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- Table of Contents
Plan BCLAF1 chromogenic IHC in paraffin sections using its predominantly nuclear tissue pattern and high staining in bone marrow hematopoietic cells (HPA tissue IHC). This guide covers fixation consistency, antibody selection and interpretation of staining.
Expected localisation, validated protocols, controls and antibodies — the at-a-glance facts below, then the full design guide.
| Expected localisation | Nuclear in tissue; cytoplasmic location also annotated (HPA tissue IHC; UniProt) | |
| Staining pattern | Widespread nuclear staining; high in marrow cells (HPA tissue IHC) | |
| Antigen retrieval | EDTA pH 8.0 HIER, heat-mediated (datasheet A04100-3) | |
| Positive control | Adrenal gland+4 more · see all | |
| Negative control | None in HPA (detected in all 45 tissues); use no-primary + isotype controls |
| Fixation | Keep fixation consistent across paraffin sections (standard IHC practice; not target-specific) | |
| Caveat | Marrow peroxidase may mimic DAB staining (HPA tissue IHC; standard IHC practice) | |
| Regulation | Bone marrow has enhanced RNA expression (HPA tissue RNA) | |
| Isoform / epitope | 4 isoforms; no extracellular domain; epitope coverage unknown (UniProt) |
Compare the catalog antibody’s IHC protocol (datasheet A04100-3) with published methods for osteoarthritic cartilage (PMC11844276), mouse tumors (PMC11496133), and human ESCC (PMC8486183).
| Sample | Paraffin-embedded mouse brain tissue; fixative not specified (datasheet A04100-3) |
| Fixation | Image fixative and duration unreported (datasheet A04100-3); 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 A04100-3); 20 min, 95–100 °C (standard) |
| Peroxidase block | 3% H2O2, 10 min, room temperature (standard) |
| Blocking | 10% goat serum (datasheet A04100-3) |
| Primary antibody | Rabbit anti-BCLAF1, 2-5 μg/ml (datasheet A04100-3) |
| Primary incubation | Overnight at 4 °C (datasheet A04100-3) |
| Detection | HRP-conjugated secondary, DAB chromogen (datasheet A04100-3) |
| Counterstain | Hematoxylin, blue, dehydrate and mount (standard) |
| Expected result | BCLAF1-positive staining in glandular cells of adrenal gland (HPA tissue IHC: High). HPA tissue profile: Ubiquitous nuclear expression. No signal in the no-primary control. |
BCLAF1 should appear predominantly in nuclei across many cell types (HPA: ubiquitous nuclear expression; UniProt Q9NYF8: nucleus and nucleoplasm). High staining is reported in bone marrow hematopoietic cells, bronchial respiratory epithelium, and several glandular cell populations (HPA: tissue IHC). HPA rates the tissue pattern Enhanced because antibody staining is consistent with RNA expression (HPA: reliability description). BCLAF1 has no transmembrane segment (UniProt Q9NYF8: topology).
| Distinct nuclear chromogen in bone marrow hematopoietic cells or bronchial respiratory epithelial cells. | This matches reported high staining in those cells and the broadly nuclear tissue pattern (HPA: tissue IHC). Compare signal with a nuclear counterstain so cytoplasmic pigment is not scored as nuclear staining (general IHC practice). |
| Strong cytoplasmic or membrane staining with little or no nuclear signal. | An exclusively extranuclear IHC pattern conflicts with the reported nuclear tissue pattern (HPA: tissue IHC). Cytoplasmic localization is listed by UniProt, so limited cytoplasmic signal alone is not proof of artefact (UniProt Q9NYF8: subcellular location). Review controls and staining distribution before assigning specificity (general IHC practice). |
| Signal is concentrated in unexpected cells while the expected cells in the same section remain unstained. | For example, absent hematopoietic-cell staining in bone marrow conflicts with its reported high level (HPA: bone marrow). Consider antibody cross-reactivity or endogenous chromogen-generating activity (general IHC practice). BCLAF1 is broadly expressed, so staining in another cell type alone does not establish a false positive (HPA: ubiquitous nuclear expression). |
| Diffuse color covers nuclei, cytoplasm, and extracellular spaces without clear cell boundaries. | This is poor localization rather than a convincing nuclear result (HPA: ubiquitous nuclear expression). Nonspecific antibody binding, inadequate washing, or detection background can produce diffuse chromogen (general IHC practice); assess the negative reagent control before scoring (general IHC practice). |
| No nuclear signal in a known-positive tissue, including bone marrow hematopoietic cells. | A blank result is inconsistent with the reported high staining in that cell population (HPA: bone marrow). Check the assay controls and detection steps before concluding that the specimen lacks BCLAF1 (general IHC practice). HPA tissue data do not identify a BCLAF1-specific fixation sensitivity (HPA: tissue IHC scope). |
| Tissue and cell population (HPA: tissue IHC) | HPA reports ubiquitous nuclear expression and high staining in listed glandular, hematopoietic, respiratory epithelial, and selected neural cell populations. Use the relevant cell population within the section as the comparison, rather than treating every nucleus as equally intense (HPA: tissue IHC). |
| Subcellular resolution (HPA: subcellular ICC-IF; UniProt Q9NYF8: location) | ICC-IF places BCLAF1 in nuclear speckles, while tissue IHC reports a nuclear pattern (HPA: subcellular ICC-IF; HPA: tissue IHC). Chromogenic IHC need not resolve speckles to support a nuclear call (general IHC practice). UniProt also lists nucleoplasm and cytoplasm (UniProt Q9NYF8: location). |
| Antibody validation (HPA: antibodies; HPA: tissue reliability) | HPA lists Enhanced IHC validation for HPA006669 and HPA027770, while HPA006484 has Enhanced ICC validation without an IHC designation (HPA: antibodies). Those ratings support the stated assays; they do not validate every catalog antibody or transfer ICC image detail directly to paraffin IHC (HPA: antibodies). |
| Protein forms and topology (UniProt Q9NYF8: isoforms and processing) | Four isoforms are listed, but the supplied record does not assign separate tissue staining patterns to them (UniProt Q9NYF8: isoforms; HPA: tissue IHC). No signal peptide, propeptide, or transmembrane segment is annotated, so these data give no basis to predict a membrane or secreted staining pattern (UniProt Q9NYF8: topology and processing). |
| Situation | Likely cause | Next action |
|---|---|---|
| A positive-control bone marrow section shows no nuclear stain (HPA: bone marrow). | The expected hematopoietic-cell signal is missing; assay failure is one possibility (HPA: bone marrow; general IHC practice). | Verify that the control section, primary antibody, detection reagents, and chromogen worked, then review the validated IHC procedure used for that antibody (general IHC practice). |
| Only cytoplasm or cell borders stain in a tissue expected to show nuclear BCLAF1 (HPA: tissue IHC). | The compartment disagrees with the reported tissue pattern; nonspecific binding or detection background is possible (HPA: tissue IHC; general IHC practice). | Compare the signal with the nuclear counterstain and a negative reagent control, and reassess antibody and detection conditions (general IHC practice). |
| Staining appears in unexpected cells, but reported high-staining cells are blank (HPA: tissue IHC). | Cross-reactivity or endogenous detection activity may explain the distribution; cell identity alone cannot prove either cause (general IHC practice). | Check cell identity on the section, compare a negative reagent control, and use an independently validated antibody if available (general IHC practice; HPA: antibody validation). |
| Brown color is spread across the section and obscures nuclear boundaries (general IHC practice). | Diffuse nonspecific binding or detection background can prevent localization-based interpretation (general IHC practice). | Inspect negative controls, washing, blocking, and chromogen development; score only cells whose nuclear signal can be distinguished from background (general IHC practice). |
| An IF image shows speckles, but the chromogenic section shows broader nuclear staining (HPA: subcellular ICC-IF; HPA: tissue IHC). | The assays present nuclear localization at different visual resolution (general IHC practice); HPA reports speckles for ICC-IF and a nuclear tissue pattern for IHC (HPA: subcellular ICC-IF; HPA: tissue IHC). | Evaluate this section against the nuclear tissue pattern; use the separate IF/ICC guide when punctate subnuclear localization is the experimental question (HPA: tissue IHC; HPA: subcellular ICC-IF). |
| The investigator attributes weak staining to a BCLAF1-specific fixation effect. | The supplied UniProt and HPA records do not establish target-specific fixation sensitivity (UniProt Q9NYF8: supplied record; HPA: tissue IHC scope). | Check section and assay controls first; record fixation and retrieval conditions as general IHC workflow variables without assigning a BCLAF1-specific cause (general IHC practice). |
Comprehensive Human Protein Atlas IHC scoring per tissue (reliability: Enhanced — High 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 → |
| Appendix | Glandular cells | High | Protein (IHC) | HPA → |
| Bone marrow | Hematopoietic cells | High | Protein (IHC) | HPA → |
| Breast | Glandular cells | High | Protein (IHC) | HPA → |
| Bronchus | Respiratory epithelial cells | High | Protein (IHC) | HPA → |
| Tissue | Cell type | Level | Evidence | Source |
|---|---|---|---|---|
| None in HPA: BCLAF1 is detected in all 45 scored tissues. Use a no-primary (secondary-only) and an isotype control instead. | ||||
Troubleshoot BCLAF1 staining in paraffin sections by checking retrieval, nuclear localisation, assay background and cell-specific scoring.
Anti-BCLAF1 antibodies have IHC images from mouse and rat brain paraffin sections and an IF image from HeLa cells (catalog image captions).
A04100-3 has IHC images from mouse and rat brain paraffin sections and an IF/ICC image from HeLa cells (catalog image captions). A04100-1 has an IHC image from mouse brain tissue and lists IHC-P among its applications (catalog image caption; catalog applications).
Which to pick: For tissue IHC, choose A04100-3 when a documented paraffin-section workflow or images from both mouse and rat brain matter; A04100-1 has a mouse brain IHC image (each SKU’s IHC image caption). For IF/ICC, choose A04100-3 because IF and ICC are listed applications with a HeLa cell image; A04100-1 lists neither application, and neither rendered SKU reports a clone (catalog applications; catalog IF image caption; catalog clone fields). Both list human, mouse and rat reactivity, but A04100-3 has IHC images from two species; the fixative is unreported in both SKUs’ IHC captions (catalog reactivity; each SKU’s IHC image caption).