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COX6C / Cytochrome c oxidase subunit 6C · IHC design guide
Design Immunohistochemistry for COX6C
Plan COX6C chromogenic IHC in paraffin sections around its granular cytoplasmic tissue pattern (HPA tissue IHC). Compare high staining in breast glandular cells with low staining in adipocytes (HPA tissue IHC), using the catalog antibody's 1:50–1:200 IHC dilution (datasheet).
Evidence assembled Oct 2026 · For research use; verify linked source records and product datasheet before use
COX6C 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 | Granular cytoplasm (HPA tissue IHC); inner mitochondrial membrane (UniProt) | |
| Staining pattern | Granular cytoplasmic staining; high in glandular cells (HPA tissue IHC) | |
| Antigen retrieval | Citrate pH 6.0 HIER, 95–98 °C, 20 min (rule: cytoplasmic / membrane antigen) | |
| Positive control | Adrenal gland+4 more · see all | |
| Negative control | None in HPA (detected in all 45 tissues); use no-primary + isotype controls |
Important caveats
Reasons your staining may differ from the expected pattern.
| Fixation | Keep fixation consistent across sections (standard IHC practice; not target-specific) | |
| Caveat | Adipocytes and chondrocytes show low staining (HPA tissue IHC) | |
| Regulation | Expression regulation unreported (UniProt) | |
| Isoform / epitope | No isoforms; one unprocessed 1–75 chain (UniProt) |
Section 1
Recommended COX6C IHC & IF Protocols
The catalog antibody IHC-P protocol is paired with one published COX6C tissue microarray IHC protocol (PMC10799076).
| Sample | Paraffin-embedded human breast carcinoma tissue; fixative not specified (datasheet A11443-1) |
| Fixation | Image fixative and duration unreported (datasheet A11443-1); verify before use. |
| Sectioning | 4–5 µm sections on charged slides (standard) |
| Deparaffinisation | Xylene, graded ethanol series to water (standard) |
| Antigen retrieval | Heat-induced epitope retrieval in citrate buffer, pH 6.0, 20 min at 95–98 °C (standard rule: cytoplasmic / membrane antigen) |
| Peroxidase block | 3% H2O2, 10 min, room temperature (standard) |
| Blocking | 10% normal serum of the secondary host, 30 min, room temperature (standard) |
| Primary antibody | Rabbit anti-COX6C, 1:50-1:200 (datasheet A11443-1) |
| Primary incubation | Overnight at 4 °C (standard) |
| Detection | HRP-polymer secondary, DAB chromogen 5–10 min (standard) |
| Counterstain | Hematoxylin, blue, dehydrate and mount (standard) |
| Expected result | COX6C-positive staining in glandular cells of adrenal gland (HPA tissue IHC: High). HPA tissue profile: General cytoplasmic expression with a granular pattern. No signal in the no-primary control. |
💡Decision noteStart with citrate pH 6.0 retrieval at 95–98 °C for 20 min (page antigen-retrieval setting); the published protocol does not specify retrieval conditions (PMC10799076).
Section 2
What Is the Expected COX6C Staining Pattern?
COX6C is an inner mitochondrial membrane protein spanning residues 14–54, with termini facing the matrix and intermembrane space (UniProt P09669 topology). In paraffin-section IHC, expect granular cytoplasmic staining in cells such as colon glandular cells and cerebral cortex neurons, both recorded as High (HPA: tissue IHC). The tissue profile has Enhanced reliability, reflecting consistency between antibody staining and RNA expression (HPA: tissue IHC).
| Granular cytoplasmic signal in colon or appendix glandular cells. | This matches the reported general granular cytoplasmic profile and High staining in these cells (HPA: tissue IHC). Interpret the granules as consistent with mitochondrial localisation (UniProt P09669 subcellular location); chromogenic IHC alone does not prove that each granule is a mitochondrion. |
| Predominantly nuclear or sharply plasma-membrane staining. | These compartments conflict with COX6C's inner mitochondrial membrane location (UniProt P09669 subcellular location). Treat the pattern as suspect, inspect morphology and controls, and avoid scoring it as specific COX6C signal until it is independently resolved (general IHC practice). |
| Strong staining concentrated in adipocytes or chondrocytes while expected positive cells are weak. | HPA reports Low staining in adipocytes and chondrocytes and High staining in several glandular cell groups (HPA: tissue IHC). The mismatch raises possible cross-reactivity or endogenous detection activity; Low is not an absence call, so examine no-primary controls before assigning a cause (general IHC practice). |
| Diffuse colour across cells, extracellular space, or the entire section. | A broad, unstructured deposit obscures the reported granular cytoplasmic pattern (HPA: tissue IHC). Background from detection chemistry or nonspecific binding is possible; assess no-primary and tissue-background controls before interpreting intensity (general IHC practice). |
| No discernible signal in colon glandular cells or cerebral cortex neurons. | Both cell groups are recorded as High in HPA tissue IHC, so a blank result warrants a technical check (HPA: tissue IHC). Confirm tissue identity, positive-control performance, primary antibody application, retrieval conditions, and chromogen development before calling the sample negative (general IHC practice). |
💡Expected COX6C appearanceCall a result positive when expected glandular or neuronal cells show clear granular cytoplasmic staining, potentially strong in HPA High groups; isolated nuclear signal or uniform section-wide colour is suspect (HPA: tissue IHC; UniProt P09669 subcellular location; general IHC practice).
| Compartment and epitope accessibility | COX6C crosses the inner mitochondrial membrane at residues 14–54; residues 1–13 face the matrix and 55–75 the intermembrane space (UniProt P09669 topology). Epitope location could matter when interpreting access, but no antibody epitope or COX6C-specific retrieval response is supplied. |
| Cell selection for a positive control | Colon glandular cells, bronchial respiratory epithelial cells, and cerebral cortex neurons are each reported High (HPA: tissue IHC). Use the relevant cell population within a control section when judging staining, because a whole-section average can hide cell-specific differences (general IHC practice). |
| How much weight to give the HPA pattern | The tissue profile is rated Enhanced for antibody-staining and RNA consistency (HPA: tissue IHC). HPA014295 and CAB016244 are each rated Enhanced for IHC (HPA: antibody validation). These ratings support the reference pattern but do not validate an unlisted antibody or every staining condition. |
| IF/ICC Q: What localisation should I expect? | A: Mitochondrial localisation is the enhanced main location; HPA lists ICC-IF images from A-431, U-251MG, and U2OS (HPA: subcellular). Use that as a localisation cross-check. IF/ICC optimisation belongs in its own guide; this row gives no IF protocol. |
| Situation | Likely cause | Next action |
|---|---|---|
| The known-positive control is blank. | A failed reagent, missed primary-antibody step, unsuitable retrieval, or incomplete chromogen development is possible (general IHC practice). | Check run controls and recorded steps, then repeat with an HPA High cell group such as colon glandular cells (HPA: tissue IHC; general IHC practice). No COX6C-specific retrieval condition is established by the supplied sources. |
| Most cells and spaces have similar colour. | Nonspecific binding, residual detection activity, or excessive chromogen development may produce diffuse background (general IHC practice). | Compare a no-primary section and review blocking, washes, and development time (general IHC practice). Score only a resolved granular cytoplasmic pattern consistent with HPA tissue IHC. |
| Signal is mainly nuclear. | That distribution conflicts with the inner mitochondrial membrane assignment (UniProt P09669 subcellular location); artefact or off-target binding is possible. | Check no-primary staining and tissue morphology; compare the same cell population with the granular cytoplasmic reference pattern (HPA: tissue IHC; general IHC practice). |
| Adipocytes or chondrocytes look stronger than the expected positive cells. | Those cells are recorded Low by HPA, so the contrast merits investigation; endogenous activity or off-target staining is possible (HPA: tissue IHC; general IHC practice). | Inspect a no-primary control and compare staining within named HPA High cell groups. Do not use Low cells as an absolute negative control (HPA: tissue IHC; general IHC practice). |
| Granules are visible, but their location is uncertain. | Chromogenic granules can be hard to assign to an organelle from appearance alone (general IHC practice). | Check that staining is cytoplasmic in the expected cell type (HPA: tissue IHC). For a separate localisation assessment, HPA ICC-IF reports mitochondria as the enhanced main location (HPA: subcellular). |
| One antibody gives the expected pattern and another does not. | Antibodies can differ in recognised epitope or off-target binding (general IHC practice); the supplied record gives no epitope mapping. | Compare matched sections and controls, document each antibody, and use the HPA granular cytoplasmic profile and validated-antibody ratings as reference evidence (HPA: tissue IHC; HPA: antibody validation). |
Experiment evidence
IHC & IF images showing COX6C staining
A11443-1 · IHCImmunohistochemistry (IHC) analyzes of COX6c (R40) pAb in paraffin-embedded human breast carcinoma tissue at 1:100.
HPA · Cerebral cortexHuman Protein Atlas IHC, Cerebral cortex. Source: https://www.proteinatlas.org/ENSG00000164919-COX6C/tissue/cerebral+cortex#imid_11981847
HPA · ColonHuman Protein Atlas IHC, Colon. Source: https://www.proteinatlas.org/ENSG00000164919-COX6C/tissue/colon#imid_11981781
HPA · LiverHuman Protein Atlas IHC, Liver. Source: https://www.proteinatlas.org/ENSG00000164919-COX6C/tissue/liver#imid_11981774
HPA · KidneyHuman Protein Atlas IHC, Kidney. Source: https://www.proteinatlas.org/ENSG00000164919-COX6C/tissue/kidney#imid_11981783
HPA · ICC-IF A-431Human Protein Atlas immunofluorescence, A-431, antibody HPA014295; green = COX6C, blue = nucleus, red = microtubules.
HPA · ICC-IF A-431Human Protein Atlas immunofluorescence, A-431, antibody HPA014295; green = COX6C, blue = nucleus, red = microtubules.
← swipe / scroll for more images →
Real IHC / IF data behind the staining-pattern expectations in this section.
Sample controls for COX6C IHC & IF
🧪Run breast tissue first and expect staining in glandular cells (HPA: High in breast glandular cells). HPA detects COX6C in all 45 scored tissues, so there is no supported negative tissue; use no-primary and isotype controls, and judge cells without cytoplasmic staining against background rather than assuming they are true internal negatives (HPA: no negative tissue rows; UniProt P09669: mitochondrial inner membrane).
Positive control tissue: Adrenal gland (Glandular cells, HPA High)
Negative control tissue: None in HPA: COX6C is detected in all 45 scored tissues. Use a no-primary (secondary-only) and an isotype control instead.
ICC-IF cell lines (HPA subcellular resource): HPA ICC-IF images show COX6C in A-431, U-251MG, U2OS, with annotated localisation: Mitochondria (enhanced) (HPA subcellular).
Technical controls: Include a no-primary, secondary-only control and an isotype control matched to the primary antibody’s host species and clonality; use COX6C knockout material as a biological negative where available (standard IHC practice). For chromogenic breast IHC, block endogenous peroxidase and assess endogenous biotin if using avidin–biotin detection (standard IHC practice).
⚠️Feasibility: The selected paraffin-section breast carcinoma caption reports a 1:100 dilution but does not report the fixative; no target-specific fixation window or retrieval dependency is established by the supplied evidence (selected SKU A11443-1 caption). Optimize antigen retrieval for the IHC-validated antibody, and check breast-section background during scoring (standard IHC practice). HPA shows mitochondrial IF localization, but the supplied evidence does not establish whether frozen sections or IF are easier than paraffin IHC (HPA: subcellular mitochondria).
HPA tissue IHC evidence for COX6C
Comprehensive Human Protein Atlas IHC scoring per tissue (reliability: Enhanced — High 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 |
|---|---|---|---|---|
| Adrenal gland | Glandular cells | High | Protein (IHC) | HPA → |
| Appendix | Glandular cells | High | Protein (IHC) | HPA → |
| Breast | Glandular cells | High | Protein (IHC) | HPA → |
| Bronchus | Respiratory epithelial cells | High | Protein (IHC) | HPA → |
| Cerebellum | Cells in granular layer | High | Protein (IHC) | HPA → |
Undetected expression · recommended negative controls
| Tissue | Cell type | Level | Evidence | Source |
|---|---|---|---|---|
| None in HPA: COX6C is detected in all 45 scored tissues. Use a no-primary (secondary-only) and an isotype control instead. | ||||
Section 3
Advanced COX6C IHC Tips
COX6C is an inner mitochondrial membrane component of complex IV (UniProt P09669); assess its granular cytoplasmic staining in cell context (HPA tissue IHC).
How should I retrieve COX6C in paraffin sections when staining is weak?
Use citrate pH 6.0 heat-induced antigen retrieval at 95–98 °C for 20 min for COX6C paraffin IHC (page retrieval rule). If staining is weak, first confirm complete deparaffinisation and consistent heating, then compare retrieved and unretrieved sections from the same block (standard IHC practice). Interpret any gain alongside morphology and background: COX6C should show a granular cytoplasmic pattern, consistent with its mitochondrial location (HPA tissue IHC; HPA subcellular). Because the selected antibody caption reports paraffin sections but no retrieval conditions, treat this schedule as the page protocol rather than a demonstrated condition for SKU A11443-1 (selected tissue-IHC caption).
Could fixation explain weak or uneven COX6C staining?
Target-specific fixation sensitivity is unknown: the selected paraffin-section caption does not state a fixative or fixation duration (selected tissue-IHC caption, SKU A11443-1). Record fixative, time in fixative, section age and processing history before comparing signal across blocks, since these variables can affect IHC staining (standard IHC practice). Run a known staining control through the same processing and citrate pH 6.0 retrieval schedule, then compare signal and morphology across matched sections (page retrieval rule; standard IHC practice). Do not attribute a weak result specifically to COX6C fixation sensitivity without controlled evidence; the expected granular cytoplasmic pattern helps assess signal distribution, not fixation tolerance (HPA tissue IHC).
Where should convincing COX6C signal appear in tissue sections?
Expect granular cytoplasmic staining at light-microscope resolution, matching the reported tissue IHC profile and mitochondrial localisation (HPA tissue IHC; HPA subcellular). COX6C resides in the inner mitochondrial membrane, with residues 1–13 facing the matrix, 14–54 spanning the membrane and 55–75 facing the intermembrane space (UniProt P09669 topology). Assess staining within intact cells and compare nearby structures under identical exposure or brightfield settings, since diffuse extracellular colour or nuclear-only staining would conflict with that localisation (UniProt P09669; standard IHC practice). High staining is reported in breast glandular cells, providing a cell-context reference, although the selected carcinoma image alone does not establish tumour-cell specificity (HPA tissue IHC; selected tissue-IHC caption).
How can epitope placement affect interpretation of this small membrane protein?
The supplied record lists one 75-amino-acid COX6C chain, no annotated isoforms, and no annotated glycosylation sites or modified residues (UniProt P09669). Its membrane-spanning segment covers residues 14–54, while the termini face opposite mitochondrial compartments, so epitope accessibility may depend on antibody binding site and processing (UniProt P09669 topology; standard IHC practice). The selected tissue caption does not identify an epitope, so do not claim that retrieval exposes a particular terminus or distinguishes a protein isoform (selected tissue-IHC caption; UniProt P09669). If results disagree between antibodies, compare their documented immunogens, staining patterns and controls before assigning a COX6C-specific biological difference (standard IHC practice).
How should I check COX6C localisation by multiplex IF?
Use a mitochondrial reference stain and a marker identifying the expected cell population, then assess whether COX6C puncta occur within the relevant cells (HPA subcellular; standard IF practice). Choose a COX6C fluorophore channel with low tissue autofluorescence, and examine unstained and single-stained controls before interpreting apparent overlap (standard IF practice). Because residues 1–13 face the matrix and 55–75 face the intermembrane space, optimise permeabilisation against the antibody's documented epitope and verify that mitochondrial structure remains discernible (UniProt P09669 topology; standard IF practice). The supplied antibody caption documents paraffin IHC at 1:100, so establish IF conditions independently rather than treating that dilution as IF validation (selected tissue-IHC caption).
What causes apparent widespread COX6C colour in chromogenic IHC?
First compare the test section with a no-primary control to identify detection-system colour unrelated to primary-antibody binding (standard chromogenic IHC practice). Use an appropriate endogenous peroxidase block for a peroxidase and DAB workflow, and inspect pigment or precipitate before assigning brown signal to COX6C (standard chromogenic IHC practice). COX6C has low RNA tissue specificity and a reported general granular cytoplasmic IHC pattern, so widespread cellular staining alone is not evidence of nonspecific background (HPA tissue IHC). Titrate the IHC-validated antibody around the captioned 1:100 condition while preserving matched retrieval, detection and imaging settings; the caption does not establish an optimal dilution for every specimen (selected tissue-IHC caption; standard IHC practice).
How should I score COX6C staining across samples? ⚠ ANSWER MARKED FOR VERIFICATION
Define the cell population and regions before scoring, then record the percentage of positive cells and cytoplasmic intensity or calculate an H-score using consistent intensity bins (standard IHC practice). Restrict scoring to intact cells with plausible granular cytoplasmic signal, since that is the reported COX6C pattern (HPA tissue IHC). Normalise positive-cell counts to the number of evaluable cells in that population, or normalise stained area to tissue area in mm², rather than comparing raw stained area across unequal sections (standard IHC practice). Keep retrieval, antibody dilution, chromogen development and image settings matched across samples, and report the scoring threshold and excluded regions (standard IHC practice).
How can I distinguish true COX6C staining from section artefacts?
A plausible positive result is intracellular granular cytoplasmic staining in intact cells, consistent with COX6C mitochondrial localisation and the tissue IHC profile (HPA subcellular; HPA tissue IHC). Check cell identity against the section morphology: high staining is reported in breast glandular cells, while adipocytes and chondrocytes are listed as low-staining contexts (HPA tissue IHC). Treat signal concentrated at section edges, necrotic areas or extracellular deposits cautiously, and compare adjacent intact regions and a no-primary control (standard IHC practice). In a peroxidase and DAB assay, persistent colour in the no-primary control suggests endogenous enzyme activity or detection background rather than confirmed COX6C binding (standard chromogenic IHC practice).
Boster reagents
Best COX6C / Cytochrome c oxidase subunit 6C IHC Antibodies
The IHC-tested COX6C antibody A11443-1 has an IHC image from paraffin-embedded human breast carcinoma (catalog image caption). Listed reactivity includes human, mouse, and rat (catalog).
Real IHC data
Anti-COX6c (R40) Antibody
Cat # A11443-1
A11443-1 is the sole card and shows IHC staining of paraffin-embedded human breast carcinoma at 1:100 (catalog image caption). Its listed application is IHC, and its listed reactivity is human, mouse, and rat (catalog).
Which to pick: Choose A11443-1 for paraffin-section tissue IHC: it is a rabbit polyclonal antibody listed for IHC, with a human breast carcinoma image (catalog; catalog image caption). Its human, mouse, and rat reactivity is listed, while the supplied image documents human tissue only (catalog; catalog image caption). No IF/ICC application or image is listed for A11443-1 (catalog); the paraffin-section caption does not report a fixative (catalog image caption).
Each figure is that product's own IHC / IF validation image from its datasheet.
References
- UniProt Consortium. UniProt entry P09669 (COX6C_HUMAN, Cytochrome c oxidase subunit 6C).
- Human Protein Atlas. COX6C tissue IHC expression (reliability: Enhanced).
- Human Protein Atlas. COX6C subcellular location (ICC-IF): Localized to the mitochondria..
- Human Protein Atlas. COX6C antibody validation summary (2 antibodies).
- COX6C expression driven by copy amplification of 8q22.2 regulates cell proliferation via mediation of mitosis by ROS-AMPK signaling in lung adenocarcinoma. Cell death & disease 2024 — PMC10799076.
- PubMed PMID:2849755 — UniProt-cited evidence.
- PubMed PMID:10072584 — UniProt-cited evidence.
- PubMed PMID:14702039 — UniProt-cited evidence.
Immunohistochemistry protocol sheet for COX6C (Cytochrome c oxidase subunit 6C). Expected localisation Granular cytoplasm (HPA tissue IHC); inner mitochondrial membrane (UniProt). Antigen retrieval: Citrate pH 6.0 HIER, 95–98 °C, 20 min (rule: cytoplasmic / membrane antigen). Validated IHC antibody: A11443-1 at 1:50-1:200 (the product's own IHC validation image is shown). Controls (HPA): positive Adrenal gland (Glandular cells); negative None in HPA (detected in all 45 tissues); use no-primary + isotype controls. IHC-P workflow on paraffin sections; fixative unspecified. Protocol steps: 1. Sample: Paraffin-embedded human breast carcinoma tissue; fixative not specified (datasheet A11443-1); 2. Fixation: Image fixative and duration unreported (datasheet A11443-1); 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-induced epitope retrieval in citrate buffer, pH 6.0 , 20 min at 95–98 °C…; 6. Peroxidase block: 3% H2O2, 10 min , room temperature (standard); 7. Blocking: 10% normal serum of the secondary host, 30 min , room temperature (standard); 8. Primary antibody: Rabbit anti-COX6C, 1:50-1:200 (datasheet A11443-1); 9. Primary incubation: Overnight at 4 °C (standard). Watch for: Fixation: Keep fixation consistent across sections (standard IHC practice; not target-specific); Caveat: Adipocytes and chondrocytes show low staining (HPA tissue IHC); Isoform / epitope: No isoforms; one unprocessed 1–75 chain (UniProt); Regulation: Expression regulation unreported (UniProt). Evidence: UniProt P09669, HPA tissue IHC · Enhanced, HPA ICC-IF · mitochondria., Datasheet A11443-1, PMC10799076. QR code links to https://www.bosterbio.com/bosterbio-gene-info-cards/COX6C/immunohistochemistry-ihc-guide.