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ARID1B / AT-rich interactive domain-containing protein 1B · IHC design guide
Design Immunohistochemistry for ARID1B
Plan ARID1B paraffin IHC around mainly nuclear staining (HPA tissue IHC). Cerebral cortex neuronal cells and bone marrow hematopoietic cells show high staining (HPA tissue IHC); start the catalog antibody at 1:100–1:300 (datasheet A02556-1).
Evidence assembled Oct 2026 · For research use; verify linked source records and product datasheet before use
ARID1B 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 | Mainly nuclear staining (HPA tissue IHC) | |
| Staining pattern | Mainly nuclear staining in cells across tissues (HPA tissue IHC) | |
| Antigen retrieval | Tris-EDTA pH 8.0 HIER, heat-mediated (datasheet A02556-1) | |
| Positive control | Bone marrow+4 more · see all | |
| Negative control | None in HPA (detected in all 44 tissues); use no-primary + isotype controls |
Important caveats
Reasons your staining may differ from the expected pattern.
| Fixation | Keep fixation consistent across sections (standard IHC practice; not target-specific) | |
| Caveat | Antibody staining and RNA show medium consistency (HPA tissue IHC) | |
| Regulation | Higher levels in heart, skeletal muscle and kidney (UniProt) | |
| Isoform / epitope | 4 isoforms; epitope coverage needs validation (UniProt) |
Section 1
Recommended ARID1B IHC & IF Protocols
The catalog antibody’s IHC-P protocol is accompanied by 4 published ARID1B protocols (PMC6032401; PMC6396229; PMC8034473; PMC5687163).
| Sample | Paraffin-embedded Human breast cancer tissue; fixative not specified (datasheet A02556-1) |
| Fixation | Image fixative and duration unreported (datasheet A02556-1); verify before use. |
| Sectioning | 4–5 µm sections on charged slides (standard) |
| Deparaffinisation | Xylene, graded ethanol series to water (standard) |
| Antigen retrieval | Heat retrieval: Tris-EDTA pH 8.0 (datasheet A02556-1); 20 min, 95–100 °C (standard) |
| 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 anti-ARID1B, 1:100-1:300 (datasheet A02556-1) |
| 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 | ARID1B-positive staining in hematopoietic cells of bone marrow (HPA tissue IHC: High). HPA tissue profile: Mainly nuclear expression in all tissues. No signal in the no-primary control. |
💡Decision noteStart with heat-mediated Tris-EDTA, pH 8.0 (datasheet A02556-1); two published protocols use sodium citrate retrieval (PMC6032401; PMC6396229).
Section 2
What Is the Expected ARID1B Staining Pattern?
ARID1B is a nuclear, non-transmembrane chromatin regulator (UniProt Q8NFD5: nucleus; no transmembrane segment). In paraffin-section IHC, expect mainly nuclear staining across tissues, including neuronal, epithelial and hematopoietic cells reported as high by HPA (HPA tissue IHC: mainly nuclear; listed high cells). HPA rates its tissue IHC profile Approved, with medium consistency between staining and RNA data (HPA tissue IHC: reliability).
| Distinct nuclear staining in cerebral cortex neuronal cells or bone marrow hematopoietic cells. | This matches the expected compartment and two reported high-staining cell populations (HPA tissue IHC: mainly nuclear; High in cerebral cortex neuronal cells and bone marrow hematopoietic cells). Judge nuclei against neighboring cells on the same section; a high HPA category is a reference pattern, not a fixed intensity cutoff (HPA tissue IHC: reported levels; standard IHC interpretation). |
| Predominantly cytoplasmic or membrane staining, with little nuclear signal. | Treat this as discordant with tissue IHC, then inspect controls and staining conditions for artefact (HPA tissue IHC: mainly nuclear; standard IHC practice). HPA ICC-IF reports uncertain additional cytosol and plasma-membrane localization; that uncertainty does not establish a predominant extranuclear pattern in paraffin-section IHC (HPA subcellular: supported nucleoplasm; additional locations uncertain). |
| Strong chromogen in cells expected to stain weakly, or in areas without a clear cellular pattern. | Compare with the reported cell types before calling the signal specific; liver cholangiocytes and prostate glandular cells are low, not established negatives (HPA tissue IHC: Low in cholangiocytes and prostate glandular cells; negative list empty). Cross-reactivity or endogenous detection activity is possible if the signal fails compartment and control checks (standard IHC practice). |
| Haze or precipitate spreads across nuclei, cytoplasm and cell-free areas. | A diffuse pattern cannot establish ARID1B localization (HPA tissue IHC: mainly nuclear; standard IHC interpretation). Check background on a reagent-control section and inspect blocking, washes and chromogen development as general IHC workflow variables (standard IHC practice); the supplied sources give no ARID1B-specific background mechanism. |
| No nuclear signal in a section containing a reported high-staining population. | First verify that the expected cells are present and assess a known-positive control processed in the same run (HPA tissue IHC: listed High populations; standard IHC practice). Absent staining may reflect an assay failure, but one negative slide does not establish biological absence, especially when HPA reports mainly nuclear expression across tissues (HPA tissue IHC: profile). |
💡Expected ARID1B appearanceCall a result consistent when chromogen is mainly nuclear in the relevant cells, with conspicuous staining in HPA high populations; predominant extranuclear colour or diffuse cell-free deposit is suspect (HPA tissue IHC: profile and High cells; standard IHC interpretation).
| Tissue and cell population | HPA reports High staining in cerebral cortex neuronal cells, bone marrow hematopoietic cells and esophageal squamous epithelial cells, but Low staining in liver cholangiocytes and smooth muscle cells (HPA tissue IHC: cell-level entries). Use those differences to choose comparison fields; Low is not a validated negative control (HPA tissue IHC: negative list empty). |
| Antibody evidence | HPA016511 is Approved for IHC, while the tissue profile is Approved with medium staining–RNA consistency (HPA antibodies: HPA016511 IHC Approved; HPA tissue IHC: reliability). Those ratings support use of the reported pattern as a reference; they do not prove that every coloured cell on a new slide is specific (standard IHC interpretation). |
| Nuclear target and chromogenic readout | ARID1B is nuclear and lacks a transmembrane segment (UniProt Q8NFD5: subcellular location and topology). Assess chromogen in relation to nuclei and a counterstain (standard IHC practice). If colour obscures nuclear boundaries, shorten development or review the detection conditions before scoring localization (standard IHC practice). |
| IF/ICC Q&A | Q: Where should IF/ICC signal localize? A: Mainly the nucleoplasm; HPA supports that location and marks additional plasma-membrane and cytosol locations uncertain (HPA subcellular: location assessments). Its ICC-IF images include A-431, U-251MG, U2OS, RT-4 and KOLF2.1J (HPA subcellular: imaged cell lines). |
| Situation | Likely cause | Next action |
|---|---|---|
| Reported high-staining cells show no nuclear colour. | The cells may be absent from the section, or the IHC run may have failed; neither can be resolved from a blank field alone (HPA tissue IHC: High cell entries; standard IHC practice). | Identify the expected cells on the counterstained section, then review a concurrently processed positive control and reagent steps (standard IHC practice). |
| Signal is strongest outside nuclei. | The pattern conflicts with mainly nuclear tissue IHC; nonspecific detection or a localization artefact is possible (HPA tissue IHC: profile; standard IHC practice). | Compare nuclear and extranuclear colour in reported high-staining cells, and check reagent controls before accepting the pattern (HPA tissue IHC: High cells; standard IHC practice). |
| Weakly reported cells appear as intense as high-staining cells. | The contrast differs from HPA's cell-level observations, although HPA levels are not universal intensity thresholds (HPA tissue IHC: High and Low entries; standard IHC interpretation). | Check compartment, section morphology and control staining; repeat the comparison within the same run before assigning a biological difference (standard IHC practice). |
| Colour appears without a primary antibody. | Primary-independent chromogenic signal can arise from endogenous detection activity or other reagent background (standard IHC practice). | Address the implicated detection or blocking step using the assay's established controls, then reassess the nuclear pattern (standard IHC practice; HPA tissue IHC: mainly nuclear). |
| Diffuse colour makes individual nuclei hard to score. | Excess background or overdevelopment may obscure cellular boundaries (standard IHC practice). | Inspect wash and chromogen-development conditions and compare a reagent-control section; score only interpretable nuclei (standard IHC practice). |
| A section differs from the HPA reference despite acceptable controls. | HPA reports medium consistency between antibody staining and RNA expression, so its tissue profile is a qualified reference (HPA tissue IHC: reliability description). | Record the tissue, cell type, compartment and control results; describe the discrepancy without treating an HPA Low entry as an established negative (HPA tissue IHC: Low entries; negative list empty; standard IHC reporting). |
Experiment evidence
IHC & IF images showing ARID1B staining
A02556-1 · IHCImmunohistochemical analysis of paraffin-embedded Human breast cancer. Antibody was diluted at 1:100 (4° overnight). High-pressure and tempe
A02556-1 · IFImmunofluorescence analysis of HUVEC cells, using BAF250B Antibody. The picture on the right is blocked with the synthesized peptide.
A30528 · IHCImmunohistochemical analysis of paraffin-embedded Human breast cancer. Antibody was diluted at 1:100(4° overnight). High-pressure and temper
A30528 · IFImmunofluorescence analysis of HUVEC cells, using BAF250B Antibody. The picture on the right is blocked with the synthesized peptide.
HPA · Cerebral cortexHuman Protein Atlas IHC, Cerebral cortex. Source: https://www.proteinatlas.org/ENSG00000049618-ARID1B/tissue/cerebral+cortex#imid_4434744
HPA · ColonHuman Protein Atlas IHC, Colon. Source: https://www.proteinatlas.org/ENSG00000049618-ARID1B/tissue/colon#imid_4434686
HPA · LiverHuman Protein Atlas IHC, Liver. Source: https://www.proteinatlas.org/ENSG00000049618-ARID1B/tissue/liver#imid_4434687
HPA · KidneyHuman Protein Atlas IHC, Kidney. Source: https://www.proteinatlas.org/ENSG00000049618-ARID1B/tissue/kidney#imid_4434680
HPA · ICC-IF A-431Human Protein Atlas immunofluorescence, A-431, antibody HPA016511; green = ARID1B, blue = nucleus, red = microtubules.
HPA · ICC-IF A-431Human Protein Atlas immunofluorescence, A-431, antibody HPA016511; green = ARID1B, blue = nucleus, red = microtubules.
← swipe / scroll for more images →
Real IHC / IF data behind the staining-pattern expectations in this section.
Sample controls for ARID1B IHC & IF
🧪Run cerebral cortex first and look for nuclear staining in neuronal cells (HPA: High in cerebral cortex neuronal cells; UniProt Q8NFD5: nucleus). HPA detects ARID1B in all 44 scored tissues, so there is no supported negative tissue; use no-primary and isotype controls, and regard any cells without nuclear chromogen on the positive slide as background comparisons rather than validated negative cells (HPA: no negative tissue rows).
Positive control tissue: Bone marrow (Hematopoietic cells, HPA High)
Negative control tissue: None in HPA: ARID1B is detected in all 44 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 ARID1B in A-431, U-251MG, U2OS, RT-4, KOLF2.1J, with annotated localisation: Nucleoplasm (supported) (HPA subcellular).
Technical controls: Run a no-primary, secondary-only section and an isotype-matched control appropriate to the primary antibody’s host species and clonality; use ARID1B knockout material or a validated immunogen-peptide block as a biological specificity control (standard IHC practice; selected-SKU caption: peptide-block control). For chromogenic cerebral cortex IHC, quench endogenous peroxidase and assess pigment-associated background against the controls (standard IHC practice).
⚠️Feasibility: A target-specific fixation window or fixation effect is unreported in the supplied evidence, and the fixative is unreported in the selected A02556-1 paraffin-section caption (selected-SKU caption). That caption uses high-pressure, high-temperature Tris-EDTA retrieval at pH 8.0; use it as a starting condition, since retrieval dependence in cerebral cortex is unreported (selected-SKU caption). Frozen sections or IF/ICC are not established as easier by the supplied evidence; IF/ICC can help assess nucleoplasmic localisation, while cerebral cortex autofluorescence requires background controls (HPA: supported nucleoplasmic localisation; standard IF practice).
HPA tissue IHC evidence for ARID1B
Comprehensive Human Protein Atlas IHC scoring per tissue (reliability: Approved — Medium consistency between antibody staining and RNA expression data.). Rows are taken directly from the HPA tissue chart — click any row's HPA link to view the source.
Positive expression · recommended positive controls
| Tissue | Cell type | Level | Evidence | Source |
|---|---|---|---|---|
| Bone marrow | Hematopoietic cells | High | Protein (IHC) | HPA → |
| Cerebellum | Cells in molecular layer | High | Protein (IHC) | HPA → |
| Cerebral cortex | Neuronal cells | High | Protein (IHC) | HPA → |
| Epididymis | Glandular cells | High | Protein (IHC) | HPA → |
| Esophagus | Squamous epithelial cells | High | Protein (IHC) | HPA → |
Undetected expression · recommended negative controls
| Tissue | Cell type | Level | Evidence | Source |
|---|---|---|---|---|
| None in HPA: ARID1B is detected in all 44 scored tissues. Use a no-primary (secondary-only) and an isotype control instead. | ||||
Section 3
Advanced ARID1B IHC Tips
Troubleshoot ARID1B chromogenic IHC by checking nuclear localisation, retrieval, controls and scoring; the IF entry addresses multiplex imaging.
How should I adjust retrieval when ARID1B nuclear staining is weak or uneven?
Start with heat-mediated Tris-EDTA antigen retrieval at pH 8.0 for paraffin sections (datasheet A02556-1). The selected product image used high-pressure, high-temperature retrieval with that buffer, followed by antibody at 1:100 overnight at 4°C; use those conditions as a reference while optimising your own run (caption A02556-1). If nuclear signal is weak, compare a modestly longer retrieval with the starting condition on adjacent sections, checking tissue integrity and background at the same time (standard IHC practice). Keep section thickness, detection and imaging consistent across that comparison, and judge improvement by nuclear staining in an appropriate positive control rather than by total chromogen intensity (HPA: mainly nuclear tissue expression; standard IHC practice).
Could fixation explain absent ARID1B staining in paraffin sections?
Target-specific fixation sensitivity is unknown: the selected paraffin-section caption does not state a fixative, so its result cannot establish how ARID1B responds to fixation (caption A02556-1). Record the fixative and fixation duration for each specimen, then compare sections with similar handling before changing antibody concentration or retrieval (standard IHC practice). If a section is weak, inspect morphology and stain a comparably processed positive control alongside it to distinguish a specimen-handling problem from a run-wide failure (standard IHC practice). Interpret any recovery after retrieval adjustment as an observation for that preparation, rather than evidence that a particular fixation condition alters ARID1B antigenicity (standard IHC practice).
What staining pattern should count as ARID1B in chromogenic IHC?
Score predominantly nuclear chromogen: ARID1B is annotated in the nucleus, and tissue IHC shows mainly nuclear expression across tissues (UniProt Q8NFD5: subcellular location; HPA: tissue profile). Nucleoplasmic localisation is supported by cell imaging, whereas reported plasma-membrane and cytosolic locations are uncertain; treat isolated nonnuclear staining cautiously in a chromogenic section (HPA: subcellular localisation). Use a nuclear counterstain to confirm that signal lies within intact nuclei, and compare the pattern with a no-primary control processed through the same detection steps (standard IHC practice). If cytoplasmic or membrane colour dominates, review retrieval, antibody concentration and detection background before assigning it to ARID1B (HPA: subcellular localisation; standard IHC practice).
Can an epitope or isoform difference explain discordant ARID1B IHC results?
ARID1B has 4 listed isoforms, but the supplied product caption does not map the antibody epitope or establish isoform coverage (UniProt Q8NFD5: isoforms; caption A02556-1). The protein contains an ARID domain at residues 1136–1227 and several annotated modified residues, yet those annotations alone cannot predict whether this antibody binds after paraffin processing (UniProt Q8NFD5: domains and modified residues). Check the antibody's documented immunogen and epitope information before interpreting disagreement with another assay, and avoid assigning an IHC difference to a specific isoform without direct evidence (standard IHC practice). Compare nuclear patterns across matched sections and controls while holding retrieval and detection constant, so technical variation does not masquerade as epitope-dependent biology (standard IHC practice).
How can IF help assess a questionable ARID1B IHC pattern?
For a separate IF assessment, multiplex ARID1B with a validated marker of the cell population under study, then check whether ARID1B signal occupies those cells' nuclei (HPA: mainly nuclear tissue expression; standard IF practice). Choose fluorophores after measuring tissue autofluorescence, favouring a spectrally distinct channel for the weaker target signal and including single-label controls to assess bleed-through (standard IF practice). ARID1B has no annotated transmembrane segment and is primarily nuclear, so optimise permeabilisation for access to an intracellular nuclear epitope while monitoring morphology (UniProt Q8NFD5: topology and location; standard IF practice). Use the IF result to investigate compartment and cell identity, and evaluate the chromogenic IHC pattern against its own section controls (standard IHC/IF practice).
How do I reduce diffuse or granular background without losing nuclear ARID1B signal?
Compare the stained section with no-primary and detection-only controls to locate background arising from the detection system (standard IHC practice). For peroxidase-based chromogenic detection, check that the peroxidase block is effective, then optimise protein blocking and washes using adjacent sections (standard IHC practice). The selected image used 1:100 antibody overnight at 4°C; if background is strong, titrate around that starting condition while keeping retrieval and development time constant (caption A02556-1; standard IHC practice). Assess each change by preservation of crisp nuclear signal and reduced extranuclear colour, since tissue expression is mainly nuclear and broad diffuse staining is less informative (HPA: tissue profile; standard IHC practice).
How should I score ARID1B across sections with different cell mixtures? ⚠ ANSWER MARKED FOR VERIFICATION
Define the cell population before scoring, then record the percentage of cells with nuclear staining and nuclear intensity using a consistent threshold across sections (HPA: mainly nuclear tissue expression; standard IHC practice). An H-score can combine intensity categories with the percentage in each category; report the scoring bins and count enough sampled fields to represent the section (standard IHC practice). Normalise to the number of intact nuclei in the specified population, or report positive nuclei per mm² when area-based density answers the study question (standard IHC practice). Keep retrieval, chromogen development and image settings matched, and analyse cell populations separately when their proportions differ between specimens (standard IHC practice).
Which findings argue that an apparent ARID1B-positive IHC result is artefactual?
A convincing result has staining in intact nuclei, consistent with ARID1B's nuclear annotation and the mainly nuclear tissue-IHC profile (UniProt Q8NFD5: subcellular location; HPA: tissue profile). Diffuse cytoplasmic or membrane colour without nuclear signal deserves review because those additional locations have uncertain support in cell imaging (HPA: subcellular localisation). Compare the claimed positive cells with the expected population and matched controls; HPA reports high staining in several populations, including bone-marrow hematopoietic cells and cerebral-cortex neurons, but these are reference observations, not universal controls (HPA: tissue positives; standard IHC practice). Exclude section edges, necrotic regions and deposits that persist in no-primary controls, and investigate endogenous peroxidase signal before calling the staining ARID1B-positive (standard IHC practice).
Boster reagents
Best ARID1B / AT-rich interactive domain-containing protein 1B IHC Antibodies
Two anti-ARID1B antibodies have paraffin-section IHC images from human breast cancer and IF images from HUVEC cells (catalog image captions); both list human and rat reactivity (catalog reactivity).
Real IHC data
Anti-BAF250b ARID1B Antibody
Cat # A02556-1
Real IHC data
Anti-BAF250B ARID1B Antibody
Cat # A30528
A02556-1 lists IHC and IF, with a human breast cancer paraffin-section IHC image and a HUVEC IF image (A02556-1 catalog applications and image captions). A30528 lists IHC, IF and ICC, with its own human breast cancer paraffin-section IHC image and a HUVEC IF image (A30528 catalog applications and image captions).
Which to pick: For tissue IHC, either rabbit polyclonal SKU has its own paraffin-section image using 1:100 antibody dilution and Tris-EDTA retrieval at pH 8.0; the fixative is unreported in both captions (A02556-1 and A30528 catalog records and IHC image captions). For IF/ICC, choose A30528 when ICC is required; both SKUs list IF and show HUVEC IF images, while only A30528 lists ICC (catalog applications and IF image captions). For rat samples, either SKU lists rat reactivity, but both IHC images are from human tissue (catalog reactivity and IHC image captions).
Each figure is that product's own IHC / IF validation image from its datasheet.
References
- UniProt Consortium. UniProt entry Q8NFD5 (ARI1B_HUMAN, AT-rich interactive domain-containing protein 1B).
- Human Protein Atlas. ARID1B tissue IHC expression (reliability: Approved).
- Human Protein Atlas. ARID1B subcellular location (ICC-IF): Mainly localized to the nucleoplasm. In addition localized to the plasma membrane and cytosol..
- Human Protein Atlas. ARID1B antibody validation summary (2 antibodies).
- ARID1B as a Potential Therapeutic Target for ARID1A-Mutant Ovarian Clear Cell Carcinoma. International journal of molecular sciences 2018 — PMC6032401.
- Upregulated expression of AT-rich interactive domain-containing protein 1B predicts poor prognosis in patients with triple-negative breast cancer. Oncology letters 2019 — PMC6396229.
- ARID1B/SUB1-activated lncRNA HOXA-AS2 drives the malignant behaviour of hepatoblastoma through regulation of HOXA3. Journal of cellular and molecular medicine 2021 — PMC8034473.
- Expression of ARID1B Is Associated With Poor Outcomes and Predicts the Benefit from Adjuvant Chemotherapy in Bladder Urothelial Carcinoma. Journal of Cancer 2017 — PMC5687163.
- PubMed PMID:14574404 — UniProt-cited evidence.
- PubMed PMID:9804814 — UniProt-cited evidence.
- PubMed PMID:8896557 — UniProt-cited evidence.
Immunohistochemistry protocol sheet for ARID1B (AT-rich interactive domain-containing protein 1B). Expected localisation Mainly nuclear staining (HPA tissue IHC). Antigen retrieval: Tris-EDTA pH 8.0 HIER, heat-mediated (datasheet A02556-1). Validated IHC antibody: A02556-1 at 1:100-1:300 (the product's own IHC validation image is shown). Controls (HPA): positive Bone marrow (Hematopoietic cells); negative None in HPA (detected in all 44 tissues); use no-primary + isotype controls. IHC workflow; specimen preparation unspecified. Protocol steps: 1. Sample: Paraffin-embedded Human breast cancer tissue; fixative not specified (datasheet A02556-1); 2. Fixation: Image fixative and duration unreported (datasheet A02556-1); 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: Tris-EDTA pH 8.0 (datasheet A02556-1); 20 min, 95–100 °C (standard); 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 anti-ARID1B, 1:100-1:300 (datasheet A02556-1); 9. Primary incubation: Overnight at 4 °C (standard). Watch for: Fixation: Keep fixation consistent across sections (standard IHC practice; not target-specific); Caveat: Antibody staining and RNA show medium consistency (HPA tissue IHC); Isoform / epitope: 4 isoforms; epitope coverage needs validation (UniProt); Regulation: Higher levels in heart, skeletal muscle and kidney (UniProt). Evidence: UniProt Q8NFD5, HPA tissue IHC · Approved, HPA ICC-IF · Mainly localized to the nucleoplasm. In addition localized to the…, Datasheet A02556-1, PMC6032401, PMC6396229. QR code links to https://www.bosterbio.com/bosterbio-gene-info-cards/ARID1B/immunohistochemistry-ihc-guide.