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SSX1 / Protein SSX1 · IHC design guide
Design Immunohistochemistry for SSX1
Plan SSX1 chromogenic IHC on paraffin sections using nuclear staining in testis pachytene spermatocytes as the expected tissue pattern (HPA tissue IHC). The human-reactive catalog antibody A07363 has an IHC dilution of 1:100 (datasheet); interpret staining with the reported cross-gene caution (HPA tissue IHC).
Evidence assembled Oct 2026 · For research use; verify linked source records and product datasheet before use
SSX1 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 | Nuclear staining observed in testis (HPA tissue IHC) | |
| Staining pattern | Nuclear staining in pachytene spermatocytes (HPA tissue IHC) | |
| Antigen retrieval | Citrate pH 6.0 HIER, 95–98 °C, 20 min (rule: cytoplasmic / membrane antigen) | |
| Positive control | Testis | |
| Negative control | Adipose tissue+4 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 | Staining may detect proteins from more than one gene (HPA tissue IHC) | |
| Regulation | High in testis; low in thyroid (UniProt) | |
| Isoform / epitope | No annotated isoforms; one 1–188 chain (UniProt) |
Section 1
Recommended SSX1 IHC & IF Protocols
The catalog antibody’s IHC-P protocol is paired with one published SSX1 chromogenic IHC protocol for paraffin sections (PMC10088888).
| Sample | Paraffin-embedded human skin tissue; fixative not specified (datasheet A07363) |
| Fixation | Image fixative and duration unreported (datasheet A07363); 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-SSX1, 1:100 (datasheet A07363) |
| 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 | SSX1-positive staining in pachytene spermatocytes of testis (HPA tissue IHC: High). HPA tissue profile: Nuclear expression in testis. No signal in the no-primary control. |
💡Decision noteStart with citrate pH 6.0 HIER at 95–98 °C for 20 min (page retrieval rule); compare the published 100 °C, 5 min condition (PMC10088888).
Section 2
What Is the Expected SSX1 Staining Pattern?
SSX1 staining is expected mainly in the nuclei of pachytene spermatocytes in testis, where HPA reports high staining and a Supported tissue IHC pattern (HPA: tissue IHC). UniProt describes SSX1 as lacking a transmembrane segment and also annotates cytoplasm, cytoskeleton and flagellum axoneme locations (UniProt Q16384). HPA cautions that its staining evidence includes antibodies targeting proteins from more than one gene (HPA: tissue IHC).
| Strong nuclear staining in pachytene spermatocytes, with little staining in surrounding cells (HPA: tissue IHC). | This matches HPA’s high testis signal and nuclear tissue pattern (HPA: tissue IHC). Score the named cell population and compartment, rather than calling the whole section uniformly positive. HPA rates the tissue pattern Supported, while warning that the antibody evidence can include other gene products (HPA: tissue IHC). |
| Predominantly cytoplasmic or diffuse staining replaces the expected nuclear testis pattern (HPA: tissue IHC). | Treat this as a possible artefact and review controls and morphology. UniProt also annotates cytoplasm, cytoskeleton and flagellum axoneme, so compartment alone cannot prove an artefact; the slide-level comparison is with HPA’s observed nuclear tissue pattern (UniProt Q16384; HPA: tissue IHC). |
| Strong staining appears in cells outside the expected pachytene spermatocyte population (HPA: tissue IHC). | Check for cross-reactivity or endogenous detection activity before assigning SSX1 expression. HPA’s tissue result identifies pachytene spermatocytes as high and cautions that antibodies can target proteins from multiple genes (HPA: tissue IHC). Distribution across cell types is therefore part of the interpretation. |
| Haze, widespread weak color, or staining that obscures nuclei spans the section. | This is nonspecific background until controls show otherwise (general IHC practice). Compare the slide with a negative reagent control and the expected cell-specific nuclear pattern in testis (HPA: tissue IHC). Background that follows section edges or covers many cell types should not be scored as SSX1. |
| No convincing nuclear signal appears in morphologically intact testis pachytene spermatocytes (HPA: tissue IHC). | First assess the run using a known-positive testis section and detection controls (general IHC practice). Absence of the HPA high-staining cell population calls the assay result into question; it does not alone establish SSX1 absence in the specimen (HPA: tissue IHC). |
💡Expected SSX1 appearanceCall a positive result when pachytene spermatocytes show high nuclear staining (HPA: tissue IHC); broad staining of unrelated cells or diffuse haze is suspect, especially given HPA’s multiple-gene antibody caution (HPA: tissue IHC).
| Cell and tissue distribution | HPA identifies high staining in testis pachytene spermatocytes and no detected staining in the listed negative cell populations, including adipocytes and adrenal glandular cells (HPA: tissue IHC). Use those reported patterns to judge cell-specific signal; they do not guarantee that every section or antibody will behave identically. |
| Compartment evidence | HPA tissue IHC reports nuclear expression in testis, whereas UniProt annotates cytoplasm, cytoskeleton and flagellum axoneme (HPA: tissue IHC; UniProt Q16384). Base the paraffin-section decision on the observed tissue IHC pattern and document discordant staining for review. |
| Antibody interpretation | The HPA tissue assessment is Supported for consistency with RNA data, but HPA warns that antibodies target proteins from more than one gene (HPA: tissue IHC). A matching pattern supports the result without proving SSX1-specific binding in each stained cell. |
| Topology and processing | UniProt reports no transmembrane segment, no signal peptide or propeptide, and one 1–188 protein chain (UniProt Q16384). These annotations do not establish an SSX1-specific retrieval condition or fixation sensitivity; optimize those assay settings by general IHC practice. |
| Situation | Likely cause | Next action |
|---|---|---|
| Testis positive control has no nuclear staining in pachytene spermatocytes (HPA: tissue IHC). | The run may have failed, or the expected cells may be absent from the section; a blank slide alone cannot distinguish these possibilities (general IHC practice). | Confirm the cells by morphology, then check antibody, retrieval and detection steps against the assay’s validated settings; repeat with a known-positive section (general IHC practice). |
| Only cytoplasmic staining is visible in testis. | It differs from HPA’s nuclear tissue IHC pattern, although UniProt lists cytoplasmic and cytoskeletal locations (HPA: tissue IHC; UniProt Q16384). | Check nuclear morphology, counterstain and negative reagent control; record the compartment before interpreting the signal (general IHC practice). Do not call this the expected tissue IHC pattern (HPA: tissue IHC). |
| Many unrelated cell types stain strongly. | Cross-reactivity or endogenous detection activity is possible (general IHC practice); HPA cautions that its antibody evidence can include multiple gene products (HPA: tissue IHC). | Compare with the reported pachytene spermatocyte pattern and negative reagent control; review blocking and detection controls before scoring unrelated cells as positive (HPA: tissue IHC; general IHC practice). |
| Diffuse brown haze makes individual nuclei hard to assess. | Nonspecific reagent binding or incomplete blocking can produce broad background (general IHC practice). | Review negative controls, blocking, washes and detection development; score only resolved cellular signal after the background is controlled (general IHC practice). |
| A reported negative tissue shows staining. | HPA reports no detected staining in several sampled cell populations, such as adipocytes and adrenal glandular cells; an unexpected signal needs verification (HPA: tissue IHC). | Verify the stained cell type and compare matched controls. Investigate background and detection activity before treating the difference as biological expression (general IHC practice). |
| Q: How should an IF/ICC nuclear signal be read here? | HPA reports approved nucleoplasm and nucleoli locations, with a multiple-gene antibody caution, in ICC-IF (HPA: subcellular). | A: Use that observation as context for compartment interpretation; assess IF/ICC on its own guide page. For this paraffin IHC result, use HPA’s nuclear testis pattern in pachytene spermatocytes (HPA: subcellular; HPA: tissue IHC). |
Experiment evidence
IHC & IF images showing SSX1 staining
A07363 · IHCImmunohistochemical analysis of paraffin-embedded human-skin, antibody was diluted at 1:100
HPA · Cerebral cortexHuman Protein Atlas IHC, Cerebral cortex. Source: https://www.proteinatlas.org/ENSG00000126752-SSX1/tissue/cerebral+cortex#imid_21105699
HPA · ColonHuman Protein Atlas IHC, Colon. Source: https://www.proteinatlas.org/ENSG00000126752-SSX1/tissue/colon#imid_21105633
HPA · LiverHuman Protein Atlas IHC, Liver. Source: https://www.proteinatlas.org/ENSG00000126752-SSX1/tissue/liver#imid_21105634
HPA · KidneyHuman Protein Atlas IHC, Kidney. Source: https://www.proteinatlas.org/ENSG00000126752-SSX1/tissue/kidney#imid_21105627
HPA · ICC-IF PC-3Human Protein Atlas immunofluorescence, PC-3, antibody HPA045683; green = SSX1, blue = nucleus, red = microtubules.
HPA · ICC-IF PC-3Human Protein Atlas immunofluorescence, PC-3, antibody HPA045683; green = SSX1, blue = nucleus, red = microtubules.
← swipe / scroll for more images →
Real IHC / IF data behind the staining-pattern expectations in this section.
Sample controls for SSX1 IHC & IF
🧪Run testis first: pachytene spermatocytes should stain strongly (HPA: High in pachytene spermatocytes). Use adipose tissue as a negative comparator (HPA: Not detected in adipocytes); on the testis slide, assess other cell types as an internal background reference without assuming they lack SSX1.
Positive control tissue: Testis (Pachytene spermatocytes, HPA High)
Negative control tissue: Adipose tissue (HPA Not detected)
ICC-IF cell lines (HPA subcellular resource): HPA ICC-IF images show SSX1 in PC-3, Rh30, U2OS, with annotated localisation: Nucleoplasm (approved), Nucleoli (approved) (HPA subcellular).
Technical controls: Include a no-primary, secondary-only control; a host-species- and isotype-matched control for a monoclonal primary or matched nonimmune IgG for a polyclonal primary; and a biological negative such as SSX1 knockout tissue or a validated peptide block (standard IHC practice). For chromogenic IHC, quench endogenous peroxidase and check background from blood-rich areas of testis; for IF, assess tissue autofluorescence with the no-primary control (standard IHC/IF practice).
⚠️Feasibility: A target-specific fixation window or fixation effect is unreported, and the selected paraffin-section caption does not state its fixative (A07363 caption: fixative not stated). Retrieval dependence is unreported; optimize antigen retrieval empirically for paraffin IHC (standard IHC practice). The supplied evidence does not establish that frozen sections or IF are easier; score pachytene spermatocytes specifically so staining in other testicular cells does not obscure the expected pattern (HPA: High in pachytene spermatocytes).
HPA tissue IHC evidence for SSX1
Comprehensive Human Protein Atlas IHC scoring per tissue (reliability: Supported — High consistency between antibody staining and RNA expression data. Caution, targets protein from more than one gene.). 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 |
|---|---|---|---|---|
| Testis | Pachytene spermatocytes | High | Protein (IHC) | HPA → |
Undetected expression · recommended negative controls
| Tissue | Cell type | Level | Evidence | Source |
|---|---|---|---|---|
| Adipose tissue | Adipocytes | Not detected | Protein (IHC) | HPA → |
| Adrenal gland | Glandular cells | Not detected | Protein (IHC) | HPA → |
| Appendix | Glandular cells | Not detected | Protein (IHC) | HPA → |
| Bone marrow | Hematopoietic cells | Not detected | Protein (IHC) | HPA → |
| Breast | Adipocytes | Not detected | Protein (IHC) | HPA → |
Section 3
Advanced SSX1 IHC Tips
Use compartment and cell-type controls when optimizing SSX1 staining; the available tissue and subcellular evidence requires careful interpretation.
How should I retrieve SSX1 in paraffin sections when staining is weak?
Start with citrate buffer at pH 6.0, heated to 95–98 °C for 20 min (page retrieval setting). Run testis alongside the study sections and assess pachytene spermatocytes, where staining is reported as high (HPA tissue IHC). If signal remains weak, compare a second retrieval condition on adjacent sections while holding antibody dilution, detection chemistry and exposure to chromogen constant (standard IHC practice). Do not treat increased staining throughout the section as improved specificity: the tissue IHC antibody can recognize proteins from more than one gene (HPA tissue IHC). Record nuclear and cytoplasmic staining separately because the reported locations differ between sources (HPA tissue IHC; UniProt Q16384).
Could fixation explain weak or uneven SSX1 staining in my sections?
SSX1-specific sensitivity to fixation is unknown from the supplied evidence; the paraffin-section image for SKU A07363 does not state a fixative (catalog caption A07363). Compare sections with documented fixation histories using the same citrate pH 6.0, 95–98 °C, 20 min retrieval setting (page retrieval setting; standard IHC practice). Include testis on each run so a processing problem can be distinguished from low staining in the study tissue; pachytene spermatocytes are a reported positive population (HPA tissue IHC). Assess morphology, staining gradients and section edges before changing antibody concentration (standard IHC practice). Do not infer a fixation effect from SSX1 topology or phosphorylation annotations (UniProt Q16384).
Should SSX1 staining be scored in nuclei or cytoplasm?
Score nuclear and cytoplasmic signal separately because tissue IHC reports nuclear expression in testis, whereas UniProt lists cytoplasm, cytoskeleton and flagellum axoneme (HPA tissue IHC; UniProt Q16384). The subcellular IF profile lists approved nucleoplasm and nucleoli locations but cautions that its antibodies target proteins from multiple genes (HPA subcellular). Examine pachytene spermatocytes first, since they have reported high tissue staining, then compare each compartment with matched negative controls (HPA tissue IHC; standard IHC practice). Avoid assigning diffuse cytoplasmic color to SSX1 solely because it matches the UniProt annotation (UniProt Q16384). Report the compartment, cell population and fraction stained together so readers can evaluate the discrepancy (standard IHC practice).
How can I assess whether an SSX1 staining pattern is epitope dependent?
The supplied record lists 0 isoforms, a KRAB-related region at residues 20–83 and phosphoserine at residue 123 (UniProt Q16384). Those annotations do not identify the catalog antibody's epitope or establish that phosphorylation changes tissue staining (UniProt Q16384; catalog caption A07363). If epitope information becomes available, map it against the annotated region and modification before interpreting retrieval-dependent differences (UniProt Q16384; standard IHC practice). Compare serial sections with an independent, appropriately characterized SSX1 reagent and the same cell-level scoring scheme (standard IHC practice). Interpret agreement cautiously because the supplied HPA tissue and IF profiles warn of antibodies recognizing proteins from multiple genes (HPA tissue IHC; HPA subcellular).
How should I check an SSX1 IHC finding by multiplex immunofluorescence?
Pair SSX1 with a validated marker that identifies pachytene spermatocytes, the population reported to stain strongly in testis, and inspect the overlap at single-cell resolution (HPA tissue IHC; standard IF practice). Choose fluorophores after measuring tissue autofluorescence in unstained controls, favoring a spectrally separated channel with low background for the weaker signal (standard IF practice). SSX1 has no annotated transmembrane segment, so permeabilize for intracellular epitopes and titrate the detergent to preserve nuclear morphology (UniProt Q16384; standard IF practice). Include single-stain and secondary-only controls when checking bleed-through and nonspecific fluorescence (standard IF practice). Compare nucleoplasmic and nucleolar signal with caution because the HPA subcellular evidence can include proteins from multiple genes (HPA subcellular).
What should I change when brown staining appears across the section?
First compare the section with a no-primary control and inspect whether color follows tissue edges, pigment or damaged areas (standard IHC practice). Block endogenous peroxidase before chromogenic detection, then check secondary-reagent specificity and shorten DAB development if controls remain colored (standard IHC practice). Titrate the antibody around the caption's 1:100 dilution using identical processing; that caption documents paraffin-embedded skin staining but does not report its fixative or establish specificity (catalog caption A07363). Compare suspect staining with the reported high signal in testis pachytene spermatocytes and reported absence in several other sampled cell populations (HPA tissue IHC). Widespread color alone is weak evidence for SSX1 because the HPA tissue antibody may recognize proteins from more than one gene (HPA tissue IHC).
How should I quantify SSX1 staining across tissue samples? ⚠ ANSWER MARKED FOR VERIFICATION
Define the cell population and compartment before scoring; testis pachytene spermatocytes have reported high nuclear staining, while localization sources disagree on other compartments (HPA tissue IHC; UniProt Q16384). For nuclear chromogenic signal, record the percentage of positive eligible cells and an H-score from intensity categories 0–3 across the same sampled area (standard IHC practice). Normalize positive-cell counts to the number of eligible cells, or report positive-cell density per mm² of viable tissue when cell identification is difficult (standard IHC practice). Exclude folds, necrosis and section edges using rules set before scoring (standard IHC practice). Keep retrieval, development and image settings consistent, and report background-adjusted compartment scores separately (standard IHC practice).
When does SSX1 staining warrant a positive interpretation?
A credible result localizes to the relevant cells and compartment, exceeds matched control staining and repeats across sections processed together (standard IHC practice). In testis, high staining of pachytene spermatocytes and a nuclear tissue profile provide a reference, although the HPA antibody may recognize proteins from more than one gene (HPA tissue IHC). Treat signal in an unexpected cell population or solely at section edges, necrotic regions or pigment deposits as requiring further verification (standard IHC practice). Check a no-primary control for endogenous enzyme activity before interpreting brown precipitate as antigen signal (standard IHC practice). Report nuclear and cytoplasmic findings separately because HPA nuclear observations and UniProt cytoplasmic annotations do not agree (HPA tissue IHC; UniProt Q16384).
Boster reagents
Best SSX1 / Protein SSX1 IHC Antibodies
A07363 is a human-reactive SSX1 antibody listed for IHC and IF (catalog: applications and reactivity). Its IHC image shows paraffin-embedded human skin (catalog: IHC image caption).
Real IHC data
Anti-SSX SSX1 Antibody
Cat # A07363
A07363 will render with an IHC image of paraffin-embedded human skin at 1:100 (catalog: IHC image caption). A07363 is also listed for human IF, but no IF image is supplied (catalog: applications, reactivity, and image captions).
Which to pick: For tissue IHC, choose A07363: its own image documents paraffin-embedded human skin, while the fixative is unreported (catalog: IHC image caption). For IF, A07363 is listed at 1:50, but the payload supplies no IF image or separate ICC validation (catalog: applications, IF dilution, and image captions). Cross-species use is unverified because A07363 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 Q16384 (SSX1_HUMAN, Protein SSX1).
- Human Protein Atlas. SSX1 tissue IHC expression (reliability: Supported).
- Human Protein Atlas. SSX1 subcellular location (ICC-IF): Localized to the nucleoplasm and nucleoli. Caution: Based on antibodies targeting proteins from multiple genes..
- Human Protein Atlas. SSX1 antibody validation summary (2 antibodies).
- The inhibitory effect of KIAA1456 on the proliferation and metastasis of epithelial ovarian cancer through SSX1 and AKT signaling pathway. Journal of Cancer 2023 — PMC10088888.
- SYT-SSX1 enhances the invasiveness and maintains stem-like cell properties in synovial sarcoma via induction of TGF-β1/Smad signaling. BMC cancer 2022 — PMC8841078.
- BCOR upregulation in a poorly differentiated synovial sarcoma with SS18L1-SSX1 fusion-A pathologic and molecular pitfall. Genes, chromosomes & cancer 2017 — PMC5546405.
- Sarcomas with sclerotic epithelioid phenotype harboring novel EWSR1-SSX1 fusions. Genes, chromosomes & cancer 2021 — PMC8266753.
- PubMed PMID:7539744 — UniProt-cited evidence.
- PubMed PMID:15772651 — UniProt-cited evidence.
- PubMed PMID:15489334 — UniProt-cited evidence.
Immunohistochemistry protocol sheet for SSX1 (Protein SSX1). Expected localisation Nuclear staining observed in testis (HPA tissue IHC). Antigen retrieval: Citrate pH 6.0 HIER, 95–98 °C, 20 min (rule: cytoplasmic / membrane antigen). Validated IHC antibody: A07363 at 1:100 (the product's own IHC validation image is shown). Controls (HPA): positive Testis (Pachytene spermatocytes); negative Adipose tissue. IHC workflow; specimen preparation unspecified. Protocol steps: 1. Sample: Paraffin-embedded human skin tissue; fixative not specified (datasheet A07363); 2. Fixation: Image fixative and duration unreported (datasheet A07363); 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-SSX1, 1:100 (datasheet A07363); 9. Primary incubation: Overnight at 4 °C (standard). Watch for: Fixation: Keep fixation consistent across sections. (standard IHC practice; not target-specific); Caveat: Staining may detect proteins from more than one gene (HPA tissue IHC); Isoform / epitope: No annotated isoforms; one 1–188 chain (UniProt); Regulation: High in testis; low in thyroid (UniProt). Evidence: UniProt Q16384, HPA tissue IHC · Supported, HPA ICC-IF · nucleoplasm and nucleoli. Caution: Based on antibodies targeting…, Datasheet A07363, PMC10088888. QR code links to https://www.bosterbio.com/bosterbio-gene-info-cards/SSX1/immunohistochemistry-ihc-guide.