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- Table of Contents
Plan chromogenic ATG9A IHC in paraffin sections using the cytoplasmic tissue pattern as a reference (HPA tissue IHC). Start the IHC-validated antibody at 2–5 μg/mL and include specificity controls because tissue staining awaits external verification (datasheet A03757-3; HPA tissue IHC).
Expected localisation, validated protocols, controls and antibodies — the at-a-glance facts below, then the full design guide.
| Expected localisation | Cytoplasmic in tissue (HPA tissue IHC); mainly TGN/endosomal at molecular level (UniProt) | |
| Staining pattern | Cytoplasmic staining in several tissues, including glandular cells (HPA tissue IHC) | |
| Antigen retrieval | EDTA pH 8.0 HIER, heat-mediated (datasheet A03757-3) | |
| Positive control | Adrenal gland+4 more · see all | |
| Negative control | Adipose tissue+4 more · see all |
| Fixation | Keep fixation consistent across sections. (standard IHC practice; not target-specific) | |
| Caveat | Tissue staining awaits external verification (HPA tissue IHC) | |
| Regulation | Starvation redistributes ATG9A to PAS (UniProt) | |
| Isoform / epitope | 3 isoforms; check splice coverage and cytoplasmic versus lumenal epitope (UniProt) |
The catalog antibody uses EDTA pH 8.0 retrieval (datasheet: A03757-3). These published ATG9A IHC protocols cover mouse central nervous system, mouse tissue, and rat extraction sockets (PMC4076416; PMC9296391; PMC10520003; PMC12314380).
| Sample | Paraffin-embedded human glioma tissue; fixative not specified (datasheet A03757-3) |
| Fixation | Image fixative and duration unreported (datasheet A03757-3); 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 A03757-3); 20 min, 95–100 °C (standard) |
| Peroxidase block | 3% H2O2, 10 min, room temperature (standard) |
| Blocking | 10% goat serum (datasheet A03757-3) |
| Primary antibody | Rabbit anti-ATG9A, 2-5μg/ml (datasheet A03757-3) |
| Primary incubation | Overnight at 4 °C (datasheet A03757-3) |
| Detection | Streptavidin-biotin complex (SABC), DAB chromogen (datasheet A03757-3) |
| Counterstain | Hematoxylin, blue, dehydrate and mount (standard) |
| Expected result | ATG9A-positive staining in glandular cells of adrenal gland (HPA tissue IHC: Medium). HPA tissue profile: Cytoplasmic expression in several tissues. No signal in the no-primary control. |
ATG9A is a membrane protein that mainly cycles between the trans-Golgi network and endosomal system (UniProt Q7Z3C6 subcellular location; UniProt Q7Z3C6 topology). In paraffin-section IHC, look for cytoplasmic staining in the relevant cells: HPA reports medium staining in bronchial respiratory epithelial cells and several glandular cell populations (HPA tissue IHC). Treat this as a provisional expectation because HPA rates its tissue IHC reliability Uncertain, pending external verification (HPA tissue IHC).
| Cytoplasmic staining in bronchial respiratory epithelial cells or adrenal glandular cells (HPA tissue IHC). | This fits HPA's medium-staining observations for those cell populations (HPA tissue IHC). A granular or perinuclear emphasis is plausible from ATG9A's TGN and endosomal location, but chromogenic IHC alone cannot identify the stained organelle (UniProt Q7Z3C6 subcellular location; general IHC practice). |
| Predominantly nuclear staining, with little cytoplasmic signal. | A nuclear-dominant pattern conflicts with ATG9A's annotated membrane locations and HPA's cytoplasmic tissue profile (UniProt Q7Z3C6 subcellular location; HPA tissue IHC). Review controls and staining conditions before scoring it as ATG9A (general IHC practice). |
| Strong staining in adipocytes or bone-marrow hematopoietic cells. | HPA reports ATG9A as not detected in those specific cell populations (HPA tissue IHC). Unexpected signal warrants checks for antibody cross-reactivity or endogenous chromogenic activity; HPA's Uncertain IHC reliability means the discrepancy alone does not prove either cause (HPA tissue IHC; general IHC practice). |
| Diffuse colour across tissue compartments, including areas outside cells. | Broad background obscures the cell-specific cytoplasmic pattern reported by HPA (HPA tissue IHC). Compare a primary-antibody-omission control, then review blocking, antibody concentration and washing as general IHC checks (general IHC practice). |
| No staining in bronchial respiratory epithelium despite an interpretable section. | HPA reports medium staining in this cell population, so absence merits investigation (HPA tissue IHC). Check section quality, retrieval and detection with appropriate controls before calling the sample negative; the HPA observation remains provisionally reliable (general IHC practice; HPA tissue IHC). |
| Cell population and tissue selection | HPA reports medium staining in bronchial respiratory epithelial cells, adrenal and several other glandular populations, but no detection in adipocytes or bone-marrow hematopoietic cells (HPA tissue IHC). Choose and score the specified cell population, not the tissue as a whole (general IHC practice). |
| Intracellular distribution | ATG9A mainly cycles between the TGN and endosomal system; starvation or rapamycin can redistribute it toward the phagophore assembly site (UniProt Q7Z3C6 subcellular location). A changed cytoplasmic distribution needs biological context and controls before interpretation (general IHC practice). |
| Topology and antibody epitope | UniProt annotates four transmembrane segments and both cytoplasmic and lumenal regions (UniProt Q7Z3C6 topology). The supplied antibody record gives no epitope position, so it cannot establish which region this IHC assay detects or a target-specific retrieval requirement (HPA antibody record; general IHC practice). |
| Strength of IHC evidence | HPA rates the tissue IHC profile Uncertain, pending external verification, and lists HPA059551 as Uncertain for IHC (HPA tissue IHC; HPA antibody record). Use the reported medium and not-detected examples as provisional comparators, with controls for the actual antibody and run (general IHC practice). |
| IF/ICC: what pattern is expected? | HPA reports vesicles as the supported main ICC-IF location and lists HPA059551 as Supported for ICC (HPA subcellular ICC-IF; HPA antibody record). This supports a vesicular IF interpretation; it does not upgrade that antibody's Uncertain IHC status or supply an IHC tissue result (HPA antibody record; HPA tissue IHC). |
| Situation | Likely cause | Next action |
|---|---|---|
| No signal in an HPA medium-staining cell population. | The run may have inadequate retrieval or detection, or the specimen may differ from HPA's provisional observation (general IHC practice; HPA tissue IHC). | Check section integrity and assay controls, then review retrieval and detection settings; keep the HPA reliability rating in view when interpreting persistent absence (general IHC practice; HPA tissue IHC). |
| Nuclear-dominant signal. | The observed compartment conflicts with the annotated membrane locations and cytoplasmic tissue profile (UniProt Q7Z3C6 subcellular location; HPA tissue IHC). | Compare the primary-antibody-omission control and reassess antibody concentration and detection before assigning ATG9A positivity (general IHC practice). |
| Colour in HPA not-detected cell populations. | Cross-reactivity or endogenous chromogenic activity is possible, although the HPA IHC pattern awaits external verification (general IHC practice; HPA tissue IHC). | Inspect cell identity, compare omission and detection controls, and verify the pattern with an independent antibody if available (general IHC practice). |
| Haze obscures cell borders or cytoplasmic detail. | Nonspecific background can prevent assessment of HPA's reported cytoplasmic expression (general IHC practice; HPA tissue IHC). | Review blocking, primary-antibody concentration and washes; use the omission control to distinguish detection background from primary-antibody-associated staining (general IHC practice). |
| Apparently uniform staining throughout a tissue. | Scoring the whole section can conceal differences between cell populations; HPA assigns staining levels to specified cells (HPA tissue IHC). | Score the named cell types separately, using the counterstain for orientation and including both reported medium and not-detected populations where available (HPA tissue IHC; general IHC practice). |
| Vesicular IF looks convincing, but IHC remains equivocal. | HPA supports the ICC location while rating both its tissue IHC profile and HPA059551 IHC result Uncertain (HPA subcellular ICC-IF; HPA tissue IHC; HPA antibody record). | Interpret each application against its own controls and evidence; do not treat the ICC result as validation of chromogenic IHC staining (general IHC practice; HPA antibody record). |
Comprehensive Human Protein Atlas IHC scoring per tissue (reliability: Uncertain — Pending external verification.). 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 | Medium | Protein (IHC) | HPA → |
| Appendix | Glandular cells | Medium | Protein (IHC) | HPA → |
| Bronchus | Respiratory epithelial cells | Medium | Protein (IHC) | HPA → |
| Cerebellum | Cells in granular layer | Medium | Protein (IHC) | HPA → |
| Cerebral cortex | Neuropil | Medium | 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 → |
| Breast | Adipocytes | Not detected | Protein (IHC) | HPA → |
| Caudate | Glial cells | Not detected | Protein (IHC) | HPA → |
| Cervix | Glandular cells | Not detected | Protein (IHC) | HPA → |
Use the catalog antibody’s paraffin-section result as a starting point, then judge staining against ATG9A localisation and cell-level controls.
IHC images cover human heart, glioma and lung cancer tissue, and mouse brain; IF images cover human heart tissue and A549 cells (catalog image captions).
A03757-3 has IHC images from human glioma and mouse brain, while A03757 has IHC and IF images from human heart tissue (catalog image captions). M03757 has an IHC image from human lung cancer, and A03757-2 has an IF/ICC image from A549 cells (catalog image captions).
Which to pick: For paraffin-section IHC, choose A03757-3: its glioma caption specifies EDTA pH 8 retrieval and 2 μg/mL primary antibody; the fixative is unreported (A03757-3 IHC caption). For IF/ICC, choose A03757-2, which lists both applications and shows staining in A549 cells (A03757-2 applications and IF caption). For work across species, A03757-3 lists human, mouse and rat reactivity and includes a mouse brain IHC image (A03757-3 catalog reactivity and IHC captions).