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- Table of Contents
Plan chromogenic paraffin IHC for ATP1A1 using kidney collecting ducts as a high-staining reference (HPA tissue IHC). Score membrane staining by cell type and compare its distribution with the expected basolateral location (UniProt).
Expected localisation, validated protocols, controls and antibodies — the at-a-glance facts below, then the full design guide.
| Expected localisation | Membranous in tissue (HPA tissue IHC); basolateral expected (UniProt) | |
| Staining pattern | Membranous staining in most tissues (HPA tissue IHC) | |
| Antigen retrieval | EDTA pH 8.0 HIER, heat-mediated (datasheet PB9482) | |
| Positive control | Adrenal gland+4 more · see all | |
| Negative control | Adipose tissue+4 more · see all |
| Fixation | Keep paraffin-section fixation consistent (standard IHC practice; not target-specific) | |
| Caveat | RNA and IHC show medium consistency (HPA tissue IHC) | |
| Regulation | Alpha-isoform expression varies by tissue (UniProt) | |
| Isoform / epitope | 4 isoforms; map the epitope to cytoplasmic or extracellular regions (UniProt) |
The catalog antibody’s IHC-P protocol is followed by three published ATP1A1 chromogenic IHC protocols for tumor sections, breast cancer tissue microarrays, and kidney sections (PMC12442677; PMC11083557; PMC9204326).
| Sample | Paraffin-embedded human ovarian cancer tissue; fixative not specified (datasheet PB9482) |
| Fixation | Image fixative and duration unreported (datasheet PB9482); 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 PB9482); 20 min, 95–100 °C (standard) |
| Peroxidase block | 3% H2O2, 10 min, room temperature (standard) |
| Blocking | 10% goat serum (datasheet PB9482) |
| Primary antibody | Rabbit anti-ATP1A1, 2-5 μg/ml (datasheet PB9482) |
| Primary incubation | Overnight at 4 °C (datasheet PB9482) |
| Detection | HRP-conjugated secondary, DAB chromogen (datasheet PB9482) |
| Counterstain | Hematoxylin, blue, dehydrate and mount (standard) |
| Expected result | ATP1A1-positive staining in glandular cells of adrenal gland (HPA tissue IHC: High). HPA tissue profile: Membranous expression in most tissues. No signal in the no-primary control. |
ATP1A1 is a ten-pass membrane protein found at the cell membrane, including basolateral membranes (UniProt P05023 topology and subcellular annotation). In paraffin-section IHC, expect predominantly membranous staining in many tissues, with high staining in kidney collecting ducts and glandular cells of the breast and adrenal gland (HPA tissue IHC). HPA rates the tissue IHC evidence Enhanced, while reporting medium consistency between staining and RNA expression (HPA tissue IHC).
| Distinct cell borders in kidney collecting ducts, with strong staining relative to nearby background. | This fits the expected positive: HPA reports High staining in collecting ducts, and UniProt places ATP1A1 at the cell membrane (HPA tissue IHC; UniProt P05023 subcellular annotation). Assess the named cell population rather than calling the whole kidney uniformly positive (HPA tissue IHC). |
| Strong signal confined to nuclei, or diffuse cytoplasmic staining that obscures cell borders. | A nuclear-only pattern conflicts with the reported membrane location (UniProt P05023; HPA tissue IHC). HPA also records cytoplasm/membrane staining in cerebellar granular cells, so cytoplasmic signal alone is insufficient to reject a section; judge its cell type, distribution and background (HPA tissue IHC). |
| Prominent staining in adipocytes, cardiomyocytes or skeletal-muscle myocytes. | HPA reports ATP1A1 as Not detected in those specific cell populations (HPA tissue IHC). Check the annotated cells before suspecting cross-reactivity or endogenous detection activity; a tissue-wide negative claim would exceed the HPA observation (HPA tissue IHC; general IHC interpretation). |
| Brown deposit appears across cells and empty spaces, with little separation between them. | This is difficult to score as cell-associated membrane staining (UniProt P05023 subcellular annotation; general IHC interpretation). Review the no-primary control and detection background before assigning ATP1A1 positivity; widespread deposit alone does not establish target localization (general IHC practice). |
| No discernible signal in kidney collecting ducts or breast glandular cells. | These are HPA High populations, so their absence makes a negative result elsewhere hard to interpret (HPA tissue IHC; general IHC interpretation). Verify that the control contains the named cells and that the staining run worked before scoring the test section negative (general IHC practice). |
| Membrane topology and epitope location | ATP1A1 has 10 transmembrane segments and both cytoplasmic and extracellular regions (UniProt P05023 topology). Epitope position could affect antibody access, but the supplied record gives no catalog-antibody epitope, so it cannot predict a retrieval condition or staining strength (UniProt P05023 topology; evidence limit). |
| Cell population selected for scoring | HPA reports High staining in kidney collecting ducts and several glandular or endocrine populations, but Not detected in selected adipocytes and muscle cells (HPA tissue IHC). Those labels apply to the specified cells, not every cell in each tissue (HPA tissue IHC). |
| Antibody validation | The two listed antibodies, CAB018702 and CAB069993, each have Enhanced IHC status; HPA defines this as support from independent antibodies or orthogonal data (HPA antibody validation). The tissue profile still carries HPA's medium staining-to-RNA consistency qualifier (HPA tissue IHC). |
| Isoform interpretation | UniProt lists 4 ATP1A1 isoforms (UniProt P05023 isoforms). No antibody epitope or isoform-specific IHC pattern is supplied, so a positive cell cannot be assigned to a particular isoform from this staining alone (UniProt P05023 isoforms; evidence limit). |
| IF/ICC Q&A: what localization is reported? | HPA reports approved plasma-membrane and vesicle localization in ICC-IF, with images from A-431, U-251MG and U2OS (HPA subcellular ICC-IF). This is an IF/ICC localization reference; the primary application here is paraffin-section IHC (HPA subcellular ICC-IF; guide scope). |
| Situation | Likely cause | Next action |
|---|---|---|
| The positive-control section has no staining in kidney collecting ducts. | The expected High population may be absent from the section, or the staining run may have failed (HPA tissue IHC; general IHC practice). | Confirm collecting ducts are present; then check primary-antibody application, antigen-retrieval execution and detection steps against the run record (general IHC practice). No ATP1A1-specific retrieval setting is established here (evidence limit). |
| Membrane signal is weak and difficult to distinguish from counterstain. | Low contrast or a weak run can obscure cell borders (general IHC interpretation); HPA intensity also varies by named cell population (HPA tissue IHC). | Compare the test section with an HPA High control in the same run, then review catalog-antibody dilution and detection settings (HPA tissue IHC; general IHC practice). |
| Staining is mainly nuclear. | Nuclear-only staining does not fit the reported cell-membrane localization (UniProt P05023 subcellular annotation; HPA tissue IHC). | Check the no-primary control, staining distribution and cell identity; score ATP1A1 only where convincing target-associated staining survives those checks (general IHC practice). |
| An HPA Not detected cell population appears strongly positive. | Possible explanations include cross-reactivity or endogenous detection activity; HPA's negative call is specific to the annotated cell population (HPA tissue IHC; general IHC interpretation). | Confirm cell identity, compare a no-primary control and repeat with a separately validated antibody if needed (general IHC practice; HPA antibody validation). |
| Brown staining spreads beyond cell outlines or into empty spaces. | Diffuse detection background can mimic a widespread positive result (general IHC interpretation). | Inspect no-primary and reagent controls; review blocking, washing and detection timing before interpreting compartment-specific staining (general IHC practice). |
| Brown signal persists when primary antibody is omitted. | The signal can arise from the detection system rather than ATP1A1; endogenous peroxidase is a consideration for peroxidase-based chromogenic IHC (general IHC practice). | Review the detection chemistry and its endogenous-activity blocking step, then rerun the no-primary control alongside the sample (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 | Endocrine cells | High | Protein (IHC) | HPA → |
| Breast | Glandular cells | High | Protein (IHC) | HPA → |
| Cerebellum | Granular cells - cytoplasm/membrane | High | Protein (IHC) | HPA → |
| Colon | Endocrine 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 → |
| Heart muscle | Cardiomyocytes | Not detected | Protein (IHC) | HPA → |
| Hippocampus | Glial cells | Not detected | Protein (IHC) | HPA → |
| Lymph node | Germinal center cells | Not detected | Protein (IHC) | HPA → |
Troubleshoot ATP1A1 staining in paraffin sections by checking retrieval, compartment, cell identity and controls before comparing chromogenic signal across samples.
Two anti-ATP1A1 antibodies have IHC images from paraffin sections of human and rat tissues (catalog IHC captions). Both list human, mouse and rat reactivity; IF is also listed for both (catalog applications/reactivity).
PB9482 has IHC images from paraffin sections of human ovarian, colon, endometrioid adenocarcinoma and liver cancer tissue (PB9482 IHC captions). M00956 has IHC images from paraffin sections of rat cerebral cortex and heart and human cervical and thyroid cancer tissue; IF and ICC are listed applications (M00956 IHC captions; catalog applications).
Which to pick: For tissue IHC, PB9482 offers a documented starting condition of 2 μg/ml after EDTA retrieval at pH 8.0 in a paraffin section (PB9482 IHC caption); the fixative is unreported (PB9482 IHC caption). For IF/ICC, choose the rabbit monoclonal M00956 because both applications are listed (M00956 catalog applications/clone); its paraffin IHC caption likewise does not report a fixative (M00956 IHC caption). For work across human, mouse and rat, either SKU lists all three species as reactive (catalog reactivity).