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COX6C / Cytochrome c oxidase subunit 6C · IHC design guide
Design Immunohistochemistry for COX6C
Plan chromogenic COX6C IHC in paraffin sections using granular cytoplasmic staining as the tissue reference (HPA tissue IHC). Compare high staining in glandular cells with low staining in adipocytes and chondrocytes (HPA tissue IHC), and titrate the catalog antibody within 1:50–1:200 (datasheet: IHC).
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 cytoplasm in glandular cells and neurons (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 paraffin sections. (standard IHC practice; not target-specific) | |
| Caveat | Adipocytes and chondrocytes may stain weakly (HPA tissue IHC) | |
| Regulation | Regulation unreported (UniProt) | |
| Isoform / epitope | No isoforms or processing annotated; one 75-aa chain (UniProt) |
Section 1
Recommended COX6C IHC & IF Protocols
The catalog antibody’s IHC-P protocol and one published COX6C tissue microarray staining workflow (PMC10799076) provide starting conditions for paraffin sections.
| 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 rule); the published study does not report retrieval conditions (PMC10799076).
Section 2
What Is the Expected COX6C Staining Pattern?
COX6C is an inner mitochondrial membrane component with a transmembrane segment spanning residues 14–54 (UniProt P09669 topology). On IHC sections, expect granular cytoplasmic staining, especially in the glandular, respiratory epithelial, and neuronal populations reported as High by HPA (HPA tissue IHC). HPA rates the tissue staining evidence Enhanced, reflecting high consistency between antibody staining and RNA expression data (HPA tissue IHC).
| Granular cytoplasmic staining in adrenal or colon glandular cells. | This matches HPA’s reported pattern and High staining in those cells (HPA tissue IHC). The appearance is consistent with mitochondrial localisation (UniProt P09669; HPA subcellular), though chromogenic granules alone do not prove organelle identity (standard IHC interpretation). Assess staining within the named cell population rather than assigning one score to the entire tissue (standard IHC practice). |
| Predominantly nuclear or sharply outlined plasma membrane staining. | That compartment conflicts with the inner mitochondrial membrane annotation and reported granular cytoplasmic IHC pattern (UniProt P09669 topology; HPA tissue IHC). Treat it as a possible nonspecific result, and compare the same tissue with appropriate staining controls before interpreting it as COX6C (standard IHC practice). |
| Strong staining in an unexpected cell population, especially where the reference pattern is Low. | HPA reports Low staining in adipocytes and chondrocytes, but does not designate them negative (HPA tissue IHC). A strong result there warrants checks for cross-reactivity or endogenous detection activity (standard IHC practice). Tissue-wide expression is plausible because HPA reports low RNA tissue specificity, so cell identity and staining pattern matter (HPA tissue IHC). |
| Uniform haze or widespread chromogen that obscures cell boundaries. | This does not resemble the reported granular cytoplasmic pattern (HPA tissue IHC). Background may arise from nonspecific reagent binding, endogenous detection activity, or excessive chromogen development (standard IHC practice). A background pattern alone cannot establish whether COX6C is present or absent in the affected cells (standard IHC interpretation). |
| No visible signal in a well-preserved adrenal gland or colon glandular compartment. | HPA reports High staining in these glandular cells, so an entirely blank expected-positive compartment calls for a run check (HPA tissue IHC). Review slide integrity, retrieval, antibody application, and detection controls (standard IHC practice). One negative run does not establish biological absence or a COX6C-specific fixation effect. |
💡Expected COX6C appearanceCall a positive result when the expected cells show clearly discernible granular cytoplasmic staining, with High staining reported in adrenal or colon glandular cells (HPA tissue IHC); nuclear staining or uniform section-wide haze is a possible false-positive pattern (UniProt P09669 topology; HPA tissue IHC; standard IHC interpretation).
| Cell and tissue context | HPA reports High staining in adrenal, appendix, breast, cervix, and colon glandular cells; bronchial respiratory epithelial cells; and selected cerebellar and cortical cells (HPA tissue IHC). It reports Low staining in adipocytes and chondrocytes, with no negative population listed (HPA tissue IHC). Choose comparison fields by named cell population. |
| Topology and epitope information | COX6C spans the inner mitochondrial membrane at residues 14–54, with residues 1–13 on the matrix side and 55–75 on the intermembrane side (UniProt P09669 topology). The supplied record does not locate either antibody’s epitope; topology therefore cannot predict an antibody-specific retrieval requirement or fixation sensitivity. |
| Validation and molecular annotations | HPA assigns Enhanced reliability to tissue IHC and Enhanced IHC validation to HPA014295 and CAB016244 (HPA tissue IHC; HPA antibodies). UniProt lists no annotated isoforms, glycosylation sites, modified residues, signal sequence, or propeptide (UniProt P09669). These annotations do not establish why an individual slide stains weakly or strongly. |
| IF/ICC Q: What localisation should be expected? | A: HPA reports mitochondrial localisation, rated enhanced, with ICC-IF images in A-431, U-251MG, and U2OS cells (HPA subcellular). This supports a mitochondrial localisation check for IF/ICC; it does not supply an IF/ICC protocol or change the IHC slide criteria. |
| Situation | Likely cause | Next action |
|---|---|---|
| Expected-positive glandular cells have no stain. | The run may have failed; HPA reports High staining in adrenal and colon glandular cells (HPA tissue IHC). | Confirm tissue identity and examine retrieval, primary-antibody, and detection controls using the IHC workflow (standard IHC practice). Do not infer target-specific fixation sensitivity from this result. |
| Signal is mainly nuclear or at the cell surface. | The location disagrees with mitochondrial COX6C and HPA’s granular cytoplasmic pattern (UniProt P09669; HPA tissue IHC). | Check a reported High cell population and review a primary-omission control for nonspecific detection (HPA tissue IHC; standard IHC practice). |
| Diffuse brown background obscures granules. | Nonspecific binding, endogenous detection activity, or overdevelopment are possible (standard IHC practice). | Inspect a primary-omission control; review blocking, washing, and chromogen development within the IHC workflow (standard IHC practice). |
| Adipocytes or chondrocytes stain strongly. | HPA reports Low staining in these cells, so the result merits scrutiny; Low is not an absence claim (HPA tissue IHC). | Confirm cell identity, compare a reported High population, and inspect controls for cross-reactivity or endogenous activity (HPA tissue IHC; standard IHC practice). |
| Staining appears widespread but varies between cell populations. | COX6C has low RNA tissue specificity, while HPA’s protein staining levels vary by named cell type (HPA tissue IHC). | Score identifiable cells separately and compare each with HPA’s cell-specific pattern; retain granular cytoplasmic localisation as a check (HPA tissue IHC; standard IHC interpretation). |
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 first: glandular cells should stain (HPA: High in breast glandular cells; selected IHC caption: breast carcinoma section). HPA detects COX6C in all 45 scored tissues, so there is no supported negative tissue; use no-primary and isotype controls, and treat cells showing counterstain alone on the positive slide as background comparators, not verified COX6C-negative cells (HPA: detected in all 45 scored tissues).
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 a nonimmune isotype control matched to the primary antibody’s host species and immunoglobulin class; a validated COX6C knockout specimen, if available, provides a biological negative. Quench endogenous peroxidase for chromogenic detection and check the breast section’s no-primary control for background staining; use a no-primary control to assess autofluorescence if performing IF.
⚠️Feasibility: No target-specific fixation window, fixation effect, or antigen-retrieval dependency is reported in the supplied evidence; assess retrieval empirically for paraffin sections. The selected 1:100 breast carcinoma IHC caption does not state a fixative (selected SKU A11443-1 caption: paraffin-embedded breast carcinoma, 1:100). Frozen sections or IF cannot be called easier from these data, although mitochondrial localization offers an IF pattern to assess (HPA: mitochondria; UniProt P09669: inner mitochondrial membrane); no breast-specific artefact is reported.
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
Troubleshoot COX6C staining in chromogenic paraffin section IHC using its mitochondrial location, tissue staining profile, and the available antibody evidence.
How should I retrieve COX6C in paraffin sections when granular staining is weak?
Start with citrate buffer at pH 6.0, heated to 95–98 °C for 20 min (page retrieval rule). Allow sections to cool in the buffer before washing, and process comparison sections together so retrieval time is the only planned variable. The selected antibody has a paraffin section image at 1:100, but its caption gives no retrieval conditions (catalog antibody A11443-1 caption). If staining remains weak, compare a slightly longer citrate retrieval on an adjacent section while checking whether tissue structure deteriorates. Granular cytoplasmic staining is the expected tissue pattern; diffuse staining alone is a poor basis for increasing retrieval intensity (HPA tissue IHC profile).
Can fixation explain inconsistent COX6C staining between paraffin blocks?
Target specific fixation sensitivity is unknown: the selected paraffin section caption does not state a fixative (catalog antibody A11443-1 caption). For a prospective comparison, use one documented routine fixation procedure across specimens, such as 10% neutral buffered formalin, and record fixation duration and processing dates. Apply the same citrate pH 6.0, 95–98 °C, 20 min retrieval to sections from each block (page retrieval rule). Compare intact regions and a shared positive control before attributing a difference to fixation. Neither the granular tissue profile nor the inner membrane topology establishes a COX6C specific fixation effect (HPA tissue IHC profile; UniProt P09669 topology).
Where should convincing COX6C chromogenic staining appear within tissue cells?
Look for granular cytoplasmic staining rather than a nuclear pattern, consistent with the reported tissue profile (HPA tissue IHC profile). COX6C resides in the mitochondrial inner membrane, with residues 1–13 facing the matrix and 55–75 facing the intermembrane space (UniProt P09669 topology). Review staining at a magnification that resolves cytoplasmic granularity, using the counterstain to locate nuclei and cell boundaries. Glandular cells in breast and colon show high staining in the tissue dataset and can anchor a comparison of cell compartments (HPA tissue IHC). If the signal fills nuclei or extracellular material, inspect a no primary control and adjacent sections before scoring it as COX6C.
Does COX6C topology change how I should assess an antibody epitope?
Check the antibody's stated immunogen or epitope before interpreting a failed retrieval comparison; the supplied paraffin image caption does not identify one (catalog antibody A11443-1 caption). The 75 residue COX6C chain has one annotated membrane spanning segment at residues 14–54, flanked by matrix and intermembrane space regions (UniProt P09669 topology). No isoforms, glycosylation sites, or modified residues are annotated in the supplied record (UniProt P09669 record). Do not assume that either exposed end is the antibody's binding site without epitope evidence. Compare staining with a separately validated mitochondrial marker on adjacent sections if a plausible granular pattern is absent.
How can IF help check an ambiguous COX6C IHC pattern?
Use IF as a separate localisation cross check when chromogenic granules cannot be assigned confidently to cells; COX6C is mitochondrial (HPA subcellular; UniProt P09669 localisation). Multiplex with a marker for the expected cell population, such as glandular epithelial cells in breast, where high glandular staining is reported (HPA tissue IHC). Choose a far red COX6C fluorophore and inspect unstained tissue and single channel controls for autofluorescence or bleed through. If the antibody epitope is known, tune permeabilisation to expose its matrix or intermembrane side; those regions are residues 1–13 and 55–75, respectively (UniProt P09669 topology). The supplied caption provides paraffin IHC evidence, not IF conditions (catalog antibody A11443-1 caption).
How do I separate COX6C granules from diffuse DAB background?
Include a no primary section and inspect whether brown deposits persist after the same chromogenic detection steps. A routine peroxidase block, for example 3% hydrogen peroxide for 10 min, and controlled DAB development address background from the detection workflow; neither is COX6C specific. The selected paraffin image uses antibody at 1:100, which is a documented starting comparison rather than a proven optimum for every tissue (catalog antibody A11443-1 caption). If diffuse colour remains, compare shorter DAB development and antibody titration on adjacent sections while holding retrieval constant. Retain granular cytoplasmic signal as the pattern to assess (HPA tissue IHC profile).
What is a defensible way to score COX6C IHC across specimens? ⚠ ANSWER MARKED FOR VERIFICATION
Define the cell population and viable tissue area before scoring, then apply identical imaging, threshold, and DAB development settings across the comparison. Record percentage of positive cells and intensity classes 0–3; their weighted sum gives an H score from 0–300. Normalize counts to the number of evaluable cells, or report positive cell density per mm² of viable tissue, with glandular and other compartments assessed separately. This matters because high glandular staining and low adipocyte or chondrocyte staining are reported in different tissues (HPA tissue IHC). Exclude folds, necrosis, and tissue edges by a rule set before reviewing group labels.
When should a positive COX6C IHC signal be treated as artefact?
A credible signal is granular within cytoplasm, matching the tissue profile and mitochondrial assignment (HPA tissue IHC profile; HPA subcellular). Strong nuclear or extracellular staining conflicts with that localisation and warrants review against a no primary section (UniProt P09669 localisation). Check whether colour follows intact cells rather than tissue edges, folds, or necrotic debris, and whether it remains after a routine peroxidase block. Compare cell populations: high staining is reported in breast glandular cells, while adipocytes are listed as low (HPA tissue IHC). Neither a brown precipitate nor staining in an unexpected compartment alone establishes COX6C identity; assess pattern, controls, and tissue integrity together.
Boster reagents
Best COX6C / Cytochrome c oxidase subunit 6C IHC Antibodies
The catalog provides one COX6C antibody with IHC data from a paraffin-embedded human breast carcinoma section (catalog image caption); its listed reactivity includes human, mouse and rat (catalog reactivity).
Real IHC data
Anti-COX6c (R40) Antibody
Cat # A11443-1
A11443-1 has an IHC image from paraffin-embedded human breast carcinoma tissue at 1:100 (catalog image caption). Its listed application is IHC, and its listed reactivity is human, mouse and rat (catalog applications and reactivity).
Which to pick: Choose A11443-1 for paraffin-section IHC: its own image shows staining in paraffin-embedded human breast carcinoma tissue at 1:100 (catalog image caption), and it is a rabbit polyclonal antibody (catalog host and dilution record). There is no IF/ICC option in this catalog: A11443-1 lists IHC only (catalog applications). For mouse or rat tissue, A11443-1 lists reactivity with both species, although its supplied IHC image is from human tissue (catalog reactivity; catalog image caption); the fixative is unreported (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 paraffin sections. (standard IHC practice; not target-specific); Caveat: Adipocytes and chondrocytes may stain weakly (HPA tissue IHC); Isoform / epitope: No isoforms or processing annotated; one 75-aa chain (UniProt); Regulation: 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.