ATP6V1A / V-type proton ATPase catalytic subunit A · IHC design guide

Design Immunohistochemistry for ATP6V1A

Plan chromogenic IHC on paraffin sections using antibody A10401-2 at 2–5 μg/ml (datasheet A10401-2). Interpret cytoplasmic and nuclear staining against the broad tissue pattern, with high signal in colon glandular cells and no detected signal in liver cholangiocytes (HPA tissue IHC).

Evidence assembled Oct 2026 · For research use; verify linked source records and product datasheet before use
Immunohistochemistry protocol sheet for ATP6V1A (IHC for ATP6V1A): expected localisation Cytoplasmic and nuclear tissue staining (HPA tissue IHC), antibody A10401-2, validated IHC image, and IHC protocol steps
Printable ATP6V1A IHC protocol sheet — expected localisation Cytoplasmic and nuclear tissue staining (HPA tissue IHC), antibody A10401-2, controls and protocol steps. Open the full ATP6V1A IHC guide →

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 Cytoplasmic and nuclear tissue staining (HPA tissue IHC)
Staining pattern Widespread cytoplasmic and nuclear signal (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 consistent across sections. (standard IHC practice; not target-specific)
Caveat Liver cholangiocytes show no detected signal (HPA tissue IHC)
Regulation Low tissue specificity (HPA tissue RNA)
Isoform / epitope 2 isoforms; epitope differences unspecified (UniProt)
Section 1

Recommended ATP6V1A IHC & IF Protocols

The catalog antibody protocol uses EDTA pH 8.0 heat retrieval (datasheet A10401-2). The published IHC protocol below examines ATP6V1A in human invasive ductal carcinoma (PMC8721851).

Recommended immunohistochemistry (IHC-P) protocol parameters
SampleParaffin-embedded human adenocarcinoma of the right colon tissue; fixative not specified (datasheet A10401-2)
FixationImage fixative and duration unreported (datasheet A10401-2); verify before use.
Sectioning4–5 µm sections on charged slides (standard)
DeparaffinisationXylene, graded ethanol series to water (standard)
Antigen retrievalHeat retrieval: EDTA pH 8.0 (datasheet A10401-2); 20 min, 95–100 °C (standard)
Peroxidase block3% H2O2, 10 min, room temperature (standard)
Blocking10% goat serum (datasheet A10401-2)
Primary antibodyRabbit anti-ATP6V1A, 2-5 μg/ml (datasheet A10401-2)
Primary incubationOvernight at 4 °C (datasheet A10401-2)
DetectionHRP-conjugated secondary, DAB chromogen (datasheet A10401-2)
CounterstainHematoxylin, blue, dehydrate and mount (standard)
Expected resultATP6V1A-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 EDTA pH 8.0 heat retrieval (datasheet A10401-2); the published breast carcinoma protocol does not report a retrieval method (PMC8721851).
Section 2

What Is the Expected ATP6V1A Staining Pattern?

ATP6V1A should appear mainly in the cytoplasm, including vesicle-associated regions, with some nuclear staining possible (UniProt P38606 localization; HPA: ubiquitous cytoplasmic and nuclear IHC expression; HPA: vesicles and cytosol in ICC-IF, additional nucleoplasm). Expect staining across many cell types, with strong examples in adrenal glandular and cerebellar Purkinje cells (HPA: High). The subunit has no transmembrane segment (UniProt P38606 topology). HPA rates its tissue IHC profile Approved, with medium staining–RNA consistency and external verification pending (HPA: reliability).

What am I looking at on my slide?
Cytoplasmic staining, sometimes granular, in adrenal glandular cells or cerebellar Purkinje cells (HPA: High).This matches reported IHC-positive cells (HPA: High). A granular component is compatible with vesicle localization (HPA: ICC-IF vesicles; UniProt P38606 localization). Chromogenic IHC may not resolve individual vesicles; judge the cell and overall compartment before interpreting fine puncta.
Nuclear signal accompanies cytoplasmic staining, or appears alongside a vesicular pattern (HPA: tissue IHC profile; HPA: ICC-IF nucleoplasm).Do not reject nuclear signal solely because ATP6V1A functions in a proton pump: HPA reports nuclear IHC expression and additional nucleoplasmic ICC-IF localization (HPA: tissue IHC profile; HPA: ICC-IF nucleoplasm). A nuclear-only pattern needs comparison with a known-positive control and the negative reagent control.
Strong signal is confined to cell borders or extracellular deposits, with little cytoplasmic signal.This is discordant with the reported cytoplasmic and vesicular distribution (HPA: tissue IHC profile; HPA: ICC-IF vesicles and cytosol). Check whether the apparent border signal follows tissue folds or chromogen deposits; repeat with controls before assigning a membrane-specific ATP6V1A pattern (UniProt P38606 localization).
Cholangiocytes stain strongly in liver, despite little signal in the expected positive control.HPA reports ATP6V1A as not detected in liver cholangiocytes (HPA: Not detected). Consider antibody cross-reactivity or endogenous detection activity; inspect the reagent-negative control and verify cell identity. This comparison applies to cholangiocytes, not to every cell in liver.
Diffuse color covers cells and empty tissue spaces, or known-positive adrenal glandular cells remain unstained (HPA: High).Diffuse staining outside cells suggests background from the detection workflow; weak or absent staining in a reported positive population suggests a failed or insufficiently sensitive run. Neither finding alone establishes ATP6V1A absence. Compare matched control sections before interpreting the specimen (HPA: adrenal glandular cells High).
💡Expected ATP6V1A appearanceA convincing positive has cytoplasmic staining, potentially granular, in reported positive cells such as adrenal glandular or cerebellar Purkinje cells (HPA: High; HPA: ICC-IF vesicles and cytosol); nuclear signal may coexist (HPA: tissue IHC profile), while dominant extracellular deposits or border-only color warrant an artefact check.
How each factor affects the staining
Compartment and resolutionATP6V1A is cytosolic and associated with vesicles and lysosome membranes (UniProt P38606 localization); ICC-IF resolves vesicles more directly than chromogenic paraffin IHC (HPA: ICC-IF vesicles; standard microscopy practice). Interpret IHC granularity conservatively.
Cell and tissue choiceHPA reports High staining in adrenal glandular cells, cerebellar Purkinje cells, and several other populations, but Not detected in liver cholangiocytes (HPA: tissue IHC). Use the named cell population when selecting or reading controls; an entire organ is not uniformly positive or negative.
Strength of evidenceThe tissue IHC profile is Approved, with medium consistency against RNA and external verification pending (HPA: reliability). CAB006910 is IHC Approved; HPA035084 has ICC Supported status without an IHC status in this payload (HPA: antibody validation). Match claims to the assay and antibody actually used.
Topology and epitopeATP6V1A has no transmembrane segment or signal peptide and is the catalytic V1 subunit (UniProt P38606 topology, processing, function). These facts support an intracellular interpretation but do not locate the catalog antibody's epitope or predict which antigen retrieval condition will work.
Isoforms and modificationsUniProt lists two isoforms and three modified residues, including phosphorylation sites (UniProt P38606 isoforms, modified residues). Without an antibody epitope or isoform-specific validation, differences in staining cannot be assigned to an isoform or modification.
Fixation and retrieval evidenceNo ATP6V1A-specific fixation sensitivity or retrieval condition is established by the supplied UniProt and HPA records. Antigen retrieval is a general paraffin-IHC optimization step; compare conditions using the same positive control before attributing a signal change to target biology.
Why is my staining missing, weak or wrong?
SituationLikely causeNext action
Known-positive adrenal glandular cells are blank or very weak (HPA: High).The run may lack sufficient usable signal; the HPA tissue result alone cannot identify which preparation or detection step failed.Check that the positive section and detection reagents worked, then optimize the catalog antibody dilution and antigen retrieval using matched sections. Record each condition; no ATP6V1A-specific dilution or retrieval recipe is supplied.
Color is widespread, including empty spaces or section edges.Chromogen precipitate, insufficient washing, or nonspecific detection can produce diffuse background (standard IHC practice). This pattern does not track the reported cellular localization (HPA: tissue IHC profile).Inspect a reagent-negative section, remove visible precipitate, and review washing and blocking. Reassess whether signal remains inside cells after background is reduced; use the same exposure and scoring criteria across sections.
Liver cholangiocytes show strong staining (HPA: Not detected).Possible cell misidentification, cross-reactivity, or endogenous detection activity; HPA's finding is specific to cholangiocytes, and its IHC evidence has medium RNA consistency (HPA: reliability).Confirm the stained cell type on the counterstained section. Compare a reagent-negative control and a reported positive cell population, then repeat or seek independent antibody evidence if the discordance persists.
The slide appears exclusively membranous or extracellular.That distribution conflicts with cytoplasmic IHC and vesicle/cytosol ICC-IF findings (HPA: tissue IHC profile; HPA: ICC-IF localization). Tissue folds or localized background may mimic borders (standard IHC practice).Review morphology at higher magnification, including intact cells away from edges. Check a reagent-negative control and compare with a reported positive tissue before scoring the border signal as ATP6V1A.
Nuclear staining seems unexpected.Nuclear staining is reported in tissue IHC, and nucleoplasm is an additional ICC-IF location (HPA: tissue IHC profile; HPA: ICC-IF nucleoplasm). Nuclear signal alone does not prove artefact.Score nuclear and cytoplasmic compartments separately. Compare distribution in a reported positive cell type and inspect reagent-negative staining; investigate a nuclear-only pattern that lacks the expected cytoplasmic component.
IF/ICC puncta and paraffin IHC staining look different.HPA reports vesicles and cytosol in ICC-IF, while its tissue IHC profile describes broader cytoplasmic and nuclear expression (HPA: ICC-IF localization; HPA: tissue IHC profile). The methods reveal different levels of spatial detail.Use the ICC-IF finding as localization context, not an IHC protocol setting. Judge the paraffin section against IHC cell-type and compartment expectations; consult the separate IF/ICC guide for that assay.

Sample controls for ATP6V1A IHC & IF

🧪Run cerebellum first; Purkinje cells should stain (HPA: High in cerebellar Purkinje cells). Use liver cholangiocytes as the negative tissue compartment (HPA: Not detected in liver cholangiocytes); on the cerebellar slide, cells without specific staining should show only counterstain or background, although HPA does not identify a validated negative cerebellar cell type (HPA: cerebellar Purkinje cell row).
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; rabbit IgG matched to the primary’s clonality and concentration as an isotype control; and ATP6V1A knockout material, if available, as a biological negative (caption: rabbit anti-ATP6V1A primary; standard IHC control practice). For cerebellar DAB staining, quench endogenous peroxidase and check for neuronal lipofuscin pigment that could resemble chromogen (caption: HRP/DAB; 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 (caption: fixative unreported). Heat-mediated retrieval in EDTA at pH 8.0 is documented, but retrieval dependency and whether frozen sections or IF are easier are unreported (caption: EDTA heat retrieval; HPA: ICC-IF images). In cerebellum, assess granular cytoplasmic signal against pigment and control-slide background (UniProt P38606: cytosol and vesicles; standard IHC practice: neuronal lipofuscin).

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

TissueCell typeLevelEvidenceSource
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

TissueCell typeLevelEvidenceSource
Liver Cholangiocytes Not detected Protein (IHC) HPA →
Section 3

Advanced ATP6V1A IHC Tips

Troubleshoot ATP6V1A staining in paraffin sections by checking retrieval, compartment patterns, controls and scoring before interpreting differences between samples.

How should I retrieve ATP6V1A in paraffin sections when staining is weak?
Start with heat-mediated retrieval in EDTA at pH 8.0 (datasheet A10401-2). The selected paraffin-section image used this retrieval before staining with 2 μg/ml antibody overnight at 4°C, so those conditions provide a documented starting point (caption A10401-2). If staining remains weak, check that sections stayed submerged and that heating and cooling were consistent across the batch (standard IHC practice). Change retrieval time in a small side-by-side series while holding antibody concentration and detection constant (standard IHC practice). A different buffer or pH is a fallback to test only after the documented EDTA condition has been assessed (datasheet A10401-2; standard IHC practice).
Could fixation explain variable ATP6V1A staining between paraffin blocks?
Target-specific fixation sensitivity is unknown because the selected tissue-IHC caption does not state a fixative (caption A10401-2). Record each block’s fixative and fixation duration, and compare sections of similar thickness processed in the same run (standard IHC practice). Use the documented EDTA retrieval at pH 8.0 and 2 μg/ml antibody condition as fixed starting variables when assessing block-to-block variation (datasheet A10401-2; caption A10401-2). Include a reference section from one block in every run to reveal processing or detection drift (standard IHC practice). Do not assign a fixation effect to ATP6V1A from its tissue staining pattern or protein topology alone (HPA tissue IHC; UniProt P38606 topology).
Which compartments should show ATP6V1A staining in chromogenic IHC?
Assess cytoplasmic staining, including punctate vesicle-associated signal, because ATP6V1A is reported in cytosol and vesicles and has no transmembrane segment (UniProt P38606 localisation and topology; HPA subcellular). HPA tissue IHC also describes widespread cytoplasmic and nuclear expression, while subcellular imaging lists nucleoplasm as an additional location (HPA tissue IHC; HPA subcellular). Nuclear colour therefore needs comparison with cytoplasmic staining and controls before interpretation (HPA tissue IHC; standard IHC practice). Examine a documented high-staining population, such as colon glandular cells, alongside the study tissue (HPA: High in colon glandular cells). Score compartments separately at a consistent magnification and exposure to the chromogen (standard IHC practice).
Could isoforms or epitope position change the ATP6V1A IHC pattern?
ATP6V1A has 2 annotated isoforms, but the supplied evidence does not map this antibody’s epitope to either one (UniProt P38606 isoforms; caption A10401-2). The protein is a 617-residue catalytic V1 subunit without an annotated transmembrane segment, so membrane-adjacent puncta do not by themselves locate the antibody epitope (UniProt P38606 chain, function and topology). Reported modifications include phosphorylation at residues 136 and 384; their effect on this antibody’s IHC staining is unestablished (UniProt P38606 modified residues; caption A10401-2). If staining differs between specimens, compare retrieval and controls before attributing it to an isoform or modification (standard IHC practice). Request epitope mapping or isoform-reactivity evidence before making that attribution (standard IHC practice).
How should I assess ATP6V1A by multiplex IF alongside this IHC guide?
For the separate IF/ICC assessment, pair ATP6V1A with a marker identifying the expected cell population, such as a glandular-cell marker when studying colon glands (HPA: High in colon glandular cells; standard IF practice). Inspect unstained tissue first, then choose spectrally separated fluorophores; a far-red channel near 647 nm can help assess signal against shorter-wavelength tissue autofluorescence (standard IF practice). ATP6V1A lacks a transmembrane segment and is reported in cytosol and vesicles, so intracellular epitope access requires permeabilisation to be assessed (UniProt P38606 topology and localisation; standard IF practice). Check single-stain controls for bleed-through and compare puncta with the cell marker and nuclear counterstain (standard IF practice). The supplied IHC caption does not establish IF fixation or antibody conditions (caption A10401-2).
How can I distinguish ATP6V1A staining from diffuse DAB background?
Compare test sections with a primary-antibody omission control and inspect whether colour follows cell boundaries or instead coats edges, folds and damaged areas (standard IHC practice). The selected paraffin-section image used 10% goat serum blocking, 2 μg/ml primary antibody overnight at 4°C, and DAB development (caption A10401-2). If background is widespread, check blocking and washing, then titrate primary antibody around the documented concentration while keeping retrieval unchanged (caption A10401-2; standard IHC practice). Include a peroxidase block before HRP detection to assess endogenous enzyme contribution; this is a general chromogenic IHC step (standard IHC practice). Judge improvement by preserved cellular signal and reduced staining in omission controls (standard IHC practice).
How should I quantify ATP6V1A staining across tissue sections? ⚠ ANSWER MARKED FOR VERIFICATION
Define the tissue region and cell population before scoring, and keep retrieval, staining run and image settings comparable across samples (standard IHC practice). For cellular DAB staining, record the percentage of positive cells and intensity grades 0–3, then calculate an H-score from 0–300 (standard IHC practice). Score cytoplasmic and nuclear signal separately because both appear in the supplied tissue profile, while vesicles and cytosol are supported subcellular locations (HPA tissue IHC; HPA subcellular). Normalise counts to the number of evaluable cells, or positive-cell density to viable tissue area in mm² (standard IHC practice). Exclude folds, section edges and necrotic regions by a prespecified rule, and report the excluded area (standard IHC practice).
What makes an ATP6V1A-positive IHC result credible rather than artefactual?
A credible result follows cellular anatomy and a plausible cytoplasmic or vesicular pattern; nuclear staining is also reported, so evaluate it separately (UniProt P38606 localisation; HPA tissue IHC and subcellular). Compare with a documented high-staining population such as colon glandular cells, and note that liver cholangiocytes were reported as not detected in the supplied tissue profile (HPA tissue IHC). Signal confined to section edges, folds or necrotic areas warrants review for artefact (standard IHC practice). Check a primary-antibody omission control and peroxidase blocking when diffuse DAB colour could reflect endogenous enzyme activity (standard IHC practice). HPA rates tissue staining as Approved with medium RNA concordance and pending external verification, so interpret unexpected cell-specific claims cautiously (HPA tissue IHC reliability).
Boster reagents

Best ATP6V1A / V-type proton ATPase catalytic subunit A IHC Antibodies

Anti-ATP6V1A antibodies have human paraffin-section IHC and human cell IF images (catalog image captions); listed reactivity covers human, mouse, rat, and, for one SKU, monkey (catalog reactivity).

Real IHC data IHC analysis of ATP6V1A using anti-ATP6V1A antibody (A10401-2). ATP6V1A was detected in a paraffin-embedded section of human adenocarcinoma of the right colon tissue. Heat mediated antigen retrieval was performed in EDTA buffer (pH 8.0, epitope retrieval solution). The tissue section was blocked with 10% goat serum. The tissue section was then incubated with 2 μg/ml rabbit anti-ATP6V1A Antibody (A10401-2) overnight at 4°C. Peroxidase Conjugated Goat Anti-rabbit IgG was used as secondary antibody and incubated for 30 minutes at 37°C. The tissue section was developed using HRP Conjugated Rabbit IgG Super Vision Assay Kit (Catalog # SV0002) with DAB as the chromogen.
Anti-ATP6V1A Antibody ®
Cat # A10401-2
Real IF data IF analysis of ATP6V1A using anti-ATP6V1A antibody (A10401-1). ATP6V1A was detected in an immunocytochemical section of Hela cells. Enzyme antigen retrieval was performed using IHC enzyme antigen retrieval reagent (AR0022) for 15 mins. The cells were blocked with 10% goat serum. And then incubated with 5 μg/mL rabbit anti-ATP6V1A Antibody (A10401-1) overnight at 4°C. DyLight®488 Conjugated Goat Anti-Rabbit IgG (BA1127) was used as secondary antibody at 1:100 dilution and incubated for 30 minutes at 37°C. The section was counterstained with DAPI. Visualize using a fluorescence microscope and filter sets appropriate for the label used.
Anti-ATP6V1A Antibody ®
Cat # A10401-1

A10401-2 is listed for IHC and IF, with IHC images of human paraffin sections and an IF image of A549 cells (catalog applications; A10401-2 image captions). A10401-1 is listed for ICC/IF and has a HeLa cell IF image (catalog applications; A10401-1 image caption).

Which to pick: Choose A10401-2 for tissue IHC: its own caption documents staining of human paraffin sections, but does not report the fixative (A10401-2 IHC image caption). For IF/ICC, either SKU is listed, with A10401-1 imaged in HeLa cells and A10401-2 in A549 cells (catalog applications; respective IF image captions). Both are rabbit antibodies; A10401-1 additionally lists monkey reactivity, while neither catalog entry establishes IHC staining in species beyond human (catalog host, reactivity, and IHC image captions).

Each figure is that product's own IHC / IF validation image from its datasheet.

References

  1. UniProt Consortium. UniProt entry P38606 (VATA_HUMAN, V-type proton ATPase catalytic subunit A).
  2. Human Protein Atlas. ATP6V1A tissue IHC expression (reliability: Approved).
  3. Human Protein Atlas. ATP6V1A subcellular location (ICC-IF): Mainly localized to vesicles and cytosol. In addition localized to the nucleoplasm..
  4. Human Protein Atlas. ATP6V1A antibody validation summary (2 antibodies).
  5. circSnx12 Is Involved in Ferroptosis During Heart Failure by Targeting miR-224-5p. Frontiers in cardiovascular medicine 2021 — PMC8097164.
  6. 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.
  7. Renoprotective effects of tubular glucagon receptor activation mediated by V-ATPase. Science advances 2026 — PMC13440415.
  8. Discovering novel mechanisms of taxane resistance in human breast cancer by whole-exome sequencing. Oncology letters 2022 — PMC8721851.
  9. PubMed PMID:8463241 — UniProt-cited evidence.
  10. PubMed PMID:10931946 — UniProt-cited evidence.
  11. PubMed PMID:14702039 — UniProt-cited evidence.