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ATP6V1A / V-type proton ATPase catalytic subunit A · IHC design guide
Design Immunohistochemistry for ATP6V1A
Plan chromogenic IHC on paraffin sections with antibody A10401-2 at 2–5 μg/ml (datasheet A10401-2). Assess cytoplasmic and nuclear staining across cell types, bearing in mind that liver cholangiocytes were reported as unstained (HPA tissue IHC).
Evidence assembled Oct 2026 · For research use; verify linked source records and product datasheet before use
ATP6V1A Immunohistochemistry Experimental Design Guide
Expected localisation, validated protocols, controls and antibodies — the at-a-glance facts below, then the full design guide.
Must know before staining
| Expected localisation | Observed cytoplasmic and nuclear tissue staining (HPA tissue IHC) | |
| Staining pattern | Across cell types: cytoplasmic and nuclear staining (HPA tissue IHC) | |
| Antigen retrieval | EDTA pH 8.0 HIER, heat-mediated (datasheet A10401-2) | |
| Positive control | Adrenal gland+4 more · see all | |
| Negative control | Liver |
Important caveats
Reasons your staining may differ from the expected pattern.
| Fixation | Keep fixation conditions consistent between samples. (standard IHC practice; not target-specific) | |
| Caveat | Liver cholangiocytes may be unstained (HPA tissue IHC) | |
| Regulation | High expression in skin (UniProt) | |
| Isoform / epitope | 2 isoforms; check epitope coverage; no transmembrane segment (UniProt) |
Section 1
Recommended ATP6V1A IHC & IF Protocols
The catalog antibody has an IHC-P protocol (datasheet A10401-2); one published protocol stains ATP6V1A in human breast cancer tissue (PMC8721851).
| Sample | Paraffin-embedded human adenocarcinoma of the right colon tissue; fixative not specified (datasheet A10401-2) |
| Fixation | Image fixative and duration unreported (datasheet A10401-2); 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 A10401-2); 20 min, 95–100 °C (standard) |
| Peroxidase block | 3% H2O2, 10 min, room temperature (standard) |
| Blocking | 10% goat serum (datasheet A10401-2) |
| Primary antibody | Rabbit anti-ATP6V1A, 2-5 μg/ml (datasheet A10401-2) |
| Primary incubation | Overnight at 4 °C (datasheet A10401-2) |
| Detection | HRP-conjugated secondary, DAB chromogen (datasheet A10401-2) |
| Counterstain | Hematoxylin, blue, dehydrate and mount (standard) |
| Expected result | ATP6V1A-positive staining in glandular cells of adrenal gland (HPA tissue IHC: High). HPA tissue profile: Ubiquitous cytoplasmic and nuclear expression. No signal in the no-primary control. |
💡Decision noteStart with heat-mediated EDTA retrieval at pH 8.0 for the catalog antibody (datasheet A10401-2); the published ATP6V1A protocol does not specify retrieval (PMC8721851).
Section 2
What Is the Expected ATP6V1A Staining Pattern?
ATP6V1A is a cytosolic V-ATPase subunit associated with vesicles and lysosome membranes; it has no transmembrane segment (UniProt P38606). In paraffin-section IHC, expect staining in many cell types, including adrenal glandular cells, cortical neurons and cerebellar Purkinje cells (HPA tissue IHC: High). HPA describes ubiquitous cytoplasmic and nuclear expression, but rates its tissue IHC profile Approved with medium consistency against RNA data and pending external verification (HPA tissue IHC).
| Cytoplasmic staining in adrenal glandular cells, cortical neurons or Purkinje cells. | These are reported high-staining cells (HPA tissue IHC: High). A vesicular component is compatible with the protein’s cytosolic and vesicle-associated locations (UniProt P38606); the record does not prescribe a precise chromogenic texture. |
| Nuclear staining accompanies cytoplasmic staining. | This can fit the reported tissue profile (HPA tissue IHC: ubiquitous cytoplasmic and nuclear expression). Nucleoplasm is also an additional ICC-IF location (HPA subcellular: Approved). Nuclear signal alone should therefore be judged against the tissue pattern and controls. |
| Signal is confined to an unexpected compartment, such as extracellular deposits. | Extracellular-only staining does not fit the listed intracellular locations (UniProt P38606; HPA subcellular). Treat it as a possible artefact and check the no-primary control and tissue morphology before assigning it to ATP6V1A (general IHC practice). |
| Strong staining appears in liver cholangiocytes. | HPA reports these cells as not detected (HPA tissue IHC: liver). Unexpected signal may reflect cross-reactivity or endogenous detection activity (general IHC practice). One discordant specimen is not decisive because the HPA tissue profile has medium consistency and awaits external verification (HPA tissue IHC). |
| Known high-staining tissue has diffuse background or no discernible cellular signal. | Loss of contrast or absent staining prevents a reliable localisation call (general IHC practice). Check the tissue and detection controls first; an HPA High designation identifies a useful comparator, not a guaranteed result in every section (HPA tissue IHC: High; Approved, medium consistency). |
💡Expected ATP6V1A appearanceCall a positive result when discernible cytoplasmic staining, potentially vesicle-associated, appears in an HPA high-staining cell population; assess nuclear signal in context, and treat extracellular-only deposits or unexplained cholangiocyte staining as suspect (UniProt P38606; HPA tissue IHC; HPA subcellular).
| Subcellular context | ATP6V1A is a soluble V1 catalytic subunit with no transmembrane segment, listed in cytosol, vesicles and lysosome membrane (UniProt P38606). Judge localisation at the cellular level rather than requiring a continuous membrane outline. |
| Tissue and cell selection | Adrenal glandular cells, cortical neurons and Purkinje cells are High, whereas liver cholangiocytes are not detected (HPA tissue IHC). Include a high-staining population as a positive comparator when available. |
| Confidence in the tissue reference | The tissue IHC profile is Approved, with medium staining–RNA consistency and external verification pending (HPA tissue IHC). Use its levels as interpretation guides, not absolute cutoffs for individual specimens. |
| Antibody validation | CAB006910 has Approved IHC status; HPA035084 has Supported ICC status and no listed IHC status (HPA antibodies). An ICC result does not establish performance in paraffin-section IHC. |
| Isoforms and processing | Two isoforms are listed, with a full-length chain at residues 1–617 and no annotated signal peptide or propeptide (UniProt P38606). The payload gives no epitope position, so it cannot predict isoform coverage or cleavage-related staining. |
| Retrieval and fixation evidence | No target-specific retrieval or fixation effect is supplied (UniProt P38606; HPA tissue IHC). Set retrieval and detection from the IHC-validated antibody’s documented method, then verify with tissue controls (general IHC practice). |
| IF/ICC question: should its image pattern guide IHC interpretation? | Yes, as localisation context: vesicles and cytosol are main ICC-IF locations, with nucleoplasm additional (HPA subcellular). ICC-IF images and Supported ICC status do not supply a paraffin IHC protocol (HPA subcellular; HPA antibodies). |
| Situation | Likely cause | Next action |
|---|---|---|
| No signal in a high-staining comparator. | The staining run may have failed, or the selected section may differ from the reference profile (general IHC practice; HPA tissue IHC: Approved, medium consistency). | Confirm tissue identity and preservation, then review the antibody’s IHC instructions, positive control and detection reagents before interpreting the specimen as negative (general IHC practice). |
| Diffuse chromogen obscures cell boundaries. | Nonspecific binding or excess detection background can reduce contrast (general IHC practice). | Inspect the no-primary control; review blocking, antibody concentration, washes and chromogen development using the validated IHC workflow (general IHC practice). |
| Staining is prominent in cholangiocytes. | This conflicts with the reported not-detected pattern and could reflect nonspecific staining or endogenous detection activity (HPA tissue IHC: liver; general IHC practice). | Compare a no-primary control and an HPA high-staining tissue in the same run; check detection-system blocking before calling the cholangiocyte signal specific (HPA tissue IHC: High; general IHC practice). |
| Signal appears only outside intact cells. | An extracellular-only pattern conflicts with the listed intracellular locations and may be precipitate or tissue artefact (UniProt P38606; HPA subcellular; general IHC practice). | Examine morphology and the no-primary control, then repeat with the validated chromogen development conditions if deposits persist (general IHC practice). |
| Nuclear signal seems stronger than cytoplasmic signal. | Nuclear staining is reported in tissue IHC, while nucleoplasm is an additional ICC-IF location; intensity balance is not specified (HPA tissue IHC; HPA subcellular). | Compare cellular morphology, cytoplasmic signal and controls across the section. Do not reject nuclear staining solely because it is nuclear (HPA tissue IHC; general IHC practice). |
| An ICC-supported antibody gives an uncertain paraffin-section result. | Supported ICC status alone does not validate paraffin IHC; only CAB006910 has listed Approved IHC status here (HPA antibodies). | Use an IHC-validated antibody and its documented paraffin-section method; confirm the run with an HPA high-staining tissue comparator (HPA antibodies; HPA tissue IHC: High). |
Experiment evidence
IHC & IF images showing ATP6V1A staining
A10401-2 · IHCIHC analysis of ATP6V1A using anti-ATP6V1A antibody (A10401-2). ATP6V1A was detected in a paraffin-embedded section of human adenocarcinoma
A10401-2 · IHCIHC analysis of ATP6V1A using anti-ATP6V1A antibody (A10401-2). ATP6V1A was detected in a paraffin-embedded section of human cervical cancer
A10401-2 · IFIF analysis of ATP6V1A using anti-ATP6V1A antibody (A10401-2). ATP6V1A was detected in an immunocytochemical section of A549 cells. Enzyme a
A10401-1 · IFIF analysis of ATP6V1A using anti-ATP6V1A antibody (A10401-1). ATP6V1A was detected in an immunocytochemical section of Hela cells. Enzyme a
HPA · Cerebral cortexHuman Protein Atlas IHC, Cerebral cortex. Source: https://www.proteinatlas.org/ENSG00000114573-ATP6V1A/tissue/cerebral+cortex#imid_1849800
HPA · ColonHuman Protein Atlas IHC, Colon. Source: https://www.proteinatlas.org/ENSG00000114573-ATP6V1A/tissue/colon#imid_1849734
HPA · LiverHuman Protein Atlas IHC, Liver. Source: https://www.proteinatlas.org/ENSG00000114573-ATP6V1A/tissue/liver#imid_1849735
HPA · KidneyHuman Protein Atlas IHC, Kidney. Source: https://www.proteinatlas.org/ENSG00000114573-ATP6V1A/tissue/kidney#imid_1849728
HPA · ICC-IF A-431Human Protein Atlas immunofluorescence, A-431, antibody HPA035084; green = ATP6V1A, blue = nucleus, red = microtubules.
HPA · ICC-IF A-431Human Protein Atlas immunofluorescence, A-431, antibody HPA035084; green = ATP6V1A, blue = nucleus, red = microtubules.
← swipe / scroll for more images →
Real IHC / IF data behind the staining-pattern expectations in this section.
Sample controls for ATP6V1A IHC & IF
🧪Run bone marrow first: hematopoietic cells should stain (HPA: High in bone marrow hematopoietic cells). Use liver cholangiocytes as the negative tissue (HPA: Not detected); cells without specific cytoplasmic or vesicular staining on the positive slide should remain at background, although the supplied HPA rows do not identify a validated internal negative marrow cell type (HPA: bone marrow hematopoietic cells High).
Positive control tissue: Adrenal gland (Glandular cells, HPA High)
Negative control tissue: Liver (HPA Not detected)
ICC-IF cell lines (HPA subcellular resource): HPA ICC-IF images show ATP6V1A in A-431, A-549, U2OS, with annotated localisation: Vesicles (approved), Cytosol (supported) (HPA subcellular).
Technical controls: Include a no-primary, secondary-only control, a concentration-matched rabbit IgG isotype control, and ATP6V1A knockout tissue or cells as a biological negative (selected A10401-2 caption: rabbit primary; standard IHC practice). Quench endogenous peroxidase in bone marrow before HRP/DAB detection and check the no-primary slide for residual signal (standard IHC practice).
⚠️Feasibility: A target-specific fixation window or fixation effect is unreported, and the selected A10401-2 paraffin-section caption does not state a fixative (selected A10401-2 tissue-IHC caption). The caption uses heat-mediated EDTA retrieval at pH 8.0, which is a starting condition; dependence on retrieval is unreported (selected A10401-2 tissue-IHC caption). Whether frozen sections or IF are easier is unreported; endogenous peroxidase in bone marrow hematopoietic cells can produce misleading DAB signal (standard IHC practice).
HPA tissue IHC evidence for ATP6V1A
Comprehensive Human Protein Atlas IHC scoring per tissue (reliability: Approved — Medium consistency between antibody staining and RNA expression data. Pending external verification.). Rows are taken directly from the HPA tissue chart — click any row's HPA link to view the source.
Positive expression · recommended positive controls
| Tissue | Cell type | Level | Evidence | Source |
|---|---|---|---|---|
| Adrenal gland | Glandular cells | High | Protein (IHC) | HPA → |
| Bone marrow | Hematopoietic cells | High | Protein (IHC) | HPA → |
| Bronchus | Respiratory epithelial cells | High | Protein (IHC) | HPA → |
| Cerebellum | Purkinje cells | High | Protein (IHC) | HPA → |
| Cerebral cortex | Neuronal cells | High | Protein (IHC) | HPA → |
Undetected expression · recommended negative controls
| Tissue | Cell type | Level | Evidence | Source |
|---|---|---|---|---|
| Liver | Cholangiocytes | Not detected | Protein (IHC) | HPA → |
Section 3
Advanced ATP6V1A IHC Tips
Troubleshooting ATP6V1A staining in paraffin sections with chromogenic detection, with one companion question for IF/ICC.
Which retrieval condition should I start with for ATP6V1A in paraffin sections?
Start with heat mediated retrieval in EDTA pH 8.0 for paraffin sections (datasheet A10401-2). The catalog image used that condition before overnight incubation at 4°C with 2 μg/ml antibody (datasheet A10401-2). If staining is weak, first check that the section stayed covered during heating and cooling, then compare a shorter and longer heating interval on adjacent sections (standard IHC practice). Keep antibody concentration and detection conditions constant during that comparison so retrieval is the tested variable (standard IHC practice). A different buffer is a fallback only after this documented condition has been checked; record its pH and heating time alongside tissue morphology (standard IHC practice).
How should I troubleshoot ATP6V1A staining when fixation history is uncertain?
The selected paraffin section caption does not report its fixative, so target specific fixation sensitivity is unknown (datasheet A10401-2). Record the actual fixative, time in fixative, tissue thickness and processing history for each specimen before comparing staining (standard IHC practice). On adjacent sections, apply the documented EDTA pH 8.0 retrieval and 2 μg/ml antibody condition consistently, then assess both staining and preserved morphology (datasheet A10401-2; standard IHC practice). If specimens with different fixation histories disagree, repeat the comparison using matched processing before assigning a biological explanation (standard IHC practice). Do not use the reported tissue pattern or protein modifications to predict fixation effects without direct testing (HPA tissue IHC; UniProt P38606).
What ATP6V1A staining pattern is plausible in tissue sections?
Expect predominantly cytoplasmic staining, potentially with a punctate component: ATP6V1A is reported in cytosol and vesicles, including secretory vesicles and lysosome associated compartments (UniProt P38606 subcellular; HPA subcellular). ATP6V1A is a V1 catalytic subunit with no transmembrane segment, so a continuous membrane outline alone deserves scrutiny (UniProt P38606 function and topology). HPA also reports nuclear tissue staining and additional nucleoplasmic localisation, so nuclear signal cannot be dismissed solely by compartment (HPA tissue IHC; HPA subcellular). Compare cellular distribution with an adjacent section and a no primary control, using identical DAB development times (standard IHC practice). Resolve unexpected patterns with an independent antibody or orthogonal assay before calling them ATP6V1A specific (standard IHC practice).
Can the antibody distinguish ATP6V1A isoforms or modified epitopes in IHC?
ATP6V1A has 2 listed isoforms, but the supplied caption does not identify the antibody epitope or establish isoform selectivity (UniProt P38606 isoforms; datasheet A10401-2). The protein has no annotated transmembrane segment and has listed modifications including Thr136 phosphorylation, Ser384 phosphorylation by AMPK and Ala2 acetylation (UniProt P38606 topology and modified residues). Those annotations do not establish that any modification changes this antibody’s staining (UniProt P38606; datasheet A10401-2). Check the antibody’s immunogen or epitope documentation before interpreting isoform specific or modification dependent differences (standard IHC practice). If that information remains unavailable, report staining as ATP6V1A immunoreactivity and test a second mapped epitope for any stronger claim (standard IHC practice).
How can IF/ICC help assess the ATP6V1A pattern seen by chromogenic IHC?
Use IF/ICC as a companion localisation check, selecting a marker for the expected cell population rather than treating overlap as proof of ATP6V1A identity (standard IF practice). HPA places ATP6V1A mainly in vesicles and cytosol, with additional nucleoplasmic localisation; assess those compartments separately when comparing with IHC (HPA subcellular). Choose spectrally separated fluorophores and inspect an unstained specimen for autofluorescence before assigning puncta to either marker (standard IF practice). Because ATP6V1A lacks a transmembrane segment and occupies intracellular compartments, optimise permeabilisation for access to the mapped epitope and preserve vesicle structure (UniProt P38606 topology and subcellular; standard IF practice). The supplied IHC caption provides no IF/ICC fixation or permeabilisation condition for this antibody (datasheet A10401-2).
What should I check when ATP6V1A DAB staining looks diffuse or widespread?
Widespread signal may be plausible because HPA describes ubiquitous cytoplasmic and nuclear tissue expression, but its tissue IHC assessment has medium consistency and awaits external verification (HPA tissue IHC). Compare a no primary control with the stained section, and block endogenous peroxidase before HRP and DAB development (standard IHC practice). The selected caption used 10% goat serum, 2 μg/ml primary antibody overnight at 4°C, and a peroxidase conjugated secondary for 30 minutes at 37°C (datasheet A10401-2). If background persists, titrate primary antibody and shorten chromogen development while holding retrieval constant (standard IHC practice). Review edges, damaged areas and stromal deposits separately from intact cells (standard IHC practice).
How should I score ATP6V1A IHC across heterogeneous sections? ⚠ ANSWER MARKED FOR VERIFICATION
Define the cell population and compartment before scoring, because HPA reports both cytoplasmic and nuclear tissue staining (HPA tissue IHC). For intensity, calculate an H-score from the percentage of cells at each intensity level; also report the percentage of positive cells rather than collapsing both measures into one label (standard IHC practice). For spatial comparisons, count positive cells per mm² of viable tissue and normalise to the number of eligible cells or measured tissue area (standard IHC practice). Keep section thickness, retrieval, DAB development, imaging and scoring thresholds consistent across samples (standard IHC practice). Exclude folds and necrotic areas, and report cytoplasmic and nuclear scores separately when both are evaluated (standard IHC practice).
How can I distinguish specific ATP6V1A staining from artefact?
Assess whether signal occurs in intact cells with a plausible cytosolic or vesicular pattern; ATP6V1A is a V1 subunit without a transmembrane segment (UniProt P38606 subcellular, function and topology). Nuclear signal can occur, but isolated nuclear staining should be checked against HPA’s additional nucleoplasmic localisation and an independent specificity control (HPA subcellular; standard IHC practice). Compare expected cell populations: HPA reports high staining in colon glandular cells and no detected staining in liver cholangiocytes, with medium consistency for its tissue IHC profile (HPA tissue IHC). Treat edge staining, necrotic deposits and signal in a no primary control as possible artefacts; test endogenous peroxidase contribution when DAB persists (standard IHC practice). Corroborate surprising cell specific patterns before assigning biological meaning (standard IHC practice).
Boster reagents
Best ATP6V1A / V-type proton ATPase catalytic subunit A IHC Antibodies
The catalog shows ATP6V1A staining in human paraffin sections and human cells; both antibodies list Human, Mouse and Rat reactivity, and A10401-1 also lists Monkey (catalog image captions; reactivity).
Real IHC data
Anti-ATP6V1A Antibody ®
Cat # A10401-2
Real IF data
Anti-ATP6V1A Antibody ®
Cat # A10401-1
A10401-2 has IHC images from human paraffin sections of right-colon adenocarcinoma, cervical cancer, lienal rupture and liver cancer, plus IF in A549 cells (catalog image captions). A10401-1 has an IF image in Hela cells and lists ICC/IF, but does not list IHC (catalog image caption; applications).
Which to pick: Choose A10401-2 for chromogenic paraffin-section IHC: its own caption reports EDTA retrieval at pH 8.0, a 10% goat-serum block, 2 μg/ml primary antibody overnight at 4°C, and peroxidase/DAB detection; the fixative is unreported (A10401-2 IHC caption). For IF/ICC, either SKU lists those applications and has a human cell image; A10401-1 additionally lists Monkey reactivity, while both list Human, Mouse and Rat (catalog applications, reactivity and IF captions). Neither SKU reports a clone, so clonality cannot guide the choice (catalog clone fields).
Each figure is that product's own IHC / IF validation image from its datasheet.
References
- UniProt Consortium. UniProt entry P38606 (VATA_HUMAN, V-type proton ATPase catalytic subunit A).
- Human Protein Atlas. ATP6V1A tissue IHC expression (reliability: Approved).
- Human Protein Atlas. ATP6V1A subcellular location (ICC-IF): Mainly localized to vesicles and cytosol. In addition localized to the nucleoplasm..
- Human Protein Atlas. ATP6V1A antibody validation summary (2 antibodies).
- circSnx12 Is Involved in Ferroptosis During Heart Failure by Targeting miR-224-5p. Frontiers in cardiovascular medicine 2021 — PMC8097164.
- Interspecific comparisons of anuran embryonic epidermal landscapes and energetic trade-offs in response to changes in salinity. Developmental dynamics : an official publication of the American Association of Anatomists 2025 — PMC12678683.
- Renoprotective effects of tubular glucagon receptor activation mediated by V-ATPase. Science advances 2026 — PMC13440415.
- Discovering novel mechanisms of taxane resistance in human breast cancer by whole-exome sequencing. Oncology letters 2022 — PMC8721851.
- PubMed PMID:8463241 — UniProt-cited evidence.
- PubMed PMID:10931946 — UniProt-cited evidence.
- PubMed PMID:14702039 — UniProt-cited evidence.
Immunohistochemistry protocol sheet for ATP6V1A (V-type proton ATPase catalytic subunit A). Expected localisation Observed cytoplasmic and nuclear tissue staining (HPA tissue IHC). Antigen retrieval: EDTA pH 8.0 HIER, heat-mediated (datasheet A10401-2). Validated IHC antibody: A10401-2 at 2-5 μg/ml (the product's own IHC validation image is shown). Controls (HPA): positive Adrenal gland (Glandular cells); negative Liver. IHC-P workflow on paraffin sections; fixative unspecified. Protocol steps: 1. Sample: Paraffin-embedded human adenocarcinoma of the right colon tissue; fixative not specified (datasheet A10401-2); 2. Fixation: Image fixative and duration unreported (datasheet A10401-2); verify before use.; 3. Sectioning: 4–5 µm sections on charged slides (standard); 4. Deparaffinisation: Xylene, graded ethanol series to water (standard); 5. Antigen retrieval: Heat retrieval: EDTA pH 8.0 (datasheet A10401-2); 20 min, 95–100 °C (standard); 6. Peroxidase block: 3% H2O2, 10 min , room temperature (standard); 7. Blocking: 10% goat serum (datasheet A10401-2); 8. Primary antibody: Rabbit anti-ATP6V1A, 2-5 μg/ml (datasheet A10401-2); 9. Primary incubation: Overnight at 4 °C (datasheet A10401-2). Watch for: Fixation: Keep fixation conditions consistent between samples. (standard IHC practice; not target-specific); Caveat: Liver cholangiocytes may be unstained (HPA tissue IHC); Isoform / epitope: 2 isoforms; check epitope coverage; no transmembrane segment (UniProt); Regulation: High expression in skin (UniProt). Evidence: UniProt P38606, HPA tissue IHC · Approved, HPA ICC-IF · Mainly localized to vesicles and cytosol. In addition localized to…, Datasheet A10401-2, PMC8721851. QR code links to https://www.bosterbio.com/bosterbio-gene-info-cards/ATP6V1A/immunohistochemistry-ihc-guide.