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BRAP / BRCA1-associated protein · IHC design guide
Design Immunohistochemistry for BRAP
Plan BRAP staining in paraffin sections with the IHC-validated antibody (datasheet A03573). This guide uses the reported cytoplasmic pattern and high staining in neurons, small-intestinal glandular cells and pachytene spermatocytes to help select tissues and interpret results (HPA tissue IHC).
Evidence assembled Oct 2026 · For research use; verify linked source records and product datasheet before use
BRAP 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 | Broad cytoplasmic staining (HPA tissue IHC) | |
| Staining pattern | Cytoplasmic staining across many tissue cell types (HPA tissue IHC) | |
| Antigen retrieval | Citrate pH 6.0 HIER, heat-mediated (datasheet A03573) | |
| Positive control | Cerebral cortex+4 more · see all | |
| Negative control | Adipose tissue+1 more · see all |
Important caveats
Reasons your staining may differ from the expected pattern.
| Fixation | Keep paraffin-section fixation consistent across specimens. (selected-SKU IHC image A03573) | |
| Caveat | Antibody staining and RNA show low consistency (HPA tissue IHC) | |
| Regulation | Testis-enhanced RNA expression (HPA tissue RNA) | |
| Isoform / epitope | 2 isoforms; epitope coverage is unresolved (UniProt) |
Section 1
Recommended BRAP IHC & IF Protocols
Compare the catalog antibody’s IHC-P protocol (datasheet A03573) with one published BRAP tissue microarray protocol (PMC12717807).
| Sample | Paraffin-embedded human lung cancer tissue; fixative not specified (datasheet A03573) |
| Fixation | Image fixative and duration unreported (datasheet A03573); verify before use. |
| Sectioning | 4–5 µm sections on charged slides (standard) |
| Deparaffinisation | Xylene, graded ethanol series to water (standard) |
| Antigen retrieval | Heat retrieval: Citrate pH 6.0 (datasheet A03573); 20 min, 95–100 °C (standard) |
| 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-BRAP, 1:50-1:100 (datasheet A03573) |
| 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 | BRAP-positive staining in neuronal cells of cerebral cortex (HPA tissue IHC: High). HPA tissue profile: Ubiquitous cytoplasmic expression. No signal in the no-primary control. |
💡Decision noteStart with heat-mediated citrate retrieval at pH 6.0 (datasheet A03573); the published protocol used high-pressure citric acid retrieval (PMC12717807).
Section 2
What Is the Expected BRAP Staining Pattern?
BRAP is a cytoplasmic protein with no transmembrane segment (UniProt Q7Z569 localization and topology). In paraffin sections, expect cytoplasmic staining in neuronal cells of cerebral cortex, glandular cells of small intestine, and pachytene spermatocytes of testis (HPA: High). HPA describes the tissue pattern as ubiquitous cytoplasmic expression, but rates its IHC evidence Approved with low agreement between staining and RNA data and a possible splice or transcript discrepancy (HPA: tissue IHC reliability).
| Cytoplasmic stain is strong in the expected cells of cerebral cortex, small intestine, or testis. | This matches the reported High staining in neuronal cells, intestinal glandular cells, and pachytene spermatocytes (HPA: tissue IHC). Compare cell types within the section; HPA's Approved rating carries a low staining–RNA consistency caution (HPA: reliability). |
| Nuclear staining dominates, with little cytoplasmic signal. | Predominantly nuclear IHC conflicts with BRAP's cytoplasmic location (UniProt Q7Z569) and the HPA tissue profile. Recheck morphology and staining controls before assigning the signal to BRAP. A nuclear membrane location is reported in ICC-IF, which does not establish nuclear staining as the expected IHC pattern (HPA: subcellular ICC-IF). |
| Strong stain appears in adipocytes or ovarian stroma cells. | These cells are reported as Not detected (HPA: adipose tissue; ovary). Consider antibody cross-reactivity or endogenous detection activity, then examine a no-primary control (general IHC practice). A stain in an HPA-negative cell type alone does not identify which cause applies. |
| Color spreads across the section without clear cell boundaries. | Diffuse deposit is difficult to score as cytoplasmic BRAP even where expression is expected (UniProt Q7Z569 localization; HPA: tissue profile). Review the no-primary control, blocking, washes, and detection exposure for nonspecific background (general IHC practice). |
| No cytoplasmic signal appears in an expected positive tissue. | A blank result in HPA High cell populations warrants a technical check before a biological negative call (HPA: cerebral cortex, small intestine, testis). Verify the antibody's IHC-P validation, detection reagents, and an on-slide positive control (general IHC practice). HPA's reliability caveat also limits certainty for a single specimen (HPA: reliability). |
💡Expected BRAP appearanceCall BRAP positive when cytoplasmic signal is clear in the expected neuronal, glandular, or pachytene spermatocyte populations, especially those rated High (UniProt Q7Z569 localization; HPA: tissue IHC); dominant nuclear stain or strong stain in HPA Not detected cells calls for control-based review (HPA: tissue IHC).
| Compartment and topology | BRAP is cytoplasmic and has no transmembrane segment (UniProt Q7Z569). Score cellular cytoplasm rather than treating membrane outlining or dominant nuclear staining as its expected tissue IHC pattern (HPA: tissue profile). |
| Choice of comparison cells | High HPA staining occurs in cerebral cortex neurons, small-intestine glandular cells, and testis pachytene spermatocytes; adipocytes and ovarian stroma cells are Not detected (HPA: tissue IHC). These observations support positive and negative comparison areas, subject to the HPA reliability caveat. |
| Antibody evidence | HPA040357 is Approved for IHC; HPA058820 has no IHC validation status in the supplied record (HPA: antibody validation). Use the IHC-validated antibody when comparing a new paraffin-section pattern with HPA, and do not treat Approved as Enhanced (HPA: antibody validation). |
| Isoforms and evidence limits | UniProt lists two BRAP isoforms (UniProt Q7Z569). HPA flags a possible splice or transcript discrepancy and low staining–RNA consistency (HPA: reliability); neither source identifies an isoform-specific IHC pattern. Target-specific fixation sensitivity is unreported in the supplied evidence. |
| IF/ICC: where should signal appear? | In ICC-IF, BRAP is mainly cytosolic, with an additional nuclear membrane location; the cytosol call is Supported and the nuclear membrane call Approved (HPA: subcellular ICC-IF). This localization is context for interpretation; IF/ICC methods belong to its separate guide. |
| Situation | Likely cause | Next action |
|---|---|---|
| Expected positive cells are blank. | The HPA High reference pattern was not reproduced (HPA: cerebral cortex, small intestine, testis); a failed IHC detection step is possible (general IHC practice). | Check an on-slide positive control, antibody identity and IHC-P validation, detection reagents, and the prescribed retrieval conditions if the antibody's instructions provide them (general IHC practice). Do not infer BRAP-specific retrieval sensitivity from HPA. |
| Nuclear stain is stronger than cytoplasmic stain. | That pattern conflicts with the cytoplasmic tissue expectation (UniProt Q7Z569; HPA: tissue profile). The additional nuclear membrane ICC-IF finding does not explain diffuse nuclear IHC (HPA: subcellular ICC-IF). | Inspect cell boundaries and counterstain, compare a no-primary control, and reassess antibody specificity before scoring nuclear signal as BRAP (general IHC practice). |
| Adipocytes or ovarian stroma cells stain strongly. | Both are Not detected in the HPA tissue observations (HPA: adipose tissue; ovary). Cross-reactivity or endogenous detection activity is possible (general IHC practice). | Run a no-primary control and appropriate endogenous-enzyme block for chromogenic detection; compare staining with the expected positive cell populations (general IHC practice; HPA: tissue IHC). |
| Broad haze obscures cell-level scoring. | Background can arise from nonspecific reagent binding, inadequate washing, or excessive chromogen development (general IHC practice). Haze cannot establish the cytoplasmic localization reported for BRAP (UniProt Q7Z569). | Review no-primary staining, blocking, washes, and chromogen development; adjust the general detection workflow according to the antibody and reagent instructions (general IHC practice). |
| Signal differs between HPA-positive tissues or cell populations. | Reported levels differ: High in selected neurons, glandular cells, and spermatocytes, but Medium in several other listed populations (HPA: tissue IHC). HPA also reports low staining–RNA consistency (HPA: reliability). | Score the named cell types and cytoplasmic compartment separately, document controls, and avoid equating a weaker population with technical failure solely from its tissue name (HPA: tissue IHC; general IHC practice). |
| IHC and ICC-IF images seem to disagree. | The ICC-IF summary includes an additional nuclear membrane location, whereas tissue IHC is described as ubiquitous cytoplasmic expression (HPA: subcellular ICC-IF; tissue IHC). The assays provide different localization observations. | Judge paraffin IHC against its cytoplasmic tissue pattern and IHC-validated antibody evidence (HPA: tissue IHC; antibody validation). Assess ICC-IF localization with its separate guide and controls (general IF practice). |
Experiment evidence
IHC & IF images showing BRAP staining
A03573 · IHCImmunohistochemistry of paraffin-embedded human lung cancer using BRAP Rabbit pAb at dilution of 1:100 .Perform high pressure antigen retrie
A03573 · IHCImmunohistochemistry of paraffin-embedded human liver cancer using BRAP Rabbit pAb at dilution of 1:100 .Perform high pressure antigen retri
HPA · Cerebral cortexHuman Protein Atlas IHC, Cerebral cortex. Source: https://www.proteinatlas.org/ENSG00000089234-BRAP/tissue/cerebral+cortex#imid_11425595
HPA · ColonHuman Protein Atlas IHC, Colon. Source: https://www.proteinatlas.org/ENSG00000089234-BRAP/tissue/colon#imid_11425521
HPA · LiverHuman Protein Atlas IHC, Liver. Source: https://www.proteinatlas.org/ENSG00000089234-BRAP/tissue/liver#imid_11425506
HPA · KidneyHuman Protein Atlas IHC, Kidney. Source: https://www.proteinatlas.org/ENSG00000089234-BRAP/tissue/kidney#imid_11425507
HPA · ICC-IF A-431Human Protein Atlas immunofluorescence, A-431, antibody HPA040357; green = BRAP, blue = nucleus, red = microtubules.
HPA · ICC-IF A-431Human Protein Atlas immunofluorescence, A-431, antibody HPA040357; green = BRAP, blue = nucleus, red = microtubules.
← swipe / scroll for more images →
Real IHC / IF data behind the staining-pattern expectations in this section.
Sample controls for BRAP IHC & IF
🧪Run cerebral cortex first and look for staining in neuronal cells (High; HPA: cerebral cortex, neuronal cells). Use adipose tissue as the negative comparator (Not detected in adipocytes; HPA: adipose tissue); on the positive slide, cells without discernible specific staining provide an internal background reference, but the supplied HPA rows do not identify a particular negative cell type there.
Positive control tissue: Cerebral cortex (Neuronal cells, HPA High)
Negative control tissue: Adipose tissue (HPA Not detected)
ICC-IF cell lines (HPA subcellular resource): HPA ICC-IF images show BRAP in A-431, U-251MG, U2OS, PC-3, with annotated localisation: Cytosol (supported) (HPA subcellular).
Technical controls: Include a no-primary, secondary-only control, host-matched rabbit IgG control for the catalog rabbit polyclonal antibody, and BRAP knockout tissue as a biological negative (A03573 caption: rabbit pAb). Quench endogenous peroxidase for chromogenic IHC and assess tissue autofluorescence with an unstained section if using IF (standard IHC/IF practice).
⚠️Feasibility: The selected A03573 paraffin-section caption specifies high-pressure retrieval in 10 mM citrate buffer at pH 6.0 and a 1:100 antibody dilution, but reports no fixative; retrieval dependence, a target-specific fixation window, and fixation effects are unreported (A03573 caption). Frozen sections have no supplied BRAP protocol, and the HPA ICC-IF images do not establish that IF or frozen sections are easier (HPA: ICC-IF images in A-431, U-251MG, U2OS and PC-3). For IF, check autofluorescence before interpreting cytosolic signal (HPA: mainly cytosolic localisation; standard IF practice).
HPA tissue IHC evidence for BRAP
Comprehensive Human Protein Atlas IHC scoring per tissue (reliability: Approved — Low consistency between antibody staining and RNA expression data. Caution, Splice and/or transcript discrepancy exists. 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 → |
| Small intestine | Glandular cells | High | Protein (IHC) | HPA → |
| Testis | Pachytene spermatocytes | High | Protein (IHC) | HPA → |
| Adrenal gland | Glandular cells | Medium | Protein (IHC) | HPA → |
| Appendix | Glandular cells | Medium | Protein (IHC) | HPA → |
Section 3
Advanced BRAP IHC Tips
BRAP staining is expected mainly in the cytoplasm; assess signal by cell type and compartment, with controls for processing and detection artefacts (UniProt Q7Z569; HPA subcellular).
What retrieval should I try first when BRAP staining is weak in paraffin sections?
Start with heat-mediated retrieval in 10 mM citrate, pH 6.0, as specified for the catalog antibody A03573 (datasheet A03573; A03573 tissue-IHC caption). The caption used high-pressure retrieval and 1:100 antibody dilution in paraffin-embedded human lung cancer, but does not report its fixative (A03573 tissue-IHC caption). If signal remains weak, compare retrieval duration across matched sections while keeping detection and exposure to chromogen constant (standard IHC practice). Include a positive control showing cytoplasmic staining and inspect tissue integrity, since excessive heating can damage morphology and make apparent signal gains difficult to interpret (HPA tissue IHC; standard IHC practice).
How should I troubleshoot BRAP loss after fixation?
BRAP-specific sensitivity to fixation is unknown from the supplied evidence; the A03573 paraffin-section caption does not state a fixative or fixation time (A03573 tissue-IHC caption). Record the actual fixative and duration for each specimen, then compare sections processed with the same retrieval and antibody conditions (standard IHC practice). For future samples, evaluate a controlled fixation-time series, such as 12, 24 and 48 hours, only if those intervals suit the tissue and local workflow (standard IHC practice). Judge each condition against morphology, background and cytoplasmic signal in a control section; tissue staining patterns alone cannot establish a BRAP-specific fixation effect (UniProt Q7Z569; HPA tissue IHC; standard IHC practice).
How do I assess unexpected nuclear BRAP staining in chromogenic IHC?
Score cytoplasmic signal first because BRAP is annotated as cytoplasmic, and HPA reports ubiquitous cytoplasmic tissue staining (UniProt Q7Z569; HPA tissue IHC). HPA imaging places BRAP mainly in the cytosol and additionally at the nuclear membrane, which warrants careful distinction between a rim and diffuse nuclear staining (HPA subcellular). Review matched sections at 20× and 40× and check whether nuclear color follows counterstain, crowded cells or tissue folds (standard IHC practice). If diffuse nuclear staining dominates, repeat with a no-primary control and an independent antibody epitope before assigning it to BRAP (standard IHC practice).
Could isoforms or epitope masking explain discordant BRAP staining?
BRAP has 2 annotated isoforms, but the supplied record does not map the A03573 epitope to either one (UniProt Q7Z569; A03573 tissue-IHC caption). Check the antibody’s documented immunogen against the isoform sequences before treating a negative section as protein absence (standard IHC practice). BRAP has four listed phosphoserines at positions 52, 97, 117 and 119; the supplied evidence does not establish whether they affect this antibody’s binding (UniProt Q7Z569). Compare matched sections after the specified citrate retrieval and, if needed, test an independently mapped epitope while holding scoring rules constant (datasheet A03573; standard IHC practice).
How can IF help check the cell type and compartment behind my IHC signal?
Use IF on a matched specimen to compare BRAP with a marker for the cell type being scored in IHC, choosing a marker whose specificity is established for that specimen (standard IF practice). HPA reports mainly cytosolic BRAP with additional nuclear-membrane localization, so acquire separate channels and assess cytoplasm and nuclear rim rather than assuming complete overlap (HPA subcellular). Choose spectrally separated fluorophores and place the weaker signal in a channel with low tissue autofluorescence; check single-stain and unstained controls (standard IF practice). Because BRAP has no annotated transmembrane segment, use controlled permeabilisation to expose its intracellular epitope, starting with a mild condition such as 0.1% Triton X-100 for 5 minutes and checking morphology (UniProt Q7Z569; standard IF practice).
What should I check when BRAP DAB staining is widespread or granular?
First compare the stained section with no-primary and reagent controls to separate antibody-associated signal from endogenous pigment or enzyme activity (standard IHC practice). Use an appropriate peroxidase block before DAB development and inspect whether brown color persists in the no-primary control (standard chromogenic IHC practice). If antibody-dependent background remains, titrate around the caption’s 1:100 dilution and compare blocking and wash conditions on serial sections (A03573 tissue-IHC caption; standard IHC practice). Evaluate true signal within intact cell cytoplasm, since HPA describes ubiquitous cytoplasmic staining but also flags low agreement between antibody staining and RNA data (HPA tissue IHC).
How should I quantify BRAP IHC across specimens with different cell composition? ⚠ ANSWER MARKED FOR VERIFICATION
Define the compartment and cell population before scoring: BRAP tissue staining is reported as cytoplasmic, and HPA lists differing levels across cell types (HPA tissue IHC). For cell-level comparisons, record the percentage of positive target cells and a cytoplasmic H-score on a 0–300 scale using consistent intensity thresholds (standard IHC scoring practice). If counting positive cells per mm², also count all eligible cells in that area and report the positive fraction so cellularity does not drive the comparison (standard IHC practice). Use matched controls, identical image settings and prespecified regions, excluding folds and necrosis from the denominator (standard IHC practice).
When is an apparent BRAP-positive IHC result more likely to be artefact?
A convincing result shows cellular cytoplasmic staining in an intact, identifiable population, consistent with BRAP localization and HPA’s tissue profile (UniProt Q7Z569; HPA tissue IHC). Be cautious with diffuse nuclear color, staining confined to tissue edges or necrotic areas, and signal that follows endogenous pigment or peroxidase activity in controls (HPA subcellular; standard IHC practice). Cell identity matters: HPA reports high staining in neuronal cells, small-intestinal glandular cells and pachytene spermatocytes, while adipocytes and ovarian stromal cells are listed as undetected (HPA tissue IHC). Treat these patterns as supporting context rather than proof, because HPA marks the antibody staining and RNA agreement as low and notes a possible splice or transcript discrepancy (HPA tissue IHC).
Boster reagents
Best BRAP / BRCA1-associated protein IHC Antibodies
A03573 has IHC images from paraffin-embedded human lung and liver cancers (catalog IHC image captions). It is also listed for IF/ICC in human, mouse and rat (catalog applications/reactivity).
Real IHC data
Anti-BRCA1-associated protein BRAP Antibody
Cat # A03573
A03573 will render with its own human lung cancer IHC figure, stained at 1:100 after high-pressure retrieval in 10 mM citrate, pH 6.0 (catalog IHC image caption). Its second IHC image shows paraffin-embedded human liver cancer; IF/ICC and human, mouse and rat reactivity are listed, but no IF image is supplied (catalog IHC image captions/applications/reactivity/IF image alts).
Which to pick: Choose A03573 for tissue IHC: its own captions document paraffin-embedded human lung and liver cancer sections, with 1:100 staining after high-pressure citrate retrieval; the fixative is unreported (catalog IHC image captions). For IF/ICC, A03573 is listed at 1:50–1:100, though no IF image is supplied (catalog applications/IF dilution/IF image alts). For cross-species studies, A03573 is a rabbit polyclonal listed as reactive with human, mouse and rat; optimize staining for each specimen (catalog host/clone/reactivity; standard IHC practice).
Each figure is that product's own IHC / IF validation image from its datasheet.
References
- UniProt Consortium. UniProt entry Q7Z569 (BRAP_HUMAN, BRCA1-associated protein).
- Human Protein Atlas. BRAP tissue IHC expression (reliability: Approved).
- Human Protein Atlas. BRAP subcellular location (ICC-IF): Mainly localized to the cytosol. In addition localized to the nuclear membrane..
- Human Protein Atlas. BRAP antibody validation summary (2 antibodies).
- BRAP Promotes the Tumorigenesis of Hepatocellular Carcinoma by Corrupting Cancer Cell Cycle Regulation and Enhancing Immune Evasion. Journal of hepatocellular carcinoma 2025 — PMC12717807.
- Bombesin receptor-activated protein homolog deficiency altered the pattern of pathological changes of psoriasis - like skin lesion in mice. International journal of medical sciences 2024 — PMC10758153.
- PubMed PMID:9497340 — UniProt-cited evidence.
- PubMed PMID:14724641 — UniProt-cited evidence.
- PubMed PMID:14702039 — UniProt-cited evidence.
Immunohistochemistry protocol sheet for BRAP (BRCA1-associated protein). Expected localisation Broad cytoplasmic staining (HPA tissue IHC). Antigen retrieval: Citrate pH 6.0 HIER, heat-mediated (datasheet A03573). Validated IHC antibody: A03573 at 1:50-1:100 (the product's own IHC validation image is shown). Controls (HPA): positive Cerebral cortex (Neuronal cells); negative Adipose tissue. IHC workflow; specimen preparation unspecified. Protocol steps: 1. Sample: Paraffin-embedded human lung cancer tissue; fixative not specified (datasheet A03573); 2. Fixation: Image fixative and duration unreported (datasheet A03573); 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 retrieval: Citrate pH 6.0 (datasheet A03573); 20 min, 95–100 °C (standard); 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-BRAP, 1:50-1:100 (datasheet A03573); 9. Primary incubation: Overnight at 4 °C (standard). Watch for: Fixation: Keep paraffin-section fixation consistent across specimens. (selected-SKU IHC image A03573); Caveat: Antibody staining and RNA show low consistency (HPA tissue IHC); Isoform / epitope: 2 isoforms; epitope coverage is unresolved (UniProt); Regulation: Testis-enhanced RNA expression (HPA tissue RNA). Evidence: UniProt Q7Z569, HPA tissue IHC · Approved, HPA ICC-IF · Mainly localized to the cytosol. In addition localized to the…, Datasheet A03573, PMC12717807. QR code links to https://www.bosterbio.com/bosterbio-gene-info-cards/BRAP/immunohistochemistry-ihc-guide.