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SLFN11 / Schlafen family member 11 · IHC design guide
Design Immunohistochemistry for SLFN11
Plan chromogenic SLFN11 IHC on paraffin sections using the catalog antibody at 2–5 μg/mL (datasheet A08259). Assess cytoplasmic tissue staining (HPA tissue IHC) alongside the protein’s nuclear and chromosomal localisation (UniProt), and interpret the tissue pattern with its uncertain reliability in mind (HPA tissue IHC).
Evidence assembled Oct 2026 · For research use; verify linked source records and product datasheet before use
SLFN11 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 | Cytoplasmic tissue staining (HPA tissue IHC); nuclear/chromosomal localisation (UniProt) | |
| Staining pattern | Cytoplasmic staining across several tissue cell types (HPA tissue IHC) | |
| Antigen retrieval | EDTA pH 8.0 HIER, heat-mediated (datasheet A08259) | |
| Positive control | Adipose tissue+4 more · see all | |
| Negative control | Appendix+4 more · see all |
Important caveats
Reasons your staining may differ from the expected pattern.
| Fixation | Keep paraffin-section fixation consistent (standard IHC practice; not target-specific) | |
| Caveat | Tissue staining reliability is uncertain (HPA tissue IHC) | |
| Regulation | Interferon-induced expression (UniProt) | |
| Isoform / epitope | No annotated isoforms; single chain, residues 1–901 (UniProt) |
Section 1
Recommended SLFN11 IHC & IF Protocols
The catalog antibody’s IHC-P protocol is accompanied by published SLFN11 staining conditions for soft tissue sarcoma, ovarian serous carcinoma, and bladder cancer (PMC13008703; PMC13576481; PMC8819307).
| Sample | Paraffin-embedded human liver cancer tissue; fixative not specified (datasheet A08259) |
| Fixation | Image fixative and duration unreported (datasheet A08259); 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 A08259); 20 min, 95–100 °C (standard) |
| Peroxidase block | 3% H2O2, 10 min, room temperature (standard) |
| Blocking | 10% goat serum (datasheet A08259) |
| Primary antibody | Rabbit anti-SLFN11, 2-5μg/ml (datasheet A08259) |
| Primary incubation | Overnight at 4 °C (datasheet A08259) |
| Detection | Streptavidin-biotin complex (SABC), DAB chromogen (datasheet A08259) |
| Counterstain | Hematoxylin, blue, dehydrate and mount (standard) |
| Expected result | SLFN11-positive staining in adipocytes of adipose tissue (HPA tissue IHC: Medium). HPA tissue profile: Cytoplasmic expression in several different tissue types. No signal in the no-primary control. |
💡Decision noteStart with heat-mediated EDTA pH 8.0 retrieval for the catalog antibody (datasheet A08259). Use each article’s stated conditions when reproducing its protocol (PMC13008703; PMC13576481).
Section 2
What Is the Expected SLFN11 Staining Pattern?
SLFN11 is assigned to the nucleus and chromosomes and has no transmembrane segment (UniProt Q7Z7L1). Nuclear staining in expressing cells is therefore biologically plausible. HPA instead reports cytoplasmic tissue IHC staining across several tissues, with uncertain reliability; its ICC-IF data support nucleoplasmic localisation (HPA tissue IHC; HPA subcellular). Interpret compartment and cell type together, and treat either IHC pattern as requiring antibody and control review.
| Nuclear signal in cells of endometrial stroma, with limited background. | Nuclear localisation agrees with UniProt and supported HPA ICC-IF nucleoplasmic localisation (UniProt Q7Z7L1; HPA subcellular). HPA rates endometrial stromal tissue staining medium, but its tissue IHC reliability is uncertain; this slide alone does not validate the IHC antibody (HPA tissue IHC). |
| Predominantly cytoplasmic staining in adipocytes or adrenal glandular cells. | HPA reports medium staining in those cells and describes its tissue IHC profile as cytoplasmic (HPA tissue IHC). This differs from UniProt nuclear localisation and supported HPA ICC-IF nucleoplasmic localisation (UniProt Q7Z7L1; HPA subcellular). Record it as an observed, uncertain IHC pattern rather than proof of cytoplasmic SLFN11. |
| Strong staining confined to cell membranes, with little nuclear or cytoplasmic signal. | A membrane-only pattern conflicts with UniProt nuclear localisation and the absence of a transmembrane segment (UniProt Q7Z7L1). Check antibody specificity and detection background before assigning it to SLFN11. HPA's uncertain cytoplasmic tissue IHC pattern does not support a membrane-only interpretation (HPA tissue IHC). |
| Prominent signal in appendix glandular cells or bronchial respiratory epithelium. | HPA lists those cell types as not detected (HPA tissue IHC). If signal is convincing, assess cross-reactivity or endogenous detection activity with appropriate controls (general IHC practice). Because HPA rates its tissue IHC evidence uncertain, a discrepant result warrants investigation rather than an automatic false-positive label (HPA tissue IHC). |
| No signal in adipocytes despite intact tissue and a working counterstain. | HPA reports medium adipocyte staining, making them a useful comparison within this evidence set, although the tissue IHC profile remains uncertain (HPA tissue IHC). Check the antibody and detection controls, retrieval conditions and reagent dilution (general IHC practice). A negative slide alone cannot establish absent SLFN11 expression. |
💡Expected SLFN11 appearanceA credible positive shows cell-associated nuclear signal, consistent with UniProt and HPA ICC-IF, in a cell type with reported HPA staining, such as endometrial stromal cells; HPA tissue IHC may instead show medium cytoplasmic signal and is uncertain, while membrane-only or widespread cell-free colour calls for control review (UniProt Q7Z7L1; HPA subcellular; HPA tissue IHC; general IHC practice).
| Compartment evidence | UniProt assigns SLFN11 to the nucleus and chromosomes; HPA ICC-IF supports nucleoplasm, whereas HPA tissue IHC describes cytoplasmic staining with uncertain reliability (UniProt Q7Z7L1; HPA subcellular; HPA tissue IHC). Keep the assay-specific discrepancy visible when scoring. |
| Tissue and cell selection | HPA reports medium staining in adipocytes and endometrial stromal cells, low staining in glial cells, and no detection in appendix glandular cells (HPA tissue IHC). Compare the named cell populations, rather than treating an entire section as uniformly positive or negative. |
| Antibody evidence | HPA023030 is rated uncertain for IHC and supported for ICC; HPA062062 has no listed IHC status and is supported for ICC (HPA antibodies). An ICC rating does not establish performance in paraffin-section IHC. HPA also rates its tissue IHC profile uncertain (HPA tissue IHC). |
| Protein topology and processing | UniProt lists no transmembrane segment, signal peptide, propeptide or annotated glycosylation site for SLFN11 (UniProt Q7Z7L1). These annotations support caution with a membrane-only pattern; they do not predict how fixation or antigen retrieval affects the IHC signal. |
| IF/ICC Q: what pattern should be expected? | A: Mainly nucleoplasmic signal is supported; additional cytosolic localisation is uncertain (HPA subcellular). That ICC-IF observation helps interpret localisation, but it cannot substitute for validation of chromogenic paraffin-section IHC (HPA subcellular; HPA antibodies). |
| Situation | Likely cause | Next action |
|---|---|---|
| Nuclear signal is absent but cytoplasmic colour is present. | HPA describes uncertain cytoplasmic tissue IHC, while UniProt and supported ICC-IF favour nuclear localisation (HPA tissue IHC; UniProt Q7Z7L1; HPA subcellular). | Record both compartment and named cell type; compare antibody and detection controls before interpreting the cytoplasmic colour as SLFN11 (general IHC practice). |
| Signal appears only along membranes. | Membrane-only localisation is unsupported by UniProt's nuclear assignment and lack of a transmembrane segment (UniProt Q7Z7L1). | Review antibody specificity and a no-primary control, then reassess localisation in intact cells (general IHC practice). |
| Unexpected epithelial cells stain strongly. | Appendix glandular and bronchial respiratory epithelial cells are listed as not detected by HPA, although its tissue IHC evidence is uncertain (HPA tissue IHC). | Confirm the cell identity and compare a no-primary control; investigate cross-reactivity or endogenous detection activity before scoring a new positive pattern (general IHC practice). |
| Colour is diffuse across tissue or appears in cell-free areas. | Diffuse colour prevents a reliable cell-level or compartment-level assignment (general IHC practice). | Compare a no-primary control and review blocking, washes and chromogen development; score only distinguishable cellular signal (general IHC practice). |
| No staining appears in adipocytes or endometrial stromal cells. | Both are reported at medium staining by HPA, but the overall tissue IHC profile has uncertain reliability (HPA tissue IHC). | Verify section integrity, antibody dilution, retrieval and detection controls; document the negative finding without assuming biological absence (general IHC practice). |
| An ICC-IF result is nucleoplasmic while paraffin IHC is cytoplasmic. | That difference mirrors supported HPA ICC-IF localisation and its uncertain cytoplasmic tissue IHC profile (HPA subcellular; HPA tissue IHC). | Report assay and compartment separately; assess the IHC antibody and controls within paraffin sections before reconciling the results (HPA antibodies; general IHC practice). |
Experiment evidence
IHC & IF images showing SLFN11 staining
A08259 · IHCIHC analysis of SLFN11 using anti-SLFN11 antibody (A08259). SLFN11 was detected in a paraffin-embedded section of human liver cancer tissue.
A08259 · IHCIHC analysis of SLFN11 using anti-SLFN11 antibody (A08259). SLFN11 was detected in a paraffin-embedded section of human lung cancer tissue.
HPA · Cerebral cortexHuman Protein Atlas IHC, Cerebral cortex. Source: https://www.proteinatlas.org/ENSG00000172716-SLFN11/tissue/cerebral+cortex#imid_5831764
HPA · ColonHuman Protein Atlas IHC, Colon. Source: https://www.proteinatlas.org/ENSG00000172716-SLFN11/tissue/colon#imid_5831690
HPA · LiverHuman Protein Atlas IHC, Liver. Source: https://www.proteinatlas.org/ENSG00000172716-SLFN11/tissue/liver#imid_5831683
HPA · KidneyHuman Protein Atlas IHC, Kidney. Source: https://www.proteinatlas.org/ENSG00000172716-SLFN11/tissue/kidney#imid_5831684
HPA · ICC-IF A-431Human Protein Atlas immunofluorescence, A-431, antibody HPA023030; green = SLFN11, blue = nucleus, red = microtubules.
HPA · ICC-IF A-431Human Protein Atlas immunofluorescence, A-431, antibody HPA023030; green = SLFN11, blue = nucleus, red = microtubules.
← swipe / scroll for more images →
Real IHC / IF data behind the staining-pattern expectations in this section.
Sample controls for SLFN11 IHC & IF
🧪Run adipose tissue first and score SLFN11 staining in adipocytes (Medium; HPA: adipose tissue, adipocytes). Use appendix glandular cells as the negative comparator (HPA: appendix, glandular cells, Not detected); on the adipose slide, treat cells without specific nuclear staining as internal background references rather than assuming a particular cell population is negative (UniProt Q7Z7L1: nucleus).
Positive control tissue: Adipose tissue (Adipocytes, HPA Medium)
Negative control tissue: Appendix (HPA Not detected)
ICC-IF cell lines (HPA subcellular resource): HPA ICC-IF images show SLFN11 in A-431, U-251MG, U2OS, HEK293, Rh30, with annotated localisation: Nucleoplasm (supported) (HPA subcellular).
Technical controls: Include no-primary (secondary-only) and concentration-matched rabbit IgG isotype controls, plus SLFN11 knockout material or a validated peptide-block control where available (selected-SKU caption: rabbit primary antibody; standard IHC practice). Block endogenous peroxidase before chromogenic detection and assess endogenous biotin if using the caption’s biotin-based detection system (selected-SKU caption: biotinylated secondary, streptavidin–biotin complex and DAB; standard IHC practice).
⚠️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 alone does not establish fixation (selected-SKU caption: fixative not stated). The caption uses heat retrieval in EDTA at pH 8.0, so start there and optimize against the positive and negative tissues; a retrieval dependency is not established by the supplied evidence (selected-SKU caption: EDTA retrieval; HPA: adipocytes Medium, appendix glandular cells Not detected). Frozen sections or IF cannot be judged easier from these data; in adipose tissue, large lipid spaces leave thin cytoplasm, so assess nuclear staining in identifiable adipocytes (HPA: adipose tissue, adipocytes; UniProt Q7Z7L1: nucleus; standard histology practice). The selected A08259 tissue-IHC caption documents paraffin sections, but does not specify the fixative (selected-SKU IHC image A08259).
HPA tissue IHC evidence for SLFN11
Comprehensive Human Protein Atlas IHC scoring per tissue (reliability: Uncertain — Medium consistency between antibody staining and RNA expression data. 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 |
|---|---|---|---|---|
| Adipose tissue | Adipocytes | Medium | Protein (IHC) | HPA → |
| Adrenal gland | Glandular cells | Medium | Protein (IHC) | HPA → |
| Caudate | Neuronal cells | Medium | Protein (IHC) | HPA → |
| Endometrium | Cells in endometrial stroma | Medium | Protein (IHC) | HPA → |
| Epididymis | Glandular cells | Medium | Protein (IHC) | HPA → |
Undetected expression · recommended negative controls
| Tissue | Cell type | Level | Evidence | Source |
|---|---|---|---|---|
| Appendix | Glandular cells | Not detected | Protein (IHC) | HPA → |
| Bronchus | Respiratory epithelial cells | Not detected | Protein (IHC) | HPA → |
| Colon | Endothelial cells | Not detected | Protein (IHC) | HPA → |
| Duodenum | Glandular cells | Not detected | Protein (IHC) | HPA → |
| Esophagus | Squamous epithelial cells | Not detected | Protein (IHC) | HPA → |
Section 3
Advanced SLFN11 IHC Tips
Troubleshoot SLFN11 staining in paraffin-section chromogenic IHC by checking retrieval, nuclear localisation, controls and cell-specific scoring (datasheet A08259; UniProt Q7Z7L1).
What should I change if SLFN11 staining is weak after antigen retrieval?
Start with heat-mediated EDTA retrieval at pH 8.0 for paraffin-section IHC (datasheet A08259). This condition accompanies staining of a human liver cancer section with 2 μg/ml primary antibody overnight at 4°C (datasheet A08259). If staining remains weak, compare heating intervals on matched sections while keeping antibody concentration and DAB development constant; excessive heating can damage morphology (standard IHC practice). Include a no-primary control and record nuclear and cytoplasmic signal separately, since SLFN11 is nuclear and an additional cytosolic location is reported with uncertain support (UniProt Q7Z7L1; HPA subcellular).
Could fixation explain inconsistent SLFN11 staining across paraffin sections?
The selected paraffin-section caption does not state a fixative, so target-specific SLFN11 fixation sensitivity is unknown (datasheet A08259). For new material, document fixation and processing conditions, then compare matched sections using pH 8.0 EDTA retrieval and 2 μg/ml primary antibody overnight at 4°C (datasheet A08259; standard IHC practice). Inspect morphology and compare the same cell population before changing retrieval, because fixation and processing can alter epitope accessibility (standard IHC practice). Neither tissue staining patterns nor the absence of an annotated transmembrane segment or glycosylation sites establishes a preferred fixative (HPA tissue; UniProt Q7Z7L1).
Should I score cytoplasmic SLFN11 staining as positive?
Score nuclear staining separately: SLFN11 is annotated in the nucleus and on chromosomes, while nucleoplasmic localisation has supported cell-imaging evidence (UniProt Q7Z7L1; HPA subcellular). HPA also describes cytoplasmic staining across several tissues, but rates its tissue-IHC reliability uncertain and its additional cytosolic localisation uncertain (HPA tissue; HPA subcellular). Compare nuclear and cytoplasmic patterns within identified cell populations on matched sections, using the documented pH 8.0 EDTA retrieval as the starting condition (datasheet A08259; standard IHC practice). Report cytoplasmic signal separately and require independent validation before treating it as definitive SLFN11 expression (standard IHC practice).
Can an unannotated isoform or epitope change explain a negative section?
The supplied record lists 0 isoforms, no signal peptide and a single 1–901 chain, so it provides no annotated isoform switch to explain staining loss (UniProt Q7Z7L1). It also lists 0 glycosylation sites and 0 modified residues, but those annotations do not establish how fixation affects the antibody epitope (UniProt Q7Z7L1; standard IHC practice). The epitope location is not supplied, so do not assign a negative section to epitope masking without testing (datasheet A08259). First compare matched sections with documented pH 8.0 EDTA retrieval and appropriate positive and no-primary controls (datasheet A08259; standard IHC practice).
How can companion IF help resolve ambiguous chromogenic SLFN11 localisation?
Use companion IF/ICC to inspect nuclear and cytosolic signal separately; nucleoplasmic localisation is supported, whereas additional cytosolic localisation is uncertain (HPA subcellular). For tissue comparisons, multiplex SLFN11 with a marker identifying the cell population being scored, such as adipocytes where HPA reports medium tissue-IHC staining (HPA tissue; standard IF practice). Choose a fluorophore channel away from strong tissue autofluorescence and include single-channel and no-primary controls before interpreting overlap (standard IF practice). Because SLFN11 has no transmembrane segment and is primarily nuclear, permeabilisation must allow antibody access to the nucleus; optimise it for the antibody’s unreported epitope (UniProt Q7Z7L1; HPA subcellular; standard IF practice).
How do I separate diffuse DAB background from SLFN11 staining?
The documented chromogenic workflow uses a biotinylated secondary, streptavidin-biotin complex and DAB, so inspect controls for background from both detection steps (datasheet A08259; standard IHC practice). Include a no-primary section, block endogenous peroxidase, and assess endogenous biotin where the avidin-biotin method gives diffuse signal (standard IHC practice). The caption used 10% goat serum before 2 μg/ml primary antibody overnight at 4°C; reproduce those conditions before changing concentration or incubation (datasheet A08259). Compare background with nucleoplasmic staining in intact cells, since nucleoplasmic localisation has stronger support than cytosolic localisation (HPA subcellular; standard IHC practice).
What should I measure when SLFN11 staining varies between cell populations? ⚠ ANSWER MARKED FOR VERIFICATION
Define the cell population and compartment before scoring, because SLFN11 is nuclear and tissue staining varies by cell type (UniProt Q7Z7L1; HPA tissue). Record the percentage of viable target cells with nuclear staining and intensity categories, then calculate a nuclear H-score from 0–300 if intensity grading is reproducible (standard IHC scoring). Normalise positive-cell counts to all viable target cells scored, or report positive-cell density per mm² of viable tissue when spatial distribution matters (standard IHC scoring). Keep cytoplasmic scores separate and record retrieval and detection conditions across specimens (HPA subcellular; datasheet A08259; standard IHC practice).
What findings would make an apparent SLFN11-positive section unreliable?
A convincing result should show signal in identifiable intact cells with a reproducible nuclear pattern, consistent with SLFN11’s nuclear annotation and supported nucleoplasmic localisation (UniProt Q7Z7L1; HPA subcellular; standard IHC practice). Treat staining limited to section edges, necrotic areas or an unexplained cell population cautiously, and compare it with morphology and a no-primary control (standard IHC practice). Diffuse DAB signal can arise from endogenous peroxidase or biotin-dependent detection, since the documented method uses a streptavidin-biotin complex (datasheet A08259; standard IHC practice). Cytoplasmic staining alone needs independent validation because tissue-IHC reliability and additional cytosolic localisation are uncertain (HPA tissue; HPA subcellular).
Boster reagents
Best SLFN11 / Schlafen family member 11 IHC Antibodies
A human-reactive anti-SLFN11 antibody has real IHC data from paraffin sections of human liver and lung cancer tissue (catalog: A08259 reactivity and IHC image captions).
Real IHC data
Anti-SLFN11 Antibody ®
Cat # A08259
A08259 is listed for human IHC and has chromogenic images from paraffin sections of human liver and lung cancer tissue (catalog: A08259 applications, reactivity and IHC image captions). IF/ICC is absent from its application list, and no IF image is supplied (catalog: A08259 applications and IF image alts).
Which to pick: Choose A08259 for human paraffin-section IHC: the rabbit antibody is listed for IHC, and its own captions document EDTA retrieval at pH 8.0 and DAB detection (catalog: A08259 host, applications and IHC image captions). The clone and fixative are unreported; the captions establish paraffin embedding, not a specific fixation method (catalog: A08259 clone and IHC image captions). No listed SKU has IF/ICC or nonhuman validation: A08259 lists human reactivity and no IF application or IF image (catalog: A08259 applications, reactivity and IF image alts).
Each figure is that product's own IHC / IF validation image from its datasheet.
References
- UniProt Consortium. UniProt entry Q7Z7L1 (SLN11_HUMAN, Schlafen family member 11).
- Human Protein Atlas. SLFN11 tissue IHC expression (reliability: Uncertain).
- Human Protein Atlas. SLFN11 subcellular location (ICC-IF): Mainly localized to the nucleoplasm. In addition localized to the cytosol..
- Human Protein Atlas. SLFN11 antibody validation summary (2 antibodies).
- Schlafen 11 as a prognostic and potentially predictive biomarker in soft tissue sarcoma: evidence from a real-world cohort. Frontiers in oncology 2026 — PMC13008703.
- Schlafen 11 (SLFN11) And Tumor-Infiltrating Lymphocytes (TILs): Dual Predictive Biomarkers In Ovarian Serous Carcinoma. Asian Pacific journal of cancer prevention : APJCP 2026 — PMC13576481.
- Immunohistochemical analysis of SLFN11 expression uncovers potential non-responders to DNA-damaging agents overlooked by tissue RNA-seq. Virchows Archiv : an international journal of pathology 2021 — PMC9175511.
- Prognostic impact of Schlafen 11 in bladder cancer patients treated with platinum-based chemotherapy. Cancer science 2022 — PMC8819307.
- PubMed PMID:14702039 — UniProt-cited evidence.
- PubMed PMID:17974005 — UniProt-cited evidence.
- PubMed PMID:16625196 — UniProt-cited evidence.
Immunohistochemistry protocol sheet for SLFN11 (Schlafen family member 11). Expected localisation Cytoplasmic tissue staining (HPA tissue IHC); nuclear/chromosomal localisation (UniProt). Antigen retrieval: EDTA pH 8.0 HIER, heat-mediated (datasheet A08259). Validated IHC antibody: A08259 at 2-5μg/ml (the product's own IHC validation image is shown). Controls (HPA): positive Adipose tissue (Adipocytes); negative Appendix. IHC-P workflow on paraffin sections; fixative unspecified. Protocol steps: 1. Sample: Paraffin-embedded human liver cancer tissue; fixative not specified (datasheet A08259); 2. Fixation: Image fixative and duration unreported (datasheet A08259); 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 A08259); 20 min, 95–100 °C (standard); 6. Peroxidase block: 3% H2O2, 10 min , room temperature (standard); 7. Blocking: 10% goat serum (datasheet A08259); 8. Primary antibody: Rabbit anti-SLFN11, 2-5μg/ml (datasheet A08259); 9. Primary incubation: Overnight at 4 °C (datasheet A08259). Watch for: Fixation: Keep paraffin-section fixation consistent (standard IHC practice; not target-specific); Caveat: Tissue staining reliability is uncertain (HPA tissue IHC); Isoform / epitope: No annotated isoforms; single chain, residues 1–901 (UniProt); Regulation: Interferon-induced expression (UniProt). Evidence: UniProt Q7Z7L1, HPA tissue IHC · Uncertain, HPA ICC-IF · Mainly localized to the nucleoplasm. In addition localized to the…, Datasheet A08259, PMC13008703, PMC13576481. QR code links to https://www.bosterbio.com/bosterbio-gene-info-cards/SLFN11/immunohistochemistry-ihc-guide.