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- Table of Contents
Plan BCL11B paraffin IHC around nuclear staining in subsets of lymphoid, squamous epithelial and neuronal cells (HPA tissue IHC). Use high-staining non-germinal center cells in appendix or lymph node as positive controls (HPA tissue IHC), and start the IHC-validated antibody at 2–5 μg/ml (datasheet A01485-2).
Expected localisation, validated protocols, controls and antibodies — the at-a-glance facts below, then the full design guide.
| Expected localisation | Nuclear in subsets of tissue cells (HPA tissue IHC) | |
| Staining pattern | Nuclei in subsets of lymphoid, squamous and neuronal cells (HPA tissue IHC) | |
| Antigen retrieval | EDTA pH 8.0 HIER, heat-mediated (datasheet A01485-2) | |
| Positive control | Appendix+4 more · see all | |
| Negative control | Adipose tissue+4 more · see all |
| Fixation | Keep fixation consistent across sections (standard IHC practice; not target-specific) | |
| Caveat | Subset staining may make a tissue appear negative (HPA tissue IHC) | |
| Regulation | Staining varies by tissue and cell type (HPA tissue IHC) | |
| Isoform / epitope | Two isoforms; check antibody epitope coverage (UniProt) |
Alongside the catalog antibody’s IHC-P protocol (datasheet A01485-2), these published protocols cover Ewing sarcoma sections (PMC7139395) and frozen mouse embryonic heads (PMC3358280).
| Sample | Paraffin-embedded human bladder urothelial carcinoma with squamous differentiation tissue; fixative not specified (datasheet A01485-2) |
| Fixation | Image fixative and duration unreported (datasheet A01485-2); 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 A01485-2); 20 min, 95–100 °C (standard) |
| Peroxidase block | 3% H2O2, 10 min, room temperature (standard) |
| Blocking | 10% goat serum (datasheet A01485-2) |
| Primary antibody | Rabbit anti-BCL11B, 2-5 μg/ml (datasheet A01485-2) |
| Primary incubation | Overnight at 4 °C (datasheet A01485-2) |
| Detection | HRP-conjugated secondary, DAB chromogen (datasheet A01485-2) |
| Counterstain | Hematoxylin, blue, dehydrate and mount (standard) |
| Expected result | BCL11B-positive staining in non-germinal center cells of appendix (HPA tissue IHC: High). HPA tissue profile: Nuclear expression in a subset of lymphoid cells, squamous epithelia, neurons and testis. No signal in the no-primary control. |
BCL11B should appear predominantly in nuclei (UniProt Q9C0K0: nucleus; HPA tissue IHC). Expect staining in subsets of lymphoid cells, squamous epithelial cells and neurons, rather than every cell in a section (HPA tissue IHC). BCL11B has no transmembrane segment (UniProt Q9C0K0 topology). HPA rates its tissue IHC profile Enhanced, with medium consistency between staining and RNA data and external verification pending (HPA tissue IHC).
| Distinct nuclear chromogen appears in non-germinal center cells of appendix or lymph node. | This matches an expected strong positive compartment and cell population: HPA reports High staining in these cells in both tissues (HPA tissue IHC). Assess the fraction of stained cells within that population; a subset pattern is expected (HPA tissue IHC). |
| The dominant signal is cytoplasmic or membrane-like while nuclei remain unstained. | That distribution conflicts with the nuclear tissue pattern and UniProt localization (HPA tissue IHC; UniProt Q9C0K0: nucleus). Treat it as a specificity or detection concern until a known-positive section shows convincing nuclear staining; morphology alone cannot identify the source of the signal (general IHC practice). |
| Prominent staining appears in an HPA-reported negative cell population. | For example, HPA reports adipocytes in adipose tissue and hematopoietic cells in bone marrow as Not detected (HPA tissue IHC). Staining there raises concern for cross-reactivity or endogenous detection activity; confirm the stained cell identity and compare control sections before assigning a cause (general IHC practice). |
| Chromogen spreads across nuclei, cytoplasm and tissue spaces without clear cell boundaries. | Diffuse background prevents a reliable nuclear call (general IHC practice). Compare a section processed without primary antibody and inspect whether the signal follows tissue structures; background by itself does not establish BCL11B expression (general IHC practice). |
| No nuclear signal is visible in appendix or lymph node non-germinal center cells. | Those cells are reported High and provide useful positive reference material (HPA tissue IHC). First verify that the expected cell population is present in the section, then review the IHC run and controls; an absent signal in one preparation does not establish biological absence (general IHC practice). |
| Choice of reference population | HPA reports High staining in appendix and lymph node non-germinal center cells, but Medium staining in caudate, cerebral cortex and hippocampal neurons and in cervix, esophagus and oral mucosa squamous epithelial cells (HPA tissue IHC). Compare cells of the same type when judging relative intensity. |
| Antibody evidence | The listed antibody, HPA049117, has Enhanced IHC status (HPA antibodies). The tissue profile still has medium staining-to-RNA consistency and awaits external verification (HPA tissue IHC); interpret an unexpected distribution with controls rather than treating validation status as proof for every section. |
| Isoform coverage | UniProt annotates 2 BCL11B isoforms (UniProt Q9C0K0). The supplied record does not establish which isoform an IHC antibody recognizes, so isoform-specific staining cannot be inferred from a positive or negative section. |
| IF/ICC Q&A: where should signal appear? | HPA places the main IF signal in the nucleoplasm and an additional signal in the nucleoli fibrillar center (HPA subcellular ICC-IF). Use that as a localization cross-check; the tissue IHC profile separately describes nuclear staining in subsets of cells (HPA tissue IHC). |
| Situation | Likely cause | Next action |
|---|---|---|
| Known-positive lymphoid tissue has no convincing nuclear chromogen. | The relevant non-germinal center cells may be absent from the sampled area, or the staining run may have failed (HPA tissue IHC; general IHC practice). | Locate the expected cells on the counterstained section and inspect the run's positive control. Review retrieval, antibody dilution and detection against the validated IHC procedure if the control also fails (general IHC practice). |
| Signal is strongest outside nuclei. | A dominant extranuclear pattern disagrees with the reported localization (HPA tissue IHC; UniProt Q9C0K0: nucleus); the specific cause is unresolved. | Compare with a known-positive nuclear pattern and a no-primary control. Reassess staining conditions only after checking that the apparent signal lies within the intended cells (general IHC practice). |
| Unexpected cell populations stain strongly. | Possible causes include cross-reactivity or endogenous detection activity (general IHC practice); HPA reports some populations as Not detected (HPA tissue IHC). | Identify the stained cells by morphology, compare the matching HPA population, and run a no-primary control. If enzyme detection is used, check the appropriate endogenous-enzyme control (general IHC practice). |
| Diffuse chromogen obscures nuclear boundaries. | Nonspecific background or excess detection signal can make compartment scoring unreliable (general IHC practice). | Compare the no-primary control; review blocking, antibody dilution, wash steps and chromogen development within the IHC workflow before rescoring nuclei (general IHC practice). |
| A no-primary section develops chromogen. | Signal without primary antibody indicates background from the detection workflow or tissue activity, rather than evidence of specific BCL11B binding (general IHC practice). | Check the detection reagents and, where relevant, endogenous-enzyme blocking. Resolve this control signal before interpreting staining in the test section (general IHC practice). |
| A low-signal area is called BCL11B-negative. | Expected intensity depends on the sampled population: HPA reports Medium staining in selected neurons and squamous epithelial cells, Low in some other populations, and Not detected in others (HPA tissue IHC). | Record the cell type and nuclear intensity, then compare that population with its HPA tissue pattern and an appropriate positive reference. Avoid applying one intensity cutoff across unlike tissues (HPA tissue IHC; general IHC practice). |
Comprehensive Human Protein Atlas IHC scoring per tissue (reliability: Enhanced — 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.
| Tissue | Cell type | Level | Evidence | Source |
|---|---|---|---|---|
| Appendix | Non-germinal center cells | High | Protein (IHC) | HPA → |
| Lymph node | Non-germinal center cells | High | Protein (IHC) | HPA → |
| Caudate | Neuronal cells | Medium | Protein (IHC) | HPA → |
| Cerebral cortex | Neuronal cells | Medium | Protein (IHC) | HPA → |
| Cervix | Squamous epithelial cells | Medium | Protein (IHC) | HPA → |
| Tissue | Cell type | Level | Evidence | Source |
|---|---|---|---|---|
| Adipose tissue | Adipocytes | Not detected | Protein (IHC) | HPA → |
| Adrenal gland | Glandular cells | Not detected | Protein (IHC) | HPA → |
| Bone marrow | Hematopoietic cells | Not detected | Protein (IHC) | HPA → |
| Breast | Adipocytes | Not detected | Protein (IHC) | HPA → |
| Bronchus | Respiratory epithelial cells | Not detected | Protein (IHC) | HPA → |
Use nuclear staining, cell type, and matched controls to troubleshoot BCL11B in chromogenic IHC of paraffin sections (UniProt Q9C0K0; HPA tissue IHC).
Two IHC-validated antibodies cover human paraffin sections (A01485-2 image captions) and human, mouse, and rat tissue (M01485-2 image captions); A01485-2 also has U2OS immunofluorescence data (A01485-2 IF caption).
A01485-2 will render with human bladder carcinoma IHC data; its additional captions show human breast cancer, chronic tonsillitis, and lung adenocarcinoma sections, plus U2OS immunofluorescence (A01485-2 image captions). M01485-2 will render with mouse spleen IHC data; its other captions show rat spleen and human tonsil IHC staining (M01485-2 image captions).
Which to pick: Choose A01485-2 for human paraffin-section IHC when its documented EDTA retrieval and 2 μg/ml starting concentration suit the experiment (A01485-2 IHC caption); the fixative is unreported (A01485-2 IHC caption). Choose A01485-2 for ICC/IF because it has a U2OS cell image at 5 μg/ml (A01485-2 IF caption); choose M01485-2 for human, mouse, or rat tissue IHC because it is monoclonal and has IHC images across those species (M01485-2 catalog entry; M01485-2 IHC captions). M01485-2 also lists IF at 1:200–1:1000, but supplies no IF image; its IHC captions do not report fixation or retrieval conditions (M01485-2 catalog entry; M01485-2 IHC captions).