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NDUFS6 / NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrial · IHC design guide
Design Immunohistochemistry for NDUFS6
Plan chromogenic IHC in paraffin sections with the IHC-validated antibody (datasheet A09082-2). Use glandular cells as positive controls and assess granular cytoplasmic staining (HPA tissue IHC), while treating the mitochondrial inner-membrane location as a molecular annotation (UniProt).
Evidence assembled Oct 2026 · For research use; verify linked source records and product datasheet before use
NDUFS6 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 | Tissue: granular cytoplasm (HPA tissue IHC); protein: mitochondrial inner membrane (UniProt) | |
| Staining pattern | General granular cytoplasmic staining (HPA tissue IHC) | |
| Antigen retrieval | EDTA pH 8.0 HIER, heat-mediated (datasheet A09082-2) | |
| Positive control | Adrenal gland+4 more · see all | |
| Negative control | Adipose tissue+1 more · see all |
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 are unstained despite broad tissue expression (HPA tissue IHC) | |
| Regulation | Tissue-enhanced RNA in skeletal muscle (HPA tissue RNA) | |
| Isoform / epitope | No isoforms annotated; mature chain spans 29–124 (UniProt) |
Section 1
Recommended NDUFS6 IHC & IF Protocols
The catalog antibody’s IHC-P protocol is paired with four published NDUFS6 protocols for ovarian, neuroblastoma, cardiac, and other paraffin-embedded tissue sections (datasheet A09082-2; PMC12635173; PMC13263444; PMC12095822; PMC12148850).
| Sample | Paraffin-embedded human breast cancer tissue; fixative not specified (datasheet A09082-2) |
| Fixation | Image fixative and duration unreported (datasheet A09082-2); verify before use. |
| Sectioning | 4–5 µm sections on charged slides (standard) |
| Deparaffinisation | Xylene, graded ethanol series to water (standard) |
| Antigen retrieval | Heat retrieval: EDTA pH 8.0 (datasheet A09082-2); 20 min, 95–100 °C (standard) |
| Peroxidase block | 3% H2O2, 10 min, room temperature (standard) |
| Blocking | 10% goat serum (datasheet A09082-2) |
| Primary antibody | Rabbit anti-NDUFS6, 2-5 μg/ml (datasheet A09082-2) |
| Primary incubation | Overnight at 4 °C (datasheet A09082-2) |
| Detection | HRP-conjugated secondary, DAB chromogen (datasheet A09082-2) |
| Counterstain | Hematoxylin, blue, dehydrate and mount (standard) |
| Expected result | NDUFS6-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 heat-mediated EDTA retrieval at pH 8.0 for the catalog antibody (datasheet A09082-2). Published retrieval conditions differ; match them to the antibody used in each study (PMC12635173; PMC13263444).
Section 2
What Is the Expected NDUFS6 Staining Pattern?
NDUFS6 is a mitochondrial inner-membrane Complex I subunit with no predicted transmembrane segment (UniProt O75380 topology). In paraffin-section IHC, expect granular cytoplasmic staining in cells such as colon glandular cells, bronchial respiratory epithelial cells, and cerebral cortical neurons (HPA: tissue IHC). HPA describes the overall pattern as general granular cytoplasmic expression and rates its tissue IHC evidence Supported, with medium consistency between staining and RNA data (HPA: tissue IHC).
| Granular cytoplasmic stain in colon glandular cells or cerebral cortical neurons (HPA: High in both). | This fits the reported tissue pattern (HPA: granular cytoplasm) and mitochondrial location (UniProt O75380). Assess the named cells rather than treating every cell in the section as an equally strong positive control (HPA: cell-specific tissue IHC). |
| Predominantly nuclear, surface, or extracellular stain in otherwise positive cells. | That distribution does not fit the granular cytoplasmic IHC profile (HPA: tissue IHC) or inner-membrane location (UniProt O75380). Treat it as suspect staining; inspect morphology, detection controls, and the antibody conditions before scoring it as NDUFS6 (standard IHC practice). |
| Strong stain in adipocytes or parathyroid glandular cells (HPA: Not detected in both). | This conflicts with the reported cell-level negatives (HPA: tissue IHC). Cross-reactivity or endogenous detection activity is possible; compare a no-primary control and the positive tissue processed in the same run before assigning a cause (standard IHC practice). |
| Uniform haze across tissue, stroma, and cells, obscuring granules. | A diffuse field is hard to reconcile with the reported granular cytoplasmic profile (HPA: tissue IHC). Review background controls, blocking, washes, and chromogen development; broad color alone cannot establish target localisation (standard IHC practice). |
| No stain in colon glandular cells or bronchial respiratory epithelial cells (HPA: High in both). | The run lacks its expected positive readout (HPA: tissue IHC). Check tissue identity and cell preservation, then review antibody dilution, retrieval, and detection controls before calling the sample negative (standard IHC practice). HPA's Supported rating is not a guarantee for every section (HPA: reliability). |
💡Expected NDUFS6 appearanceCall a positive result when the expected cells show discernible granular cytoplasmic stain, ideally strong in an HPA High cell population; isolated nuclear, extracellular, or diffuse field staining is suspect (HPA: tissue IHC; UniProt O75380 localisation).
| Cell-level tissue contrast | HPA reports High staining in adrenal, appendix, breast, colon, and duodenum glandular cells, but Not detected in parathyroid glandular cells (HPA: tissue IHC). Choose and score controls by the specified cell population, not by the organ name alone (standard IHC practice). |
| Protein location and processing | NDUFS6 resides at the mitochondrial inner membrane, has no annotated transmembrane segment, and has a mature chain at residues 29–124 (UniProt O75380). These annotations support a cytoplasmic, organelle-associated reading; they do not identify this antibody's epitope or prescribe retrieval conditions (UniProt O75380; standard IHC practice). |
| Strength of IHC evidence | The HPA tissue profile is Supported with medium staining–RNA consistency; HPA064221 is listed as IHC Supported (HPA: tissue IHC; HPA: antibody validation). Use the observed pattern as a reference and retain run controls when judging an unexpected result (standard IHC practice). |
| IF evidence boundary | HPA gives no main ICC-IF location and lists no cell lines with ICC-IF images; HPA064221 has no ICC status in the supplied record (HPA: subcellular; HPA: antibody validation). Can this establish an IF pattern? No: assess IF on its own guide page, without treating the IHC pattern as ICC-IF validation. |
| Situation | Likely cause | Next action |
|---|---|---|
| Known-positive cells remain unstained. | The run may have a tissue, retrieval, antibody, or detection problem; colon glandular cells are reported High (HPA: tissue IHC; standard IHC practice). | Confirm the expected cells are present, then review retrieval, dilution, reagent performance, and a run-matched positive control (standard IHC practice). No NDUFS6-specific retrieval setting is supplied. |
| The entire section develops brown color. | Broad color may reflect endogenous peroxidase activity or detection background rather than granular cytoplasmic NDUFS6 (standard IHC practice; HPA: tissue IHC). | Compare no-primary and detection controls; review peroxidase blocking, washes, and development time before interpreting cell-level stain (standard IHC practice). |
| Adipocytes or parathyroid glandular cells stain strongly. | Those populations are reported Not detected (HPA: tissue IHC); cross-reactivity or detection background is possible (standard IHC practice). | Inspect a no-primary control and an HPA High population from the same run; score only a credible granular cytoplasmic pattern (HPA: tissue IHC; standard IHC practice). |
| Nuclear staining dominates a positive tissue. | A nuclear pattern disagrees with granular cytoplasmic IHC and mitochondrial localisation (HPA: tissue IHC; UniProt O75380). | Check counterstain separation and no-primary controls, then reassess antibody and detection conditions before assigning target-specific signal (standard IHC practice). |
| Positive tissue shows weak, patchy granules. | HPA assigns High staining to particular cells, not every cell in an organ; uneven section quality or run performance can complicate scoring (HPA: tissue IHC; standard IHC practice). | Score the named cell population, compare a run-matched positive control, and inspect tissue preservation and detection consistency (standard IHC practice). |
| An IF image is requested as proof of the IHC result. | The supplied HPA subcellular record has no ICC-IF images or assigned main location, and the antibody has no listed ICC status (HPA: subcellular; HPA: antibody validation). | Use the IHC tissue pattern and IHC controls for this callout (HPA: tissue IHC; standard IHC practice). Evaluate IF separately on its own guide page; this record supplies no ICC-IF validation. |
Experiment evidence
IHC & IF images showing NDUFS6 staining
A09082-2 · IHCIHC analysis of NDUFS6 using anti-NDUFS6 antibody (A09082-2). NDUFS6 was detected in a paraffin-embedded section of human breast cancer tiss
A09082-2 · IHCIHC analysis of NDUFS6 using anti-NDUFS6 antibody (A09082-2). NDUFS6 was detected in a paraffin-embedded section of human ovarian cancer tis
HPA · Cerebral cortexHuman Protein Atlas IHC, Cerebral cortex. Source: https://www.proteinatlas.org/ENSG00000145494-NDUFS6/tissue/cerebral+cortex#imid_17792624
HPA · ColonHuman Protein Atlas IHC, Colon. Source: https://www.proteinatlas.org/ENSG00000145494-NDUFS6/tissue/colon#imid_17792548
HPA · LiverHuman Protein Atlas IHC, Liver. Source: https://www.proteinatlas.org/ENSG00000145494-NDUFS6/tissue/liver#imid_17792541
HPA · KidneyHuman Protein Atlas IHC, Kidney. Source: https://www.proteinatlas.org/ENSG00000145494-NDUFS6/tissue/kidney#imid_17792542
← swipe / scroll for more images →
Real IHC / IF data behind the staining-pattern expectations in this section.
Sample controls for NDUFS6 IHC & IF
🧪Run breast first: glandular cells should stain (HPA: High in breast glandular cells). Use adipose tissue as the negative comparator (HPA: Not detected in adipocytes); on the breast slide, assess non-glandular areas for background against the no-primary control rather than assuming those cells lack NDUFS6.
Positive control tissue: Adrenal gland (Glandular cells, HPA High)
Negative control tissue: Adipose tissue (HPA Not detected)
ICC-IF cell lines (HPA subcellular resource): HPA carries no ICC-IF cell line for NDUFS6; derive a cell-line control from the positive tissue's cell type (Glandular cells) and confirm it by RNA or western blot first.
Technical controls: Include a no-primary, secondary-only control and an isotype control matched to the rabbit primary antibody’s host and clonality where applicable (selected SKU A09082-2 caption: rabbit primary). Use NDUFS6 knockout material or a cognate-peptide block as a biological specificity control, and quench endogenous peroxidase before interpreting DAB signal in breast tissue (selected SKU A09082-2 caption: peroxidase detection with DAB).
⚠️Feasibility: A target-specific fixation window or fixation effect is unreported, and the selected SKU A09082-2 tissue-IHC caption does not state a fixative. The demonstrated paraffin-section workflow used heat retrieval in EDTA at pH 8.0, but the caption does not establish that retrieval is required (selected SKU A09082-2 caption). Whether frozen sections or IF are easier is unreported; breast-slide DAB background should be assessed with the peroxidase and no-primary controls (selected SKU A09082-2 caption: breast cancer tissue and DAB detection).
HPA tissue IHC evidence for NDUFS6
Comprehensive Human Protein Atlas IHC scoring per tissue (reliability: Supported — 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 |
|---|---|---|---|---|
| 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 → |
Section 3
Advanced NDUFS6 IHC Tips
Use the catalog antibody’s paraffin-section IHC conditions as the starting point, then assess granular cytoplasmic staining against tissue controls and morphology.
Which antigen retrieval should I try first for NDUFS6 in paraffin sections?
Start with heat-mediated retrieval in EDTA at pH 8.0 for paraffin-section NDUFS6 IHC (datasheet A09082-2). Keep retrieval time and heating method consistent across test and control sections so staining differences remain interpretable (standard IHC practice). The catalog image used 2 μg/ml primary antibody overnight at 4°C; use that condition as a reference when assessing retrieval (datasheet A09082-2). If staining is weak, adjust heating duration in small steps while checking whether tissue morphology and background deteriorate (standard IHC practice). Compare each condition with a no-primary control and the same expected-positive tissue (standard IHC practice).
How should I troubleshoot fixation-related loss of NDUFS6 staining?
Target-specific fixation sensitivity is unknown: the catalog tissue-IHC caption identifies a paraffin section but does not state its fixative (datasheet A09082-2). Record the fixative, fixation duration and processing history for each specimen before comparing NDUFS6 staining (standard IHC practice). Test differently processed sections using identical EDTA pH 8.0 retrieval and detection conditions to isolate processing effects (datasheet A09082-2; standard IHC practice). If staining varies, inspect morphology and include a consistently processed reference section in the same run (standard IHC practice). Do not attribute a weak result to a particular fixation mechanism without a controlled comparison (standard IHC practice).
What staining pattern should I expect, and how do I assess diffuse signal?
NDUFS6 is assigned to the mitochondrial inner membrane and has no annotated transmembrane segment (UniProt O75380 topology). In tissue IHC, the reported pattern is granular cytoplasmic staining, so assess whether the signal forms cytoplasmic puncta rather than a uniform nuclear or surface rim (HPA tissue IHC). Check well-preserved cells at high magnification and compare the pattern with a no-primary section before assigning faint diffuse brown staining to NDUFS6 (standard IHC practice). Granules need not resolve individual mitochondria in chromogenic sections, so score the cellular pattern consistently across specimens (standard IHC practice). Mark strongly stained edges separately if their intensity does not match the section interior (standard IHC practice).
Could precursor processing or an isoform explain inconsistent NDUFS6 staining?
The record lists no isoforms and describes a 124-aa precursor with a mature chain spanning residues 29–124 (UniProt O75380 processing and isoforms). It also lists no annotated glycosylation sites and one modified residue, acetyllysine at position 98 (UniProt O75380 modifications). These annotations do not identify the catalog antibody’s epitope, so they cannot establish whether processing or acetylation changes its staining (UniProt O75380; datasheet A09082-2). If an epitope map becomes available, check whether it lies within the mature chain before interpreting variable signal (standard antibody-validation practice). Meanwhile, compare matched retrieval conditions and cellular patterns rather than assigning intensity differences to an unverified isoform (standard IHC practice).
How can I investigate NDUFS6 localisation by IF alongside this IHC assay?
Treat IF as a separate application requiring its own antibody validation; the supplied catalog example documents chromogenic tissue IHC (datasheet A09082-2). For multiplex IF, pair NDUFS6 with a marker for the cell population being assessed and a mitochondrial marker when compartment assignment matters (standard IF practice; UniProt O75380 localisation). Choose fluorophores after inspecting tissue autofluorescence, favouring a channel with clear separation from that background (standard IF practice). Because NDUFS6 is assigned to the mitochondrial inner membrane, optimise permeabilisation to permit antibody access to its actual epitope; the epitope’s membrane-facing side is not supplied (UniProt O75380 topology; datasheet A09082-2). Include single-stain and no-primary controls before interpreting overlap (standard IF practice).
What should I change if NDUFS6 DAB staining is widespread or uneven?
The catalog IHC example blocked the section with 10% goat serum, used 2 μg/ml primary antibody overnight at 4°C, and developed signal with DAB (datasheet A09082-2). Start troubleshooting by comparing a no-primary section with the test section and checking whether brown signal follows tissue edges or damaged areas (standard IHC practice). Apply a peroxidase block and verify wash steps before DAB development, since residual enzyme activity can produce misleading chromogen signal (standard IHC practice). If background persists, titrate primary concentration and detection time while retaining a positive reference section (standard IHC practice). Interpret diffuse staining cautiously against the reported granular cytoplasmic pattern (HPA tissue IHC).
How should I quantify NDUFS6 staining across tissue sections? ⚠ ANSWER MARKED FOR VERIFICATION
Define the cell population and analysis region before scoring, then exclude folds, necrosis and poorly preserved areas using the same rules for every section (standard IHC practice). For cellular expression, record the percentage of positive cells and a predefined intensity grade; calculate an H-score only if those grades are reproducible between observers (standard IHC practice). For spatial comparisons, report positive-cell density per mm² of viable analysed tissue and state how regions were selected (standard IHC practice). Normalise comparisons to the same cell type, viable area, staining run and reference section rather than raw whole-section brown area (standard IHC practice). The reported granular cytoplasmic pattern should guide positive-cell calls (HPA tissue IHC).
How do I distinguish convincing NDUFS6 positivity from staining artefact?
A convincing cellular result should fit granular cytoplasmic staining and the protein’s mitochondrial inner-membrane assignment (HPA tissue IHC; UniProt O75380 localisation). Compare candidate-positive cells with section morphology and a no-primary control, particularly where signal appears nuclear, membranous or diffusely extracellular (standard IHC practice). The HPA reports high staining in breast glandular cells and no detected staining in adipocytes, which can inform interpretation when those cells are present (HPA tissue IHC). Treat isolated edge staining, necrotic deposits and signal attributable to endogenous peroxidase as potential artefacts, and check them against interior tissue and the blocked control (standard IHC practice). Resolve discordant patterns with a second validated readout before making a biological claim (standard IHC practice).
Boster reagents
Best NDUFS6 / NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrial IHC Antibodies
A09082-2 has paraffin-section IHC images from human breast and ovarian cancer tissue and mouse heart (catalog image captions). No IF image is supplied (catalog payload).
Real IHC data
Anti-NDUFS6 Antibody ®
Cat # A09082-2
A09082-2 is listed for IHC in human and mouse samples (catalog: IHC dilution listing), with images from paraffin sections of human breast cancer, human ovarian cancer, and mouse heart (catalog image captions). Its general reactivity list also includes rat, but the supplied IHC images do not show rat tissue (catalog: reactivity list; image captions).
Which to pick: For tissue IHC, choose A09082-2 at the listed 2–5 μg/ml range (datasheet: IHC dilution); its captions document paraffin sections with EDTA retrieval, while the fixative is unreported (catalog image captions). No SKU in this payload is validated for IF/ICC, so there is no IF/ICC pick (catalog: application list; IF image alts). For cross-species planning, A09082-2 lists human, mouse, and rat reactivity, with IHC image evidence for human and mouse only; its clone is unreported.
Each figure is that product's own IHC / IF validation image from its datasheet.
References
- UniProt Consortium. UniProt entry O75380 (NDUS6_HUMAN, NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrial).
- Human Protein Atlas. NDUFS6 tissue IHC expression (reliability: Supported).
- Human Protein Atlas. NDUFS6 subcellular location (ICC-IF): Highest expression in HeLa: 1511.0 nTPM.
- Human Protein Atlas. NDUFS6 antibody validation summary (1 antibodies).
- Integrative machine learning-driven prognosis and immunotherapy stratification via lactylation-associated gene in ovarian cancer. NPJ precision oncology 2025 — PMC12635173.
- NDUFS6 promotes neuroblastoma progression and represents a potential therapeutic target. Translational pediatrics 2026 — PMC13263444.
- Gene therapy prevents onset of mitochondrial cardiomyopathy in neonatal mice with Ndufs6 deficiency. Cell death discovery 2025 — PMC12095822.
- Exploring the role of mitochondrial metabolism and immune infiltration in myocardial infarction: novel insights from bioinformatics and experimental validation. Frontiers in immunology 2025 — PMC12148850.
- PubMed PMID:9647766 — UniProt-cited evidence.
- PubMed PMID:15489334 — UniProt-cited evidence.
- PubMed PMID:12611891 — UniProt-cited evidence.
Immunohistochemistry protocol sheet for NDUFS6 (NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrial). Expected localisation Tissue: granular cytoplasm (HPA tissue IHC); protein: mitochondrial inner membrane (UniProt). Antigen retrieval: EDTA pH 8.0 HIER, heat-mediated (datasheet A09082-2). Validated IHC antibody: A09082-2 at 2-5 μg/ml (the product's own IHC validation image is shown). Controls (HPA): positive Adrenal gland (Glandular cells); negative Adipose tissue. IHC-P workflow on paraffin sections; fixative unspecified. Protocol steps: 1. Sample: Paraffin-embedded human breast cancer tissue; fixative not specified (datasheet A09082-2); 2. Fixation: Image fixative and duration unreported (datasheet A09082-2); verify before use.; 3. Sectioning: 4–5 µm sections on charged slides (standard); 4. Deparaffinisation: Xylene, graded ethanol series to water (standard); 5. Antigen retrieval: Heat retrieval: EDTA pH 8.0 (datasheet A09082-2); 20 min, 95–100 °C (standard); 6. Peroxidase block: 3% H2O2, 10 min , room temperature (standard); 7. Blocking: 10% goat serum (datasheet A09082-2); 8. Primary antibody: Rabbit anti-NDUFS6, 2-5 μg/ml (datasheet A09082-2); 9. Primary incubation: Overnight at 4 °C (datasheet A09082-2). Watch for: Fixation: Keep fixation consistent across sections. (standard IHC practice; not target-specific); Caveat: Adipocytes are unstained despite broad tissue expression (HPA tissue IHC); Isoform / epitope: No isoforms annotated; mature chain spans 29–124 (UniProt); Regulation: Tissue-enhanced RNA in skeletal muscle (HPA tissue RNA). Evidence: UniProt O75380, HPA tissue IHC · Supported, HPA cell-line RNA · Highest expression in HeLa: 1511.0 nTPM, Datasheet A09082-2, PMC12635173, PMC13263444. QR code links to https://www.bosterbio.com/bosterbio-gene-info-cards/NDUFS6/immunohistochemistry-ihc-guide.