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SND1 / Staphylococcal nuclease domain-containing protein 1 · IHC design guide
Design Immunohistochemistry for SND1
Plan SND1 IHC in paraffin sections around its variable cytoplasmic tissue staining (HPA tissue IHC). Use cell-specific positive controls and score staining by cell population (HPA tissue IHC; standard IHC practice).
Evidence assembled Oct 2026 · For research use; verify linked source records and product datasheet before use
SND1 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 | Predominantly cytoplasmic in tissue; nuclear location annotated (HPA tissue IHC; UniProt) | |
| Staining pattern | Variable cytoplasmic staining across tissue cell types (HPA tissue IHC) | |
| Antigen retrieval | EDTA pH 8.0 HIER, heat-mediated (datasheet M02602-2) | |
| Positive control | Bone marrow+4 more · see all | |
| Negative control | Adipose tissue+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 | Cell-type variation can complicate intensity scoring (HPA tissue IHC) | |
| Regulation | Tissue expression varies (HPA tissue IHC) | |
| Isoform / epitope | No listed isoforms; mature chain spans residues 2–910 (UniProt) |
Section 1
Recommended SND1 IHC & IF Protocols
The catalog antibody’s IHC-P protocol (datasheet: M02602-2) accompanies published SND1 IHC methods for prostate microarrays (PMC11390458), liver microarrays (PMC4050181), and cartilage (PMC10518936).
| Sample | Paraffin-embedded human liver cancer tissue; fixative not specified (datasheet M02602-2) |
| Fixation | Image fixative and duration unreported (datasheet M02602-2); 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 M02602-2); 20 min, 95–100 °C (standard) |
| Peroxidase block | 3% H2O2, 10 min, room temperature (standard) |
| Blocking | 10% goat serum (datasheet M02602-2) |
| Primary antibody | Mouse monoclonal (clone 6G3B4) anti-SND1, 2 μg/ml (datasheet M02602-2) |
| Primary incubation | Overnight at 4 °C (datasheet M02602-2) |
| Detection | Streptavidin-biotin complex (SABC), DAB chromogen (datasheet M02602-2) |
| Counterstain | Hematoxylin, blue, dehydrate and mount (standard) |
| Expected result | SND1-positive staining in hematopoietic cells of bone marrow (HPA tissue IHC: High). HPA tissue profile: Ubiquitous cytoplasmic expression at variable levels. No signal in the no-primary control. |
💡Decision noteStart with heat-mediated EDTA retrieval at pH 8.0 for the catalog antibody (datasheet: M02602-2); optimize against the tissue and antibody used.
Section 2
What Is the Expected SND1 Staining Pattern?
SND1 is predominantly cytoplasmic in tissue IHC, with variable staining across cell types (HPA: ubiquitous cytoplasmic expression). Expect strong staining in selected glandular, neuronal, hematopoietic and other documented positive cells (HPA: High in listed cell types). UniProt also lists nuclear and melanosomal localization; SND1 has no transmembrane segment (UniProt Q7KZF4: localization and topology). HPA rates tissue IHC reliability Enhanced, with medium consistency between staining and RNA expression (HPA: tissue IHC).
| Clear cytoplasmic staining in endometrial glandular cells or pancreatic exocrine glandular cells. | This fits documented high staining in both cell types (HPA: High in endometrium and pancreas). Judge intensity against nearby cells and the slide controls; a positive tissue need not stain uniformly (HPA: variable levels). |
| Predominantly nuclear staining, with little cytoplasmic signal. | This departs from the usual tissue IHC pattern (HPA: ubiquitous cytoplasmic expression). Nuclear SND1 is possible, particularly with IL-4 stimulation (UniProt Q7KZF4: nucleus and STAT6 colocalization); investigate context and controls before calling it artefact. |
| Strong staining in adipocytes, cardiomyocytes or skeletal myocytes. | These cell types are listed as not detected (HPA: adipocytes, cardiomyocytes and skeletal myocytes). Check for nonspecific antibody binding or endogenous detection activity; an unexpected signal alone does not establish cross-reactivity. |
| Diffuse color across tissue, including areas without defined cells. | This does not match a cell-associated cytoplasmic pattern (HPA: tissue IHC profile). In chromogenic IHC, inadequate blocking, excess antibody or residual detection activity can cause background (general IHC practice). |
| No signal in a documented high-staining cell type. | Absence in the chosen positive cells conflicts with the HPA pattern (HPA: High in listed cell types). First check whether the cells are present and whether controls developed; then review the IHC workflow (general IHC practice). |
💡Expected SND1 appearanceCall the stain positive when defined cells show predominantly cytoplasmic signal, potentially high in endometrial glandular or pancreatic exocrine cells (HPA: tissue IHC); broad haze or staining confined to documented not-detected cells is suspect (HPA: tissue IHC; general IHC practice).
| Tissue and cell selection | Expression is widespread but variable (HPA: tissue IHC; UniProt Q7KZF4: ubiquitous expression). Select a documented high-staining cell type for a positive reference; adipocytes or cardiomyocytes offer documented not-detected comparisons (HPA: tissue IHC). |
| Compartment and topology | Cytoplasm is the dominant tissue IHC pattern, and SND1 lacks a transmembrane segment (HPA: tissue IHC; UniProt Q7KZF4: topology). A membrane-only outline is therefore unexpected; review morphology and controls before assigning it to SND1. |
| Context for nuclear signal | UniProt lists nucleus and reports colocalization with STAT6 in IL-4-stimulated cells (UniProt Q7KZF4: subcellular location). This supports a context-dependent possibility, not a prediction that an unstimulated paraffin section should stain mainly in nuclei. |
| Antibody validation | HPA lists IHC Enhanced for HPA002529 and HPA002632, and Supported for CAB019323 (HPA: antibody validation). Those ratings support interpretation of their reported staining; they do not establish how an unlisted antibody will perform. |
| IF/ICC Q: What pattern is reported? | A: Predominantly cytosolic signal (HPA: ICC-IF, Cytosol enhanced). UniProt also lists nucleus and melanosome (UniProt Q7KZF4: localization). The ICC-IF summary reports no additional location, so use the IF/ICC guide for assay-specific design. |
| Situation | Likely cause | Next action |
|---|---|---|
| Positive reference tissue is blank. | The selected high-staining cells may be absent, or the staining run may have failed (HPA: High in listed cell types; general IHC practice). | Locate the named cells on a counterstained section, confirm the run control, then check retrieval, primary antibody and detection steps (general IHC practice). |
| All cells show uniform brown haze. | Excess antibody, incomplete blocking or residual endogenous detection activity may obscure cell boundaries (general chromogenic IHC practice). | Compare a no-primary control; optimize blocking, washes and antibody concentration within the assay's validated range (general IHC practice). |
| Only nuclei appear positive. | The pattern differs from predominant cytoplasmic tissue staining (HPA: tissue IHC), although nuclear SND1 is documented in a specific stimulated context (UniProt Q7KZF4: IL-4/STAT6). | Check cytoplasmic signal and negative controls, then assess whether the experimental context supports nuclear localization before scoring it as specific. |
| Cardiomyocytes or adipocytes stain strongly. | These cells are reported as not detected (HPA: heart muscle and adipose tissue); nonspecific binding or endogenous chromogenic activity is possible (general IHC practice). | Compare no-primary and detection controls, inspect cell morphology, and repeat with an IHC-validated antibody if the unexpected pattern persists (HPA: antibody validation). |
| A documented positive cell type stains weakly. | HPA reports high staining in selected cells but variable expression across tissue (HPA: tissue IHC). Sampling and assay conditions can affect what is visible (general IHC practice). | Confirm cell identity, assess the positive control, and optimize retrieval and antibody dilution using the assay instructions (general IHC practice). |
| Signal outlines cell membranes without cytoplasmic staining. | A membrane-only pattern conflicts with the reported cytoplasmic profile and lack of a transmembrane segment (HPA: tissue IHC; UniProt Q7KZF4: topology). | Inspect a no-primary control and neighboring cell morphology; confirm the pattern with an independently validated IHC antibody (general IHC practice; HPA: antibody validation). |
Experiment evidence
IHC & IF images showing SND1 staining
M02602-2 · IHCIHC analysis of SND1 using anti-SND1 antibody (M02602-2). SND1 was detected in a paraffin-embedded section of human liver cancer tissue. Hea
M02602-2 · IHCIHC analysis of SND1 using anti-SND1 antibody (M02602-2). SND1 was detected in a paraffin-embedded section of human metaplasia of squamous c
M02602-2 · IFIF analysis of SND1 using anti-SND1 antibody (M02602-2). SND1 was detected in an immunocytochemical section of PC-3 cells. Enzyme antigen re
M02602-1 · IHCIHC analysis of SND1 using anti-SND1 antibody (M02602-1). SND1 was detected in a paraffin-embedded section of human Hodgkin's lymphoma tissu
M02602-1 · IHCIHC analysis of SND1 using anti-SND1 antibody (M02602-1). SND1 was detected in a paraffin-embedded section of human liver cancer tissue. Hea
M02602-1 · IFIF analysis of SND1 using anti-SND1 antibody (M02602-1). SND1 was detected in an immunocytochemical section of PC-3 cells. Enzyme antigen re
A02602-3 · IHCIHC analysis of SND1 using anti-SND1 antibody (A02602-3). SND1 was detected in paraffin-embedded section of human breast cancer tissue. Heat
A02602-3 · IHCIHC analysis of SND1 using anti-SND1 antibody (A02602-3). SND1 was detected in paraffin-embedded section of human placenta tissue. Heat medi
A02602-3 · IFIF analysis of SND1 using anti-SND1 antibody (A02602-3). SND1 was detected in immunocytochemical section of PC-3 cells. Enzyme antigen retri
HPA · Cerebral cortexHuman Protein Atlas IHC, Cerebral cortex. Source: https://www.proteinatlas.org/ENSG00000197157-SND1/tissue/cerebral+cortex#imid_994088
HPA · ColonHuman Protein Atlas IHC, Colon. Source: https://www.proteinatlas.org/ENSG00000197157-SND1/tissue/colon#imid_994014
HPA · LiverHuman Protein Atlas IHC, Liver. Source: https://www.proteinatlas.org/ENSG00000197157-SND1/tissue/liver#imid_994015
HPA · PancreasHuman Protein Atlas IHC, Pancreas. Source: https://www.proteinatlas.org/ENSG00000197157-SND1/tissue/pancreas#imid_993958
HPA · ICC-IF A-431Human Protein Atlas immunofluorescence, A-431, antibody CAB019323; green = SND1, blue = nucleus, red = microtubules.
HPA · ICC-IF A-431Human Protein Atlas immunofluorescence, A-431, antibody CAB019323; green = SND1, blue = nucleus, red = microtubules.
← swipe / scroll for more images →
Real IHC / IF data behind the staining-pattern expectations in this section.
Sample controls for SND1 IHC & IF
🧪Run bone marrow first and confirm staining in hematopoietic cells (High; HPA: bone marrow). Use skeletal muscle myocytes as the negative tissue (Not detected; HPA: skeletal muscle); adipocytes, if present on the marrow slide, can serve as an internal negative reference, but assess them separately from hematopoietic cells (HPA: adipose tissue adipocytes not detected).
Positive control tissue: Bone marrow (Hematopoietic cells, HPA High)
Negative control tissue: Adipose tissue (HPA Not detected)
ICC-IF cell lines (HPA subcellular resource): HPA ICC-IF images show SND1 in A-431, U-251MG, U2OS, U2OS, siRNA 1 (10x), U2OS, siRNA 1 (40x), U2OS, scrambled (10x), U2OS, scrambled (40x), NIH 3T3, with annotated localisation: Cytosol (enhanced) (HPA subcellular).
Technical controls: Include a no-primary (secondary-only) control, a concentration-matched mouse isotype control for the catalog antibody, and a SND1 knockout specimen or validated peptide-block control (selected-SKU caption: mouse anti-SND1). For chromogenic marrow IHC, quench endogenous peroxidase and check background from endogenous biotin when using the caption’s biotin–streptavidin detection (selected-SKU caption: SABC with DAB).
⚠️Feasibility: A target-specific fixation window or fixation effect is unreported, and the selected-SKU paraffin-section caption does not state the fixative (selected-SKU caption: fixative not stated). The caption provides an IHC-P starting condition of heat retrieval in EDTA at pH 8.0, but does not establish that retrieval is required across specimens (selected-SKU caption: EDTA retrieval). Relative ease of frozen-section staining or IF is unreported; marrow interpretation should account for endogenous peroxidase and biotin background under the caption’s chromogenic detection scheme (selected-SKU caption: SABC with DAB).
HPA tissue IHC evidence for SND1
Comprehensive Human Protein Atlas IHC scoring per tissue (reliability: Enhanced — 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 |
|---|---|---|---|---|
| Bone marrow | Hematopoietic cells | High | Protein (IHC) | HPA → |
| Cerebellum | Cells in molecular layer | High | Protein (IHC) | HPA → |
| Cerebral cortex | Neuronal cells | High | Protein (IHC) | HPA → |
| Endometrium | Glandular cells | High | Protein (IHC) | HPA → |
| Gallbladder | Glandular cells | High | Protein (IHC) | HPA → |
Undetected expression · recommended negative controls
| Tissue | Cell type | Level | Evidence | Source |
|---|---|---|---|---|
| Adipose tissue | Adipocytes | Not detected | Protein (IHC) | HPA → |
| Heart muscle | Cardiomyocytes | Not detected | Protein (IHC) | HPA → |
| Skeletal muscle | Myocytes | Not detected | Protein (IHC) | HPA → |
| Soft tissue | Chondrocytes | Not detected | Protein (IHC) | HPA → |
Section 3
Advanced SND1 IHC Tips
Troubleshoot SND1 staining in paraffin sections against the catalog antibody’s demonstrated workflow and the expected cytoplasmic pattern (datasheet M02602-2; HPA tissue IHC).
How should I adjust retrieval when SND1 staining is weak?
Begin with heat-mediated antigen retrieval in EDTA at pH 8.0 for paraffin sections (datasheet M02602-2). Use the demonstrated workflow as a benchmark: 10% goat serum block, 2 μg/ml primary overnight at 4°C, and DAB detection (datasheet M02602-2). If staining remains weak, verify deparaffinisation and heating consistency, then compare retrieval times on adjacent sections while holding antibody exposure and detection constant (standard IHC practice). Score cytoplasmic staining against a positive reference section, since SND1 staining varies across tissues and cells (HPA tissue IHC).
Could fixation explain inconsistent SND1 staining between paraffin blocks?
Target-specific fixation sensitivity for SND1 is unknown because the selected paraffin-section caption does not report its fixative (datasheet M02602-2). Record fixative, fixation duration, tissue thickness, and processing delay for each block; compare adjacent sections before changing retrieval or antibody concentration (standard IHC practice). Keep pH 8.0 EDTA heat retrieval and 2 μg/ml overnight primary incubation as initial constants, then change one variable at a time (datasheet M02602-2; standard IHC practice). Inspect morphology and internal positive cells alongside staining, since poor preservation can mimic low antigen abundance (standard IHC practice).
Should SND1 appear in the nucleus or cytoplasm on IHC?
Expect predominantly cytoplasmic staining in routine tissue IHC: the tissue profile describes ubiquitous cytoplasmic expression at variable levels (HPA tissue IHC). SND1 also has a reported nuclear location, including colocalisation with STAT6 after IL-4 stimulation, so a nuclear signal requires context and independent validation (UniProt Q7KZF4). Compare nuclear and cytoplasmic staining separately within morphologically intact cells, using the same exposure and scoring rules across sections (standard IHC practice). Melanosome-fraction identification by mass spectrometry does not establish a distinctive melanosomal pattern in these paraffin sections (UniProt Q7KZF4; standard IHC practice).
Can SND1 domains or modifications explain patchy staining?
The supplied record lists 0 isoforms, so it provides no alternative isoform pattern to assign to patchy IHC staining (UniProt Q7KZF4). SND1 contains 4 TNase-like domains and a Tudor domain at residues 729–787, but the selected caption does not identify the antibody epitope (UniProt Q7KZF4; datasheet M02602-2). Document retrieval and processing variation before proposing epitope masking, and compare staining with an independently validated antibody if available (standard IHC practice). Reported phosphorylation and acetylation sites establish modifications, not that they alter this antibody’s binding in sections (UniProt Q7KZF4).
How can IF help check a disputed SND1 IHC pattern?
Use IF as an orthogonal localisation check, pairing SND1 with a marker for the expected cell type, such as a cytotrophoblast marker when examining placenta (HPA tissue IHC; standard IF practice). Choose spectrally separated fluorophores and consider a far-red SND1 channel where tissue autofluorescence obscures shorter wavelengths; include unstained and secondary-only controls (standard IF practice). SND1 is intracellular and has no transmembrane segment, so include a controlled permeabilisation step to expose cytosolic epitopes (UniProt Q7KZF4; standard IF practice). Compare cellular localisation with IHC, while recording IF fixation separately because the selected IHC caption supplies no fixation condition (datasheet M02602-2; standard IF practice).
What causes diffuse brown background in SND1 IHC?
First inspect no-primary and secondary-only controls for signal from the detection system, and compare them with a morphology-matched stained section (standard IHC practice). The demonstrated method uses a biotinylated goat anti-mouse secondary, streptavidin-biotin complex, and DAB, so assess endogenous biotin and peroxidase activity with appropriate controls and blocking (datasheet M02602-2; standard IHC practice). Titrate the 2 μg/ml primary concentration downward and check wash stringency if staining persists outside cells (datasheet M02602-2; standard IHC practice). Preserve a positive reference: broadly distributed cytoplasmic SND1 staining alone is not evidence of background (HPA tissue IHC).
How should I quantify SND1 staining across specimens? ⚠ ANSWER MARKED FOR VERIFICATION
Define the cell population and compartment before scoring, then report cytoplasmic percent-positive cells and intensity, or an H-score calculated as the sum of each intensity category’s percentage multiplied by its score (HPA tissue IHC; standard IHC practice). An H-score on a 0–3 intensity scale ranges from 0–300 (standard IHC practice). Normalise counts to eligible intact cells or stained area to tissue area, and exclude necrosis, folds, and section edges consistently (standard IHC practice). Keep retrieval, detection, imaging, and scoring thresholds constant across specimens, with a reference section to monitor batch variation (standard IHC practice).
When is an apparent SND1-positive cell likely an artefact?
Treat intact cytoplasmic staining in the expected cell population as more convincing than signal confined to damaged edges, folds, or necrotic areas (HPA tissue IHC; standard IHC practice). Check whether strongly stained cells fit the tissue context: high staining is reported in placental cytotrophoblasts, whereas adipocytes are listed as not detected (HPA tissue IHC). A predominantly nuclear-only result needs corroboration, because routine tissue staining is cytoplasmic although nuclear localisation is reported under specific conditions (HPA tissue IHC; UniProt Q7KZF4). If DAB persists in no-primary controls, investigate endogenous enzyme or detection-system signal before calling SND1 positive (standard IHC practice).
Boster reagents
Best SND1 / Staphylococcal nuclease domain-containing protein 1 IHC Antibodies
Anti-SND1 antibodies have paraffin-section IHC images from human tissues and IF/ICC images from PC-3 cells (catalog image captions); listed reactivity includes human, mouse, and rat (catalog reactivity).
Real IHC data
Anti-SND1 Antibody ® (monoclonal, 6G3B4)
Cat # M02602-2
Real IHC data
Anti-SND1 Antibody ® (monoclonal, 5F5E9)
Cat # M02602-1
Real IHC data
Anti-SND1 Antibody ®
Cat # A02602-3
M02602-2 has an IHC image from human liver cancer, and M02602-1 has one from human Hodgkin's lymphoma (respective IHC captions). A02602-3 has an IHC image from human breast cancer, while all three have IF/ICC images from PC-3 cells (respective image captions).
Which to pick: For paraffin-section IHC, choose M02602-2 for the liver cancer example, M02602-1 for the Hodgkin's lymphoma example, or A02602-3 for the breast cancer example (respective IHC captions); the captions do not report a fixative. For IF/ICC, choose A02602-3 if a rabbit primary suits the detection setup, or either mouse monoclonal, M02602-1 or M02602-2; each has a PC-3 IF/ICC image (catalog host and clone fields; respective IF captions). For cross-species IHC planning, the monoclonals list human, mouse, and rat for paraffin-section IHC, while A02602-3 lists human and mouse for that application (catalog dilution_raw); the cited IHC images show human samples only (respective IHC captions).
Each figure is that product's own IHC / IF validation image from its datasheet.
References
- UniProt Consortium. UniProt entry Q7KZF4 (SND1_HUMAN, Staphylococcal nuclease domain-containing protein 1).
- Human Protein Atlas. SND1 tissue IHC expression (reliability: Enhanced).
- Human Protein Atlas. SND1 subcellular location (ICC-IF): Localized to the cytosol..
- Human Protein Atlas. SND1 antibody validation summary (3 antibodies).
- [Identification and Analysis of SND1 as an Oncogene and Prognostic Biomarker for Lung Adenocarcinoma]. Zhongguo fei ai za zhi = Chinese journal of lung cancer 2024 — PMC10895293.
- Androgen receptor modulatory miR-1271-5p can promote hormone sensitive prostate cancer cell growth. Frontiers in oncology 2024 — PMC11390458.
- Staphylococcal nuclease domain containing-1 (SND1) promotes migration and invasion via angiotensin II type 1 receptor (AT1R) and TGFβ signaling. FEBS open bio 2014 — PMC4050181.
- SND1 aggravates mitochondrial damage, apoptosis and extracellular matrix degradation in IL-1β-stimulated chondrocytes via PINK1/BECN1 pathway. European journal of medical research 2023 — PMC10518936.
- PubMed PMID:7651391 — UniProt-cited evidence.
- PubMed PMID:15489334 — UniProt-cited evidence.
- PubMed PMID:12234934 — UniProt-cited evidence.
Immunohistochemistry protocol sheet for SND1 (Staphylococcal nuclease domain-containing protein 1). Expected localisation Predominantly cytoplasmic in tissue; nuclear location annotated (HPA tissue IHC; UniProt). Antigen retrieval: EDTA pH 8.0 HIER, heat-mediated (datasheet M02602-2). Validated IHC antibody: M02602-2 at 2 μg/ml (the product's own IHC validation image is shown). Controls (HPA): positive Bone marrow (Hematopoietic cells); negative Adipose tissue. IHC-P workflow on paraffin sections; fixative unspecified. Protocol steps: 1. Sample: Paraffin-embedded human liver cancer tissue; fixative not specified (datasheet M02602-2); 2. Fixation: Image fixative and duration unreported (datasheet M02602-2); 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 M02602-2); 20 min, 95–100 °C (standard); 6. Peroxidase block: 3% H2O2, 10 min , room temperature (standard); 7. Blocking: 10% goat serum (datasheet M02602-2); 8. Primary antibody: Mouse monoclonal (clone 6G3B4) anti-SND1, 2 μg/ml (datasheet M02602-2); 9. Primary incubation: Overnight at 4 °C (datasheet M02602-2). Watch for: Fixation: Keep fixation consistent across samples. (standard IHC practice; not target-specific); Caveat: Cell-type variation can complicate intensity scoring (HPA tissue IHC); Isoform / epitope: No listed isoforms; mature chain spans residues 2–910 (UniProt); Regulation: Tissue expression varies (HPA tissue IHC). Evidence: UniProt Q7KZF4, HPA tissue IHC · Enhanced, HPA ICC-IF · cytosol., Datasheet M02602-2, PMC11390458, PMC4050181. QR code links to https://www.bosterbio.com/bosterbio-gene-info-cards/SND1/immunohistochemistry-ihc-guide.