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SMARCE1 / SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily E member 1 · IHC design guide
Design Immunohistochemistry for SMARCE1
Plan SMARCE1 chromogenic IHC around the ubiquitous nuclear tissue pattern (HPA tissue IHC). The catalog antibody has a human paraffin-section range of 2–5 μg/ml (datasheet A03739-2); keep fixation consistent and score nuclear staining by cell type (standard IHC practice).
Evidence assembled Oct 2026 · For research use; verify linked source records and product datasheet before use
SMARCE1 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 | Ubiquitous nuclear staining (HPA tissue IHC) | |
| Staining pattern | Nuclear staining across tissue cell types (HPA tissue IHC) | |
| Antigen retrieval | EDTA pH 8.0 HIER, heat-mediated (datasheet A03739-2) | |
| Positive control | Adrenal gland+4 more · see all | |
| Negative control | None in HPA (detected in all 45 tissues); use no-primary + isotype controls |
Important caveats
Reasons your staining may differ from the expected pattern.
| Fixation | Keep fixation consistent across paraffin sections. (standard IHC practice; not target-specific) | |
| Caveat | Widespread nuclear staining can complicate cell-type scoring (HPA tissue IHC) | |
| Regulation | No staining-intensity regulator specified (UniProt) | |
| Isoform / epitope | Six isoforms; isoform-specific epitope coverage is unknown (UniProt) |
Section 1
Recommended SMARCE1 IHC & IF Protocols
The catalog antibody’s IHC-P protocol (datasheet A03739-2) is followed by published SMARCE1 IHC methods for gastric cancer and clear cell meningioma (PMC10225191; PMC7847462; PMC6498956).
| Sample | Paraffin-embedded human breast cancer tissue; fixative not specified (datasheet A03739-2) |
| Fixation | Image fixative and duration unreported (datasheet A03739-2); 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 A03739-2); 20 min, 95–100 °C (standard) |
| Peroxidase block | 3% H2O2, 10 min, room temperature (standard) |
| Blocking | 10% goat serum (datasheet A03739-2) |
| Primary antibody | Rabbit anti-SMARCE1, 2-5 μg/ml (datasheet A03739-2) |
| Primary incubation | Overnight at 4 °C (datasheet A03739-2) |
| Detection | HRP-conjugated secondary, DAB chromogen (datasheet A03739-2) |
| Counterstain | Hematoxylin, blue, dehydrate and mount (standard) |
| Expected result | SMARCE1-positive staining in glandular cells of adrenal gland (HPA tissue IHC: High). HPA tissue profile: Ubiquitous nuclear expression. No signal in the no-primary control. |
💡Decision noteStart with heat-mediated EDTA pH 8.0 retrieval (datasheet A03739-2); sodium citrate pH 6.0 is a published alternative for gastric cancer sections (PMC6498956).
Section 2
What Is the Expected SMARCE1 Staining Pattern?
SMARCE1 is a nuclear SWI/SNF chromatin-remodeling protein with no transmembrane segment (UniProt Q969G3). Expect staining in nuclei across many cell populations: HPA describes ubiquitous nuclear expression and low tissue RNA specificity (HPA tissue IHC). Its tissue IHC profile is rated Supported, with high consistency between antibody staining and RNA expression (HPA tissue IHC).
| Distinct nuclear staining appears in glandular cells of breast or appendix, respiratory epithelial cells of bronchus, or hematopoietic cells of bone marrow (HPA tissue IHC: High). | This fits the reported broad nuclear pattern (HPA tissue IHC: ubiquitous nuclear expression). Judge the signal by its nuclear location and contrast with local background; a High HPA rating describes reported staining, not a required intensity for every section or run (HPA tissue IHC). |
| Brown chromogen is mainly cytoplasmic or outlines cell membranes while nuclei are pale (UniProt Q969G3: Nucleus; HPA ICC-IF: nucleoplasm). | This conflicts with the supported compartment. Check morphology and counterstain first, then compare a known-positive section and a no-primary control under the same detection conditions (general IHC practice). HPA does not establish a specific cause for cytoplasmic signal (HPA tissue IHC). |
| Strong color is confined to an unexpected cell population while nuclei in a reported High population remain blank (HPA tissue IHC: listed High cell populations). | Consider cross-reactivity or endogenous detection activity, especially if the signal persists without primary antibody (general IHC practice). Do not reject a cell type solely because it is absent from HPA's examples: the overall profile is ubiquitous, and no negative cell population is supplied (HPA tissue IHC). |
| Diffuse color covers nuclei and surrounding tissue with little nuclear contrast (UniProt Q969G3: Nucleus; HPA tissue IHC: ubiquitous nuclear expression). | The distribution is hard to score as SMARCE1 even if some nuclei look brown. Review the no-primary control, blocking and detection steps, and primary-antibody concentration as general IHC checks; the supplied sources do not identify a SMARCE1-specific background mechanism (general IHC practice). |
| Nuclei show no signal in bone marrow hematopoietic cells or cerebellar granular-layer cells reported as High (HPA tissue IHC: High). | Treat this as a failed or inconclusive run until section integrity and assay controls are checked (general IHC practice). A blank field alone does not establish true SMARCE1 absence; HPA reports ubiquitous nuclear expression and provides no negative tissue comparator (HPA tissue IHC). |
💡Expected SMARCE1 appearanceCall a positive when cell nuclei show clear chromogenic staining above local background in reported High populations, such as breast glandular cells or bone marrow hematopoietic cells (HPA tissue IHC: High; HPA tissue IHC: ubiquitous nuclear expression); dominant cytoplasmic or membrane color is discordant (UniProt Q969G3: Nucleus; HPA ICC-IF: nucleoplasm).
| Compartment and topology (UniProt Q969G3: Nucleus; no transmembrane segment). | Score nuclear signal within intact cells. The nucleoplasmic location is independently supported by ICC-IF images (HPA ICC-IF: Nucleoplasm, supported). A membrane-dominant pattern needs investigation rather than a positive call (UniProt Q969G3; HPA ICC-IF). |
| Breadth of expression (HPA tissue IHC: ubiquitous nuclear expression; low tissue RNA specificity). | High staining is reported in glandular, respiratory epithelial, hematopoietic, glial and cerebellar granular-layer cells (HPA tissue IHC: High). The supplied profile lists no negative or Low tissue, so it cannot define a reliable negative-tissue control (HPA tissue IHC). |
| Antibody evidence (HPA antibodies: HPA003916 IHC Supported; CAB037318 IHC Supported). | These labels support IHC use for the listed antibodies, but do not by themselves establish that every nuclear signal is specific in a new run (HPA antibodies: IHC Supported). Compare observed localization with the tissue profile and run controls (general IHC practice). |
| Isoforms and epitope information (UniProt Q969G3: six isoforms). | The record lists isoforms 1–6 but supplies no antibody epitope or isoform coverage (UniProt Q969G3; HPA antibodies). Do not attribute different staining across cells to a particular isoform without additional evidence. |
| Situation | Likely cause | Next action |
|---|---|---|
| Reported High tissue is blank in the test and positive-control sections (HPA tissue IHC: High). | The run may have failed; a blank known-positive section does not identify whether retrieval, antibody binding or detection is responsible (general IHC practice). | Check section integrity, antigen retrieval, primary-antibody and detection steps with the assay controls (general IHC practice). Reassess nuclear staining before scoring tissue negative (HPA tissue IHC: ubiquitous nuclear expression). |
| Signal is mainly cytoplasmic or membrane-associated (UniProt Q969G3: Nucleus; HPA ICC-IF: nucleoplasm). | The location conflicts with both source profiles; its specific cause is unresolved by the supplied evidence (UniProt Q969G3; HPA ICC-IF). | Compare with a reported High section and a no-primary control; confirm nuclei with the counterstain (HPA tissue IHC: High; general IHC practice). |
| Unexpected cells stain strongly while expected nuclei do not (HPA tissue IHC: ubiquitous nuclear expression). | Cross-reactivity or endogenous detection activity is possible, but HPA provides no negative cell-type list that could settle specificity (HPA tissue IHC; general IHC practice). | Inspect the no-primary control and compare nuclear localization in reported High cells; keep the result inconclusive if controls do not resolve it (HPA tissue IHC: High; general IHC practice). |
| Diffuse background obscures nuclear borders (UniProt Q969G3: Nucleus). | Background from blocking, antibody concentration or detection can reduce contrast; no SMARCE1-specific background mechanism is supplied (general IHC practice). | Check the no-primary control and review blocking, washing, primary-antibody concentration and detection conditions (general IHC practice). |
| Only scattered nuclei stain in a tissue expected to show broad expression (HPA tissue IHC: ubiquitous nuclear expression). | Uneven staining may reflect section or assay variation; the HPA profile alone cannot assign a cause to patchiness (HPA tissue IHC; general IHC practice). | Compare nearby intact cells and the positive-control section, then check whether retrieval and reagent coverage were even across the slide (general IHC practice). |
| IF/ICC shows a different compartment from IHC (HPA ICC-IF: Nucleoplasm, supported; HPA tissue IHC: ubiquitous nuclear expression). | The source profiles agree on nuclear localization; the discrepancy needs assay-specific review rather than an assumed biological relocalization (HPA ICC-IF; HPA tissue IHC). | Assess each assay's controls and nuclear counterstain separately. For IF/ICC interpretation, use its dedicated guide (general IHC/IF practice). |
Experiment evidence
IHC & IF images showing SMARCE1 staining
A03739-2 · IHCIHC analysis of BAF57/SMARCE1 using anti-BAF57/SMARCE1 antibody (A03739-2). BAF57/SMARCE1 was detected in a paraffin-embedded section of hum
A03739-2 · IHCIHC analysis of BAF57/SMARCE1 using anti-BAF57/SMARCE1 antibody (A03739-2). BAF57/SMARCE1 was detected in a paraffin-embedded section of hum
A03739-2 · IFIF analysis of BAF57/SMARCE1 using anti-BAF57/SMARCE1 antibody (A03739-2). BAF57/SMARCE1 was detected in an immunocytochemical section of U2
HPA · Cerebral cortexHuman Protein Atlas IHC, Cerebral cortex. Source: https://www.proteinatlas.org/ENSG00000073584-SMARCE1/tissue/cerebral+cortex#imid_9723788
HPA · ColonHuman Protein Atlas IHC, Colon. Source: https://www.proteinatlas.org/ENSG00000073584-SMARCE1/tissue/colon#imid_9723722
HPA · LiverHuman Protein Atlas IHC, Liver. Source: https://www.proteinatlas.org/ENSG00000073584-SMARCE1/tissue/liver#imid_9723707
HPA · KidneyHuman Protein Atlas IHC, Kidney. Source: https://www.proteinatlas.org/ENSG00000073584-SMARCE1/tissue/kidney#imid_9723716
HPA · ICC-IF A-431Human Protein Atlas immunofluorescence, A-431, antibody HPA003916; green = SMARCE1, blue = nucleus, red = microtubules.
HPA · ICC-IF A-431Human Protein Atlas immunofluorescence, A-431, antibody HPA003916; green = SMARCE1, blue = nucleus, red = microtubules.
← swipe / scroll for more images →
Real IHC / IF data behind the staining-pattern expectations in this section.
Sample controls for SMARCE1 IHC & IF
🧪Run breast first and look for nuclear staining in glandular cells (HPA: High in breast glandular cells; UniProt Q969G3: Nucleus). HPA detects SMARCE1 in all 45 scored tissues, so there is no supported negative tissue; use no-primary and isotype controls, and treat cells without nuclear staining on the positive slide as background references rather than validated internal negatives (HPA: no negative tissue rows; UniProt Q969G3: Nucleus).
Positive control tissue: Adrenal gland (Glandular cells, HPA High)
Negative control tissue: None in HPA: SMARCE1 is detected in all 45 scored tissues. Use a no-primary (secondary-only) and an isotype control instead.
ICC-IF cell lines (HPA subcellular resource): HPA ICC-IF images show SMARCE1 in A-431, U-251MG, U2OS, KOLF2.1J, with annotated localisation: Nucleoplasm (supported) (HPA subcellular).
Technical controls: Run a secondary-only slide without primary antibody and a slide with host-matched nonimmune rabbit IgG; confirm specificity with a SMARCE1 knockout sample processed alongside the test sample (selected IHC caption: rabbit primary antibody; standard IHC controls). For chromogenic breast sections, block endogenous peroxidase and check for DAB background (selected IHC caption: breast tissue and HRP–DAB detection; standard IHC practice).
⚠️Feasibility: No target-specific fixation window or fixation effect is reported in the supplied evidence, and the selected A03739-2 paraffin-section caption does not state the fixative (selected IHC caption: fixative unreported). The documented IHC procedure uses heat-mediated retrieval in EDTA at pH 8.0; this supports starting with that condition but does not establish a retrieval requirement across specimens (selected IHC caption: EDTA retrieval at pH 8.0). The supplied evidence does not establish whether frozen sections or IF are easier, and it reports no breast-specific artefact; assess peroxidase background on the breast control slide (selected IHC caption: breast tissue and HRP–DAB detection; standard IHC practice).
HPA tissue IHC evidence for SMARCE1
Comprehensive Human Protein Atlas IHC scoring per tissue (reliability: Supported — High 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 |
|---|---|---|---|---|
| Adrenal gland | Glandular cells | High | Protein (IHC) | HPA → |
| Appendix | Glandular cells | High | Protein (IHC) | HPA → |
| Bone marrow | Hematopoietic cells | High | Protein (IHC) | HPA → |
| Breast | Glandular cells | High | Protein (IHC) | HPA → |
| Bronchus | Respiratory epithelial cells | High | Protein (IHC) | HPA → |
Undetected expression · recommended negative controls
| Tissue | Cell type | Level | Evidence | Source |
|---|---|---|---|---|
| None in HPA: SMARCE1 is detected in all 45 scored tissues. Use a no-primary (secondary-only) and an isotype control instead. | ||||
Section 3
Advanced SMARCE1 IHC Tips
Troubleshoot SMARCE1 staining in paraffin sections by checking retrieval, nuclear localisation and cell-level controls before comparing chromogenic signal.
How should I troubleshoot weak SMARCE1 staining after antigen retrieval?
Start with heat-mediated retrieval in EDTA at pH 8.0 for paraffin sections (datasheet A03739-2). The selected tissue-IHC example used that retrieval before applying 2 μg/ml catalog antibody overnight at 4°C (datasheet A03739-2). If nuclear staining is weak, compare sections from the same block while changing only retrieval duration or heat exposure, and inspect morphology for damage (standard IHC practice). Use a known positive section alongside each run: SMARCE1 is nuclear (UniProt Q969G3: nucleus), and glandular cells in breast show high staining (HPA: High in breast glandular cells). Record the retrieval conditions for each section before changing antibody concentration.
Could fixation explain variable SMARCE1 staining between paraffin blocks?
Target-specific fixation sensitivity is unknown: the selected paraffin-section caption does not state a fixative (datasheet A03739-2: fixative not stated). Record each block’s fixative and fixation interval, then compare blocks processed with the same retrieval, antibody concentration and detection run (standard IHC practice). Assess nuclear detail and tissue integrity before treating a weak signal as loss of SMARCE1; its expected compartment is the nucleus (UniProt Q969G3: nucleus). Include a positive section in each run and compare like cell populations, since breast glandular cells show high staining in the reference tissue profile (HPA: High in breast glandular cells).
What should I check when SMARCE1 staining looks predominantly cytoplasmic?
Treat a predominantly cytoplasmic DAB pattern as a reason to investigate staining specificity, because SMARCE1 is nuclear (UniProt Q969G3: nucleus) and the supported subcellular location is nucleoplasm (HPA: Nucleoplasm supported). Check the counterstain at high magnification to distinguish nuclear signal from pigment overlying adjacent cytoplasm (standard IHC practice). Compare the pattern with a no-primary control and a positive section processed in the same run, then review peroxidase blocking and washing if diffuse colour persists (standard IHC practice). SMARCE1 has no annotated transmembrane segment, so a crisp membrane pattern also warrants scrutiny (UniProt Q969G3: topology).
How could SMARCE1 isoforms or epitope changes affect IHC results?
SMARCE1 has 6 annotated isoforms, so check the antibody’s stated epitope against the isoform sequences before interpreting discordant sections (UniProt Q969G3: isoforms 1–6). The supplied product caption establishes paraffin-section staining conditions but does not identify an epitope or demonstrate isoform-specific recognition (datasheet A03739-2). Document whether the proposed epitope includes an annotated modified residue, including methylarginine at positions 4 or 40, or phosphoserine at 265 (UniProt Q969G3: modified residues). Those annotations alone do not establish an effect on antibody binding; test any suspected epitope effect with a reagent whose recognition region is documented.
How should I investigate SMARCE1 localisation by IF alongside this IHC guide?
Use the chromogenic IHC pattern as a compartment reference: SMARCE1 is nuclear (UniProt Q969G3: nucleus), with supported nucleoplasmic localisation (HPA: Nucleoplasm supported). For a separate IF/ICC experiment, pair SMARCE1 with a validated marker of the expected cell population, such as a glandular-cell marker when examining breast glandular cells (HPA: High in breast glandular cells). Inspect an unstained specimen’s autofluorescence before choosing spectrally separated fluorophores, and include single-colour controls when multiplexing (standard IF practice). Because SMARCE1 has no transmembrane segment and the expected signal is nuclear, assess permeabilisation for access to the nuclear epitope (UniProt Q969G3: topology; HPA: Nucleoplasm supported).
How can I reduce diffuse or granular background in SMARCE1 IHC?
The selected paraffin-section example used 10% goat serum blocking, 2 μg/ml primary antibody overnight at 4°C, a peroxidase-conjugated secondary, and DAB detection (datasheet A03739-2). Reproduce those stated conditions first, then change one variable at a time while comparing tissue sections from the same block (standard IHC practice). Include a no-primary control to reveal secondary or detection background, and check peroxidase blocking when DAB appears outside nuclei (standard IHC practice). Evaluate whether colour follows tissue edges, folds or damaged areas rather than nuclei, the expected SMARCE1 compartment (UniProt Q969G3: nucleus).
How should I quantify SMARCE1 staining across paraffin sections? ⚠ ANSWER MARKED FOR VERIFICATION
Score nuclear staining within a prespecified cell population, because SMARCE1 is nuclear (UniProt Q969G3: nucleus) and the tissue profile describes ubiquitous nuclear expression (HPA: tissue IHC profile). Report the percentage of positive nuclei and, when intensity grades are reproducible, an H-score calculated from the proportion of cells at each intensity (standard IHC practice). Normalize counts to the total evaluable nuclei in that population, or report positive nuclei per mm² of evaluable tissue when density is the question (standard IHC practice). Exclude folds, necrotic regions and edge artefacts consistently, and keep staining and image-analysis settings matched across sections.
How can I distinguish true SMARCE1 signal from IHC artefact?
A convincing result places DAB signal in intact nuclei, consistent with SMARCE1’s nuclear annotation (UniProt Q969G3: nucleus) and supported nucleoplasmic localisation (HPA: Nucleoplasm supported). Compare cells in the same tissue compartment with a positive section; glandular cells in breast show high staining in the reference profile (HPA: High in breast glandular cells). Reconsider isolated cytoplasmic colour, staining concentrated at section edges, or signal within necrotic areas, and check a no-primary control for detection background (standard IHC practice). If colour persists without primary antibody, review endogenous peroxidase blocking before assigning it to SMARCE1 (standard IHC practice).
Boster reagents
Best SMARCE1 / SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily E member 1 IHC Antibodies
A03739-2 has IHC images of human breast and lung cancer paraffin sections (catalog IHC captions) and an IF image of U20S cells (catalog IF caption).
Real IHC data
Anti-BAF57/SMARCE1 Antibody ®
Cat # A03739-2
A03739-2 is the only SKU with a card here; its IHC images show human breast and lung cancer paraffin sections (catalog IHC captions). Its IF image shows U20S cells (catalog IF caption).
Which to pick: Choose A03739-2 for tissue IHC: its own captions document human paraffin sections, and the fixative is unreported (catalog IHC captions). For IF/ICC, A03739-2 has an IF image in U20S cells (catalog IF caption); M03739-1 is a rabbit monoclonal, clone 20S59, listed for ICC/IF without a supplied image (catalog clone, applications, image alts). For cross-species work, A03739-2 lists human, monkey, mouse and rat reactivity, while M03739-1 lists human, mouse and rat (catalog reactivity); the supplied IHC/IF images show human samples only (catalog image alts).
Each figure is that product's own IHC / IF validation image from its datasheet.
References
- UniProt Consortium. UniProt entry Q969G3 (SMCE1_HUMAN, SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily E member 1).
- Human Protein Atlas. SMARCE1 tissue IHC expression (reliability: Supported).
- Human Protein Atlas. SMARCE1 subcellular location (ICC-IF): Localized to the nucleoplasm..
- Human Protein Atlas. SMARCE1 antibody validation summary (2 antibodies).
- SMARCA4 and SMARCE1 in gastric cancer: Correlation with ARID1A, and microsatellite stability, and SMARCE1/ERBB2 co-amplification. Cancer medicine 2023 — PMC10225191.
- Clear cell meningiomas are defined by a highly distinct DNA methylation profile and mutations in SMARCE1. Acta neuropathologica 2021 — PMC7847462.
- High expression of SMARCE1 predicts poor prognosis and promotes cell growth and metastasis in gastric cancer. Cancer management and research 2019 — PMC6498956.
- Is location more determining than WHO grade for long-term clinical outcome in patients with meningioma in the first two decades of life?. Wiener klinische Wochenschrift 2025 — PMC11739186.
- PubMed PMID:9435219 — UniProt-cited evidence.
- PubMed PMID:14702039 — UniProt-cited evidence.
- PubMed PMID:16625196 — UniProt-cited evidence.
Immunohistochemistry protocol sheet for SMARCE1 (SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily E member 1). Expected localisation Ubiquitous nuclear staining (HPA tissue IHC). Antigen retrieval: EDTA pH 8.0 HIER, heat-mediated (datasheet A03739-2). Validated IHC antibody: A03739-2 at 2-5 μg/ml (the product's own IHC validation image is shown). Controls (HPA): positive Adrenal gland (Glandular cells); negative None in HPA (detected in all 45 tissues); use no-primary + isotype controls. IHC-P workflow on paraffin sections; fixative unspecified. Protocol steps: 1. Sample: Paraffin-embedded human breast cancer tissue; fixative not specified (datasheet A03739-2); 2. Fixation: Image fixative and duration unreported (datasheet A03739-2); 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 A03739-2); 20 min, 95–100 °C (standard); 6. Peroxidase block: 3% H2O2, 10 min , room temperature (standard); 7. Blocking: 10% goat serum (datasheet A03739-2); 8. Primary antibody: Rabbit anti-SMARCE1, 2-5 μg/ml (datasheet A03739-2); 9. Primary incubation: Overnight at 4 °C (datasheet A03739-2). Watch for: Fixation: Keep fixation consistent across paraffin sections. (standard IHC practice; not target-specific); Caveat: Widespread nuclear staining can complicate cell-type scoring (HPA tissue IHC); Isoform / epitope: Six isoforms; isoform-specific epitope coverage is unknown (UniProt); Regulation: No staining-intensity regulator specified (UniProt). Evidence: UniProt Q969G3, HPA tissue IHC · Supported, HPA ICC-IF · nucleoplasm., Datasheet A03739-2, PMC10225191, PMC7847462. QR code links to https://www.bosterbio.com/bosterbio-gene-info-cards/SMARCE1/immunohistochemistry-ihc-guide.