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SATB2 / DNA-binding protein SATB2 · IHC design guide
Design Immunohistochemistry for SATB2
Plan chromogenic SATB2 IHC in paraffin sections using nuclear staining as the readout (HPA tissue IHC). Colon or rectum endocrine cells and cortical neurons provide positive tissue references; adipocytes provide a negative cell reference (HPA tissue IHC).
Evidence assembled Oct 2026 · For research use; verify linked source records and product datasheet before use
SATB2 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 | Selective nuclear staining in intestine and brain (HPA tissue IHC) | |
| Staining pattern | Nuclear staining in intestinal endocrine cells and neuronal subsets (HPA tissue IHC) | |
| Antigen retrieval | Tris-EDTA pH 9.0 HIER, 95–98 °C, 20 min (rule: nuclear antigen) | |
| Positive control | Appendix+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 fixation consistent across paraffin sections. (standard IHC practice; not target-specific) | |
| Caveat | Intestinal staining is selective for endocrine cells (HPA tissue IHC) | |
| Regulation | Expression varies across brain regions (UniProt) | |
| Isoform / epitope | 2 isoforms; epitope coverage is unspecified (UniProt) |
Section 1
Recommended SATB2 IHC & IF Protocols
The catalog antibody protocol is paired with two published chromogenic IHC protocols for SATB2 in odontogenic tumors and sarcomas (PMC13535953; PMC5106294).
| Sample | Paraffin-embedded human stomach cancer tissue; fixative not specified (datasheet M02588) |
| Fixation | Image fixative and duration unreported (datasheet M02588); verify before use. |
| Sectioning | 4–5 µm sections on charged slides (standard) |
| Deparaffinisation | Xylene, graded ethanol series to water (standard) |
| Antigen retrieval | Heat-induced epitope retrieval in Tris-EDTA buffer, pH 9.0, 20 min at 95–98 °C (standard rule: nuclear antigen) |
| Peroxidase block | 3% H2O2, 10 min, room temperature (standard) |
| Blocking | 10% normal serum of the secondary host, 30 min, room temperature (standard) |
| Primary antibody | Rabbit monoclonal (clone ADI-19) anti-SATB2, 1:50 (datasheet M02588) |
| Primary incubation | Overnight at 4 °C (standard) |
| Detection | HRP-polymer secondary, DAB chromogen 5–10 min (standard) |
| Counterstain | Hematoxylin, blue, dehydrate and mount (standard) |
| Expected result | SATB2-positive staining in endocrine cells of appendix (HPA tissue IHC: High). HPA tissue profile: Selective nuclear expression in large intestine and subsets of neuronal cells in brain. No signal in the no-primary control. |
💡Decision noteStart with Tris-EDTA pH 9.0 at 95–98 °C for 20 min for nuclear SATB2 (page retrieval setting; UniProt: nucleus matrix). An ER2 retrieval protocol is also published (PMC5106294).
Section 2
What Is the Expected SATB2 Staining Pattern?
SATB2 is a nuclear matrix protein with no transmembrane segment (UniProt Q9UPW6 topology and subcellular location). In paraffin-section IHC, expect selective nuclear staining in large-intestine endocrine cells and subsets of brain neurons (HPA: tissue IHC profile). HPA rates the tissue pattern Enhanced, citing high consistency between antibody staining and RNA expression (HPA: tissue IHC reliability). Interpret signal by both its compartment and the identity of stained cells.
| Distinct nuclear staining in colon or rectum endocrine cells, or cerebral-cortex neuronal cells. | This matches HPA's High staining annotations for those cell and tissue pairs (HPA: tissue IHC). A positive result need not label every cell: the reported pattern is selective (HPA: tissue IHC profile). |
| Predominantly cytoplasmic staining with little or no nuclear signal in an expected positive population. | Treat this as a compartment mismatch requiring investigation: SATB2 is assigned to the nuclear matrix (UniProt Q9UPW6), while HPA reports selective nuclear tissue staining (HPA: tissue IHC). Cytoplasmic color alone does not establish a true SATB2-positive cell. |
| Strong staining across cell types outside the annotated positive population in colon or cerebral cortex. | Check for antibody cross-reactivity or endogenous chromogenic detection activity (general IHC practice). HPA assigns High staining specifically to colon endocrine cells and cerebral-cortex neuronal cells (HPA: tissue IHC); its annotations are a comparison, not an exhaustive cell atlas. |
| Diffuse color across nuclei, cytoplasm, and surrounding tissue, with poor cell boundaries. | The distribution is difficult to score against HPA's selective nuclear pattern (HPA: tissue IHC profile). Review blocking, wash conditions, chromogen development, and detection controls as general IHC troubleshooting steps. |
| No nuclear staining in a run that includes colon endocrine cells or cerebral-cortex neuronal cells. | Both are annotated High by HPA (HPA: tissue IHC), so an entirely negative known-positive control raises concern about assay performance. Check tissue preservation, primary-antibody handling, retrieval, and detection using general IHC practice; HPA supplies no SATB2-specific fixation effect. |
💡Expected SATB2 appearanceCall a slide positive when discrete nuclear signal marks the appropriate endocrine or neuronal cells at the annotated High level (HPA: colon, rectum, cerebral cortex); isolated cytoplasmic or widespread off-pattern color warrants investigation (UniProt Q9UPW6 subcellular location; HPA: tissue IHC profile).
| Compartment | SATB2 is assigned to the nuclear matrix and has no transmembrane segment (UniProt Q9UPW6). Score nuclear staining first; broad membrane staining conflicts with that topology and with HPA's selective nuclear IHC profile (HPA: tissue IHC). |
| Tissue and cell selection | Appendix, colon, and rectum endocrine cells and cerebral-cortex neurons are High; small-intestine endocrine cells and testis pachytene spermatocytes are Medium (HPA: tissue IHC). Compare like cell types when judging intensity, because a whole-section average can obscure selective staining. |
| Low and undetected comparators | HPA reports Low neuronal staining in hippocampus and caudate, Low signal in kidney proximal tubules, and Not detected staining in adipocytes of adipose tissue (HPA: tissue IHC). A low-signal tissue is a weaker run control than an annotated High population. |
| Evidence strength | HPA labels tissue IHC reliability Enhanced and lists multiple antibodies with Enhanced IHC validation (HPA: tissue IHC; HPA: antibody validation). This supports the reported pattern but does not validate every new antibody, retrieval condition, or interpretation of an atypical cell. |
| Protein forms and retrieval | UniProt lists two isoforms, a 1–733 SATB2 chain, and phosphorylation sites (UniProt Q9UPW6). These records do not specify the catalog antibody's epitope or isoform coverage. Antigen retrieval may be optimized as general paraffin-IHC practice; no SATB2-specific fixation or retrieval effect is supplied. |
| IF/ICC Q&A: where should signal appear? | Mainly in the nucleoplasm (HPA: ICC-IF, supported). HPA also lists cytosol, centrosome, and basal body as uncertain additional locations (HPA: ICC-IF). Those uncertain observations do not override the nuclear expectation for tissue IHC (HPA: tissue IHC profile). |
| Situation | Likely cause | Next action |
|---|---|---|
| Known-positive tissue is entirely blank. | A failed staining step is possible when annotated High cells show no signal (HPA: colon endocrine cells; HPA: cerebral-cortex neuronal cells). The supplied sources do not identify a SATB2-specific fixation cause. | Confirm that the expected cells are present, then review the primary antibody, retrieval setup, detection reagents, and a run control in that order (general IHC practice). Do not infer target absence from a failed positive control. |
| Signal appears weak in hippocampus or caudate. | HPA records Low staining in neuronal cells at both sites (HPA: tissue IHC). Weak signal there can fit the reference pattern and is less decisive than absence from a High reference population. | Assess nuclear localization and compare with a High annotated population, such as cerebral-cortex neuronal cells, on a suitable control (HPA: tissue IHC; general IHC practice). |
| A chromogenic slide shows mainly cytoplasmic or membranous color. | That distribution disagrees with SATB2's nuclear matrix assignment and HPA's selective nuclear tissue pattern (UniProt Q9UPW6; HPA: tissue IHC). Background or nonspecific detection is possible (general IHC practice). | Check nuclear counterstain alignment, examine a negative reagent control, and review primary-antibody dilution and washes (general IHC practice). Base the SATB2 call on convincing nuclear signal. |
| Many unexpected cells stain strongly within an otherwise plausible tissue. | HPA's High calls specify particular endocrine or neuronal cells (HPA: tissue IHC). Cross-reactivity or endogenous detection activity can create extra signal (general IHC practice); an HPA annotation alone cannot identify its cause. | Map stained cells against morphology, run an appropriate primary-antibody omission control, and assess the detection system's endogenous activity controls (general IHC practice). |
| Diffuse background obscures selective nuclear staining. | Excess background can mask the expected cell-restricted pattern (HPA: tissue IHC profile). Inadequate blocking or washing, excessive antibody concentration, and prolonged chromogen development are general IHC possibilities. | Inspect controls and adjust blocking, washes, primary-antibody concentration, or chromogen development one variable at a time (general IHC practice). Reassess whether signal resolves to nuclei in the annotated cells. |
| An HPA Not detected comparator appears strongly positive. | Strong staining in adipose-tissue adipocytes or bone-marrow hematopoietic cells conflicts with their HPA Not detected annotations (HPA: tissue IHC). HPA annotations are reference observations, not proof that every sample must be negative. | Verify cell identity and control performance, then investigate nonspecific staining and endogenous detection activity (general IHC practice). Report the discrepancy instead of converting it into a new expected SATB2 pattern. |
Experiment evidence
IHC & IF images showing SATB2 staining
M02588 · IHCImmunohistochemical analysis of paraffin-embedded human stomach cancer, using SATB2 Antibody.
M02588 · IHCImmunohistochemical analysis of paraffin-embedded Human testis cancer, using the Antibody at 1:100 dilution.
M02588 · IFImmunofluorescent analysis of SH-SY5Y cells, using SATB2 Antibody .
A02588 · IFImmunofluorescence of SATB2 in Human Brain cells with SATB2 antibody at 20 μg/mL.
HPA · Cerebral cortexHuman Protein Atlas IHC, Cerebral cortex. Source: https://www.proteinatlas.org/ENSG00000119042-SATB2/tissue/cerebral+cortex#imid_18793810
HPA · ColonHuman Protein Atlas IHC, Colon. Source: https://www.proteinatlas.org/ENSG00000119042-SATB2/tissue/colon#imid_18793736
HPA · RectumHuman Protein Atlas IHC, Rectum. Source: https://www.proteinatlas.org/ENSG00000119042-SATB2/tissue/rectum#imid_18793696
HPA · LiverHuman Protein Atlas IHC, Liver. Source: https://www.proteinatlas.org/ENSG00000119042-SATB2/tissue/liver#imid_18793729
HPA · ICC-IF A-431Human Protein Atlas immunofluorescence, A-431, antibody HPA001042; green = SATB2, blue = nucleus, red = microtubules.
HPA · ICC-IF A-431Human Protein Atlas immunofluorescence, A-431, antibody HPA001042; green = SATB2, blue = nucleus, red = microtubules.
← swipe / scroll for more images →
Real IHC / IF data behind the staining-pattern expectations in this section.
Sample controls for SATB2 IHC & IF
🧪Run colon first: endocrine cells should show strong nuclear staining (HPA: High in colon endocrine cells; UniProt: nuclear matrix localization). Use adipose tissue as the negative tissue; adipocytes are expected to lack staining (HPA: Not detected in adipocytes). On the colon slide, compare endocrine nuclei with adjacent non-endocrine cells, which should lack comparable nuclear signal (HPA: High is assigned to endocrine cells).
Positive control tissue: Appendix (Endocrine cells, HPA High)
Negative control tissue: Adipose tissue (HPA Not detected)
ICC-IF cell lines (HPA subcellular resource): HPA ICC-IF images show SATB2 in A-431, U-251MG, U2OS, RPTEC/TERT1, hTERT-RPE1 (serum starved), KOLF2.1J, with annotated localisation: Nucleoplasm (supported) (HPA subcellular).
Technical controls: Include a no-primary control, a secondary-only control, and an isotype control matched to the primary antibody’s host species and clonality; use SATB2 knockout material or an immunizing-peptide block, if available, as a biological specificity control (standard IHC practice). For colon, quench endogenous peroxidase and check for endogenous biotin if using avidin–biotin detection (standard IHC practice).
⚠️Feasibility: A target-specific fixation window and the effect of antigen retrieval are unreported in the supplied evidence; optimize retrieval empirically for the paraffin IHC assay (supplied target/application evidence; standard IHC practice). The selected M02588 caption shows paraffin-section stomach cancer IHC but does not report the fixative (selected-SKU tissue-IHC caption). Whether frozen sections or IF are easier is unreported; endogenous biotin may complicate avidin–biotin detection in colon (supplied target/application evidence; standard IHC practice).
HPA tissue IHC evidence for SATB2
Comprehensive Human Protein Atlas IHC scoring per tissue (reliability: Enhanced — 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 |
|---|---|---|---|---|
| Appendix | Endocrine cells | High | Protein (IHC) | HPA → |
| Cerebral cortex | Neuronal cells | High | Protein (IHC) | HPA → |
| Colon | Endocrine cells | High | Protein (IHC) | HPA → |
| Rectum | Endocrine cells | High | Protein (IHC) | HPA → |
| Small intestine | Endocrine 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 → |
| Bronchus | Respiratory epithelial cells | Not detected | Protein (IHC) | HPA → |
Section 3
Advanced SATB2 IHC Tips
Troubleshoot SATB2 staining by checking nuclear localisation, cell type and matched controls before changing the chromogenic IHC workflow (UniProt: nuclear matrix; HPA: selective nuclear expression).
How should I troubleshoot weak SATB2 staining after antigen retrieval?
Use Tris-EDTA pH 9.0 HIER at 95–98 °C for 20 min (page retrieval setting: nuclear antigen). Check a known positive section alongside the test section: SATB2 shows selective nuclear staining in large intestine and subsets of brain neurons (HPA: tissue IHC). If both sections are weak, confirm that the bath reached the specified temperature and that sections remained immersed for the full time (standard IHC practice). If staining remains weak, compare a second retrieval condition on matched sections while holding antibody and detection conditions constant (standard IHC practice). Judge improvement by nuclear signal and tissue preservation together (UniProt: nuclear matrix; standard IHC practice).
Could fixation explain weak or uneven SATB2 staining?
Target-specific sensitivity of SATB2 to fixation is unknown from the supplied evidence; the catalog image identifies paraffin-embedded human stomach cancer but does not state its fixative (M02588 caption). Record the specimen's actual fixative and fixation interval before comparing staining across cases (standard IHC practice). On matched sections, keep thickness, retrieval and chromogenic detection constant while assessing whether staining varies with the documented processing history (standard IHC practice). Include a positive tissue section in each run to distinguish a specimen-specific failure from a run-wide failure (HPA: selective nuclear expression in large intestine; standard IHC practice). Do not assign a SATB2-specific fixation effect without a controlled comparison (standard IHC practice).
Where should convincing SATB2 signal appear in a paraffin section?
Score crisp nuclear staining as the primary SATB2 pattern: the protein associates with the nuclear matrix, and tissue IHC shows selective nuclear expression (UniProt: subcellular location; HPA: tissue IHC). Nucleoplasmic localisation is also supported by cell imaging, while reported cytosolic, centrosomal and basal-body locations are uncertain (HPA: subcellular). Compare suspected positive cells with neighboring cells in the same section and with a known positive control (standard IHC practice). Diffuse cytoplasmic chromogen without a matching nuclear pattern warrants checks of primary-antibody concentration, washing and detection background before biological interpretation (UniProt: nuclear matrix; standard IHC practice). Use morphology to identify the stained cell population (standard IHC practice).
Could isoforms or epitope accessibility change the SATB2 IHC pattern?
SATB2 has 2 listed isoforms, but the supplied evidence does not map the catalog antibody's epitope or establish isoform-specific IHC staining (UniProt: isoforms; supplied antibody evidence). Interpret a missing nuclear signal cautiously if the epitope location is unknown (UniProt: nuclear matrix; standard IHC practice). The record lists phosphorylation at residues 20, 39, 454, 467 and 594; it does not show that these modifications affect this antibody (UniProt: modified residues; supplied antibody evidence). Compare retrieval conditions on adjacent sections and use the same antibody lot and detection conditions when investigating epitope access (standard IHC practice). Avoid calling an isoform difference from chromogenic staining alone (standard IHC practice).
How can I follow up a SATB2 IHC result with multiplex IF?
Treat IF as a separate assay requiring its own antibody validation and controls; the supplied catalog caption documents paraffin-section IHC, not IF performance (M02588 caption). Pair SATB2 with a validated marker of the expected cell population, such as neuronal cells in cerebral cortex, and confirm that the SATB2 channel remains nuclear (HPA: cerebral cortex neuronal cells; UniProt: nuclear matrix). Choose spectrally separated fluorophores and place the weaker signal in a channel with less tissue autofluorescence, checking unstained tissue first (standard IF practice). Because SATB2 has no transmembrane segment and is nuclear, optimise permeabilisation for access to an intracellular epitope after fixation (UniProt: topology and subcellular location; standard IF practice).
What should I check when SATB2 chromogen appears throughout the section?
First compare the pattern with a section processed without primary antibody to assess secondary-reagent and detection background (standard IHC practice). For peroxidase-based chromogenic detection, verify the endogenous peroxidase block and inspect areas that retain chromogen in the control (standard IHC practice). If the control is clean, titrate the primary antibody and review blocking and wash conditions while retaining a known positive section (standard IHC practice; HPA: selective nuclear expression in large intestine). SATB2 interpretation depends on nuclear staining in appropriate cells, so widespread diffuse cytoplasmic colour is suspect (UniProt: nuclear matrix; HPA: tissue IHC). Compare section edges with the interior for uneven staining (standard IHC practice).
How should I quantify SATB2 nuclear staining across cases? ⚠ ANSWER MARKED FOR VERIFICATION
Define the cell population and analysis region before scoring, then report the percentage of eligible cells with nuclear SATB2 signal (UniProt: nuclear matrix; standard IHC practice). If intensity matters, use a nuclear H-score from 0 to 300, recording the percentage at each intensity level (standard IHC practice). For spatial comparisons, report positive-cell density per mm² of viable annotated tissue and state the counting method (standard IHC practice). Normalise positive counts to all evaluable nuclei of the same cell population, and exclude necrosis, folds and section edges consistently (standard IHC practice). Keep retrieval and detection conditions consistent across cases (standard IHC practice).
How do I distinguish true SATB2 positivity from an IHC artefact?
A persuasive positive result is nuclear and occurs in an appropriate cell population; tissue IHC reports selective nuclear expression in large intestine and subsets of brain neurons (HPA: tissue IHC). Compare the test section with a positive control and a section processed without primary antibody in the same run (standard IHC practice). Question colour confined to section edges, folds or necrotic areas, or colour that persists in the no-primary control (standard IHC practice). Diffuse cytoplasmic staining alone conflicts with the principal nuclear localisation, although cell imaging reports uncertain additional cytosolic localisation (UniProt: nuclear matrix; HPA: subcellular). Check endogenous enzyme background before assigning biological meaning to chromogen deposits (standard IHC practice).
Boster reagents
Best SATB2 / DNA-binding protein SATB2 IHC Antibodies
The catalog lists SATB2 antibodies reactive with human, mouse and rat samples (catalog: M02588, A02588). The figures show paraffin-section IHC and human brain cell IF, respectively (image captions: M02588, A02588).
Real IHC data
Anti-SATB2 Rabbit Monoclonal Antibody
Cat # M02588
Real IF data
Anti-DNA-binding protein SATB2 SATB2 Antibody
Cat # A02588
M02588 lists IHC and ICC/IF, with an IHC image of paraffin-embedded human stomach cancer (catalog: applications; image caption: M02588). A02588 lists IHC-P and IF, with an IF image of human brain cells (catalog: applications; image caption: A02588).
Which to pick: For tissue IHC, choose M02588: its own image shows staining in a paraffin-embedded human stomach cancer section; the fixative is unreported (image caption: M02588). For IF/ICC, choose M02588 when ICC is required, or A02588 for the pictured human brain cell IF experiment (catalog: applications; image caption: A02588). Both list human, mouse and rat reactivity; M02588 is a rabbit monoclonal, while A02588 has no clone designation in the catalog (catalog: reactivity, host, clone).
Each figure is that product's own IHC / IF validation image from its datasheet.
References
- UniProt Consortium. UniProt entry Q9UPW6 (SATB2_HUMAN, DNA-binding protein SATB2).
- Human Protein Atlas. SATB2 tissue IHC expression (reliability: Enhanced).
- Human Protein Atlas. SATB2 subcellular location (ICC-IF): Mainly localized to the nucleoplasm. In addition localized to the cytosol, centrosome and basal body..
- Human Protein Atlas. SATB2 antibody validation summary (8 antibodies).
- Special AT-rich sequence binding protein 2 (SATB2), β-catenin, and CD10 immunohistochemistry provides insights into the histopathologic features and cellular differentiation of adenomatoid odontogenic tumor. Journal of dental sciences 2026 — PMC13535953.
- BCOR Overexpression Is a Highly Sensitive Marker in Round Cell Sarcomas With BCOR Genetic Abnormalities. The American journal of surgical pathology 2016 — PMC5106294.
- Effect of Dietary Amino Acids L-Arginine and Lysine on Implant Osseointegration. Journal of pharmacy & bioallied sciences 2022 — PMC9469227.
- Transiently elevated expression of different forms of brain-derived neurotrophic factor in the neonatal medial prefrontal cortex affected anxiety and depressive-like behaviors in adolescence. PeerJ 2024 — PMC11608019.
- PubMed PMID:10470851 — UniProt-cited evidence.
- PubMed PMID:14702039 — UniProt-cited evidence.
- PubMed PMID:15815621 — UniProt-cited evidence.
Immunohistochemistry protocol sheet for SATB2 (DNA-binding protein SATB2). Expected localisation Selective nuclear staining in intestine and brain (HPA tissue IHC). Antigen retrieval: Tris-EDTA pH 9.0 HIER, 95–98 °C, 20 min (rule: nuclear antigen). Validated IHC antibody: M02588 at 1:50 (the product's own IHC validation image is shown). Controls (HPA): positive Appendix (Endocrine cells); negative Adipose tissue. IHC workflow; specimen preparation unspecified. Protocol steps: 1. Sample: Paraffin-embedded human stomach cancer tissue; fixative not specified (datasheet M02588); 2. Fixation: Image fixative and duration unreported (datasheet M02588); verify before use.; 3. Sectioning: 4–5 µm sections on charged slides (standard); 4. Deparaffinisation: Xylene, graded ethanol series to water (standard); 5. Antigen retrieval: Heat-induced epitope retrieval in Tris-EDTA buffer, pH 9.0 , 20 min at 95–98 °C…; 6. Peroxidase block: 3% H2O2, 10 min , room temperature (standard); 7. Blocking: 10% normal serum of the secondary host, 30 min , room temperature (standard); 8. Primary antibody: Rabbit monoclonal (clone ADI-19) anti-SATB2, 1:50 (datasheet M02588); 9. Primary incubation: Overnight at 4 °C (standard). Watch for: Fixation: Keep fixation consistent across paraffin sections. (standard IHC practice; not target-specific); Caveat: Intestinal staining is selective for endocrine cells (HPA tissue IHC); Isoform / epitope: 2 isoforms; epitope coverage is unspecified (UniProt); Regulation: Expression varies across brain regions (UniProt). Evidence: UniProt Q9UPW6, HPA tissue IHC · Enhanced, HPA ICC-IF · Mainly localized to the nucleoplasm. In addition localized to the…, Datasheet M02588, PMC13535953, PMC5106294. QR code links to https://www.bosterbio.com/bosterbio-gene-info-cards/SATB2/immunohistochemistry-ihc-guide.