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SQOR / Sulfide:quinone oxidoreductase, mitochondrial · IHC design guide
Design Immunohistochemistry for SQOR
Use the granular cytoplasmic pattern and high staining in kidney tubules to plan SQOR tissue IHC controls (HPA tissue IHC). This guide covers consistent fixation, chromogenic scoring, and the catalog antibody’s IHC range of 2–5 μg/ml (datasheet A31817).
Evidence assembled Oct 2026 · For research use; verify linked source records and product datasheet before use
SQOR 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); mitochondrion (UniProt) | |
| Staining pattern | Granular cytoplasm in most tissues; high in kidney tubules (HPA tissue IHC) | |
| Antigen retrieval | EDTA pH 8.0 HIER, heat-mediated (datasheet A31817) | |
| Positive control | Appendix+4 more · see all | |
| Negative control | Hippocampus+3 more · see all |
Important caveats
Reasons your staining may differ from the expected pattern.
| Fixation | Keep fixation consistent across samples. (standard IHC practice; not target-specific) | |
| Caveat | Staining may include proteins from other genes (HPA tissue IHC) | |
| Regulation | Expression regulation not annotated (UniProt) | |
| Isoform / epitope | No annotated isoforms; epitope variation is unknown (UniProt) |
Section 1
Recommended SQOR IHC & IF Protocols
The catalog antibody’s IHC-P protocol is followed by 3 published SQOR IHC methods (PMC10746537; PMC11576178; PMC11584973).
| Sample | Paraffin-embedded human breast cancer tissue; fixative not specified (datasheet A31817) |
| Fixation | Image fixative and duration unreported (datasheet A31817); 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 A31817); 20 min, 95–100 °C (standard) |
| Peroxidase block | 3% H2O2, 10 min, room temperature (standard) |
| Blocking | 10% goat serum (datasheet A31817) |
| Primary antibody | Rabbit anti-SQOR, 2-5 μg/ml (datasheet A31817) |
| Primary incubation | Overnight at 4 °C (datasheet A31817) |
| Detection | HRP-conjugated secondary, DAB chromogen (datasheet A31817) |
| Counterstain | Hematoxylin, blue, dehydrate and mount (standard) |
| Expected result | SQOR-positive staining in endocrine cells of appendix (HPA tissue IHC: High). HPA tissue profile: Cytoplasmic expression with a granular pattern in most tissues. No signal in the no-primary control. |
💡Decision noteStart with heat-mediated EDTA pH 8.0 retrieval (datasheet A31817), then check staining against appropriate controls (standard IHC practice).
Section 2
What Is the Expected SQOR Staining Pattern?
SQOR is mitochondrial (UniProt Q9Y6N5; HPA subcellular: supported). In tissue IHC, expect granular cytoplasmic staining, with high signal in kidney tubule cells, intestinal endocrine cells, and skeletal myocytes (HPA tissue IHC). SQOR has no annotated transmembrane segment (UniProt Q9Y6N5 topology). HPA rates the tissue profile Enhanced but notes medium agreement with RNA, possible staining of proteins from more than one gene, and pending external verification (HPA tissue IHC).
| Granular cytoplasmic chromogen in kidney tubule cells, with less signal in neighboring cell populations. | This fits the reported high tubule-cell staining and granular tissue profile (HPA tissue IHC). Score the named cell population rather than calling the entire kidney uniformly positive. |
| Predominantly nuclear or surface staining where granular cytoplasmic signal is absent. | That distribution conflicts with mitochondrial localization and the reported tissue pattern (UniProt Q9Y6N5; HPA tissue IHC). Check morphology and controls before assigning it to SQOR. |
| Strong staining in a cell population reported as undetected, such as ovarian follicle cells. | HPA reports no detection in that cell population (HPA tissue IHC). Consider antibody cross-reactivity or endogenous detection activity; a discordant result alone cannot identify its cause. |
| Uniform haze or chromogen across many cell types and extracellular areas. | This obscures the expected granular cytoplasmic pattern (HPA tissue IHC). Background from detection chemistry or inadequate blocking is possible (general IHC practice); judge specificity using controls. |
| No staining in an otherwise evaluable positive cell population, such as kidney tubule cells. | That is discordant with the reported high signal (HPA tissue IHC). Check that the intended cells are present, then review retrieval, antibody incubation, and detection controls (general IHC practice). |
💡Expected SQOR appearanceCall a result positive when the relevant cells show distinct granular cytoplasmic staining, especially high signal in kidney tubule cells or intestinal endocrine cells (HPA tissue IHC); isolated nuclear, surface, or widespread diffuse signal is discordant with mitochondrial localization (UniProt Q9Y6N5; HPA subcellular).
| Compartment and morphology | Mitochondrial localization (UniProt Q9Y6N5; HPA subcellular: supported) agrees with the granular cytoplasmic tissue pattern (HPA tissue IHC). Assess punctate or granular cytoplasmic signal within recognizable cells. |
| Choice of positive tissue and cell population | HPA reports high staining in appendix, colon, duodenum, and rectum endocrine cells; kidney tubule cells; and skeletal myocytes (HPA tissue IHC). Use the annotated cell population when judging a control. |
| Choice of low or undetected comparison | HPA reports no detection in hippocampal glial cells, ovarian follicle cells, smooth muscle cells, and vaginal squamous epithelial cells (HPA tissue IHC). These are cell-level observations, not whole-tissue negatives. |
| Strength of validation evidence | The overall tissue profile is Enhanced, with medium RNA agreement, a multi-gene staining caution, and external verification pending (HPA tissue IHC). HPA017079 is IHC Enhanced; HPA041589 is IHC Supported (HPA antibodies). |
| Retrieval and target-specific fixation effects | Target-specific fixation effects are not established by the supplied assay evidence. Verify with a matched IHC source before attributing a result to fixation. |
| Situation | Likely cause | Next action |
|---|---|---|
| A kidney tubule positive control is blank. | The result conflicts with high tubule-cell staining (HPA tissue IHC); the failed step cannot be identified from this observation alone. | Confirm tubules are present, then check the antibody and detection controls and review retrieval conditions (general IHC practice). |
| Most of the section is diffusely brown. | Diffuse coverage does not match granular cytoplasmic SQOR staining (HPA tissue IHC). Detection background or endogenous activity is possible (general IHC practice). | Inspect a no-primary control and review blocking, washing, and chromogen development (general IHC practice); interpret cell-level staining only after background is controlled. |
| Signal is mainly nuclear or follows cell borders. | The compartment conflicts with mitochondrial localization (UniProt Q9Y6N5; HPA subcellular: supported). | Verify the morphology and compare with a reported positive cell population; use controls to assess whether the pattern comes from the staining workflow (general IHC practice). |
| Ovarian follicle cells stain strongly. | HPA reports these cells as not detected (HPA tissue IHC); cross-reactivity or detection activity is possible, but the stain alone does not prove either. | Compare with a no-primary control and a reported positive population; seek independent antibody or orthogonal confirmation before assigning the signal to SQOR (HPA tissue IHC: verification pending). |
| A whole section is scored from its strongest cells. | SQOR levels vary by cell population: kidney tubule cells are high, while ovarian follicle cells are not detected (HPA tissue IHC). | Score the named cell types separately and record granular cytoplasmic signal and intensity within each population (HPA tissue IHC). |
| How should an IF/ICC image be interpreted? | HPA supports mitochondrial localization and lists images from A-431, A-549, and U2OS cells (HPA subcellular); those images do not establish an IHC staining condition. | Look for mitochondrial signal rather than treating diffuse or nuclear fluorescence as confirmation (HPA subcellular: supported). Use the separate IF/ICC guide for its workflow. |
Experiment evidence
IHC & IF images showing SQOR staining
A31817 · IHCIHC analysis of SQRDL/SQOR using anti-SQRDL/SQOR antibody (A31817). SQRDL/SQOR was detected in a paraffin-embedded section of human breast c
A31817 · IHCIHC analysis of SQRDL/SQOR using anti-SQRDL/SQOR antibody (A31817). SQRDL/SQOR was detected in a paraffin-embedded section of human colorect
A31817 · IFIF analysis of SQRDL/SQOR using anti-SQRDL/SQOR antibody (A31817). SQRDL/SQOR was detected in an immunocytochemical section of PC-3 cells. E
HPA · Cerebral cortexHuman Protein Atlas IHC, Cerebral cortex. Source: https://www.proteinatlas.org/ENSG00000137767-SQOR/tissue/cerebral+cortex#imid_14930064
HPA · ColonHuman Protein Atlas IHC, Colon. Source: https://www.proteinatlas.org/ENSG00000137767-SQOR/tissue/colon#imid_14929974
HPA · LiverHuman Protein Atlas IHC, Liver. Source: https://www.proteinatlas.org/ENSG00000137767-SQOR/tissue/liver#imid_14929983
HPA · KidneyHuman Protein Atlas IHC, Kidney. Source: https://www.proteinatlas.org/ENSG00000137767-SQOR/tissue/kidney#imid_14929976
HPA · ICC-IF A-431Human Protein Atlas immunofluorescence, A-431, antibody HPA017079; green = SQOR, blue = nucleus, red = microtubules.
HPA · ICC-IF A-431Human Protein Atlas immunofluorescence, A-431, antibody HPA017079; green = SQOR, blue = nucleus, red = microtubules.
← swipe / scroll for more images →
Real IHC / IF data behind the staining-pattern expectations in this section.
Sample controls for SQOR IHC & IF
🧪Run colon first: endocrine cells should stain strongly (HPA: High in colon endocrine cells). Use smooth muscle as the negative tissue (HPA: Not detected in smooth muscle cells); smooth muscle cells within the colon section, if present, should show no specific staining and provide an internal comparator (HPA: Not detected in smooth muscle cells).
Positive control tissue: Appendix (Endocrine cells, HPA High)
Negative control tissue: Hippocampus (HPA Not detected)
ICC-IF cell lines (HPA subcellular resource): HPA ICC-IF images show SQOR in A-431, A-549, U2OS, with annotated localisation: Mitochondria (supported) (HPA subcellular).
Technical controls: Include a no-primary, secondary-only control; a concentration-matched rabbit IgG control for the rabbit primary (selected-SKU caption: rabbit antibody); and SQOR knockout material or a validated peptide-block control. For HRP/DAB staining, quench endogenous peroxidase and inspect the colon section for residual background (selected-SKU caption: HRP/DAB detection).
⚠️Feasibility: A target-specific fixation window or fixation effect is unreported, and the selected-SKU tissue-IHC caption does not state a fixative. Its paraffin-section example uses heat retrieval in EDTA at pH 8.0, but retrieval dependency has not been established (selected-SKU tissue-IHC caption). The supplied evidence does not establish whether frozen sections or IF are easier; assess colon background from endogenous peroxidase for IHC and autofluorescence for IF (selected-SKU caption: HRP/DAB detection).
HPA tissue IHC evidence for SQOR
Comprehensive Human Protein Atlas IHC scoring per tissue (reliability: Enhanced — Medium consistency between antibody staining and RNA expression data. Caution, targets protein from more than one gene. Pending external verification.). Rows are taken directly from the HPA tissue chart — click any row's HPA link to view the source.
Positive expression · recommended positive controls
| Tissue | Cell type | Level | Evidence | Source |
|---|---|---|---|---|
| Appendix | Endocrine cells | High | Protein (IHC) | HPA → |
| Colon | Endocrine cells | High | Protein (IHC) | HPA → |
| Duodenum | Endocrine cells | High | Protein (IHC) | HPA → |
| Kidney | Cells in tubules | High | Protein (IHC) | HPA → |
| Nasopharynx | Respiratory epithelial cells | High | Protein (IHC) | HPA → |
Undetected expression · recommended negative controls
| Tissue | Cell type | Level | Evidence | Source |
|---|---|---|---|---|
| Hippocampus | Glial cells | Not detected | Protein (IHC) | HPA → |
| Ovary | Follicle cells | Not detected | Protein (IHC) | HPA → |
| Smooth muscle | Smooth muscle cells | Not detected | Protein (IHC) | HPA → |
| Vagina | Squamous epithelial cells | Not detected | Protein (IHC) | HPA → |
Section 3
Advanced SQOR IHC Tips
Troubleshoot SQOR staining in paraffin sections by checking retrieval, granular cytoplasmic localisation, cell type and assay controls.
What retrieval should I try when SQOR staining is weak?
Start with heat-mediated retrieval in EDTA buffer at pH 8.0 (datasheet A31817). The selected paraffin-section example used this retrieval before overnight incubation at 4°C with 2 μg/ml catalog antibody, so assess retrieval alongside antibody concentration (datasheet A31817). If signal remains weak, compare a second retrieval condition on adjacent sections while holding detection and imaging constant (standard IHC practice). Include a kidney tubular-cell or intestinal endocrine-cell positive control, since these cells show high SQOR staining (HPA: high in kidney tubules and intestinal endocrine cells). Excessively harsh heating can damage section structure, so judge staining intensity together with morphology (standard IHC practice).
How should I troubleshoot variable SQOR staining between paraffin blocks?
Target-specific sensitivity to fixation is unknown: the selected paraffin-section caption does not state a fixative (datasheet A31817). Record each block’s fixative and fixation duration, then compare sections processed with the same EDTA pH 8.0 retrieval and detection workflow (datasheet A31817; standard IHC practice). For a controlled comparison, hold section thickness and antibody incubation constant; the selected example used 2 μg/ml overnight at 4°C (datasheet A31817). Check preservation of cell borders and nuclei before attributing a weak result to SQOR abundance (standard IHC practice). Include a consistently processed positive-control section in each run to distinguish block variation from staining-run variation (standard IHC practice).
Where should convincing SQOR signal appear in chromogenic IHC?
Expect granular cytoplasmic staining consistent with mitochondrial localisation, rather than a nuclear or surface-only pattern (HPA: granular cytoplasmic tissue expression; HPA subcellular: mitochondria supported; UniProt Q9Y6N5: mitochondrion). Inspect cells at 40× alongside a lower-power survey so fine granules and the tissue distribution can both be assessed (standard IHC practice). Kidney tubular cells and intestinal endocrine cells provide high-staining reference populations (HPA: kidney, appendix, colon, duodenum and rectum). Compare similarly processed negative-control sections when diffuse cytoplasmic colour obscures granules (standard IHC practice). SQOR has no annotated transmembrane segment, but that annotation alone does not establish which antibody epitopes are accessible after processing (UniProt Q9Y6N5 topology).
Could isoforms or epitope masking explain inconsistent SQOR staining?
The supplied SQOR record lists 0 isoforms, so an isoform-specific explanation is unsupported by this record (UniProt Q9Y6N5 isoforms). It lists no transmembrane segment and notes acetyllysine at 173 and phosphoserine at 343; these annotations do not identify the catalog antibody’s epitope (UniProt Q9Y6N5 topology and modified residues). If staining varies, compare the documented EDTA pH 8.0 retrieval across matched sections before assigning the difference to epitope masking (datasheet A31817; standard IHC practice). Ask for the antibody’s epitope information or test an independently validated antibody if epitope dependence is central to the experiment (standard IHC practice). Keep staining conditions and scoring thresholds constant during that comparison (standard IHC practice).
How can I assess SQOR localisation by IF alongside this IHC assay?
Use a separate IF/ICC validation workflow: the selected catalog example establishes paraffin-section chromogenic IHC, while supported mitochondrial localisation is reported independently (datasheet A31817; HPA subcellular: mitochondria supported). Multiplex SQOR with a marker identifying the expected cell population, such as kidney tubular cells, and a mitochondrial marker to assess compartment agreement (HPA: high in kidney tubules; HPA subcellular: mitochondria supported; standard IF practice). Choose spectrally separated fluorophores, favouring a far-red SQOR channel when green tissue autofluorescence is strong (standard IF practice). Permeabilise fixed cells sufficiently for access to mitochondrial epitopes, but determine detergent strength empirically because no epitope side is specified (UniProt Q9Y6N5 topology; standard IF practice). Include single-colour and no-primary controls to assess bleed-through and background (standard IF practice).
How do I reduce diffuse brown background without losing SQOR granules?
First compare the stained section with a no-primary control to separate antibody-dependent colour from detection background (standard IHC practice). The selected example blocked with 10% goat serum and used a peroxidase-conjugated secondary followed by DAB, providing a documented starting point for that antibody (datasheet A31817). Add a peroxidase-blocking step and check wash quality when endogenous enzyme activity or residual reagent produces diffuse brown staining (standard chromogenic IHC practice). Shorten DAB development consistently across sections if colour spreads beyond cell boundaries, and inspect the expected granular cytoplasmic pattern before accepting signal (standard IHC practice; HPA: granular cytoplasmic expression). Record antibody concentration; the selected example used 2 μg/ml (datasheet A31817).
How should I score SQOR IHC across samples? ⚠ ANSWER MARKED FOR VERIFICATION
Define the cell population before scoring, since SQOR staining differs by cell type within tissues (HPA: high in kidney tubular cells and intestinal endocrine cells; HPA: not detected in smooth muscle cells). For an H-score, assign intensity 0–3 and sum each intensity multiplied by its percentage of eligible cells, yielding 0–300 (standard IHC scoring practice). Alternatively report the percentage of positive eligible cells or positive-cell density per mm², using the same threshold across slides (standard IHC scoring practice). Normalise to the number or area of evaluable target cells, and exclude empty, folded or necrotic regions by a prespecified rule (standard IHC scoring practice). Report cell type and staining pattern alongside the numerical score (HPA: granular cytoplasmic expression).
How can I distinguish true SQOR positivity from staining artefact?
Give greatest weight to granular cytoplasmic colour in intact cells, consistent with mitochondrial SQOR localisation (HPA: granular cytoplasmic tissue expression; HPA subcellular: mitochondria supported; UniProt Q9Y6N5: mitochondrion). A high signal in kidney tubular cells supports plausibility, whereas strong smooth-muscle-cell staining warrants additional controls because that population was reported as not detected (HPA: high in kidney tubules; HPA: smooth muscle cells not detected). Treat nuclear-only colour, section-edge enhancement and necrotic deposits cautiously, especially if similar colour appears in a no-primary control (standard IHC practice). Check endogenous peroxidase interference with an appropriate detection control before calling diffuse DAB colour positive (standard chromogenic IHC practice). HPA tissue staining has medium agreement with RNA and may detect protein from more than one gene, so corroborate consequential calls independently (HPA: Enhanced reliability description).
Boster reagents
Best SQOR / Sulfide:quinone oxidoreductase, mitochondrial IHC Antibodies
A31817 has IHC data from human paraffin sections and ICC/IF data from PC-3 cells; the catalog lists human reactivity (A31817 image captions; catalog: reactivity).
Real IHC data
Anti-SQRDL/SQOR Antibody ®
Cat # A31817
A31817 was shown in paraffin sections of human breast cancer, colorectal adenocarcinoma, liver cancer and lung adenocarcinoma tissue (A31817 IHC captions). It was also shown by ICC/IF in PC-3 cells (A31817 IF caption).
Which to pick: Choose A31817 for tissue IHC in paraffin sections: its breast cancer IHC caption reports EDTA retrieval at pH 8.0 and 2 μg/ml primary antibody; the fixative is unreported (A31817 IHC caption). Choose the same SKU for ICC/IF because its application list includes both and its PC-3 caption reports 5 μg/ml; the catalog identifies the antibody as rabbit but does not report clonality (catalog: applications, host; A31817 IF caption). No cross-species choice is supported because the catalog lists human reactivity only (catalog: reactivity).
Each figure is that product's own IHC / IF validation image from its datasheet.
References
- UniProt Consortium. UniProt entry Q9Y6N5 (SQOR_HUMAN, Sulfide:quinone oxidoreductase, mitochondrial).
- Human Protein Atlas. SQOR tissue IHC expression (reliability: Enhanced).
- Human Protein Atlas. SQOR subcellular location (ICC-IF): Localized to the mitochondria..
- Human Protein Atlas. SQOR antibody validation summary (2 antibodies).
- Knockout of the sulfide: quinone oxidoreductase SQR reduces growth of HCT116 tumor xenograft. Redox biology 2025 — PMC12433914.
- Sulfide:quinone oxidoreductase alleviates ferroptosis in acute kidney injury via ameliorating mitochondrial dysfunction of renal tubular epithelial cells. Redox biology 2024 — PMC10746537.
- A novel hypoxia- and lactate metabolism-related prognostic signature to characterize the immune landscape and predict immunotherapy response in osteosarcoma. Frontiers in immunology 2024 — PMC11576178.
- Sulfide oxidation promotes hypoxic angiogenesis and neovascularization. Nature chemical biology 2024 — PMC11584973.
- PubMed PMID:10224084 — UniProt-cited evidence.
- PubMed PMID:10810093 — UniProt-cited evidence.
- PubMed PMID:15489334 — UniProt-cited evidence.
Immunohistochemistry protocol sheet for SQOR (Sulfide:quinone oxidoreductase, mitochondrial). Expected localisation Granular cytoplasm (HPA tissue IHC); mitochondrion (UniProt). Antigen retrieval: EDTA pH 8.0 HIER, heat-mediated (datasheet A31817). Validated IHC antibody: A31817 at 2-5 μg/ml (the product's own IHC validation image is shown). Controls (HPA): positive Appendix (Endocrine cells); negative Hippocampus. IHC-P workflow on paraffin sections; fixative unspecified. Protocol steps: 1. Sample: Paraffin-embedded human breast cancer tissue; fixative not specified (datasheet A31817); 2. Fixation: Image fixative and duration unreported (datasheet A31817); 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 A31817); 20 min, 95–100 °C (standard); 6. Peroxidase block: 3% H2O2, 10 min , room temperature (standard); 7. Blocking: 10% goat serum (datasheet A31817); 8. Primary antibody: Rabbit anti-SQOR, 2-5 μg/ml (datasheet A31817); 9. Primary incubation: Overnight at 4 °C (datasheet A31817). Watch for: Fixation: Keep fixation consistent across samples. (standard IHC practice; not target-specific); Caveat: Staining may include proteins from other genes (HPA tissue IHC); Isoform / epitope: No annotated isoforms; epitope variation is unknown (UniProt); Regulation: Expression regulation not annotated (UniProt). Evidence: UniProt Q9Y6N5, HPA tissue IHC · Enhanced, HPA ICC-IF · mitochondria., Datasheet A31817, PMC10746537, PMC11576178. QR code links to https://www.bosterbio.com/bosterbio-gene-info-cards/SQOR/immunohistochemistry-ihc-guide.