without treating Supported ICC validation as tissue IHC validation (HPA antibody validation). |
Experiment evidence
IHC & IF images showing BCL9L staining
A05905-1 · IHCImmunohistochemistry of Bcl9L in human breast tissue with Bcl9L antibody at 5 μg/ml.
A05905-1 · IFImmunocytochemistry of Bcl9L in HeLa cells with Bcl9L antibody at 10 μg/mL.
HPA · Cerebral cortexHuman Protein Atlas IHC, Cerebral cortex. Source: https://www.proteinatlas.org/ENSG00000186174-BCL9L/tissue/cerebral+cortex#imid_13838269
HPA · ColonHuman Protein Atlas IHC, Colon. Source: https://www.proteinatlas.org/ENSG00000186174-BCL9L/tissue/colon#imid_13838195
HPA · LiverHuman Protein Atlas IHC, Liver. Source: https://www.proteinatlas.org/ENSG00000186174-BCL9L/tissue/liver#imid_13838196
HPA · KidneyHuman Protein Atlas IHC, Kidney. Source: https://www.proteinatlas.org/ENSG00000186174-BCL9L/tissue/kidney#imid_13838189
HPA · ICC-IF CACO-2Human Protein Atlas immunofluorescence, CACO-2, antibody HPA049370; green = BCL9L, blue = nucleus, red = microtubules.
HPA · ICC-IF CACO-2Human Protein Atlas immunofluorescence, CACO-2, antibody HPA049370; green = BCL9L, blue = nucleus, red = microtubules.
← swipe / scroll for more images →
Real IHC / IF data behind the staining-pattern expectations in this section.
Sample controls for BCL9L IHC & IF
🧪Run adrenal gland first: its glandular cells should stain (HPA: High in adrenal gland glandular cells). Use adipose tissue as the negative tissue because adipocytes are listed as not detected (HPA: Not detected in adipocytes); on the adrenal slide, cells without specific nuclear staining should remain at background (UniProt Q86UU0: Nucleus; standard IHC practice).
Positive control tissue: Adrenal gland (Glandular cells, HPA High)
Negative control tissue: Adipose tissue (HPA Not detected)
ICC-IF cell lines (HPA subcellular resource): HPA ICC-IF images show BCL9L in CACO-2, MCF-7, U2OS, NIH 3T3, with annotated localisation: Nucleoplasm (supported) (HPA subcellular).
Technical controls: Include a no-primary (secondary-only) control, an isotype control matched to the primary antibody’s host species and clonality, and a BCL9L knockout or validated peptide-block control (standard IHC practice). For chromogenic staining, quench endogenous peroxidase and check the adrenal section for residual background before scoring (standard IHC practice).
⚠️Feasibility: A target-specific fixation window and retrieval dependency are unreported in the supplied evidence; the selected A05905-1 breast-tissue IHC caption also leaves the fixative unreported (caption: 5 μg/ml; fixative not stated). The supplied evidence does not establish whether frozen sections or IF would be easier, or identify an adrenal-specific artefact (supplied evidence). Assess nuclear staining in IHC and, if evaluating IF separately, compare it with the supported nucleoplasmic location (UniProt Q86UU0: Nucleus; HPA subcellular: Nucleoplasm supported).
HPA tissue IHC evidence for BCL9L
Comprehensive Human Protein Atlas IHC scoring per tissue (reliability: Uncertain — Low consistency between antibody staining and RNA expression data.). Rows are taken directly from the HPA tissue chart — click any row's HPA link to view the source.
Positive expression · recommended positive controls
| Tissue | Cell type | Level | Evidence | Source |
|---|---|---|---|---|
| Adrenal gland | Glandular cells | High | Protein (IHC) | HPA → |
| Cervix | Squamous epithelial cells | High | Protein (IHC) | HPA → |
| Esophagus | Squamous epithelial cells | High | Protein (IHC) | HPA → |
| Kidney | Cells in tubules | High | Protein (IHC) | HPA → |
| Oral mucosa | Squamous epithelial cells | High | Protein (IHC) | HPA → |
Undetected expression · recommended negative controls
| Tissue | Cell type | Level | Evidence | Source |
|---|---|---|---|---|
| Adipose tissue | Adipocytes | Not detected | Protein (IHC) | HPA → |
| Appendix | Glandular cells | Not detected | Protein (IHC) | HPA → |
| Bone marrow | Hematopoietic cells | Not detected | Protein (IHC) | HPA → |
| Caudate | Glial cells | Not detected | Protein (IHC) | HPA → |
| Cerebral cortex | Endothelial cells | Not detected | Protein (IHC) | HPA → |
Section 3
Advanced BCL9L IHC Tips
Use compartment-aware controls and matched tissue processing to troubleshoot BCL9L staining in chromogenic paraffin-section IHC.
How should I troubleshoot weak BCL9L staining after antigen retrieval?
Start with Tris-EDTA at pH 9.0, heated to 95–98 °C for 20 minutes (page retrieval rule: nuclear antigen). Run the same tissue with and without primary antibody, then compare nuclear staining before increasing antibody concentration; the selected breast-tissue image used 5 µg/ml (selected SKU A05905-1 caption; standard IHC practice). If staining remains weak, test a milder retrieval condition on matched sections and watch for lost morphology or diffuse background (standard IHC practice). Score nuclei separately from cytoplasm because BCL9L is nuclear by UniProt, while HPA tissue IHC reports both compartments with uncertain reliability (UniProt Q86UU0 subcellular location; HPA tissue IHC: Uncertain).
Could fixation explain weak or uneven BCL9L staining?
Target-specific sensitivity to fixation is unknown: the selected breast-tissue caption gives 5 µg/ml antibody but does not state a fixative (selected SKU A05905-1 caption). Compare sections from documented, similarly processed blocks before attributing differences to BCL9L expression; fixation and processing can change epitope accessibility in paraffin IHC (standard IHC practice). Inspect nuclear detail and tissue edges, and repeat staining on a matched section with consistent retrieval at pH 9.0 for 20 minutes (page retrieval rule: nuclear antigen; standard IHC practice). Do not infer fixation tolerance from BCL9L phosphorylation or its lack of a transmembrane segment (UniProt Q86UU0 modified residues and topology).
What should I make of predominantly cytoplasmic BCL9L staining?
Evaluate nuclear and cytoplasmic signal separately: UniProt places BCL9L in the nucleus, and HPA IF supports a mainly nucleoplasmic location with an additional nucleolar fibrillar-center location (UniProt Q86UU0 subcellular location; HPA subcellular). HPA tissue IHC also reports nuclear and cytoplasmic expression, but rates its tissue-staining reliability uncertain because antibody staining and RNA expression have low consistency (HPA tissue IHC: Uncertain). Check whether cytoplasmic color persists on a section without primary antibody, then review peroxidase blocking and counterstain contrast (standard chromogenic IHC practice). Compare matched sections under identical exposure to retrieval at pH 9.0 for 20 minutes before interpreting a compartment shift (page retrieval rule: nuclear antigen; standard IHC practice).
Could isoforms or epitope masking change the BCL9L pattern?
BCL9L has 4 annotated isoforms, but the supplied caption does not map the selected antibody’s epitope to any of them (UniProt Q86UU0 isoforms; selected SKU A05905-1 caption). Treat discordant staining as unresolved until the antibody’s immunogen or epitope and isoform coverage are documented; staining alone cannot identify an isoform (standard IHC interpretation). BCL9L has annotated phosphorylation and acetylation sites, so preserve consistent retrieval and processing when comparing sections, without claiming that a particular modification blocks this antibody (UniProt Q86UU0 modified residues; standard IHC practice). Pair the pH 9.0, 20-minute retrieval condition with a no-primary control and morphology review before changing the staining interpretation (page retrieval rule: nuclear antigen; standard IHC practice).
How can IF help resolve a BCL9L IHC localisation question?
On a separate IF/ICC workflow, multiplex BCL9L with a squamous epithelial marker such as cytokeratin when investigating the HPA-reported squamous epithelial staining pattern (HPA tissue IHC: High in squamous epithelial cells; standard IF practice). Choose a spectrally separated, preferably far-red fluorophore after checking tissue autofluorescence with an unstained control (standard IF practice). BCL9L lacks a transmembrane segment and is mainly nucleoplasmic, so use controlled permeabilisation to give antibody access to the intracellular nuclear compartment, while checking that nuclear morphology remains intact (UniProt Q86UU0 topology; HPA subcellular; standard IF practice). Compare signal with a no-primary control and keep IF/ICC localisation evidence distinct from the selected antibody’s breast-tissue IHC image at 5 µg/ml (standard IF practice; selected SKU A05905-1 caption).
How do I reduce diffuse brown background without losing nuclear signal?
First inspect a no-primary section and a matched section stained with the selected antibody at its captioned 5 µg/ml concentration (selected SKU A05905-1 caption; standard chromogenic IHC practice). Apply the usual peroxidase block before DAB detection, then compare blocking, wash stringency and antibody concentration on adjacent sections (standard chromogenic IHC practice). If color collects at section edges, folds or damaged areas, exclude those regions from interpretation and check drying and reagent coverage during staining (standard IHC practice). Retain separate nuclear and cytoplasmic observations because HPA tissue IHC describes both, while its BCL9L staining reliability is uncertain (HPA tissue IHC: nuclear and cytoplasmic expression; HPA tissue IHC: Uncertain).
How should I quantify BCL9L across differently processed sections? ⚠ ANSWER MARKED FOR VERIFICATION
Define the analysis compartment before scoring: use nuclear percent-positive cells or a nuclear H-score when testing the UniProt and HPA IF localisation expectation (UniProt Q86UU0 subcellular location; HPA subcellular; standard IHC scoring practice). Record cytoplasmic staining separately rather than merging it into a nuclear score, since HPA tissue IHC reports both compartments with uncertain reliability (HPA tissue IHC: Uncertain). Normalise positive counts to the number of evaluable cells of the same cell type, or report positive-cell density per mm² of viable annotated tissue (standard IHC scoring practice). Keep retrieval at pH 9.0 for 20 minutes, detection settings and thresholds consistent across compared sections (page retrieval rule: nuclear antigen; standard IHC practice).
When is a BCL9L-positive IHC result convincing?
A convincing result has reproducible staining in intact, identifiable cells, with a nuclear component consistent with UniProt and supported HPA IF localisation (UniProt Q86UU0 subcellular location; HPA subcellular; standard IHC interpretation). Compare the stained cell type with the tissue context: HPA reports high staining in kidney tubular cells and several squamous epithelia, but labels overall tissue IHC reliability uncertain (HPA tissue IHC: High in kidney tubular and squamous epithelial cells; HPA tissue IHC: Uncertain). Treat isolated edge staining, necrotic regions or color surviving a no-primary control as possible artefact, including endogenous enzyme activity in chromogenic detection (standard IHC practice). Require matched processing and repeatable compartment-specific signal before calling a biological difference; the selected breast-tissue caption specifies 5 µg/ml antibody but no fixative (standard IHC practice; selected SKU A05905-1 caption).
Boster reagents
Best BCL9L / B-cell CLL/lymphoma 9-like protein IHC Antibodies
Two anti-BCL9L antibodies have IHC images from human tissues; the catalog also shows rat kidney IHC and human cell IF/ICC images (catalog image captions).
Real IHC data
Anti-Bcl9L Antibody
Cat # A05905-1
A05905-1 is the rendered card, with human breast tissue IHC, human breast tissue IF, and HeLa cell ICC images (A05905-1 image captions). A05905 has IHC images from human lung, ovarian and oesophageal cancer tissues and rat kidney, plus IF/ICC images from A431 cells (A05905 image captions).
Which to pick: For human tissue IHC, A05905-1 has a paraffin-section application listing and a breast tissue image at 5 μg/mL (A05905-1 application list and IHC caption); its image caption does not report the fixative (A05905-1 IHC caption). For IF/ICC, A05905-1 lists both applications and shows human breast tissue IF and HeLa cell ICC (A05905-1 application list and image captions). For cross-species work, A05905 lists human, mouse and rat reactivity, with paraffin-section IHC images from human tissues and rat kidney; mouse IHC is not shown, and the captions do not report the fixative (A05905 reactivity and IHC captions).
Each figure is that product's own IHC / IF validation image from its datasheet.
References
- UniProt Consortium. UniProt entry Q86UU0 (BCL9L_HUMAN, B-cell CLL/lymphoma 9-like protein).
- Human Protein Atlas. BCL9L tissue IHC expression (reliability: Uncertain).
- Human Protein Atlas. BCL9L subcellular location (ICC-IF): Mainly localized to the nucleoplasm. In addition localized to the nucleoli fibrillar center..
- Human Protein Atlas. BCL9L antibody validation summary (2 antibodies).
- miR-766-3p Targeting BCL9L Suppressed Tumorigenesis, Epithelial-Mesenchymal Transition, and Metastasis Through the β-Catenin Signaling Pathway in Osteosarcoma Cells. Frontiers in cell and developmental biology 2020 — PMC7575756.
- Wnt/β-Catenin Signalling and Its Cofactor BCL9L Have an Oncogenic Effect in Bladder Cancer Cells. International journal of molecular sciences 2022 — PMC9141496.
- Role of BCL9L in transforming growth factor-β (TGF-β)-induced epithelial-to-mesenchymal-transition (EMT) and metastasis of pancreatic cancer. Oncotarget 2016 — PMC5342010.
- Cell softness regulates tumorigenicity and stemness of cancer cells. The EMBO journal 2021 — PMC7809788.
- PubMed PMID:15371335 — UniProt-cited evidence.
- PubMed PMID:15489334 — UniProt-cited evidence.
- PubMed PMID:14702039 — UniProt-cited evidence.
Immunohistochemistry protocol sheet for BCL9L (B-cell CLL/lymphoma 9-like protein). Expected localisation Nuclear and cytoplasmic in several tissues (HPA tissue IHC). Antigen retrieval: Tris-EDTA pH 9.0 HIER, 95–98 °C, 20 min (rule: nuclear antigen). Validated IHC antibody: A05905-1 at 5 μg/mL (the product's own IHC validation image is shown). Controls (HPA): positive Adrenal gland (Glandular cells); negative Adipose tissue. IHC workflow; specimen preparation unspecified. Protocol steps: 1. Sample: Tissue sections; selected-image fixative not specified (standard IHC workflow); 2. Fixation: Image fixative and duration unreported (datasheet A05905-1); 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 Tris-EDTA buffer, pH 9.0 , 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-BCL9L, 5 μg/mL (datasheet A05905-1); 9. Primary incubation: Overnight at 4 °C (standard). Watch for: Fixation: Keep fixation consistent across sections (standard IHC practice; not target-specific); Caveat: Low staining–RNA concordance limits interpretation (HPA tissue IHC); Isoform / epitope: 4 isoforms ; verify epitope coverage (UniProt); Regulation: Expression regulators unspecified (UniProt). Evidence: UniProt Q86UU0, HPA tissue IHC · Uncertain, HPA ICC-IF · Mainly localized to the nucleoplasm. In addition localized to the…, Datasheet A05905-1, PMC7575756, PMC9141496. QR code links to https://www.bosterbio.com/bosterbio-gene-info-cards/BCL9L/immunohistochemistry-ihc-guide.