This website uses cookies to ensure you get the best experience on our website.
- Table of Contents
Plan XAF1 staining in paraffin sections using cytoplasmic tissue staining as the main reference pattern (HPA tissue IHC). Compare controls and interpret intensity cautiously because antibody staining has low consistency with RNA expression (HPA tissue IHC).
Expected localisation, validated protocols, controls and antibodies — the at-a-glance facts below, then the full design guide.
| Expected localisation | Cytoplasmic tissue staining (HPA tissue IHC); nuclear location also reported (UniProt) | |
| Staining pattern | Cytoplasmic staining in most tissues, including glandular cells (HPA tissue IHC) | |
| Antigen retrieval | EDTA pH 8.0 HIER, heat-mediated (datasheet A03432-1) | |
| Positive control | Duodenum+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 A03432-1) | |
| Caveat | Antibody staining has low consistency with RNA expression (HPA tissue IHC) | |
| Regulation | Often down-regulated in cancer cell lines (UniProt) | |
| Isoform / epitope | 7 isoforms; no processing annotated; epitope coverage unknown (UniProt) |
The catalog antibody’s IHC-P protocol (datasheet: A03432-1) is followed by published XAF1 protocols for gastric cancer, renal cancer, and neuroblastoma specimens (PMC3695092; PMC3087333; PMC5085151).
| Sample | Paraffin-embedded human lung cancer tissue; fixative not specified (datasheet A03432-1) |
| Fixation | Image fixative and duration unreported (datasheet A03432-1); 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 A03432-1); 20 min, 95–100 °C (standard) |
| Peroxidase block | 3% H2O2, 10 min, room temperature (standard) |
| Blocking | 10% goat serum (datasheet A03432-1) |
| Primary antibody | Rabbit anti-XAF1, 2-5 μg/ml (datasheet A03432-1) |
| Primary incubation | Overnight at 4 °C (datasheet A03432-1) |
| Detection | HRP-conjugated secondary, DAB chromogen (datasheet A03432-1) |
| Counterstain | Hematoxylin, blue, dehydrate and mount (standard) |
| Expected result | XAF1-positive staining in glandular cells of duodenum (HPA tissue IHC: High). HPA tissue profile: Cytoplasmic expression in most tissues. No signal in the no-primary control. |
XAF1 staining in paraffin sections is expected mainly in the cytoplasm, including glandular cells and kidney tubule cells with high reported staining (HPA tissue IHC). UniProt also places XAF1 in the nucleus and mitochondrion, with no transmembrane segment (UniProt Q6GPH4). The tissue IHC profile is Approved, but antibody staining has low consistency with RNA expression data; treat the pattern as a guide, not a definitive identity test (HPA tissue IHC).
| Distinct cytoplasmic staining in duodenal glands or kidney tubules, with little staining in adjacent negative cells. | This fits the reported high staining in duodenal glandular cells and kidney tubule cells, and the mainly cytoplasmic tissue profile (HPA tissue IHC). Check both cell identity and compartment before scoring a section as positive (standard IHC practice). |
| Predominantly nuclear staining with little cytoplasmic signal in a paraffin section. | This differs from the mainly cytoplasmic tissue IHC profile (HPA tissue IHC). Nuclear XAF1 remains biologically plausible (UniProt Q6GPH4), and nucleoplasmic signal is supported in ICC/IF (HPA subcellular); compare a positive tissue and antibody controls before calling the IHC pattern specific (standard IHC practice). |
| A sharp membrane rim or extracellular deposit is the dominant signal. | Neither pattern follows the reported cytoplasmic tissue staining (HPA tissue IHC) or the no-transmembrane topology (UniProt Q6GPH4). Consider nonspecific binding or detection artefact, then inspect a matched negative control and repeat with optimized washing (standard IHC practice). |
| Strong colour appears in an HPA-negative cell population, or colour is spread diffusely across the section. | Examples of reported undetected populations are adipocytes and lung alveolar cells (HPA tissue IHC). Staining there warrants checks for cross-reactivity, endogenous detection activity, or background; an HPA 'not detected' result is not proof that every specimen must be blank (HPA tissue IHC; standard IHC practice). |
| No cellular signal appears in a duodenal or kidney section used as a positive control. | HPA reports high staining in duodenal glandular cells and kidney tubule cells (HPA tissue IHC). If tissue integrity is adequate, review staining reagents, retrieval, primary-antibody conditions, and detection before interpreting an experimental negative (standard IHC practice). |
| Tissue and cell selection | HPA reports High staining in duodenum, rectum, small intestine, thyroid gland, testis Leydig cells, and kidney tubule cells; adipocytes, lung alveolar cells, and several other listed populations were not detected (HPA tissue IHC). Choose controls by the named cell population, since a whole tissue can contain several cell types (standard IHC practice). |
| Compartment and application | Tissue IHC is mainly cytoplasmic (HPA tissue IHC), while supported ICC/IF localization is nucleoplasmic and mitochondrial (HPA subcellular); UniProt also lists cytoplasm, nucleus, and mitochondrion (UniProt Q6GPH4). Record the application and cellular context when comparing patterns. |
| Antibody evidence and transcript comparison | The listed antibody, HPA057302, is IHC Approved and ICC Supported (HPA antibodies). HPA describes low consistency between tissue antibody staining and RNA expression, despite low RNA tissue specificity (HPA tissue IHC); RNA abundance alone is an uncertain tie-breaker for a disputed stain. |
| Isoforms, topology, and processing | UniProt lists 7 isoforms, one annotated chain spanning residues 1–301, no signal peptide or propeptide, and no transmembrane segment (UniProt Q6GPH4). These annotations do not establish which isoforms the IHC antibody detects or how retrieval affects its epitope. |
| IF/ICC Q: Should nuclear or mitochondrial fluorescence match paraffin IHC? | A: Supported ICC/IF localization is mainly nucleoplasmic and mitochondrial, while tissue IHC is mainly cytoplasmic (HPA subcellular; HPA tissue IHC). Interpret each application against its own validated pattern; this section supplies no IF/ICC protocol. |
| Situation | Likely cause | Next action |
|---|---|---|
| Positive-control glandular or tubule cells show no stain. | The control misses its expected high-staining cells, or the staining run failed (HPA tissue IHC; standard IHC practice). | Confirm the named cells are present; then review reagent sequence, detection controls, retrieval, and the validated primary-antibody conditions before scoring test sections (standard IHC practice). |
| Nuclear signal dominates while cytoplasmic IHC signal is weak. | The pattern differs from HPA tissue IHC, although nuclear localization is reported by UniProt and supported by ICC/IF (HPA tissue IHC; UniProt Q6GPH4; HPA subcellular). | Record nuclear and cytoplasmic staining separately; compare the same run with an HPA-positive cell population and an appropriate negative control before assigning specificity (standard IHC practice). |
| Adipocytes or lung alveolar cells stain strongly. | These populations were reported as not detected (HPA tissue IHC); cross-reactivity or endogenous detection activity is possible (standard IHC practice). | Inspect primary-omission and detection controls, then compare staining in a high-staining reference population; avoid treating a single unexpected positive as confirmed XAF1 (standard IHC practice). |
| Uniform brown haze obscures cell borders. | Diffuse background can arise from insufficient blocking or washing, or excessive detection signal (standard IHC practice). | Use matched controls to locate the background source; adjust blocking, washing, or detection conditions while preserving a clear positive-control signal (standard IHC practice). |
| Colour concentrates on edges, folds, or extracellular material. | Those distributions do not match the mainly cytoplasmic tissue profile (HPA tissue IHC); section artefact or nonspecific signal is possible (standard IHC practice). | Assess intact, flat areas and a matched negative control; exclude deposits and damaged regions from cellular scoring (standard IHC practice). |
| Staining disagrees with an RNA-based expectation. | HPA explicitly reports low consistency between antibody staining and RNA expression data for this Approved tissue profile (HPA tissue IHC). | Report the observed cell type and compartment alongside the RNA discrepancy; rely on staining controls and independent evidence before making a target-specific conclusion (HPA tissue IHC; standard IHC practice). |
Comprehensive Human Protein Atlas IHC scoring per tissue (reliability: Approved — Low 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 |
|---|---|---|---|---|
| Duodenum | Glandular cells | High | Protein (IHC) | HPA → |
| Endometrium | Glandular cells | Medium | Protein (IHC) | HPA → |
| Kidney | Cells in tubules | High | Protein (IHC) | HPA → |
| Rectum | Glandular cells | High | Protein (IHC) | HPA → |
| Small intestine | Glandular cells | High | Protein (IHC) | HPA → |
| Tissue | Cell type | Level | Evidence | Source |
|---|---|---|---|---|
| Adipose tissue | Adipocytes | Not detected | Protein (IHC) | HPA → |
| Cerebellum | Cells in granular layer | Not detected | Protein (IHC) | HPA → |
| Cervix | Glandular cells | Not detected | Protein (IHC) | HPA → |
| Lung | Alveolar cells | Not detected | Protein (IHC) | HPA → |
| Lymph node | Non-germinal center cells | Not detected | Protein (IHC) | HPA → |
Use compartment, cell type, and matched controls to troubleshoot XAF1 staining in paraffin sections; assess IF/ICC separately.
Anti-XAF1 antibodies have image data for human tissue IHC (A03432-1 and A03432 IHC captions), human tissue IF (A03432 IF caption), and human cell IF/ICC (PA1218 IF caption).
A03432-1 shows IHC in paraffin sections of human lung cancer, placenta, and thyroid cancer (A03432-1 IHC captions). A03432 shows human spleen IHC and IF (A03432 image captions); PA1218 shows IF/ICC in human U2OS cells (PA1218 IF caption).
Which to pick: For tissue IHC, choose A03432-1 when working with human paraffin sections (A03432-1 applications and IHC captions); its captions do not report the fixative (A03432-1 IHC captions). For IF/ICC in human cells, choose PA1218, a polyclonal antibody with a U2OS IF image (PA1218 dilution_raw and IF caption). For work spanning human and mouse samples, consider A03432 because both species and IHC-P/IF are listed, while its supplied images show human spleen only (A03432 reactivity, applications, and image captions).