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- Table of Contents
Plan BCL9L paraffin-section IHC around its nuclear location (UniProt) and the nuclear and cytoplasmic tissue profile (HPA tissue IHC). This guide covers fixation consistency, staining interpretation, and the uncertain agreement between tissue staining and RNA expression (HPA tissue IHC).
Expected localisation, validated protocols, controls and antibodies — the at-a-glance facts below, then the full design guide.
| Expected localisation | Nuclear and cytoplasmic tissue staining (HPA tissue IHC); nuclear location (UniProt) | |
| Staining pattern | High squamous epithelial staining; nuclear/cytoplasmic profile (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 |
| Fixation | Keep fixation consistent across paraffin sections. (standard IHC practice; not target-specific) | |
| Caveat | Low consistency between staining and RNA expression (HPA tissue IHC) | |
| Regulation | No expression regulator specified (UniProt) | |
| Isoform / epitope | 4 isoforms; antibody epitope coverage is unreported (UniProt; datasheets) |
The catalog antibody’s IHC-P protocol is accompanied by three published BCL9L IHC methods (PMC7575756; PMC9141496; 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. |
BCL9L is a nuclear transcriptional regulator with no transmembrane segment (UniProt Q86UU0). In paraffin-section IHC, look for staining in adrenal glandular cells, kidney tubule cells, and squamous epithelium, where HPA reports high staining (HPA: tissue IHC). HPA also reports nuclear and cytoplasmic staining across several tissues, but rates its tissue IHC profile uncertain because antibody staining and RNA expression have low consistency (HPA: tissue IHC).
| Nuclear staining in adrenal glandular cells or kidney tubule cells, with identifiable tissue architecture. | This fits BCL9L's nuclear location (UniProt Q86UU0; HPA: nucleoplasm supported) and the cell populations scored high by tissue IHC (HPA: adrenal gland and kidney). Cytoplasmic staining can accompany it because HPA reports both compartments in tissue; record each compartment separately (HPA: tissue IHC, uncertain). |
| Strong membrane-edge or extracellular staining dominates, with little staining in cell interiors. | A membrane-dominant pattern lacks support from the nuclear annotation and absence of a transmembrane segment (UniProt Q86UU0). Compare it with a no-primary control and review tissue edges and detection conditions for artefact (general IHC practice). Cytoplasmic staining alone is less decisive because HPA reports cytoplasmic tissue staining (HPA: tissue IHC, uncertain). |
| Adipocytes or bone-marrow hematopoietic cells stain as strongly as the expected positive cells. | HPA scores those cell populations not detected, making the result a specificity warning rather than proof of BCL9L in them (HPA: tissue IHC, uncertain). Check for antibody cross-reactivity and signal from the detection system with matched controls (general IHC practice); the HPA comparison is provisional because its IHC reliability is uncertain (HPA: tissue IHC). |
| Brown signal coats broad areas of a chromogenic section without clear nuclear or cellular boundaries. | Diffuse background cannot establish which cells express BCL9L or whether signal is nuclear (general IHC practice). Inspect a no-primary control, blocking, washes, and the detection reagent before assigning a positive score (general IHC practice); assess any remaining cell-specific signal against HPA's reported nuclear and cytoplasmic profile (HPA: tissue IHC, uncertain). |
| An adrenal glandular-cell or kidney tubule-cell section has no interpretable staining. | These are useful positive comparators because HPA reports high staining in those specific cells (HPA: tissue IHC, uncertain). A blank result calls for checks of tissue preservation, retrieval conditions, antibody use, and chromogenic detection (general IHC practice); it does not by itself show that BCL9L is absent, particularly given the uncertain HPA IHC profile (HPA: tissue IHC). |
| Tissue comparison and confidence (HPA: tissue IHC) | HPA calls its IHC profile uncertain because staining and RNA expression have low consistency, despite high staining in several epithelial and glandular populations (HPA: tissue IHC). Use the named cell populations as comparators and avoid treating one tissue score as a definitive sensitivity or specificity standard. |
| Compartment and topology (UniProt Q86UU0; HPA: subcellular) | UniProt places BCL9L in the nucleus and lists no transmembrane segment (UniProt Q86UU0). HPA's supported ICC-IF location is mainly nucleoplasmic, with an additional nucleolar fibrillar-center signal (HPA: subcellular). Tissue IHC may also show cytoplasmic staining, so compartment calls should preserve that source-specific difference (HPA: tissue IHC, uncertain). |
| Isoforms and modifications (UniProt Q86UU0) | UniProt lists 4 isoforms and multiple modified residues (UniProt Q86UU0). The supplied record gives no antibody epitope or isoform-specific IHC validation, so it cannot predict which isoform contributes to a stained section or whether a modification alters staining. Report the observed pattern without assigning it to an isoform. |
| IF/ICC Q&A: where should BCL9L appear? (HPA: subcellular) | Mainly in the nucleoplasm, with additional signal in the nucleoli fibrillar center (HPA: ICC-IF supported). That supported ICC-IF observation helps interpret localization, while HPA's tissue IHC profile remains uncertain and includes cytoplasmic staining (HPA: tissue IHC). |
| Situation | Likely cause | Next action |
|---|---|---|
| No signal in the selected positive comparator. | The comparator may lack interpretable cells, or the IHC workflow may have failed; HPA reports high staining specifically in adrenal glandular cells and kidney tubule cells (HPA: tissue IHC, uncertain). | Verify the intended cell population on the section, then check retrieval, antibody application, detection, and counterstain against a working control (general IHC practice). Keep the HPA reliability rating in the interpretation (HPA: tissue IHC, uncertain). |
| Only a sharply membranous pattern is visible. | That distribution conflicts with the nuclear annotation and no-transmembrane topology (UniProt Q86UU0); tissue IHC instead reports nuclear and cytoplasmic staining (HPA: tissue IHC, uncertain). | Inspect a no-primary control and section edges, then reassess whether staining follows cells or a tissue artefact (general IHC practice). Do not score membrane-only signal as the expected BCL9L pattern. |
| Cytoplasmic signal appears without obvious nuclear staining. | HPA reports cytoplasmic tissue staining, so cytoplasm alone is not automatically artefactual, although UniProt and supported ICC-IF favor nuclear localization (HPA: tissue IHC, uncertain; UniProt Q86UU0; HPA: subcellular). | Score nuclear and cytoplasmic compartments separately, inspect cell boundaries and counterstain, and compare the same run with a named positive tissue and a no-primary control (general IHC practice). |
| A nominally negative population is strongly stained. | HPA scores adipocytes and bone-marrow hematopoietic cells not detected; a strong signal there raises a specificity or detection-background concern, subject to HPA's uncertain IHC reliability (HPA: tissue IHC). | Compare positive and negative populations under the same detection conditions and review the no-primary control (general IHC practice). Investigate antibody cross-reactivity if the signal persists after detection background is excluded (general IHC practice). |
| Diffuse chromogen obscures nuclei and tissue boundaries. | Broad background prevents a compartment or cell-type call (general IHC practice). If an enzyme-based detection system is used, endogenous tissue activity can also contribute to signal (general IHC practice). | Review blocking, washes, detection reagents, and the no-primary control; check the system's endogenous-activity control where applicable (general IHC practice). Rescore only signal whose cellular location can be resolved. |
| Staining varies across tissues or from the HPA examples. | HPA reports low tissue RNA specificity and rates tissue IHC uncertain because staining and RNA expression show low consistency (HPA: tissue IHC). Tissue-level comparisons alone therefore cannot establish a technical failure. | Record the exact stained cell type, compartment, and intensity; compare matched controls and repeat the relevant tissue comparison if needed (general IHC practice). Describe any discrepancy as unresolved rather than assigning BCL9L expression from staining alone (HPA: tissue IHC, uncertain). |
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.
| 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 → |
| 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 → |
Troubleshoot BCL9L chromogenic IHC by checking retrieval, nuclear localisation, tissue context and controls before interpreting staining intensity.
Anti-BCL9L IHC images cover human breast and cancer tissues and rat kidney; IF/ICC images cover human breast tissue, HeLa and A431 cells (catalog image captions).
The rendered card is A05905-1, which lists human IHC-P and shows staining in human breast tissue (A05905-1 applications, reactivity and IHC image caption). It also lists IF and ICC, with images from human breast tissue and HeLa cells (A05905-1 applications and IF image captions).
Which to pick: For human tissue IHC, A05905 has captioned paraffin-section images from lung, ovarian and oesophageal cancers, while A05905-1 lists IHC-P and shows breast tissue staining without reporting how that tissue was processed (A05905 and A05905-1 applications and IHC image captions). For IF/ICC, choose A05905-1: both applications are listed and both have images; clonality is unreported for both SKUs (A05905-1 applications and IF image captions; catalog clone fields). For cross-species IHC, choose A05905: its listed reactivity includes human, mouse and rat, with paraffin-section images from human tissues and rat kidney; no mouse IHC image is supplied, and the IHC captions do not report fixative (A05905 reactivity and IHC image captions).