This website uses cookies to ensure you get the best experience on our website.
- Table of Contents
SMARCAL1 / SNF2 related chromatin remodeling annealing helicase 1 · IHC design guide
Design Immunohistochemistry for SMARCAL1
Plan chromogenic paraffin-section IHC for SMARCAL1 using the IHC-validated antibody (datasheet A03383-2). Assess nuclear staining across tissue sections while accounting for the uncertain tissue staining profile (HPA tissue IHC).
Evidence assembled Oct 2026 · For research use; verify linked source records and product datasheet before use
SMARCAL1 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 in several tissue types (HPA tissue IHC) | |
| Staining pattern | Nuclear signal across several tissue types (HPA tissue IHC) | |
| Antigen retrieval | EDTA pH 8.0 HIER, heat-mediated (datasheet A03383-2) | |
| Positive control | Epididymis+4 more · see all | |
| Negative control | Adipose tissue+4 more · see all |
Important caveats
Reasons your staining may differ from the expected pattern.
| Fixation | Keep paraffin-section fixation consistent across samples. (standard IHC practice; not target-specific) | |
| Caveat | Staining has low consistency with RNA expression (HPA tissue IHC) | |
| Regulation | Higher expression in testis (UniProt) | |
| Isoform / epitope | No annotated isoforms; chain spans aa 2–954 (UniProt) |
Section 1
Recommended SMARCAL1 IHC & IF Protocols
The catalog antibody’s IHC-P protocol (datasheet A03383-2) is accompanied by published mouse tumor, lung adenocarcinoma, and SIOD autopsy-tissue protocols (PMC12499461; PMC12764740; PMC3568709).
| Sample | Paraffin-embedded human thyroid cancer tissue; fixative not specified (datasheet A03383-2) |
| Fixation | Image fixative and duration unreported (datasheet A03383-2); 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 A03383-2); 20 min, 95–100 °C (standard) |
| Peroxidase block | 3% H2O2, 10 min, room temperature (standard) |
| Blocking | 10% goat serum (datasheet A03383-2) |
| Primary antibody | Rabbit anti-SMARCAL1, 2-5 μg/ml (datasheet A03383-2) |
| Primary incubation | Overnight at 4 °C (datasheet A03383-2) |
| Detection | HRP-conjugated secondary, DAB chromogen (datasheet A03383-2) |
| Counterstain | Hematoxylin, blue, dehydrate and mount (standard) |
| Expected result | SMARCAL1-positive staining in glandular cells of epididymis (HPA tissue IHC: Medium). HPA tissue profile: Nuclear expression in several different tissue types. No signal in the no-primary control. |
💡Decision noteStart with heat-mediated EDTA pH 8.0 for the catalog antibody (datasheet A03383-2). The SIOD protocol reports citrate pH 6 or Tris-EDTA pH 9 (PMC3568709).
Section 2
What Is the Expected SMARCAL1 Staining Pattern?
SMARCAL1 is a nuclear protein with no transmembrane segment (UniProt Q9NZC9: location and topology). In paraffin sections, expect staining chiefly in nuclei of epithelial or glandular cells in tissues where HPA reports medium staining (HPA: tissue IHC). Treat that pattern as provisional: HPA rates its tissue staining Uncertain because antibody staining and RNA expression show low consistency (HPA: tissue IHC reliability).
| Nuclear chromogen in epithelial or glandular cells, with little surrounding stain. | This fits SMARCAL1 localisation (UniProt Q9NZC9: nucleus). HPA reports medium staining in esophageal squamous epithelium and epididymal glandular cells, among other tissues (HPA: tissue IHC). Matching location and cell type supports interpretation, subject to HPA's Uncertain reliability rating (HPA: tissue IHC). |
| Predominantly cytoplasmic, membranous, or extracellular staining. | Treat a compartment that dominates over nuclear staining as suspicious: SMARCAL1 is nuclear and has no transmembrane segment (UniProt Q9NZC9: location and topology). Review morphology, counterstain, and detection controls before assigning it to SMARCAL1 (general IHC practice). |
| Strong stain in a cell population recorded as not detected by HPA. | For example, HPA records adipocytes in adipose tissue as not detected (HPA: tissue IHC). Check whether the stain follows the expected nuclear pattern, then assess cross-reactivity or endogenous detection activity (general IHC practice). An HPA negative call is provisional because tissue IHC reliability is Uncertain (HPA: tissue IHC). |
| Diffuse chromogen obscures nuclei across the section. | A field-wide haze cannot establish the reported nuclear pattern (HPA: tissue IHC; UniProt Q9NZC9: nucleus). Compare with a no-primary control and inspect blocking, washes, and chromogen development for background from the detection workflow (general IHC practice). |
| No nuclear signal in an HPA medium-staining tissue. | First confirm that interpretable cells are present and that the detection run worked (general IHC practice). HPA reports medium staining in selected tissues, including skin keratinocytes, but rates the tissue pattern Uncertain (HPA: tissue IHC); absence in one section alone does not establish biological loss. |
💡Expected SMARCAL1 appearanceCall the result consistent with SMARCAL1 when epithelial or glandular nuclei show discernible, approximately medium staining in an HPA medium-staining tissue; dominant cytoplasmic stain or uniform haze is suspect (HPA: tissue IHC, Uncertain; UniProt Q9NZC9: nucleus).
| Nuclear localisation | UniProt places SMARCAL1 in the nucleus, and HPA reports nuclear tissue expression (UniProt Q9NZC9: location; HPA: tissue IHC). Score nuclear signal in the relevant cells; staining elsewhere needs independent support. |
| Tissue and cell selection | HPA reports medium staining in epididymal glandular cells, esophageal squamous cells, and skin keratinocytes, while several listed populations are not detected (HPA: tissue IHC). Use the named cell population when comparing sections; whole-tissue labels can obscure that distinction. |
| Strength of tissue evidence | The tissue IHC profile is Uncertain because antibody staining and RNA expression have low consistency; RNA has low tissue specificity (HPA: tissue IHC). Treat positive and negative tissue examples as observations to check, rather than definitive assay controls. |
| Antibody validation | HPA lists HPA020337 as Uncertain for IHC and Supported for ICC (HPA: antibody validation). Those application-specific ratings warrant separate interpretation; ICC support does not upgrade confidence in paraffin-section IHC. |
| Damage-associated redistribution | SMARCAL1 can be recruited to damaged DNA regions through interaction with RPA2 (UniProt Q9NZC9: location and subunit). The supplied tissue IHC record does not describe a damage-specific staining pattern (HPA: tissue IHC); do not require visible nuclear foci in routine sections. |
| Target-specific fixation sensitivity | No target-specific fixation effect is established by the supplied UniProt or HPA records. If retrieval is adjusted, judge it with section controls and nuclear localisation as a general IHC optimisation step (general IHC practice). |
| Situation | Likely cause | Next action |
|---|---|---|
| No signal in an HPA medium-staining reference tissue. | A detection or section problem is possible (general IHC practice); HPA's medium call is also provisional because tissue IHC reliability is Uncertain (HPA: tissue IHC). | Check tissue preservation and the run's detection control, then compare a second HPA-listed medium-staining cell population if available (general IHC practice; HPA: tissue IHC). Do not infer loss from one section. |
| Cytoplasm or cell borders stain more strongly than nuclei. | That distribution conflicts with the nuclear location and lack of a transmembrane segment (UniProt Q9NZC9: location and topology). | Confirm cell boundaries against the counterstain and compare a no-primary control; reassess antibody specificity if the pattern persists (general IHC practice). |
| A supposedly negative tissue shows staining. | Cross-reactivity or endogenous detection activity may contribute (general IHC practice); HPA's not-detected calls carry Uncertain reliability (HPA: tissue IHC). | Identify the stained cell type and compartment, then use appropriate detection controls (general IHC practice). Report the observation without treating the HPA negative call as an absolute exclusion. |
| Uniform brown background hides nuclear detail. | Incomplete blocking or washing, or excessive chromogen development, can raise background (general IHC practice). This pattern does not resolve the reported nuclear localisation (HPA: tissue IHC). | Compare the no-primary control, review blocking and washes, and adjust development according to the detection system (general IHC practice). Score only nuclei that remain distinguishable. |
| Scattered dark nuclei appear beside mostly faint cells. | HPA reports medium staining only for specified cell populations and rates the profile Uncertain (HPA: tissue IHC); uneven background or section quality can also complicate scoring (general IHC practice). | Score the named cell population separately, inspect morphology and the no-primary control, and record the fraction and intensity of interpretable nuclei (general IHC practice). |
| Q: Should an ICC/IF nucleoplasmic image determine the IHC result? | HPA supports nucleoplasmic ICC/IF localisation but rates tissue IHC Uncertain and HPA020337 IHC Uncertain (HPA: subcellular and antibody validation). | A: Use the ICC/IF result as a compartment check only; interpret paraffin-section staining against the tissue IHC observations and controls (HPA: subcellular and tissue IHC; general IHC practice). |
Experiment evidence
IHC & IF images showing SMARCAL1 staining
A03383-2 · IHCIHC analysis of SMARCAL1 using anti-SMARCAL1 antibody (A03383-2). SMARCAL1 was detected in a paraffin-embedded section of human thyroid canc
A03383-2 · IHCIHC analysis of SMARCAL1 using anti-SMARCAL1 antibody (A03383-2). SMARCAL1 was detected in a paraffin-embedded section of human thyroid canc
HPA · Cerebral cortexHuman Protein Atlas IHC, Cerebral cortex. Source: https://www.proteinatlas.org/ENSG00000138375-SMARCAL1/tissue/cerebral+cortex#imid_13405907
HPA · ColonHuman Protein Atlas IHC, Colon. Source: https://www.proteinatlas.org/ENSG00000138375-SMARCAL1/tissue/colon#imid_13405833
HPA · LiverHuman Protein Atlas IHC, Liver. Source: https://www.proteinatlas.org/ENSG00000138375-SMARCAL1/tissue/liver#imid_13405818
HPA · KidneyHuman Protein Atlas IHC, Kidney. Source: https://www.proteinatlas.org/ENSG00000138375-SMARCAL1/tissue/kidney#imid_13405827
HPA · ICC-IF HDLM-2Human Protein Atlas immunofluorescence, HDLM-2, antibody HPA020337; green = SMARCAL1, blue = nucleus, red = microtubules.
HPA · ICC-IF HDLM-2Human Protein Atlas immunofluorescence, HDLM-2, antibody HPA020337; green = SMARCAL1, blue = nucleus, red = microtubules.
← swipe / scroll for more images →
Real IHC / IF data behind the staining-pattern expectations in this section.
Sample controls for SMARCAL1 IHC & IF
🧪Run epididymis first and expect nuclear staining in glandular cells (HPA: Medium in epididymis glandular cells; UniProt Q9NZC9: nucleus). Run adipose tissue as the negative comparator, where adipocytes are listed as not detected; on the epididymis slide, use non-glandular cells as internal negative comparators only if they lack nuclear signal (HPA: Not detected in adipose tissue adipocytes; HPA: Medium in epididymis glandular cells).
Positive control tissue: Epididymis (Glandular cells, HPA Medium)
Negative control tissue: Adipose tissue (HPA Not detected)
ICC-IF cell lines (HPA subcellular resource): HPA ICC-IF images show SMARCAL1 in HDLM-2, HEK293, U2OS, with annotated localisation: Nucleoplasm (supported) (HPA subcellular).
Technical controls: Include a no-primary, secondary-only control; a rabbit IgG control matched to the primary antibody’s class; and SMARCAL1-knockout material processed in parallel as a biological negative (caption: rabbit primary antibody; standard IHC practice). Block endogenous peroxidase and check for background in epididymis before interpreting DAB staining (caption: HRP/DAB detection; standard IHC practice).
⚠️Feasibility: No target-specific fixation window or fixation effect is reported, and the selected A03383-2 paraffin-section caption does not state the fixative (selected-SKU caption: fixative unreported). The caption uses heat retrieval in EDTA at pH 8.0, but it does not establish that retrieval is required; the supplied evidence does not establish whether frozen sections or IF are easier (selected-SKU caption: EDTA retrieval; HPA: ICC-IF nucleoplasmic localization). In epididymis, distinguish glandular nuclear staining from luminal or diffuse background when scoring (HPA: Medium in epididymis glandular cells; UniProt Q9NZC9: nucleus; standard IHC practice).
HPA tissue IHC evidence for SMARCAL1
Comprehensive Human Protein Atlas IHC scoring per tissue (reliability: Uncertain — Low 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 |
|---|---|---|---|---|
| Epididymis | Glandular cells | Medium | Protein (IHC) | HPA → |
| Esophagus | Squamous epithelial cells | Medium | Protein (IHC) | HPA → |
| Nasopharynx | Respiratory epithelial cells | Medium | Protein (IHC) | HPA → |
| Oral mucosa | Squamous epithelial cells | Medium | Protein (IHC) | HPA → |
| Rectum | Glandular cells | Medium | 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 → |
| Bone marrow | Hematopoietic cells | Not detected | Protein (IHC) | HPA → |
| Breast | Adipocytes | Not detected | Protein (IHC) | HPA → |
| Caudate | Glial cells | Not detected | Protein (IHC) | HPA → |
Section 3
Advanced SMARCAL1 IHC Tips
Troubleshoot SMARCAL1 staining by checking retrieval, nuclear localisation, background controls and scoring before interpreting differences between samples.
How should I troubleshoot weak SMARCAL1 staining after antigen retrieval?
Start with heat-mediated retrieval in EDTA pH 8.0 for this paraffin-section IHC assay (datasheet A03383-2). The selected image used 2 μg/ml primary antibody overnight at 4°C, so compare retrieval changes while holding antibody exposure constant (datasheet A03383-2; standard IHC practice). Include a previously stained positive section in each run to distinguish retrieval failure from a low-expressing specimen (standard IHC practice). If staining remains weak, test retrieval heating time on adjacent sections and watch for tissue damage or increased background (standard IHC practice). Score nuclear signal, since SMARCAL1 is nuclear (UniProt Q9NZC9 localisation).
Can I infer the best fixative for SMARCAL1 from the published staining image?
The selected SMARCAL1 image identifies a paraffin-embedded section but does not state its fixative, so target-specific fixation sensitivity is unknown (datasheet A03383-2 caption). Record the fixative and fixation duration for every specimen, then compare sections processed together when staining differs (standard IHC practice). On test sections, keep EDTA pH 8.0 retrieval and the 2 μg/ml antibody condition constant while assessing fixation-related variation (datasheet A03383-2; standard IHC practice). Examine morphology alongside nuclear staining, since damaged or poorly preserved nuclei make localisation difficult to assess (UniProt Q9NZC9 localisation; standard IHC practice). Do not assign a target-specific fixation effect without a direct comparison (standard IHC practice).
What staining pattern should count as SMARCAL1 localisation in tissue?
Prioritise staining within intact nuclei: SMARCAL1 is nuclear, and independent cell imaging supports a nucleoplasmic location (UniProt Q9NZC9 localisation; HPA subcellular). Compare the chromogenic signal with the nuclear counterstain at high magnification, keeping the EDTA pH 8.0 retrieval condition consistent across sections (datasheet A03383-2; standard IHC practice). Its recruitment to damaged DNA regions does not make every dark nuclear focus a damage site in an unstained tissue section (UniProt Q9NZC9 localisation; standard IHC interpretation). Diffuse cytoplasmic colour should prompt checks of background and morphology before it is scored as SMARCAL1 (UniProt Q9NZC9 localisation; standard IHC practice).
Could an isoform or epitope change explain unexpected SMARCAL1 staining?
The supplied record lists 0 isoforms and places SMARCAL1 in the nucleus without a transmembrane segment (UniProt Q9NZC9 isoforms and topology). It also lists phosphorylation at residues 112, 123, 129 and 151, but the antibody epitope is unspecified, so a modification-sensitive staining effect cannot be assigned (UniProt Q9NZC9 modified residues; datasheet A03383-2). If nuclear staining changes, compare adjacent sections using the stated EDTA pH 8.0 retrieval and fixed detection conditions first (datasheet A03383-2; standard IHC practice). An antigen competition or independent-antibody control can help test specificity if a suitable validated reagent is available (standard IHC practice).
How can IF help investigate an ambiguous SMARCAL1 IHC pattern?
Use IF as a separate validation experiment and compare SMARCAL1 with a marker that identifies the expected cell population in the specimen (standard IF practice). Nuclear or nucleoplasmic colocalisation is the expected compartment, and SMARCAL1 has no transmembrane segment; use controlled permeabilisation to access its intracellular epitope (UniProt Q9NZC9 localisation and topology; HPA subcellular; standard IF practice). Choose spectrally separated fluorophores and inspect unstained tissue in each channel to avoid mistaking autofluorescence for a multiplex signal (standard IF practice). The selected EDTA pH 8.0 retrieval and 2 μg/ml antibody exposure document paraffin-section chromogenic IHC, so establish IF conditions independently (datasheet A03383-2).
What should I check when SMARCAL1 IHC shows widespread brown background?
Run a no-primary control to assess secondary-reagent or detection background, and check whether brown pigment persists without antibody (standard IHC practice). The selected image used 10% goat-serum blocking, a peroxidase-conjugated secondary and DAB chromogen, so replicate those steps consistently during troubleshooting (datasheet A03383-2). Apply a peroxidase block and adjust DAB development when endogenous enzyme activity or overdevelopment obscures nuclei (standard chromogenic IHC practice). Compare background in tissue edges, damaged areas and intact central regions before changing the 2 μg/ml primary-antibody condition (datasheet A03383-2; standard IHC practice). A convincing target pattern should remain predominantly nuclear (UniProt Q9NZC9 localisation).
How should I score SMARCAL1 across sections with different cellular composition? ⚠ ANSWER MARKED FOR VERIFICATION
Define the cell population and score only evaluable, intact nuclei, since SMARCAL1 is nuclear and tissue composition can vary between fields (UniProt Q9NZC9 localisation; standard IHC practice). Report the percentage of positive nuclei and an intensity-based H-score from 0–300, using the same thresholds for every section (standard IHC scoring practice). Normalise positive counts to the number of nuclei in the specified cell population, or report positive-cell density per mm² of viable tissue (standard IHC quantification practice). Keep retrieval at EDTA pH 8.0 and imaging or scoring settings consistent, and exclude necrotic or folded areas (datasheet A03383-2; standard IHC practice).
When is apparent SMARCAL1 positivity likely to be an artefact?
Treat staining outside intact nuclei cautiously because SMARCAL1 is nuclear and supported as nucleoplasmic in cell imaging (UniProt Q9NZC9 localisation; HPA subcellular). Check whether positive cells match the population being scored; HPA reports nuclear expression in several tissues but rates its tissue-IHC reliability Uncertain (HPA tissue IHC). Signal concentrated at section edges, folds or necrotic regions warrants comparison with intact tissue and a no-primary control (standard IHC practice). Persistent brown colour in that control can indicate endogenous peroxidase or detection background with DAB (standard chromogenic IHC practice). Confirm a disputed pattern with independent specificity evidence before assigning biological meaning (standard IHC practice).
Boster reagents
Best SMARCAL1 / SNF2 related chromatin remodeling annealing helicase 1 IHC Antibodies
A03383-2 has real IHC images from paraffin sections of human thyroid cancer and mouse brain; no IF/ICC data are supplied (catalog: A03383-2 image captions and applications).
Real IHC data
Anti-SMARCAL1 Antibody ®
Cat # A03383-2
A03383-2 was shown in IHC on paraffin sections of human thyroid cancer and mouse brain (A03383-2 IHC captions). Its listed reactivity includes human, mouse, and rat, while its IHC dilution entry specifies human and mouse (catalog: A03383-2 reactivity and dilution).
Which to pick: Choose A03383-2 for paraffin-section IHC: its captions document EDTA retrieval at pH 8.0 and a 2 μg/ml primary antibody concentration; the fixative is unreported (A03383-2 IHC captions). No IF/ICC-validated SKU is supplied, and A03383-2 has no reported clone (catalog: A03383-2 applications, IF images, and clone). For cross-species IHC, A03383-2 has human and mouse image evidence; rat is listed as reactive but has no IHC image or IHC-specific dilution in this payload (catalog: A03383-2 images, reactivity, and dilution).
Each figure is that product's own IHC / IF validation image from its datasheet.
References
- UniProt Consortium. UniProt entry Q9NZC9 (SMAL1_HUMAN, SNF2 related chromatin remodeling annealing helicase 1).
- Human Protein Atlas. SMARCAL1 tissue IHC expression (reliability: Uncertain).
- Human Protein Atlas. SMARCAL1 subcellular location (ICC-IF): Localized to the nucleoplasm..
- Human Protein Atlas. SMARCAL1 antibody validation summary (1 antibodies).
- Advanced Cancer Immunotherapy via SMARCAL1 Blockade Using a Glucose-Responsive CRISPR Nanovaccine. Advanced science (Weinheim, Baden-Wurttemberg, Germany) 2025 — PMC12499461.
- Identifying and validating SMARCAL1 as a prognostic and immunotherapy predictive biomarker for NSCLC. Discover oncology 2025 — PMC12764740.
- Reduced elastogenesis: a clue to the arteriosclerosis and emphysematous changes in Schimke immuno-osseous dysplasia?. Orphanet journal of rare diseases 2012 — PMC3568709.
- Pan-cancer analysis reveals SMARCAL1 expression is associated with immune cell infiltration and poor prognosis in various cancers. Scientific reports 2025 — PMC11850860.
- PubMed PMID:10857751 — UniProt-cited evidence.
- PubMed PMID:11799392 — UniProt-cited evidence.
- PubMed PMID:15815621 — UniProt-cited evidence.
Immunohistochemistry protocol sheet for SMARCAL1 (SNF2 related chromatin remodeling annealing helicase 1). Expected localisation Nuclear staining in several tissue types (HPA tissue IHC). Antigen retrieval: EDTA pH 8.0 HIER, heat-mediated (datasheet A03383-2). Validated IHC antibody: A03383-2 at 2-5 μg/ml (the product's own IHC validation image is shown). Controls (HPA): positive Epididymis (Glandular cells); negative Adipose tissue. IHC-P workflow on paraffin sections; fixative unspecified. Protocol steps: 1. Sample: Paraffin-embedded human thyroid cancer tissue; fixative not specified (datasheet A03383-2); 2. Fixation: Image fixative and duration unreported (datasheet A03383-2); 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 A03383-2); 20 min, 95–100 °C (standard); 6. Peroxidase block: 3% H2O2, 10 min , room temperature (standard); 7. Blocking: 10% goat serum (datasheet A03383-2); 8. Primary antibody: Rabbit anti-SMARCAL1, 2-5 μg/ml (datasheet A03383-2); 9. Primary incubation: Overnight at 4 °C (datasheet A03383-2). Watch for: Fixation: Keep paraffin-section fixation consistent across samples. (standard IHC practice; not target-specific); Caveat: Staining has low consistency with RNA expression (HPA tissue IHC); Isoform / epitope: No annotated isoforms; chain spans aa 2–954 (UniProt); Regulation: Higher expression in testis (UniProt). Evidence: UniProt Q9NZC9, HPA tissue IHC · Uncertain, HPA ICC-IF · nucleoplasm., Datasheet A03383-2, PMC12499461, PMC12764740. QR code links to https://www.bosterbio.com/bosterbio-gene-info-cards/SMARCAL1/immunohistochemistry-ihc-guide.