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Plan chromogenic SOD2 IHC on paraffin sections using 0.5–1 μg/mL as the PB9442 antibody starting range (datasheet: PB9442). Assess staining by cell type and intensity against the reported cytoplasmic, mitochondrial tissue pattern (HPA tissue IHC).
Expected localisation, validated protocols, controls and antibodies — the at-a-glance facts below, then the full design guide.
| Expected localisation | Cytoplasmic, mitochondrial pattern in tissue (HPA tissue IHC) | |
| Staining pattern | General cytoplasmic staining with a mitochondrial pattern (HPA tissue IHC) | |
| Antigen retrieval | Citrate pH 6 HIER, heat-mediated (datasheet PB9442) | |
| Positive control | Adrenal gland+4 more · see all | |
| Negative control | None in HPA (detected in all 44 tissues); use no-primary + isotype controls |
| Fixation | Keep fixation consistent across sections. (standard IHC practice; not target-specific) | |
| Caveat | Staining–RNA consistency is medium; restaining is pending (HPA tissue IHC) | |
| Regulation | Bone marrow–enhanced RNA expression (HPA tissue RNA) | |
| Isoform / epitope | 4 isoforms; mature chain spans residues 25–222; verify epitope coverage (UniProt) |
The catalog antibody’s IHC-P protocol (datasheet PB9442) is followed by three published SOD2 paraffin-section protocols (PMC11481372; PMC5955150; PMC8147985).
| Sample | Paraffin-embedded human mammary cancer tissue; fixative not specified (datasheet PB9442) |
| Fixation | Image fixative and duration unreported (datasheet PB9442); verify before use. |
| Sectioning | 4–5 µm sections on charged slides (standard) |
| Deparaffinisation | Xylene, graded ethanol series to water (standard) |
| Antigen retrieval | Heat retrieval: Citrate pH 6, 20 min (datasheet PB9442) |
| Peroxidase block | 3% H2O2, 10 min, room temperature (standard) |
| Blocking | 10% goat serum (datasheet PB9442) |
| Primary antibody | Rabbit anti-SOD2, 0.5-1μg/ml (datasheet PB9442) |
| Primary incubation | Overnight at 4 °C (datasheet PB9442) |
| Detection | Streptavidin-biotin complex (SABC), DAB chromogen (datasheet PB9442) |
| Counterstain | Hematoxylin, blue, dehydrate and mount (standard) |
| Expected result | SOD2-positive staining in glandular cells of adrenal gland (HPA tissue IHC: High). HPA tissue profile: General cytoplasmic expression with a mitochondrial pattern. No signal in the no-primary control. |
SOD2 is a mitochondrial matrix protein with no transmembrane segment (UniProt P04179 topology). In paraffin section IHC, expect cytoplasmic staining with a mitochondrial pattern (HPA: tissue IHC profile), including strong staining in colon glandular cells and bronchial respiratory epithelial cells (HPA: High in each). HPA rates its tissue IHC evidence Supported, with medium agreement between staining and RNA data; restaining is pending (HPA: tissue IHC reliability).
| Strong, granular cytoplasmic staining in colon glands or bronchial respiratory epithelium. | This fits SOD2's mitochondrial matrix location (UniProt P04179 subcellular location) and the reported high staining in those cell types (HPA: colon and bronchus tissue IHC). Score staining in the identified cells and note its cytoplasmic distribution; chromogenic IHC alone does not prove that every stained structure is a mitochondrion (general IHC practice). |
| Predominantly nuclear, cell-surface, or extracellular staining. | Those compartments conflict with the expected mitochondrial matrix location (UniProt P04179 subcellular location). Treat the pattern as suspect, then inspect the negative reagent control and compare it with a known-positive tissue on the same run (general IHC practice). A wrong compartment alone does not identify the cause. |
| Strong staining mainly in cells outside the expected positive population. | For example, high staining limited to cells other than colon glandular cells would not match the reported colon pattern (HPA: High in glandular cells). Consider antibody cross-reactivity or endogenous detection activity, then compare cell morphology, controls, and the distribution in a known-positive section (general IHC practice). Do not label an unlisted cell type definitively negative. |
| Diffuse color covers tissue structures without a discernible cellular pattern. | Broad background prevents a confident call of mitochondrial-pattern cytoplasmic staining (HPA: tissue IHC profile). Check the negative reagent control, blocking and detection steps, and whether excessive primary or detection reagent increases background (general IHC practice). Avoid scoring diffuse color as positive SOD2. |
| No signal in colon glandular cells or bronchial respiratory epithelial cells. | Both are reported as high-staining populations (HPA: colon and bronchus tissue IHC), so an absent signal warrants a run-level check. Verify tissue identity, control performance, antibody dilution, retrieval, and detection according to the validated IHC procedure (general IHC practice). A failed run cannot establish biological absence. |
| Subcellular location and topology | SOD2 resides in the mitochondrial matrix and has no transmembrane segment (UniProt P04179 subcellular location and topology). Interpret signal as an intracellular cytoplasmic pattern; a membrane-outline pattern needs control review (general IHC practice). |
| Tissue and cell selection | Colon glandular cells and bronchial respiratory epithelial cells are reported High, while splenic red-pulp cells are reported Low (HPA: tissue IHC). The spleen entry is a low-staining observation, not proof that every red-pulp cell should be blank. |
| Strength of tissue evidence | HPA calls the tissue IHC pattern Supported, describes medium agreement with RNA, and notes pending restaining (HPA: tissue IHC reliability). Use its cell-level pattern to guide interpretation while checking each staining run with controls (general IHC practice). |
| Antigen retrieval and antibody setup | Follow the selected IHC-validated antibody's established paraffin-section procedure for retrieval and dilution (general IHC practice). Neither UniProt nor the supplied HPA record establishes a SOD2-specific retrieval requirement or fixation sensitivity. |
| IF/ICC Q: Where should SOD2 appear? | A: In mitochondria; HPA reports supported mitochondrial ICC-IF localisation and images in U2OS (HPA: subcellular record). This corroborates compartment choice but does not supply an IF protocol or override tissue-specific IHC observations. |
| Situation | Likely cause | Next action |
|---|---|---|
| Known-positive cells show no chromogenic signal. | The run may have failed at retrieval, primary incubation, or detection (general IHC practice); colon glands are reported High (HPA: colon tissue IHC). | Check the positive control and reagent sequence, then repeat with the IHC-validated antibody's established retrieval and dilution conditions (general IHC practice). |
| Signal is weak but restricted to the expected cells. | Weak staining may reflect assay conditions, while intensity also differs by tissue: splenic red-pulp cells are Low (HPA: tissue IHC; general IHC practice). | Compare a High control such as colon glandular cells before changing conditions; record cell type and intensity separately (HPA: colon tissue IHC; general IHC practice). |
| Nuclei dominate the staining pattern. | Nuclear staining conflicts with mitochondrial matrix localisation (UniProt P04179 subcellular location); its cause is unresolved from appearance alone. | Review the negative reagent control, tissue morphology, and staining in a known-positive section before accepting the result (general IHC practice). |
| Color is diffuse across tissue or appears in the negative reagent control. | Nonspecific reagent binding or endogenous detection activity can contribute to background (general IHC practice). | Check blocking, washes, detection controls, and reagent concentration using the validated IHC workflow; score only interpretable cellular staining (general IHC practice). |
| Unexpected cells stain more strongly than the reported positive cells. | Cross-reactivity or endogenous detection activity is possible (general IHC practice); HPA's reported pattern identifies specific High cell populations (HPA: tissue IHC). | Compare cell identity and compartment with the HPA pattern, then review negative controls and a High positive tissue before assigning SOD2 specificity (general IHC practice). |
| Results differ across sections or tissue types. | HPA reports tissue-dependent staining and only medium agreement between antibody staining and RNA, with restaining pending (HPA: tissue IHC reliability and levels). | Score each cell population and control separately, document the observed compartment and intensity, and avoid treating a Low tissue as an absolute negative control (HPA: tissue IHC; general IHC practice). |
Comprehensive Human Protein Atlas IHC scoring per tissue (reliability: Supported — Medium consistency between antibody staining and RNA expression data. Pending restaining.). Rows are taken directly from the HPA tissue chart — click any row's HPA link to view the source.
| Tissue | Cell type | Level | Evidence | Source |
|---|---|---|---|---|
| Adrenal gland | Glandular cells | High | Protein (IHC) | HPA → |
| Appendix | Glandular cells | High | Protein (IHC) | HPA → |
| Bronchus | Respiratory epithelial cells | High | Protein (IHC) | HPA → |
| Caudate | Neuronal cells | High | Protein (IHC) | HPA → |
| Cerebellum | Cells in granular layer | High | Protein (IHC) | HPA → |
| Tissue | Cell type | Level | Evidence | Source |
|---|---|---|---|---|
| None in HPA: SOD2 is detected in all 44 scored tissues. Use a no-primary (secondary-only) and an isotype control instead. | ||||
Troubleshoot SOD2 staining in paraffin sections by checking retrieval, cellular pattern, controls and scoring before interpreting differences in signal.
These anti-SOD2 antibodies have catalog IHC images from human and rat paraffin sections (catalog image captions); one also has an IF image from U2OS cells (PA1776 image caption).
PB9442 was shown on human mammary cancer, M00349-2 on human breast cancer for acetyl-K68 SOD2, and M00349-3 on human right-colon adenocarcinoma (respective IHC image captions). M00349 was shown on human liver cancer, M33970-1 on human skeletal muscle, and PA1776 on rat brain (respective IHC image captions).
Which to pick: For tissue IHC, choose rabbit monoclonal M00349 when its human liver cancer example and EDTA retrieval at pH 8.0 suit the experiment; its paraffin-section caption does not report the fixative (M00349 catalog entry and IHC image caption). For IF/ICC, choose PA1776: ICC is listed and its IF image shows U2OS cells, while its own IHC caption shows rat brain after citrate retrieval at pH 6; that paraffin-section caption does not report the fixative (PA1776 catalog entry and image captions). For work across human, mouse and rat, PB9442 and PA1776 list all three species and IHC plus ICC; PB9442’s own IHC example uses human mammary cancer paraffin sections with citrate retrieval at pH 6, with fixative unreported (PB9442 and PA1776 catalog entries; PB9442 IHC image caption).