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BRAP / BRCA1-associated protein · IHC design guide
Design Immunohistochemistry for BRAP
Plan BRAP staining in paraffin sections with the catalog antibody at 1:50–1:100 (datasheet A03573). Assess the cytoplasmic pattern against tissue examples, accounting for the reported staining and RNA discrepancy (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 | Cytoplasmic tissue staining (HPA tissue IHC) | |
| Staining pattern | Widespread cytoplasmic staining across 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 fixation consistent across sections (standard IHC practice; not target-specific) | |
| Caveat | Staining and RNA show low consistency; verify specificity (HPA tissue IHC) | |
| Regulation | No expression regulator specified (UniProt) | |
| Isoform / epitope | 2 isoforms; epitope coverage is unspecified (UniProt) |
Section 1
Recommended BRAP IHC & IF Protocols
The catalog antibody’s IHC-P protocol uses citrate pH 6.0 retrieval (datasheet A03573). One published BRAP IHC protocol for paraffin-embedded tissue microarrays is listed below (PMC12717807 methods).
| 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 pH 6.0 retrieval (datasheet A03573); the published protocol also uses citric acid retrieval under high pressure (PMC12717807 methods).
Section 2
What Is the Expected BRAP Staining Pattern?
BRAP should appear chiefly in the cytoplasm of stained cells (UniProt Q7Z569: Cytoplasm; HPA ICC-IF: cytosol supported). In paraffin-section IHC, HPA reports high staining in cerebral-cortex neurons, small-intestinal glandular cells and testicular pachytene spermatocytes (HPA tissue IHC). BRAP has no transmembrane segment (UniProt Q7Z569 topology). Treat these as reference patterns: HPA rates tissue IHC Approved but reports low agreement with RNA expression and pending external verification (HPA tissue IHC).
| Cytoplasmic stain in cerebral-cortex neurons, small-intestinal glands or pachytene spermatocytes; nearby cells vary in intensity. | This fits the reported high-staining cell populations (HPA tissue IHC: High). Score the named cell type and compartment separately; HPA describes broad cytoplasmic expression, but its tissue IHC has low agreement with RNA expression (HPA tissue IHC: Approved, pending external verification). |
| Predominantly nuclear or sharply membrane-confined chromogen replaces the expected cytoplasmic pattern. | Question the IHC result because the reported main location is cytoplasmic (UniProt Q7Z569: Cytoplasm; HPA tissue IHC: ubiquitous cytoplasmic expression). HPA ICC-IF also reports a nuclear-membrane location, so a limited nuclear-rim signal alone does not establish an IHC artefact (HPA ICC-IF: additional location approved). |
| Strong stain appears in adipocytes or ovarian stroma while reference-positive cells stain as expected. | These cells were reported as not detected in HPA tissue IHC (HPA tissue IHC: adipocytes and ovarian stroma, Not detected). Consider antibody cross-reactivity or endogenous detection activity, then assess controls before assigning BRAP positivity; the HPA observations are reference data, not absolute exclusion rules (HPA tissue IHC: low RNA agreement). |
| Chromogen coats most tissue structures without a readable cellular boundary or compartment. | Treat diffuse staining as background until controls establish a specific signal; broad staining alone cannot confirm BRAP, despite HPA's ubiquitous cytoplasmic profile (HPA tissue IHC). Compare the no-primary control and the expected cytoplasmic pattern, and review blocking, washing and detection steps (general IHC practice). |
| A reference-positive tissue has no convincing cytoplasmic stain. | First check whether the expected cells are present: HPA reports high staining specifically in neurons, intestinal glandular cells and pachytene spermatocytes (HPA tissue IHC). If present, review antibody and detection performance with suitable controls (general IHC practice); absence in one section cannot settle BRAP expression given HPA's reported low RNA agreement (HPA tissue IHC). |
💡Expected BRAP appearanceCall a result consistent with BRAP when the named HPA high-staining cells show a readable, mainly cytoplasmic signal, with intensity judged against on-slide controls; dominant nuclear or unrelated cell-type staining warrants investigation (HPA tissue IHC: High in neurons, intestinal glandular cells and pachytene spermatocytes; UniProt Q7Z569: Cytoplasm; general IHC practice).
| Compartment and membrane topology (UniProt Q7Z569; HPA ICC-IF). | BRAP is annotated as cytoplasmic with no transmembrane segment (UniProt Q7Z569). HPA ICC-IF supports cytosol as the main location and approves an additional nuclear-membrane location (HPA ICC-IF); use the cytoplasmic pattern as the principal IHC interpretation, without treating every nuclear-rim observation as proof of error. |
| Tissue reference and validation strength (HPA tissue IHC; HPA antibodies). | HPA reports high staining in three named cell populations and Not detected staining in adipocytes and ovarian stroma (HPA tissue IHC). Its tissue IHC reliability is Approved, with low staining–RNA consistency and pending external verification (HPA tissue IHC). HPA040357 is IHC Approved; the supplied status does not say IHC Enhanced (HPA antibodies). |
| Transcript and protein forms (UniProt Q7Z569; HPA tissue IHC). | UniProt lists two BRAP isoforms and a single annotated 1–592 chain, with no signal peptide or propeptide processing (UniProt Q7Z569). HPA flags a splice or transcript discrepancy (HPA tissue IHC). Without an antibody epitope map, these facts do not identify which isoform a stain detects or explain an individual negative section. |
| IF/ICC Q&A: where is BRAP seen? (HPA ICC-IF). | HPA reports mainly cytosolic signal, with an additional nuclear-membrane location, in ICC-IF (HPA ICC-IF: cytosol supported; nuclear membrane approved). This localisation can inform interpretation, but the supplied IF evidence does not define a paraffin-section IHC retrieval or detection setting. |
| Situation | Likely cause | Next action |
|---|---|---|
| Reference-positive neurons, intestinal glands or pachytene spermatocytes are unstained (HPA tissue IHC: High). | The expected cell population may be absent from the examined area, or the IHC run may have failed (HPA tissue IHC; general IHC practice). | Confirm tissue identity and cell morphology, then inspect a suitable run control and the antibody's IHC-P instructions for retrieval and detection settings (general IHC practice); do not infer a BRAP-specific fixation effect. |
| Signal is mainly nuclear rather than cytoplasmic (UniProt Q7Z569; HPA tissue IHC). | The pattern conflicts with the reported main location; a narrow nuclear rim is separately reported in ICC-IF (HPA ICC-IF). | Check morphology and no-primary background, then repeat with the IHC-validated antibody and appropriate controls if the nuclear pattern persists (general IHC practice; HPA antibodies: HPA040357 IHC Approved). |
| Adipocytes or ovarian stroma stain strongly (HPA tissue IHC: Not detected). | Possible cross-reactivity or endogenous detection activity; HPA's tissue reference has low agreement with RNA expression (general IHC practice; HPA tissue IHC). | Review the no-primary control and detection system, and compare staining with a reported high-staining cell population on a controlled run (general IHC practice; HPA tissue IHC). |
| Diffuse chromogen obscures cytoplasmic boundaries (HPA tissue IHC: cytoplasmic profile). | Background may arise from incomplete blocking, insufficient washing or detection chemistry (general IHC practice). | Inspect no-primary and reagent controls; optimise blocking, washes and detection according to the assay instructions before scoring cellular BRAP stain (general IHC practice). |
| A weaker-than-expected result occurs in breast glandular cells (HPA tissue IHC: Medium). | Medium is the reported HPA staining level in breast glands, whereas the named high-staining populations provide stronger reference examples (HPA tissue IHC). | Judge the breast result against its own morphology and controls; use a reported high-staining tissue to check assay performance rather than demanding uniformly high breast staining (HPA tissue IHC; general IHC practice). |
| IHC and ICC-IF appear to disagree about a nuclear-rim signal (HPA ICC-IF; HPA tissue IHC). | HPA records a nuclear-membrane location in ICC-IF while describing tissue IHC as ubiquitously cytoplasmic; the supplied sources do not resolve the modality difference (HPA ICC-IF; HPA tissue IHC). | Report the observed compartment and method separately, check each assay's controls, and avoid using the ICC-IF observation alone to score a paraffin-section IHC result (HPA ICC-IF; HPA tissue IHC; general IHC 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 expect staining in neuronal cells (HPA: High in cerebral cortex neuronal cells). Run adipose tissue as the negative tissue (HPA: Not detected in adipocytes); on the cortex slide, use non-neuronal cells as a background comparison, without assuming they are BRAP-negative (HPA: High designation applies to neuronal cells).
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; a concentration-matched rabbit polyclonal IgG isotype control (selected tissue-IHC caption: rabbit pAb); and BRAP knockout material, if available, as a biological negative. Quench endogenous peroxidase for chromogenic IHC, and assess pigment-related autofluorescence if examining cerebral cortex by IF (standard IHC/IF practice).
⚠️Feasibility: A BRAP-specific fixation window or fixation effect is unreported, and the selected SKU A03573 paraffin-section caption does not state a fixative (selected tissue-IHC caption: fixative not stated). Retrieval dependence in cerebral cortex is unreported; the selected lung cancer paraffin-section image used high-pressure retrieval in 10 mM citrate buffer at pH 6.0 and a 1:100 antibody dilution (selected tissue-IHC caption). The supplied evidence does not establish whether frozen sections or IF are easier; for cortex IF, assess autofluorescent pigment separately from BRAP signal (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
These questions address BRAP staining in paraffin sections with chromogenic detection; IF/ICC requires separate optimization.
Which antigen retrieval should I start with for BRAP in paraffin sections?
Start with high pressure, heat-mediated retrieval in 10 mM citrate, pH 6.0 (datasheet A03573). Compare a controlled 10–20 minute retrieval series while keeping cooling and detection conditions consistent (standard IHC practice). The selected lung cancer image used 1:100 antibody dilution after citrate retrieval; its caption does not report the fixative (datasheet A03573). Judge retrieval by cytoplasmic staining and preserved morphology, since BRAP is annotated as cytoplasmic and has no transmembrane segment (UniProt Q7Z569). If staining remains weak, test another buffer only as a documented fallback with matched controls (standard IHC practice).
How should I assess whether fixation is affecting BRAP staining?
BRAP-specific fixation sensitivity is unknown; the selected paraffin-section caption does not state a fixative (datasheet A03573). Standardise neutral buffered formalin fixation, tissue thickness, and processing across samples before comparing staining (standard IHC practice). A pilot comparing 12 and 24 hours of fixation can test workflow sensitivity without attributing any difference to BRAP itself (standard IHC practice). Hold retrieval at 10 mM citrate, pH 6.0 and keep detection conditions matched (datasheet A03573; standard IHC practice). Record morphology and cytoplasmic signal together; neither tissue staining patterns nor annotated BRAP phosphorylation establishes fixation sensitivity (HPA: tissue IHC; UniProt Q7Z569).
Where should convincing BRAP chromogenic staining appear?
Expect predominantly cytoplasmic staining: BRAP is annotated as cytoplasmic, and the HPA describes ubiquitous cytoplasmic tissue expression (UniProt Q7Z569; HPA: tissue IHC). A nuclear membrane component is plausible because HPA reports supported cytosolic localisation and an additional approved nuclear membrane location in ICC/IF (HPA: subcellular). Distinguish a membrane rim from diffuse nuclear chromogen using well-preserved cells and a nuclear counterstain (standard IHC practice). BRAP interacts with the nuclear localisation signal of BRCA1, but that interaction alone does not establish nuclear accumulation in paraffin sections (UniProt Q7Z569). Investigate predominantly nuclear staining with matched controls before interpreting it as BRAP (standard IHC practice).
Could BRAP isoforms or modifications change what this antibody detects?
BRAP has 2 annotated isoforms, so first map the antibody immunogen against both sequences if that information is available (UniProt Q7Z569; standard IHC practice). Without an established isoform-specific epitope, chromogenic staining cannot identify which isoform contributed the signal (standard IHC practice). Annotated phosphoserines include residues 52, 97, 117, and 119, but their effect on this antibody's binding is unspecified (UniProt Q7Z569). Compare staining with an independently validated epitope or orthogonal assay when isoform identity matters (standard IHC practice). Document retrieval and fixation in that comparison, since both can alter epitope accessibility in paraffin IHC (standard IHC practice).
How can IF help check a BRAP IHC localisation pattern?
Use IF as a separate localisation check, with matched positive and negative controls for the chromogenic IHC comparison (standard IF/IHC practice). Multiplex BRAP with a neuronal marker in cerebral cortex or a glandular cell marker in small intestine, where those cell types show high tissue staining (HPA: tissue IHC). Choose a far-red fluorophore when shorter wavelengths show tissue autofluorescence, and inspect single-label controls for bleed-through (standard IF practice). BRAP is mainly cytosolic and has no transmembrane segment; use mild permeabilisation for a cytosolic epitope, but verify epitope access rather than assuming its membrane-facing side (HPA: subcellular; UniProt Q7Z569; standard IF practice). HPA also reports nuclear membrane staining in ICC/IF (HPA: subcellular).
How do I distinguish BRAP staining from chromogenic background?
Compare the primary-antibody section with a matched no-primary control and inspect the same cell compartments in both (standard IHC practice). Block endogenous peroxidase before HRP and DAB detection, and optimise the block if brown signal persists in the control (standard IHC practice). Adjust primary dilution, blocking, washes, and detection time one variable at a time while preserving the validated citrate retrieval starting point (datasheet A03573; standard IHC practice). BRAP tissue staining is described as cytoplasmic, whereas HPA reports no detected signal in adipocytes and ovarian stroma cells (HPA: tissue IHC). Treat staining that tracks section folds, edges, or damaged areas as suspect until controls resolve it (standard IHC practice).
What is a defensible way to quantify BRAP IHC? ⚠ ANSWER MARKED FOR VERIFICATION
Score BRAP within a predefined cell type and cytoplasmic compartment, using consistent exposure, detection, and counterstaining across sections (HPA: tissue IHC; standard IHC practice). Report the percentage of positive viable cells and an intensity-based H-score from 0–300, with thresholds set before group comparison (standard IHC practice). If counting discrete positive cells, report density per mm² of evaluable tissue and specify excluded necrotic or folded areas (standard IHC practice). Normalise to the number of viable cells or evaluable tissue area in the same histologic compartment (standard IHC practice). Record fixation and retrieval batches because preparation differences can change measured chromogenic intensity (standard IHC practice).
What would make a BRAP-positive IHC result credible?
A credible result shows cytoplasmic staining in intact cells with the expected morphology and an appropriately quiet no-primary control (UniProt Q7Z569; standard IHC practice). HPA reports high staining in cerebral cortex neuronal cells, small-intestine glandular cells, and testis pachytene spermatocytes, providing cell-specific comparison points (HPA: tissue IHC). A nuclear membrane accent may fit HPA ICC/IF localisation, whereas diffuse nuclear-only staining needs additional verification (HPA: subcellular; standard IHC practice). Exclude edge effects, necrosis, and residual endogenous peroxidase before scoring brown signal (standard IHC practice). Interpret any tissue comparison cautiously because HPA rates the tissue staining approved while reporting low consistency with RNA expression (HPA: tissue IHC reliability).
Boster reagents
Best BRAP / BRCA1-associated protein IHC Antibodies
A03573 has real paraffin-section IHC images from human lung and liver cancer (catalog image captions); IF/ICC is listed, without an IF image (catalog applications and image records).
Real IHC data
Anti-BRCA1-associated protein BRAP Antibody
Cat # A03573
A03573 has IHC images of paraffin-embedded human lung and liver cancer at 1:100, with citrate retrieval at pH 6.0 (catalog image captions). IF/ICC is listed, and Human, Mouse, and Rat reactivity is reported; no IF image is provided (catalog applications, reactivity, and image records).
Which to pick: Choose A03573 for paraffin-section tissue IHC because its own images show human lung and liver cancer sections; the fixative is unreported (catalog image captions). A03573 is also the listed choice for IF/ICC at 1:50–1:100, though no IF image is supplied (catalog applications, IF dilution, and image records). For Mouse or Rat samples, A03573 lists reactivity with both species, but its IHC images show only Human samples; it is a rabbit polyclonal antibody (catalog reactivity, image captions, and product description).
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 Cytoplasmic tissue 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 fixation consistent across sections (standard IHC practice; not target-specific); Caveat: Staining and RNA show low consistency; verify specificity (HPA tissue IHC); Isoform / epitope: 2 isoforms; epitope coverage is unspecified (UniProt); Regulation: No expression regulator specified (UniProt). 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.