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- Table of Contents
Plan BCAT2 IHC in paraffin sections using the granular cytoplasmic tissue pattern (HPA tissue IHC) and its mitochondrial location as a molecular expectation (UniProt). This guide covers control selection, antibody use and staining assessment.
Expected localisation, validated protocols, controls and antibodies — the at-a-glance facts below, then the full design guide.
| Expected localisation | Granular cytoplasmic staining (HPA tissue IHC) | |
| Staining pattern | Widespread granular cytoplasmic staining (HPA tissue IHC) | |
| Antigen retrieval | EDTA pH 8.0 HIER, heat-mediated (datasheet A06369-1) | |
| Positive control | Adrenal gland+4 more · see all | |
| Negative control | Adipose tissue+4 more · see all |
| Fixation | Matched tissue-IHC evidence does not establish the fixation claim. Validate the specimen-specific method before use. (selected-SKU IHC image A06369-1) | |
| Caveat | Staining and RNA show medium consistency (HPA tissue IHC) | |
| Regulation | Staining-linked regulation unspecified (UniProt) | |
| Isoform / epitope | Two isoforms (A/B); verify epitope coverage (UniProt) |
The catalog antibody’s IHC-P protocol (datasheet: A06369-1) is paired with a published paraffin-heart IHC protocol (PMC8945524: Methods).
| Sample | Paraffin-embedded human colon adenocarcinoma tissue; fixative not specified (datasheet A06369-1) |
| Fixation | Image fixative and duration unreported (datasheet A06369-1); 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 A06369-1); 20 min, 95–100 °C (standard) |
| Peroxidase block | 3% H2O2, 10 min, room temperature (standard) |
| Blocking | 10% goat serum (datasheet A06369-1) |
| Primary antibody | Rabbit anti-BCAT2, 2-5 μg/ml (datasheet A06369-1) |
| Primary incubation | Overnight at 4 °C (datasheet A06369-1) |
| Detection | HRP-conjugated secondary, DAB chromogen (datasheet A06369-1) |
| Counterstain | Hematoxylin, blue, dehydrate and mount (standard) |
| Expected result | BCAT2-positive staining in glandular cells of adrenal gland (HPA tissue IHC: High). HPA tissue profile: Ubiquitous cytoplasmic expression with a granular pattern. No signal in the no-primary control. |
BCAT2 is mitochondrial and has no annotated transmembrane segment (UniProt O15382 localization and topology). In paraffin IHC, expect granular cytoplasmic staining in many cell types, including strongly stained glandular cells of colon and breast (HPA tissue IHC). Interpret this pattern with the HPA tissue IHC reliability rating of Enhanced, which carries medium consistency between antibody staining and RNA expression (HPA tissue IHC).
| Granular cytoplasmic staining in colon glandular cells, with little nuclear staining (HPA tissue IHC; UniProt O15382 localization). | This fits the reported high staining in colon glandular cells and ubiquitous granular cytoplasmic profile (HPA tissue IHC). Cytoplasmic granules are compatible with mitochondrial localization, although chromogenic IHC alone does not prove organelle identity (UniProt O15382 localization; general IHC practice). |
| Predominantly nuclear staining on a chromogenic section. | This departs from the expected mitochondrial, granular cytoplasmic IHC pattern (UniProt O15382 localization; HPA tissue IHC). Check whether the signal follows nuclei across unrelated cell types and compare it with a negative detection control before assigning it to BCAT2 (general IHC practice). |
| Strong staining in adipocytes or skeletal muscle myocytes. | HPA reports BCAT2 as not detected in those specific cell types, so strong signal there needs scrutiny (HPA tissue IHC). Review morphology and controls for cross-reactivity or endogenous detection activity; an unexpected stain alone cannot identify its cause (general IHC practice). |
| Uniform color over cells and extracellular areas, obscuring granules. | A diffuse haze prevents assessment of the reported granular cytoplasmic pattern (HPA tissue IHC). Uneven washing, excess detection reagent, or endogenous activity can cause background in chromogenic IHC; evaluate a negative detection control and reagent conditions (general IHC practice). |
| No staining in glandular cells of a colon section. | Colon glandular cells are a reported high-staining comparator (HPA tissue IHC). An absent result could reflect an assay failure, tissue quality, or variation from the reference pattern; check section morphology and same-run controls before calling BCAT2 absent (general IHC practice). |
| Cell-type comparator | Use glandular cells of colon, breast, or appendix as reported high-staining comparators; adipocytes and skeletal muscle myocytes are reported as not detected (HPA tissue IHC). Compare the named cell types, since a whole tissue can contain several cell populations (general IHC practice). |
| Antibody evidence | The listed antibody HPA054091 has Enhanced IHC validation, and the tissue profile has an Enhanced reliability rating with medium RNA–staining consistency (HPA antibodies; HPA tissue IHC). These ratings support a reference pattern, but do not make every positive pixel specific (general IHC practice). |
| Protein processing and topology | UniProt annotates a mitochondrial protein without a transmembrane segment and a mature chain spanning residues 28–392 (UniProt O15382 topology and processing). These annotations support an intracellular localization expectation; they do not locate the antibody epitope or predict retrieval response. |
| Isoforms and epitope | UniProt lists two isoforms, A and B (UniProt O15382 isoforms). The supplied record does not map an IHC epitope to either isoform, so staining intensity cannot be assigned to a specific isoform from these data alone. |
| IF/ICC Q&A | Q: Should IF show only mitochondria? A: HPA reports supported mitochondrial and uncertain nucleoplasmic localization in ICC-IF (HPA subcellular). Assess IF localization separately from paraffin IHC; the supplied evidence does not establish an IF protocol or make nuclear-only IHC a positive call. |
| Situation | Likely cause | Next action |
|---|---|---|
| Known high-staining glandular cells show no signal (HPA tissue IHC). | The assay or section may have failed; the supplied sources give no BCAT2-specific fixation or retrieval sensitivity. | Verify tissue morphology and a same-run positive control; review retrieval and detection against the chosen IHC method (general IHC practice). |
| Expected cytoplasmic granules are weak or difficult to resolve (HPA tissue IHC). | Subtle signal can be hard to distinguish from counterstain or background in chromogenic sections (general IHC practice). | Compare with a reported high-staining cell type and a negative detection control; adjust imaging and scoring consistently (HPA tissue IHC; general IHC practice). |
| Nuclei dominate the stain while cytoplasm is faint. | The pattern conflicts with mitochondrial localization and the reported granular cytoplasmic IHC profile (UniProt O15382 localization; HPA tissue IHC). | Check a negative detection control and examine whether nuclear color tracks multiple unrelated cell types before accepting the result (general IHC practice). |
| Adipocytes or skeletal muscle myocytes stain strongly. | These cell types are reported as not detected, making cross-reactivity or endogenous detection activity possible explanations (HPA tissue IHC; general IHC practice). | Confirm cell identity on the counterstained section, then compare with a negative detection control and reported high-staining cells (general IHC practice; HPA tissue IHC). |
| Color spreads into stroma or covers cells uniformly. | Diffuse background can obscure the granular cytoplasmic profile; its exact source cannot be inferred from appearance alone (HPA tissue IHC; general IHC practice). | Inspect control sections, washing, blocking, and chromogen development under the chosen IHC method (general IHC practice). |
| Results differ among ostensibly positive tissue samples. | HPA calls the profile ubiquitous but reports medium consistency between antibody staining and RNA data; cell composition also affects what is visible (HPA tissue IHC; general IHC practice). | Score the named cell population, document intensity and granularity, and compare sections processed in the same run (general IHC practice). |
Comprehensive Human Protein Atlas IHC scoring per tissue (reliability: Enhanced — Medium 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 → |
| Breast | Glandular cells | High | Protein (IHC) | HPA → |
| Bronchus | Respiratory epithelial cells | High | Protein (IHC) | HPA → |
| Cervix | Glandular cells | High | Protein (IHC) | HPA → |
| Tissue | Cell type | Level | Evidence | Source |
|---|---|---|---|---|
| Adipose tissue | Adipocytes | Not detected | Protein (IHC) | HPA → |
| Bone marrow | Hematopoietic cells | Not detected | Protein (IHC) | HPA → |
| Caudate | Glial cells | Not detected | Protein (IHC) | HPA → |
| Cerebellum | Cells in granular layer | Not detected | Protein (IHC) | HPA → |
| Hippocampus | Glial cells | Not detected | Protein (IHC) | HPA → |
Troubleshoot BCAT2 chromogenic IHC by checking retrieval, compartment, cell type and controls before comparing staining across sections.
Two anti-BCAT2 antibodies have human paraffin-section IHC images; one also has a human paraffin-section IF image (catalog image captions). Catalog reactivity includes mouse, rat, and monkey, without IHC images for those species (catalog reactivity; IHC image captions).
A06369-1 has human colon adenocarcinoma IHC and human intestinal cancer IF images; its listed reactivity is human, mouse, and rat (A06369-1 image captions; catalog reactivity). PA1502 has human ovarian cancer IHC images and lists IF/ICC among its applications, with human and monkey reactivity (PA1502 image caption; catalog applications and reactivity).
Which to pick: For tissue IHC, choose A06369-1 for the pictured human colon adenocarcinoma section or PA1502 for the pictured human ovarian cancer section; both captions describe paraffin sections with EDTA retrieval at pH 8.0, and neither reports the fixative (A06369-1 and PA1502 IHC image captions). For IF, A06369-1 has a human tissue image; for ICC, PA1502 lists that application, though it has no IF/ICC image in this payload (A06369-1 IF image caption; PA1502 catalog applications and image payload). For other species, A06369-1 lists mouse and rat and PA1502 lists monkey, but their pictured IHC evidence is human only; both are rabbit antibodies with no clone reported (catalog reactivity, host, and clone fields; IHC image captions).