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- Table of Contents
This guide uses the observed nuclear tissue pattern to plan ATF1 staining in paraffin sections (HPA tissue IHC). It covers fixation consistency, titration within 0.5–1 μg/mL (datasheet M01600-1), chromogenic detection (datasheet M01600-1), and nuclear scoring.
Expected localisation, validated protocols, controls and antibodies — the at-a-glance facts below, then the full design guide.
| Expected localisation | Nuclear staining (HPA tissue IHC) | |
| Staining pattern | General nuclear staining across tissues (HPA tissue IHC) | |
| Antigen retrieval | EDTA pH 8.0 HIER, heat-mediated (datasheet M01600-1) | |
| Positive control | Adrenal gland+4 more · see all | |
| Negative control | Nasopharynx |
| Fixation | Keep fixation conditions consistent across sections. (standard IHC practice; not target-specific) | |
| Caveat | ATF1 is not detected in nasopharyngeal basal cells (HPA tissue IHC) | |
| Regulation | Expression regulation not annotated (UniProt) | |
| Isoform / epitope | 2 isoforms; epitope differences unreported (UniProt) |
The catalog antibody’s IHC-P protocol (datasheet: M01600-1) is accompanied by one published xenograft IHC protocol for phosphorylated CREB/ATF1 (PMC8038809).
| Sample | Paraffin-embedded human lung cancer tissue; fixative not specified (datasheet M01600-1) |
| Fixation | Image fixative and duration unreported (datasheet M01600-1); 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 M01600-1); 20 min, 95–100 °C (standard) |
| Peroxidase block | 3% H2O2, 10 min, room temperature (standard) |
| Blocking | 10% goat serum (datasheet M01600-1) |
| Primary antibody | Mouse monoclonal (clone 7F8) anti-ATF1, 0.5-1μg/ml (datasheet M01600-1) |
| Primary incubation | Overnight at 4 °C (datasheet M01600-1) |
| Detection | Streptavidin-biotin complex (SABC), DAB chromogen (datasheet M01600-1) |
| Counterstain | Hematoxylin, blue, dehydrate and mount (standard) |
| Expected result | ATF1-positive staining in glandular cells of adrenal gland (HPA tissue IHC: High). HPA tissue profile: General nuclear expression. No signal in the no-primary control. |
ATF1 should show predominantly nuclear staining in a range of tissues (UniProt P18846: nucleus; HPA: general nuclear expression). Strong examples include adrenal and colon glandular cells, cerebellar Bergmann glia nuclei, and kidney glomerular cells (HPA: High). ATF1 has no transmembrane segment (UniProt P18846 topology). Interpret tissue patterns with care: HPA rates its IHC evidence Supported, with medium consistency between staining and RNA expression (HPA: tissue IHC).
| Distinct nuclear chromogen in adrenal or colon glandular cells, with relatively clear cytoplasm. | This fits the expected compartment and two documented high-staining cell populations (UniProt P18846: nucleus; HPA: High in adrenal and colon glandular cells). Compare nuclei within the same section before judging intensity; HPA's High designation describes these cell populations, not every nucleus. |
| Predominantly cytoplasmic, membranous, or extracellular staining, especially when nuclei remain clear. | The compartment conflicts with the reported nuclear pattern (UniProt P18846: nucleus; HPA: general nuclear expression). Treat it as a possible artefact or off-target signal. Morphology and control sections should guide interpretation; this appearance alone cannot identify its cause. |
| Strong signal confined to nasopharyngeal basal cells while documented high-staining cells are weak. | HPA reports ATF1 as Not detected in nasopharyngeal basal cells and High in several other cell populations (HPA: tissue IHC). This mismatch raises possible cross-reactivity or endogenous detection activity; it does not prove either. Check the control stains and tissue identity. |
| Uniform haze across nuclei, cytoplasm, and tissue spaces obscures cell boundaries. | This is difficult to score as the expected nuclear pattern (UniProt P18846: nucleus; HPA: general nuclear expression). In chromogenic IHC, widespread haze can arise from nonspecific reagent binding or detection background (general IHC practice). Compare a no-primary control before calling cells positive. |
| No nuclear signal in an intact adrenal gland or colon section. | Both contain glandular cells reported as High by HPA, so absence of signal warrants a control and workflow check (HPA: tissue IHC). It does not establish that ATF1 is absent: HPA's tissue IHC reliability is Supported, with medium staining–RNA consistency (HPA: tissue IHC). |
| Cell population and tissue context | HPA describes general nuclear expression and low tissue RNA specificity, yet its IHC levels vary by cell population: High in selected glandular and glomerular cells, Low in lung alveolar type I cells, and Not detected in nasopharyngeal basal cells (HPA: tissue IHC). Score the identified cells, not a whole-section average. |
| Antibody validation | HPA055069 and CAB016222 each have Supported IHC status; HPA055406 has no supplied IHC status (HPA: antibody validation). HPA defines tissue IHC reliability as Supported with medium staining–RNA consistency (HPA: tissue IHC). An ICC result alone does not establish performance on paraffin sections. |
| Isoforms and epitope coverage | UniProt lists two ATF1 isoforms, but the supplied evidence does not map antibody epitopes or show isoform-specific staining (UniProt P18846: isoforms 1 and 2; HPA: antibody validation). An unexpected difference between samples cannot be assigned to isoform recognition without antibody-specific evidence. |
| Target-specific fixation sensitivity | No ATF1-specific fixation or antigen-retrieval effect is established by the supplied sources (UniProt P18846; HPA: tissue IHC). Retrieval conditions may be checked as part of general paraffin-IHC troubleshooting (general IHC practice), but neither ATF1's topology nor HPA staining levels predict a fixation-dependent result. |
| IF/ICC Q&A: Where should signal appear? | In the nucleoplasm: HPA reports enhanced nucleoplasmic localisation and lists ICC-IF images, while UniProt places ATF1 in the nucleus (HPA: subcellular ICC-IF; UniProt P18846: nucleus). This localisation is useful context for IHC; ICC-IF validation supplies no paraffin-IHC protocol. |
| Situation | Likely cause | Next action |
|---|---|---|
| Known high-staining glandular cells have no nuclear signal. | A failed staining run or unsuitable assay conditions are possibilities; the absent result alone cannot distinguish them (HPA: High in adrenal and colon glandular cells; general IHC practice). | Check tissue morphology, positive-control performance, antibody instructions, retrieval, and detection reagents on matched sections (general IHC practice). Do not infer an ATF1-specific fixation effect from this result (UniProt P18846; HPA: tissue IHC). |
| Colour is mainly cytoplasmic or membranous. | The compartment disagrees with ATF1's reported nuclear localisation (UniProt P18846: nucleus; HPA: general nuclear expression). Nonspecific staining or slide interpretation is possible (general IHC practice). | Recheck cell boundaries and counterstained nuclei; compare the matched no-primary control and a documented high-staining cell population (general IHC practice; HPA: High in adrenal glandular cells). |
| Nasopharyngeal basal cells stain strongly. | That conflicts with the supplied Not detected observation; cross-reactivity or endogenous detection activity is possible, not established (HPA: nasopharynx basal cells Not detected; general IHC practice). | Compare a no-primary control and review endogenous-enzyme blocking if using enzyme-based chromogenic detection (general IHC practice). Confirm the cell type before assigning a biological difference from HPA. |
| Brown haze covers most of the section. | Diffuse deposition may reflect detection background or nonspecific binding rather than a resolvable nuclear pattern (general IHC practice; HPA: general nuclear expression). | Inspect a no-primary control; then review blocking, wash steps, antibody concentration, and chromogen development against the antibody instructions (general IHC practice). Judge nuclear staining only after cell boundaries can be resolved. |
| Signal is weak in a low-staining population. | Weakness can agree with HPA's Low observations, including lung alveolar type I cells; it is not, by itself, evidence of assay failure (HPA: tissue IHC). | Check a documented High cell population in the same run before changing conditions (HPA: High in adrenal and colon glandular cells; general IHC practice). Keep cell identity and the Supported, medium-consistency HPA rating in the interpretation (HPA: tissue IHC). |
| An ICC-IF image appears convincing, but paraffin-section staining is uncertain. | HPA's enhanced nucleoplasmic ICC-IF localisation addresses a different application; the supplied IHC statuses are Supported for HPA055069 and CAB016222 (HPA: subcellular ICC-IF; HPA: antibody validation). | Evaluate the paraffin-section result by its nuclear pattern, documented tissue controls, and the antibody's IHC validation status (UniProt P18846: nucleus; HPA: tissue IHC and antibody validation). Do not substitute an ICC-IF result for IHC evidence. |
Comprehensive Human Protein Atlas IHC scoring per tissue (reliability: Supported — 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 → |
| Cerebellum | Bergmann glia - nucleus | High | Protein (IHC) | HPA → |
| Colon | Glandular cells | High | Protein (IHC) | HPA → |
| Duodenum | Glandular cells | High | Protein (IHC) | HPA → |
| Epididymis | Glandular cells | High | Protein (IHC) | HPA → |
| Tissue | Cell type | Level | Evidence | Source |
|---|---|---|---|---|
| Nasopharynx | Basal cells | Not detected | Protein (IHC) | HPA → |
Troubleshoot ATF1 staining in paraffin sections by assessing nuclear signal, tissue controls and detection chemistry (UniProt P18846; HPA tissue IHC).
Real IHC images show ATF1 staining in human lung, rectal and colon cancer paraffin sections (IHC captions: M01600-1; A01600-1); an IF image shows A431 cells (M01600-1 IF caption).
M01600-1 has IHC images from human lung and rectal cancer paraffin sections and an IF image from A431 cells (M01600-1 image captions). A01600-1 has an IHC image from a human colon cancer paraffin section; its application list also includes IF/ICC (A01600-1 IHC caption; catalog applications).
Which to pick: For human tissue IHC, choose M01600-1 for a mouse monoclonal antibody with documented EDTA pH 8 retrieval, or A01600-1 for a rabbit polyclonal antibody with documented Tris-EDTA pH 9 retrieval (catalog host and clone; respective IHC captions). For IF/ICC, M01600-1 has a documented A431 cell IF image, while A01600-1 also lists IF/ICC applications (M01600-1 IF caption; A01600-1 catalog applications). For mouse or rat samples, A01600-1 is the listed cross-species option; its IHC image shows human tissue only, and neither IHC caption reports the fixative (A01600-1 catalog reactivity; respective IHC captions).