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ATP6V1C1 / V-type proton ATPase subunit C 1 · IHC design guide
Design Immunohistochemistry for ATP6V1C1
Plan chromogenic paraffin IHC for ATP6V1C1 using cytoplasmic staining as the expected readout (HPA tissue IHC). Esophageal squamous cells and stomach glandular cells show high staining and can help assess the assay (HPA tissue IHC).
Evidence assembled Oct 2026 · For research use; verify linked source records and product datasheet before use
ATP6V1C1 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 | General cytoplasmic tissue staining (HPA tissue IHC) | |
| Staining pattern | Squamous and glandular cells show cytoplasmic staining (HPA tissue IHC) | |
| Antigen retrieval | EDTA pH 8.0 HIER, heat-mediated (datasheet A10380-1) | |
| Positive control | Esophagus+4 more · see all | |
| Negative control | Adipose tissue+4 more · see all |
Important caveats
Reasons your staining may differ from the expected pattern.
| Fixation | Keep fixation consistent across paraffin sections (standard IHC practice; not target-specific) | |
| Caveat | Staining has medium consistency with RNA expression (HPA tissue IHC) | |
| Regulation | Ubiquitous expression; no specific regulator reported (UniProt) | |
| Isoform / epitope | No annotated isoforms or transmembrane segment (UniProt) |
Section 1
Recommended ATP6V1C1 IHC & IF Protocols
Compare the catalog antibody’s IHC-P protocol (datasheet A10380-1) with 3 published ATP6V1C1 IHC methods (PMC8806199; PMC3805834; PMC2773039).
| Sample | Paraffin-embedded human liver cancer tissue; fixative not specified (datasheet A10380-1) |
| Fixation | Image fixative and duration unreported (datasheet A10380-1); 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 A10380-1); 20 min, 95–100 °C (standard) |
| Peroxidase block | 3% H2O2, 10 min, room temperature (standard) |
| Blocking | 10% goat serum (datasheet A10380-1) |
| Primary antibody | Rabbit anti-ATP6V1C1, 1:50 recommended; image 2 μg/ml (datasheet A10380-1) |
| Primary incubation | Overnight at 4 °C (datasheet A10380-1) |
| Detection | HRP-conjugated secondary, DAB chromogen (datasheet A10380-1) |
| Counterstain | Hematoxylin, blue, dehydrate and mount (standard) |
| Expected result | ATP6V1C1-positive staining in squamous epithelial cells of esophagus (HPA tissue IHC: High). HPA tissue profile: General cytoplasmic expression. No signal in the no-primary control. |
💡Decision noteStart with heat-mediated EDTA retrieval at pH 8.0 for the catalog antibody (datasheet A10380-1). The published excerpts provide no retrieval conditions (PMC8806199; PMC3805834; PMC2773039).
Section 2
What Is the Expected ATP6V1C1 Staining Pattern?
ATP6V1C1 is a V-ATPase V1 subunit associated with cytoplasmic vesicle membranes and has no transmembrane segment (UniProt P21283). In paraffin-section IHC, expect general cytoplasmic staining, with High staining reported in esophageal squamous cells and parathyroid and stomach glandular cells (HPA tissue IHC). HPA rates the tissue IHC profile Approved, with medium consistency between staining and RNA expression (HPA tissue IHC).
| Cytoplasmic signal in esophageal squamous cells or parathyroid or stomach glandular cells. | This matches HPA's High staining in these cells and its general cytoplasmic IHC profile (HPA tissue IHC). Assess the named cell population rather than assigning one score to the whole section; adjacent cell types may stain differently. |
| Predominantly nuclear chromogenic signal with little cytoplasmic staining. | This departs from the general cytoplasmic tissue IHC profile (HPA tissue IHC). Check counterstain, detection background and antibody controls before calling it target staining. Nuclear signal cannot be dismissed across methods: nucleoplasm is the approved main ICC-IF location (HPA subcellular). |
| Strong signal in adipocytes, skeletal myocytes or liver cholangiocytes. | HPA reports ATP6V1C1 as Not detected in those specific cell types by tissue IHC (HPA tissue IHC). Unexpected staining raises possible cross-reactivity or detection activity; it does not, on its own, identify which cause applies. |
| Diffuse color across tissue spaces and several unrelated cell types, obscuring cell boundaries. | This is hard to reconcile with a cell-specific cytoplasmic interpretation (HPA tissue IHC). A technical background problem is plausible; inspect a no-primary control and the chromogenic detection steps before scoring intensity. |
| No cytoplasmic signal in esophageal squamous cells or parathyroid or stomach glandular cells. | A negative result conflicts with HPA's High IHC observations in those cell types (HPA tissue IHC). Check the section's cell identity and run quality before interpreting the absence biologically; HPA's Approved rating has medium RNA concordance (HPA tissue IHC). |
💡Expected ATP6V1C1 appearanceCall a positive paraffin-section result when cytoplasmic chromogen is evident in the appropriate cells, especially High in esophageal squamous or parathyroid or stomach glandular cells; dominant nuclear color or widespread cell-independent color warrants investigation (HPA tissue IHC).
| Cell type and tissue | HPA reports High staining in three named positive cell populations, Medium in several others, and Not detected in particular adipocytes, cholangiocytes and muscle cells (HPA tissue IHC). These are cell-specific observations, not guarantees for every cell in a tissue. |
| Compartment and topology | ATP6V1C1 is a peripheral V1-complex subunit associated with vesicle membranes and has no transmembrane segment (UniProt P21283). HPA summarizes tissue IHC as general cytoplasmic expression; the record does not require a sharply outlined membrane pattern (HPA tissue IHC). |
| Antibody validation | HPA lists HPA023943 as Approved for IHC and HPA057297 as Approved for ICC (HPA antibodies). Those statuses apply to different antibodies and assays. The tissue IHC profile has medium staining-to-RNA consistency; it is not an Enhanced IHC claim (HPA tissue IHC). |
| IF/ICC Q: Should nuclear fluorescence be expected? | A: HPA reports an approved nucleoplasmic main location and an additional approved cytosolic location in ICC-IF (HPA subcellular). Interpret that result within IF/ICC; it does not replace HPA's general cytoplasmic pattern for tissue IHC (HPA tissue IHC). |
| Fixation sensitivity | Target-specific effects of fixation on ATP6V1C1 staining are unreported in the supplied UniProt and HPA records. If an IHC run fails, evaluate retrieval and processing as general assay variables without claiming a known ATP6V1C1 fixation response. |
| Situation | Likely cause | Next action |
|---|---|---|
| Known-positive cells show no chromogen. | The section may lack the expected cells, or a general IHC step may have failed; HPA reports High signal in esophageal squamous and parathyroid or stomach glandular cells (HPA tissue IHC). | Confirm cell identity and tissue integrity, then review the antibody's IHC validation and the run's retrieval, primary incubation and detection records. Include a known-positive section in the same run. |
| Nuclei dominate the IHC signal. | This conflicts with the general cytoplasmic tissue IHC profile, although nucleoplasm is approved in ICC-IF (HPA tissue IHC; HPA subcellular). Counterstain or detection background may complicate interpretation. | Compare a no-primary control and the chromogen against the counterstain. Reassess cytoplasmic signal in a HPA-reported positive cell population before assigning an IHC localization. |
| Unexpectedly strong color appears in reported negative cell types. | HPA lists adipocytes, skeletal myocytes and liver cholangiocytes as Not detected by tissue IHC (HPA tissue IHC). Cross-reactivity or endogenous detection activity is possible. | Verify the cell type, inspect a no-primary control and check endogenous enzyme blocking for the chromogenic system. Treat the negative-cell comparison as evidence to investigate, not proof of antibody specificity. |
| Color spreads across the section and obscures cells. | Nonspecific staining or detection background may be obscuring the cell-specific cytoplasmic profile reported by HPA (HPA tissue IHC). The appearance alone cannot distinguish those causes. | Use a no-primary control; review blocking, antibody dilution, washes and chromogen development as general IHC workflow checks. Score ATP6V1C1 only where individual cells and compartments can be resolved. |
| Signal is weaker than expected in one HPA-positive tissue. | HPA staining levels describe observed cell populations, while its IHC reliability is Approved with medium RNA concordance (HPA tissue IHC). A tissue-level mismatch alone does not establish target absence or a fixation effect. | Identify and score the specified cells, compare a second HPA-reported positive population if available, and check run controls before drawing a biological conclusion. |
| IF/ICC fluorescence looks different from the paraffin-section IHC pattern. | HPA reports nucleoplasm plus cytosol for ICC-IF, but general cytoplasmic expression for tissue IHC (HPA subcellular; HPA tissue IHC). The antibody validation entries are assay-specific (HPA antibodies). | Interpret each assay against its own HPA location and antibody validation record. Do not use an ICC-approved result as evidence that an IHC nuclear chromogen pattern is correct. |
Experiment evidence
IHC & IF images showing ATP6V1C1 staining
A10380-1 · IHCIHC analysis of ATP6V1C1 using anti-ATP6V1C1 antibody (A10380-1). ATP6V1C1 was detected in a paraffin-embedded section of human liver cancer
A10380-1 · IHCIHC analysis of ATP6V1C1 using anti-ATP6V1C1 antibody (A10380-1). ATP6V1C1 was detected in a paraffin-embedded section of human liver tissue
HPA · Cerebral cortexHuman Protein Atlas IHC, Cerebral cortex. Source: https://www.proteinatlas.org/ENSG00000155097-ATP6V1C1/tissue/cerebral+cortex#imid_6315784
HPA · ColonHuman Protein Atlas IHC, Colon. Source: https://www.proteinatlas.org/ENSG00000155097-ATP6V1C1/tissue/colon#imid_6315702
HPA · LiverHuman Protein Atlas IHC, Liver. Source: https://www.proteinatlas.org/ENSG00000155097-ATP6V1C1/tissue/liver#imid_6315695
HPA · KidneyHuman Protein Atlas IHC, Kidney. Source: https://www.proteinatlas.org/ENSG00000155097-ATP6V1C1/tissue/kidney#imid_6315696
HPA · ICC-IF A-431Human Protein Atlas immunofluorescence, A-431, antibody HPA057297; green = ATP6V1C1, blue = nucleus, red = microtubules.
HPA · ICC-IF A-431Human Protein Atlas immunofluorescence, A-431, antibody HPA057297; green = ATP6V1C1, blue = nucleus, red = microtubules.
← swipe / scroll for more images →
Real IHC / IF data behind the staining-pattern expectations in this section.
Sample controls for ATP6V1C1 IHC & IF
🧪Run esophagus first and expect its squamous epithelial cells to stain (HPA: High in esophageal squamous epithelial cells). Use adipose tissue as the negative tissue, focusing on adipocytes (HPA: Not detected in adipocytes); on the esophagus slide, treat neighboring cells without specific chromogen signal as internal negatives only if that absence is observed.
Positive control tissue: Esophagus (Squamous epithelial cells, HPA High)
Negative control tissue: Adipose tissue (HPA Not detected)
ICC-IF cell lines (HPA subcellular resource): HPA ICC-IF images show ATP6V1C1 in A-431, MCF-7, U2OS, with annotated localisation: Nucleoplasm (approved) (HPA subcellular).
Technical controls: Include a no-primary, secondary-only control and a host-species- and antibody-class-matched isotype control; use validated ATP6V1C1 knockout material or peptide competition, if available, as a biological specificity control (standard IHC practice). Quench endogenous peroxidase and check for residual background in the esophagus section before interpreting DAB staining (standard chromogenic IHC practice).
⚠️Feasibility: A target-specific fixation window or fixation effect is unreported, and the selected A10380-1 paraffin-section caption does not state the fixative (selected-SKU tissue-IHC caption). That caption uses heat retrieval in EDTA at pH 8.0, but whether ATP6V1C1 staining requires that retrieval condition is unreported (selected-SKU tissue-IHC caption). Paraffin IHC has a documented example, while the supplied IF evidence consists of ICC-IF images; it does not establish that frozen sections or IF are easier (selected-SKU tissue-IHC caption; HPA: ICC-IF images in A-431, MCF-7 and U2OS).
HPA tissue IHC evidence for ATP6V1C1
Comprehensive Human Protein Atlas IHC scoring per tissue (reliability: Approved — 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.
Positive expression · recommended positive controls
| Tissue | Cell type | Level | Evidence | Source |
|---|---|---|---|---|
| Esophagus | Squamous epithelial cells | High | Protein (IHC) | HPA → |
| Parathyroid gland | Glandular cells | High | Protein (IHC) | HPA → |
| Stomach | Glandular cells | High | Protein (IHC) | HPA → |
| Adrenal gland | Glandular cells | Medium | Protein (IHC) | HPA → |
| Appendix | Glandular cells | Medium | Protein (IHC) | HPA → |
Undetected expression · recommended negative controls
| 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 → |
| Cervix | Glandular cells | Not detected | Protein (IHC) | HPA → |
| Liver | Cholangiocytes | Not detected | Protein (IHC) | HPA → |
Section 3
Advanced ATP6V1C1 IHC Tips
Troubleshoot ATP6V1C1 staining in paraffin sections by checking retrieval, controls, cell identity and compartment before interpreting signal.
Which retrieval condition should I start with for ATP6V1C1 paraffin IHC?
Start with heat-mediated retrieval in EDTA at pH 8.0 for the catalog antibody (datasheet A10380-1). The documented image used a paraffin section, followed by 10% goat serum blocking and 2 μg/ml primary antibody overnight at 4°C (caption A10380-1). If staining is weak, first check that heating was even, sections remained attached and the positive control stained before changing retrieval conditions (standard IHC practice). Compare any adjusted retrieval condition on adjacent sections, since excessive heating can damage morphology and make cytoplasmic staining difficult to score (standard IHC practice; HPA tissue IHC: general cytoplasmic expression).
Can fixation explain weak ATP6V1C1 staining in a paraffin section?
Target-specific fixation sensitivity is unknown: the catalog image identifies a paraffin section but does not report its fixative (caption A10380-1). Record the fixative, fixation duration and processing history for each specimen, then compare sections processed together when investigating weak staining (standard IHC practice). Use the documented EDTA retrieval at pH 8.0 and 2 μg/ml primary antibody as a starting point, while treating those settings as evidence for the illustrated staining workflow only (caption A10380-1). Include a known positive tissue section in the same run so a specimen-specific loss of signal can be distinguished from a run-wide staining failure (standard IHC practice; HPA tissue IHC: high expression in esophageal squamous epithelial cells).
Where should ATP6V1C1 signal appear, and how should nuclear staining be handled?
Expect predominantly cytoplasmic staining in tissue IHC, matching the reported general tissue profile (HPA tissue IHC: general cytoplasmic expression). ATP6V1C1 is a V1 complex subunit associated with cytoplasmic vesicle membranes and has no transmembrane segment, so a vesicular cytoplasmic pattern is biologically plausible (UniProt P21283: subunit, subcellular location and topology). Nuclear signal needs separate scrutiny because HPA reports approved nucleoplasmic localisation in ICC/IF as well as cytosolic localisation (HPA subcellular: nucleoplasm and cytosol approved). Compare nuclear and cytoplasmic compartments against a matched negative control, morphology and the positive tissue control before assigning either pattern to specific antigen (standard IHC practice; HPA tissue IHC: general cytoplasmic expression).
How do topology and isoform records affect epitope troubleshooting?
The supplied record lists 0 isoforms and no transmembrane segment for ATP6V1C1, but does not map this antibody’s epitope (UniProt P21283: isoforms and topology; caption A10380-1). It also lists 0 glycosylation sites and N-terminal acetylthreonine at residue 2; neither establishes an antibody-specific retrieval response (UniProt P21283: glycosylation and modified residues). If staining varies across specimens, compare matched sections using the documented EDTA pH 8.0 retrieval before attributing differences to an epitope or protein variant (caption A10380-1; standard IHC practice). Seek the antibody’s immunogen or epitope documentation before making a residue-level claim, and verify a disputed pattern with an independent specificity control (standard IHC practice).
How should I extend the IHC findings into an ATP6V1C1 multiplex IF experiment?
Treat IF/ICC as a separate assay and validate the antibody there; the supplied catalog evidence documents chromogenic paraffin IHC, while HPA reports ICC/IF localisation separately (caption A10380-1; HPA subcellular). Pair ATP6V1C1 with a marker for the expected cell population, such as an epithelial marker when examining esophageal squamous cells, and verify each channel independently (HPA tissue IHC: high in esophageal squamous epithelial cells; standard IF practice). Choose fluorophores after checking unstained tissue for autofluorescence and avoid the brightest background channel when assigning weak ATP6V1C1 signal (standard IF practice). Because ATP6V1C1 lacks a transmembrane segment and is associated with the cytoplasmic side of vesicle membranes, optimise permeabilisation for intracellular access while preserving compartment structure (UniProt P21283: topology and subcellular location; standard IF practice).
What should I check when ATP6V1C1 DAB staining looks diffuse or nonspecific?
First compare a no-primary control with the stained section to identify secondary reagent, chromogen or endogenous enzyme background (standard chromogenic IHC practice). The documented workflow used 10% goat serum blocking, 2 μg/ml rabbit primary overnight at 4°C, a peroxidase-conjugated secondary and DAB detection (caption A10380-1). If background persists, confirm adequate peroxidase blocking and washing, then titrate the primary around the documented concentration using matched sections (standard chromogenic IHC practice; caption A10380-1). Evaluate diffuse deposits alongside morphology and compartment pattern: the tissue profile is generally cytoplasmic, so uniform staining across nuclei, stroma and empty areas warrants scrutiny (HPA tissue IHC: general cytoplasmic expression; standard IHC practice).
How should I score ATP6V1C1 staining across paraffin tissue sections? ⚠ ANSWER MARKED FOR VERIFICATION
Define the cell population and compartment before scoring; the reported tissue pattern is generally cytoplasmic, and expression differs across listed cell populations (HPA tissue IHC: profile and cell-specific levels). For discrete cells, record the percentage positive and intensity to calculate an H-score; for infiltrating populations, report positive cell density per mm² of viable tissue (standard IHC quantification practice). Normalise counts to the relevant cell population or viable tissue area, and keep thresholds, counterstain and imaging settings consistent across groups (standard IHC quantification practice). Document retrieval with EDTA at pH 8.0 and antibody concentration when comparing runs, because the catalog image specifies both conditions (caption A10380-1).
How can I distinguish ATP6V1C1 positivity from staining artefact?
Prioritise staining in intact cells with a plausible cytoplasmic pattern, consistent with the reported tissue IHC profile and vesicle-associated protein location (HPA tissue IHC: general cytoplasmic expression; UniProt P21283: subcellular location). Use cell identity as a check: esophageal squamous epithelial cells are reported high, whereas adipocytes and liver cholangiocytes are reported undetected in the listed HPA observations (HPA tissue IHC: cell-specific levels). Discount signal confined to section edges, necrotic areas or a no-primary control, and check endogenous peroxidase when DAB staining appears without primary antibody (standard chromogenic IHC practice). Interpret unexpected nuclear staining cautiously because ICC/IF reports nucleoplasmic localisation, but the supplied tissue IHC profile is generally cytoplasmic (HPA subcellular: nucleoplasm approved; HPA tissue IHC: general cytoplasmic expression).
Boster reagents
Best ATP6V1C1 / V-type proton ATPase subunit C 1 IHC Antibodies
The catalog lists one anti-ATP6V1C1 antibody with IHC data from paraffin-embedded human liver and liver cancer sections (catalog image captions). Human, mouse, and rat reactivity is listed (catalog).
Real IHC data
Anti-ATP6V1C1 Antibody
Cat # A10380-1
A10380-1 will render with an IHC figure from a paraffin-embedded human liver cancer section (A10380-1 image caption). Its catalog also lists IHC and human, mouse, and rat reactivity, with a second IHC caption for paraffin-embedded human liver tissue (A10380-1 catalog).
Which to pick: Choose A10380-1 for paraffin-section IHC: its own captions document EDTA retrieval at pH 8.0, 10% goat serum blocking, primary antibody at 2 μg/ml overnight at 4°C, and HRP/DAB detection; the fixative is unreported (A10380-1 image captions). For cross-species work, A10380-1 lists human, mouse, and rat reactivity, while its supplied IHC images show human tissue only (A10380-1 catalog and image captions). No listed SKU has IF/ICC application validation or an IF image, so there is no supported IF/ICC pick here (A10380-1 applications and IF image list).
Each figure is that product's own IHC / IF validation image from its datasheet.
References
- UniProt Consortium. UniProt entry P21283 (VATC1_HUMAN, V-type proton ATPase subunit C 1).
- Human Protein Atlas. ATP6V1C1 tissue IHC expression (reliability: Approved).
- Human Protein Atlas. ATP6V1C1 subcellular location (ICC-IF): Mainly localized to the nucleoplasm. In addition localized to the cytosol..
- Human Protein Atlas. ATP6V1C1 antibody validation summary (2 antibodies).
- A novel four-gene of iron metabolism-related and methylated for prognosis prediction of hepatocellular carcinoma. Bioengineered 2021 — PMC8806199.
- Silencing of atp6v1c1 prevents breast cancer growth and bone metastasis. International journal of biological sciences 2013 — PMC3805834.
- Targeting Atp6v1c1 Prevents Inflammation and Bone Erosion Caused by Periodontitis and Reveals Its Critical Function in Osteoimmunology. PloS one 2015 — PMC4537256.
- Atp6v1c1 is an essential component of the osteoclast proton pump and in F-actin ring formation in osteoclasts. The Biochemical journal 2009 — PMC2773039.
- PubMed PMID:8250920 — UniProt-cited evidence.
- PubMed PMID:11707601 — UniProt-cited evidence.
- PubMed PMID:15489334 — UniProt-cited evidence.
Immunohistochemistry protocol sheet for ATP6V1C1 (V-type proton ATPase subunit C 1). Expected localisation General cytoplasmic tissue staining (HPA tissue IHC). Antigen retrieval: EDTA pH 8.0 HIER, heat-mediated (datasheet A10380-1). Validated IHC antibody: A10380-1 at 1:50 recommended; image 2 μg/ml (the product's own IHC validation image is shown). Controls (HPA): positive Esophagus (Squamous epithelial cells); negative Adipose tissue. IHC-P workflow on paraffin sections; fixative unspecified. Protocol steps: 1. Sample: Paraffin-embedded human liver cancer tissue; fixative not specified (datasheet A10380-1); 2. Fixation: Image fixative and duration unreported (datasheet A10380-1); 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 A10380-1); 20 min, 95–100 °C (standard); 6. Peroxidase block: 3% H2O2, 10 min , room temperature (standard); 7. Blocking: 10% goat serum (datasheet A10380-1); 8. Primary antibody: Rabbit anti-ATP6V1C1, 1:50 recommended; image 2 μg/ml (datasheet A10380-1); 9. Primary incubation: Overnight at 4 °C (datasheet A10380-1). Watch for: Fixation: Keep fixation consistent across paraffin sections (standard IHC practice; not target-specific); Caveat: Staining has medium consistency with RNA expression (HPA tissue IHC); Isoform / epitope: No annotated isoforms or transmembrane segment (UniProt); Regulation: Ubiquitous expression; no specific regulator reported (UniProt). Evidence: UniProt P21283, HPA tissue IHC · Approved, HPA ICC-IF · Mainly localized to the nucleoplasm. In addition localized to the…, Datasheet A10380-1, PMC8806199, PMC3805834. QR code links to https://www.bosterbio.com/bosterbio-gene-info-cards/ATP6V1C1/immunohistochemistry-ihc-guide.