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SSBP1 / Single-stranded DNA-binding protein, mitochondrial · IHC design guide
Design Immunohistochemistry for SSBP1
Plan SSBP1 paraffin IHC around granular cytoplasmic staining, with lung macrophages or testis spermatogonia as high-staining controls (HPA tissue IHC). This guide covers fixation, the IHC-validated antibody at 1–2 μg/ml (datasheet A05166-1), chromogenic detection and cell-aware scoring.
Evidence assembled Oct 2026 · For research use; verify linked source records and product datasheet before use
SSBP1 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); mitochondrial matrix and nucleoid expected (UniProt) | |
| Staining pattern | Granular cytoplasmic staining across cell types (HPA tissue IHC) | |
| Antigen retrieval | EDTA pH 8.0 HIER, heat-mediated (datasheet A05166-1) | |
| Positive control | Lung+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 | High lung macrophage staining may confound tissue scoring (HPA tissue IHC) | |
| Regulation | Specific staining regulator unreported (UniProt) | |
| Isoform / epitope | No isoforms listed; mature chain 17–148 informs epitope choice (UniProt) |
Section 1
Recommended SSBP1 IHC & IF Protocols
The catalog antibody uses EDTA pH 8.0 retrieval (datasheet: A05166-1). The published IHC protocols below cover gastric tumors, tumor microarrays, cervical tumors, and mouse retina (PMC5762290; PMC10225361; PMC6411633; PMC8855788).
| Sample | Paraffin-embedded human colon adenocarcinoma tissue; fixative not specified (datasheet A05166-1) |
| Fixation | Image fixative and duration unreported (datasheet A05166-1); 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 A05166-1); 20 min, 95–100 °C (standard) |
| Peroxidase block | 3% H2O2, 10 min, room temperature (standard) |
| Blocking | 10% goat serum (datasheet A05166-1) |
| Primary antibody | Rabbit anti-SSBP1, 1-2 μg/ml (datasheet A05166-1) |
| Primary incubation | Overnight at 4 °C (datasheet A05166-1) |
| Detection | HRP-conjugated secondary, DAB chromogen (datasheet A05166-1) |
| Counterstain | Hematoxylin, blue, dehydrate and mount (standard) |
| Expected result | SSBP1-positive staining in macrophages of lung (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 pH 8.0 for the catalog antibody (datasheet: A05166-1); citrate retrieval is a published alternative for other antibodies (PMC5762290; PMC10225361).
Section 2
What Is the Expected SSBP1 Staining Pattern?
SSBP1 is a mitochondrial matrix and nucleoid protein with no transmembrane segment (UniProt Q04837). In paraffin IHC, expect granular cytoplasmic staining (HPA: tissue IHC profile), especially in lung macrophages and testicular spermatogonia, where staining is high (HPA: tissue IHC). HPA rates the tissue pattern Supported, with medium consistency between staining and RNA expression (HPA: tissue IHC reliability).
| Granular cytoplasmic stain in lung macrophages or testicular spermatogonia. | This matches the reported IHC pattern and its strongest listed cell populations (HPA: granular cytoplasmic profile; High in macrophages and spermatogonia). Assess granules within identifiable cells, using a counterstain to preserve cell identity (general IHC practice). |
| Predominantly nuclear, membrane-edge, or extracellular stain. | These compartments conflict with the expected mitochondrial matrix and nucleoid location and granular cytoplasmic IHC pattern (UniProt Q04837 localization; HPA: tissue IHC profile). Treat the pattern as suspect and check control sections and detection background before assigning it to SSBP1 (general IHC practice). |
| Strong stain centered on adipocytes or skeletal myocytes. | HPA lists SSBP1 as Not detected in those cells (HPA: adipocytes; skeletal myocytes). Unexpected strong staining warrants investigation for antibody cross-reactivity or endogenous detection activity (general IHC practice); a single discrepant section does not establish either cause. |
| Diffuse color across cells, stroma, or blank areas, with little granular definition. | That distribution is hard to reconcile with HPA's granular cytoplasmic profile (HPA: tissue IHC). Compare a no-primary control and inspect blocking, washes, and chromogen development to distinguish detection background from cell-associated staining (general IHC practice). |
| No detectable stain in a section containing lung macrophages or testicular spermatogonia. | Both are listed as High by HPA, so their absence makes a negative experimental section difficult to interpret (HPA: lung macrophages; testis spermatogonia). Verify that the expected cells are present, then review the antibody and detection run (general IHC practice). |
💡Expected SSBP1 appearanceCall a positive result when identifiable cells show granular cytoplasmic stain, strongest in lung macrophages or testicular spermatogonia (HPA: profile; High in both); dominant nuclear, membrane, or extracellular color is suspect (UniProt Q04837 localization; HPA: profile).
| Intracellular location | SSBP1 resides in the mitochondrial matrix and nucleoid (UniProt Q04837); its observed paraffin IHC appearance is granular cytoplasmic staining (HPA: tissue IHC profile). These sources support compartment interpretation, not a target-specific retrieval setting. |
| Cell-specific reference levels | Macrophages and spermatogonia are High; several glandular and neuronal cell groups are Medium, while adipocytes and skeletal myocytes are Not detected (HPA: tissue IHC). Score the identified cell population, not the whole tissue indiscriminately. |
| Protein processing and topology | UniProt lists a mature chain at residues 17–148, no transmembrane segment, and no glycosylation sites (UniProt Q04837). The supplied record gives no antibody epitope, so it cannot establish whether processing affects this antibody's staining. |
| Antibody evidence | HPA002866 is rated Supported for IHC, and the overall tissue profile has medium staining-to-RNA consistency (HPA: antibody validation; tissue IHC reliability). Use that support with morphology and controls; it does not validate every unexpected compartment. |
| Fixation and retrieval evidence | Target-specific fixation sensitivity and an SSBP1 retrieval condition are unreported in the supplied UniProt and HPA records (UniProt Q04837; HPA: tissue IHC). Retrieval optimization, if needed, is a general paraffin IHC workflow decision (general IHC practice). |
| Situation | Likely cause | Next action |
|---|---|---|
| Expected positive cells are unstained. | A negative result conflicts with HPA's High staining in lung macrophages and testicular spermatogonia, but the record does not identify a cause (HPA: tissue IHC). | Confirm those cells are in the section; inspect the IHC-validated antibody, detection reagents, and a concurrent positive control before interpreting other negatives (general IHC practice). |
| Brown signal fills most of the section or appears outside cells. | Broad, poorly defined color differs from the reported granular cytoplasmic pattern (HPA: tissue IHC profile). Detection background is one possible explanation (general IHC practice). | Compare a no-primary control; review blocking, wash steps, and chromogen development, then reassess whether signal remains cell-associated (general IHC practice). |
| Strong staining appears in adipocytes or skeletal myocytes. | Those cell types are listed as Not detected (HPA: tissue IHC); cross-reactivity or endogenous detection activity is possible, but neither is proven by appearance alone (general IHC practice). | Confirm cell identity on the counterstained section and compare controls before scoring this as SSBP1 expression (general IHC practice). |
| Nuclei or cell borders dominate the stain. | That location disagrees with mitochondrial matrix and nucleoid localization and HPA's granular cytoplasmic pattern (UniProt Q04837; HPA: tissue IHC). | Recheck morphology and control sections; treat the compartment assignment as unresolved until the granular cytoplasmic pattern can be demonstrated (general IHC practice). |
| Only weak staining is seen in a proposed control. | Some listed populations are Low, including kidney tubular cells and liver cholangiocytes; tissue-wide RNA specificity is Low (HPA: tissue IHC). | Choose a section containing HPA High lung macrophages or testicular spermatogonia for a clearer positive reference, and score the relevant cells (HPA: tissue IHC). |
| IF/ICC Q: What localization should an image show? | HPA reports mitochondria as the main supported ICC-IF location; calyx and principal piece are additional approved locations (HPA: subcellular ICC-IF). | Expect predominantly mitochondrial signal when interpreting IF/ICC images (HPA: subcellular ICC-IF). Use the separate IF/ICC guide for that application. |
Experiment evidence
IHC & IF images showing SSBP1 staining
A05166-1 · IHCIHC analysis of SSBP1 using anti-SSBP1 antibody (A05166-1). SSBP1 was detected in a paraffin-embedded section of human colon adenocarcinoma
A05166-1 · IHCIHC analysis of SSBP1 using anti-SSBP1 antibody (A05166-1). SSBP1 was detected in a paraffin-embedded section of human endometrioid adenocar
A05166-1 · IFIF analysis of SSBP1 using anti-SSBP1 antibody (A05166-1). SSBP1 was detected in an immunocytochemical section of U2OS cells. Enzyme antigen
A30475 · IHCImmunohistochemistry analysis of paraffin-embedded human pancreas tissue, using MtSSB Antibody. The picture on the right is blocked with the
A30475 · IFImmunofluorescence analysis of A549 cells, using MtSSB Antibody. The picture on the right is blocked with the synthesized peptide.
HPA · Cerebral cortexHuman Protein Atlas IHC, Cerebral cortex. Source: https://www.proteinatlas.org/ENSG00000106028-SSBP1/tissue/cerebral+cortex#imid_1163136
HPA · EsophagusHuman Protein Atlas IHC, Esophagus. Source: https://www.proteinatlas.org/ENSG00000106028-SSBP1/tissue/esophagus#imid_1163108
HPA · ColonHuman Protein Atlas IHC, Colon. Source: https://www.proteinatlas.org/ENSG00000106028-SSBP1/tissue/colon#imid_1267354
HPA · LiverHuman Protein Atlas IHC, Liver. Source: https://www.proteinatlas.org/ENSG00000106028-SSBP1/tissue/liver#imid_1267355
HPA · ICC-IF A-431Human Protein Atlas immunofluorescence, A-431, antibody HPA002866; green = SSBP1, blue = nucleus, red = microtubules.
HPA · ICC-IF A-431Human Protein Atlas immunofluorescence, A-431, antibody HPA002866; green = SSBP1, blue = nucleus, red = microtubules.
← swipe / scroll for more images →
Real IHC / IF data behind the staining-pattern expectations in this section.
Sample controls for SSBP1 IHC & IF
🧪Run lung first: macrophages should stain (HPA: High in lung macrophages). Use adipose tissue adipocytes as the negative tissue (HPA: Not detected in adipocytes); on the lung slide, neighboring cells without specific staining can serve as internal negatives, while cell identity should be checked before scoring (standard IHC practice).
Positive control tissue: Lung (Macrophages, HPA High)
Negative control tissue: Adipose tissue (HPA Not detected)
ICC-IF cell lines (HPA subcellular resource): HPA ICC-IF images show SSBP1 in A-431, U-251MG, U2OS, Sperm, with annotated localisation: Mitochondria (supported) (HPA subcellular).
Technical controls: Include no-primary (secondary-only), rabbit IgG isotype matched to the primary’s clonality where known, and SSBP1 knockout material or antigen peptide competition as a biological specificity control (caption: rabbit primary; standard IHC practice). In lung, quench endogenous peroxidase and assess macrophage pigment during chromogenic scoring; check autofluorescence if using IF (standard IHC/IF practice).
⚠️Feasibility: A target-specific fixation window or fixation effect is unreported, and the selected A05166-1 paraffin-section caption does not state the fixative (selected-SKU caption). The caption uses heat retrieval in EDTA at pH 8.0, but does not establish that retrieval is required (selected-SKU caption). The supplied evidence does not establish whether frozen sections or IF are easier; macrophage pigment can complicate interpretation of lung chromogenic staining (standard IHC practice).
HPA tissue IHC evidence for SSBP1
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 |
|---|---|---|---|---|
| Lung | Macrophages | High | Protein (IHC) | HPA → |
| Testis | Spermatogonia cells | High | Protein (IHC) | HPA → |
| Adrenal gland | Glandular cells | Medium | Protein (IHC) | HPA → |
| Breast | Glandular cells | Medium | Protein (IHC) | HPA → |
| Caudate | Neuronal cells | Medium | Protein (IHC) | HPA → |
Section 3
Advanced SSBP1 IHC Tips
Troubleshoot chromogenic SSBP1 staining in paraffin sections using the catalog antibody’s tissue example, mitochondrial localisation, and cell-specific reference patterns.
Which retrieval condition should I use when SSBP1 staining is weak?
Start with heat-mediated retrieval in EDTA at pH 8.0 for paraffin sections (datasheet A05166-1). The catalog antibody’s tissue example used that condition before incubation at 2 μg/ml overnight at 4°C (datasheet A05166-1). If staining is weak, first check heating consistency, section adhesion, and the positive control before changing retrieval conditions (standard IHC practice; HPA: high staining in lung macrophages). If a fallback retrieval condition is tested, compare it alongside EDTA pH 8.0 on matched sections and assess both granular cytoplasmic signal and background (datasheet A05166-1; HPA tissue IHC: granular cytoplasmic pattern).
Could fixation explain weak or uneven SSBP1 staining?
The catalog image documents a paraffin-embedded section but does not report its fixative, so target-specific fixation sensitivity is unknown (datasheet A05166-1). Record each sample’s fixative and fixation interval, then compare similarly processed sections before attributing an intensity difference to SSBP1 abundance (standard IHC practice). Keep retrieval at EDTA pH 8.0 and antibody incubation at 2 μg/ml overnight at 4°C while assessing that variable (datasheet A05166-1). Examine section edges and tissue centres separately for uneven processing, and include a positive reference section in the same staining run (standard IHC practice; HPA: high staining in lung macrophages).
What staining pattern is plausible for SSBP1 in paraffin sections?
Expect granular cytoplasmic staining because SSBP1 is mainly mitochondrial and resides in the mitochondrial matrix and nucleoids (HPA tissue IHC: granular cytoplasmic pattern; UniProt Q04837 localisation). Evaluate granules within intact cells, using a nuclear counterstain to distinguish cytoplasm from nuclei (standard IHC practice). Strong diffuse nuclear DAB alone would conflict with the reported main location and should prompt review of background and morphology (HPA subcellular: mitochondria supported; standard IHC practice). Compare cell populations within the same section: HPA reports high staining in lung macrophages and testicular spermatogonia, but no detection in adipocytes or skeletal myocytes (HPA tissue IHC).
How should I assess an uncertain SSBP1 epitope?
Do not assign the antibody’s epitope from the staining image; the supplied caption gives no epitope sequence (datasheet A05166-1). SSBP1 has no listed isoforms, its annotated chain spans residues 17–148, and its SSB domain spans 30–141 (UniProt Q04837). Annotated modifications include phosphoserines at 67 and 79 and modified lysines at 113 and 122, but their effect on this antibody’s tissue staining is unreported (UniProt Q04837; datasheet A05166-1). If a separate epitope map becomes available, compare it with those positions and test any retrieval change on matched sections against the documented EDTA pH 8.0 condition (UniProt Q04837; datasheet A05166-1; standard IHC practice).
How can IF help assess a questionable SSBP1 IHC pattern?
Use IF as a separate localisation check: multiplex SSBP1 with a mitochondrial marker and, where relevant, a marker identifying the cell population being scored in IHC (UniProt Q04837 localisation; HPA tissue IHC cell profiles; standard IF practice). Choose fluorophores after inspecting unstained tissue autofluorescence, and keep emission channels sufficiently separated for the chosen filters (standard IF practice). Because SSBP1 is in the mitochondrial matrix and has no transmembrane segment, optimise permeabilisation to give antibody access across mitochondrial membranes without disrupting organelle morphology (UniProt Q04837 topology and localisation; standard IF practice). Confirm punctate overlap against single-stain controls, then compare the result with granular cytoplasmic DAB staining; the supplied IHC caption does not establish an IF protocol (HPA tissue IHC; datasheet A05166-1; standard IF practice).
How do I distinguish SSBP1 signal from chromogenic background?
Run a no-primary control through secondary detection and DAB development to reveal reagent or endogenous enzyme signal (standard IHC practice). Include a peroxidase-blocking step and inspect pigment and damaged areas before calling brown deposits positive (standard IHC practice). The catalog tissue example used 10% goat serum blocking, 2 μg/ml primary antibody overnight at 4°C, and an anti-rabbit secondary for 30 minutes at 37°C (datasheet A05166-1). If background persists, optimise blocking and washing on matched sections while retaining a positive reference and the expected granular cytoplasmic pattern as checks (HPA tissue IHC; standard IHC practice).
How should I score SSBP1 staining across tissue sections? ⚠ ANSWER MARKED FOR VERIFICATION
Define the cell population and viable tissue area before scoring, then use percent positive cells with an intensity grade or an H-score applied consistently across sections (standard IHC practice). If counting discrete positive cells, report their density per mm² of viable tissue and normalise comparisons to the same cell type and sampled area (standard IHC practice). Set positivity using the no-primary control and granular cytoplasmic morphology, rather than scoring all brown pixels (HPA tissue IHC: granular cytoplasmic pattern; standard IHC practice). Record retrieval at EDTA pH 8.0 and antibody concentration of 2 μg/ml when comparing runs, because these are the documented catalog conditions (datasheet A05166-1).
When should I question an apparent SSBP1-positive result?
Give greatest weight to granular cytoplasmic staining in intact cells, consistent with the reported mitochondrial location (HPA tissue IHC; UniProt Q04837 localisation). Check whether the stained cells match the sampled population: HPA reports high staining in lung macrophages and testicular spermatogonia, while adipocytes and skeletal myocytes were not detected (HPA tissue IHC). Treat isolated nuclear signal, section-edge staining, necrotic deposits, and staining reproduced in a no-primary control as reasons to investigate artefact (HPA subcellular: mitochondria supported; standard IHC practice). Interpret an unexpected result alongside morphology, a matched positive reference, and the catalog’s EDTA pH 8.0 retrieval condition (datasheet A05166-1; standard IHC practice).
Boster reagents
Best SSBP1 / Single-stranded DNA-binding protein, mitochondrial IHC Antibodies
The IHC-validated SSBP1 antibodies have paraffin-section images from human tissues (catalog IHC captions) and IF images from human tissue or cells (catalog IF captions); one also lists mouse, rat and cow reactivity (A30475 catalog).
Real IHC data
Anti-SSBP1 Antibody ®
Cat # A05166-1
Real IHC data
Anti-MtSSB SSBP1 Antibody
Cat # A30475
A05166-1 has IHC images from human colon, endometrioid, liver and lung cancers and IF images from U2OS cells and human colon and ovarian cancers (A05166-1 image captions). A30475 has an IHC image from human pancreas and an IF image from A549 cells; its listed reactivity is human, mouse, rat and cow (A30475 image captions; A30475 catalog).
Which to pick: For human tissue IHC, choose A05166-1 if you want a documented starting condition: its paraffin-section caption specifies EDTA retrieval at pH 8.0 and 2 μg/ml primary antibody (A05166-1 IHC caption). For IF/ICC, A05166-1 has U2OS cell and tissue IF examples (A05166-1 IF captions); for work across listed species, consider the polyclonal A30475, while recognizing that its pictured IHC and IF examples are human only (A30475 catalog; A30475 image captions). Both IHC captions describe paraffin sections, and neither reports the fixative (A05166-1 IHC captions; A30475 IHC caption).
Each figure is that product's own IHC / IF validation image from its datasheet.
References
- UniProt Consortium. UniProt entry Q04837 (SSBP_HUMAN, Single-stranded DNA-binding protein, mitochondrial).
- Human Protein Atlas. SSBP1 tissue IHC expression (reliability: Supported).
- Human Protein Atlas. SSBP1 subcellular location (ICC-IF): Mainly localized to the mitochondria. In addition localized to the calyx and principal piece..
- Human Protein Atlas. SSBP1 antibody validation summary (1 antibodies).
- A functional polymorphism of SSBP1 gene predicts prognosis and response to chemotherapy in resected gastric cancer patients. Oncotarget 2017 — PMC5762290.
- Systematic identification of anticancer drug targets reveals a nucleus-to-mitochondria ROS-sensing pathway. Cell 2023 — PMC10225361.
- Mitochondrial Function of CKS2 Oncoprotein Links Oxidative Phosphorylation with Cell Division in Chemoradioresistant Cervical Cancer. Neoplasia (New York, N.Y.) 2019 — PMC6411633.
- SSBP1 mutations in dominant optic atrophy with variable retinal degeneration. Annals of neurology 2019 — PMC8855788.
- PubMed PMID:8482537 — UniProt-cited evidence.
- PubMed PMID:15489334 — UniProt-cited evidence.
- PubMed PMID:19892738 — UniProt-cited evidence.
Immunohistochemistry protocol sheet for SSBP1 (Single-stranded DNA-binding protein, mitochondrial). Expected localisation Granular cytoplasm (HPA tissue IHC); mitochondrial matrix and nucleoid expected (UniProt). Antigen retrieval: EDTA pH 8.0 HIER, heat-mediated (datasheet A05166-1). Validated IHC antibody: A05166-1 at 1-2 μg/ml (the product's own IHC validation image is shown). Controls (HPA): positive Lung (Macrophages); negative Adipose tissue. IHC-P workflow on paraffin sections; fixative unspecified. Protocol steps: 1. Sample: Paraffin-embedded human colon adenocarcinoma tissue; fixative not specified (datasheet A05166-1); 2. Fixation: Image fixative and duration unreported (datasheet A05166-1); 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 retrieval: EDTA pH 8.0 (datasheet A05166-1); 20 min, 95–100 °C (standard); 6. Peroxidase block: 3% H2O2, 10 min , room temperature (standard); 7. Blocking: 10% goat serum (datasheet A05166-1); 8. Primary antibody: Rabbit anti-SSBP1, 1-2 μg/ml (datasheet A05166-1); 9. Primary incubation: Overnight at 4 °C (datasheet A05166-1). Watch for: Fixation: Keep fixation consistent across sections (standard IHC practice; not target-specific); Caveat: High lung macrophage staining may confound tissue scoring (HPA tissue IHC); Isoform / epitope: No isoforms listed; mature chain 17–148 informs epitope choice (UniProt); Regulation: Specific staining regulator unreported (UniProt). Evidence: UniProt Q04837, HPA tissue IHC · Supported, HPA ICC-IF · Mainly localized to the mitochondria. In addition localized to the…, Datasheet A05166-1, PMC5762290, PMC10225361. QR code links to https://www.bosterbio.com/bosterbio-gene-info-cards/SSBP1/immunohistochemistry-ihc-guide.