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ATXN1 / Ataxin-1 · IHC design guide
Design Immunohistochemistry for ATXN1
Plan paraffin ATXN1 staining around cytoplasmic and nuclear signal across tissues (HPA tissue IHC). This guide helps select high-staining neuronal or glandular cells and lower-staining comparison cells (HPA tissue IHC).
Evidence assembled Oct 2026 · For research use; verify linked source records and product datasheet before use
ATXN1 Immunohistochemistry Experimental Design Guide
Expected localisation, validated protocols, controls and antibodies — the at-a-glance facts below, then the full design guide.
Must know before staining
| Expected localisation | Cytoplasmic and nuclear staining across tissues (HPA tissue IHC) | |
| Staining pattern | Cytoplasmic and nuclear signal in cells across all tissues (HPA tissue IHC) | |
| Antigen retrieval | EDTA pH 8.0 HIER, heat-mediated (datasheet M01786-1) | |
| Positive control | Appendix+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 | Staining and RNA show medium consistency (HPA tissue IHC) | |
| Regulation | Widely expressed throughout the body (UniProt) | |
| Isoform / epitope | One isoform with a full-length chain (UniProt) |
Section 1
Recommended ATXN1 IHC & IF Protocols
The catalog antibody’s IHC-P protocol (datasheet M01786-1) is followed by two published ATXN1 IHC methods (PMC2722686; PMC5706899).
| Sample | Paraffin-embedded human hepatocellular carcinoma tissue; fixative not specified (datasheet M01786-1) |
| Fixation | Image fixative and duration unreported (datasheet M01786-1); verify before use. |
| Sectioning | 4–5 µm sections on charged slides (standard) |
| Deparaffinisation | Xylene, graded ethanol series to water (standard) |
| Antigen retrieval | Heat retrieval: EDTA pH 8.0 (datasheet M01786-1); 20 min, 95–100 °C (standard) |
| Peroxidase block | 3% H2O2, 10 min, room temperature (standard) |
| Blocking | 10% goat serum (datasheet M01786-1) |
| Primary antibody | Mouse monoclonal (clone 2B13G8) anti-ATXN1, 2 μg/ml (datasheet M01786-1) |
| Primary incubation | Overnight at 4 °C (datasheet M01786-1) |
| Detection | HRP-conjugated secondary, DAB chromogen (datasheet M01786-1) |
| Counterstain | Hematoxylin, blue, dehydrate and mount (standard) |
| Expected result | ATXN1-positive staining in glandular cells of appendix (HPA tissue IHC: High). HPA tissue profile: Cytoplasmic and nuclear expression in all tissues. No signal in the no-primary control. |
💡Decision noteStart with heat-mediated EDTA pH 8.0 retrieval for the catalog antibody (datasheet M01786-1); the cervical tissue study reports heating without specifying a buffer (PMC5706899).
Section 2
What Is the Expected ATXN1 Staining Pattern?
ATXN1 is observed in the cytoplasm and nuclei across tissues (HPA: tissue IHC profile), with the nucleoplasm the main ICC-IF location (HPA: supported). Expect staining in glandular, respiratory epithelial, and selected neuronal cells (HPA: High in listed tissues). The tissue IHC antibody is Approved, with medium consistency against RNA data (HPA: reliability). ATXN1 has no transmembrane segment (UniProt P54253 topology).
| Nuclear and cytoplasmic staining in colon glandular cells. | Fits the reported distribution and a High reference cell population (HPA: tissue IHC; High in colon glandular cells). Judge the pattern within cells, alongside section controls. |
| Strong, sharply outlined cell-surface staining with little nuclear or cytoplasmic signal. | An isolated surface pattern is unexpected: ATXN1 has no transmembrane segment (UniProt P54253 topology), and HPA reports nuclear and cytoplasmic staining (HPA: tissue IHC). Check specificity. |
| Signal is strongest in a cell population rated Low while the expected cells are unstained. | This conflicts with the reference pattern; consider cross-reactivity or endogenous detection activity before interpreting it as ATXN1 (HPA: tissue IHC levels; standard IHC practice). |
| Diffuse color covers tissue and empty areas without clear cell boundaries. | Treat it as background rather than a positive ATXN1 pattern (standard IHC practice). Review blocking, washing, and detection controls; HPA localization cannot validate diffuse signal (HPA: tissue IHC). |
| No staining in a section containing colon glandular cells. | Those cells are rated High (HPA: colon glandular cells). First check the run and tissue preservation; an absent signal alone does not establish absent ATXN1. |
💡Expected ATXN1 appearanceCall positive when identifiable cells show nuclear and cytoplasmic staining, especially in HPA High reference populations; isolated surface staining or diffuse color is suspect (HPA: tissue IHC; UniProt P54253 topology).
| Reference cell populations | Appendix, breast, cervix, and colon glandular cells; bronchial respiratory epithelial cells; and caudate and cortical neurons are rated High (HPA: tissue IHC). Use the cell type, not the whole tissue, as the comparison. |
| Compartment and antibody evidence | HPA reports cytoplasmic and nuclear tissue staining, but the IHC antibody is Approved with medium RNA agreement, not Enhanced (HPA: tissue IHC; HPA: HPA008335 IHC Approved). Interpret unexpected patterns with controls. |
| Protein features | ATXN1 is a 1–815 chain with one listed isoform and no signal peptide or transmembrane segment (UniProt P54253). The supplied sources give no epitope or target-specific fixation-sensitivity result. |
| IF/ICC Q&A: Where should signal appear? | Mainly in nucleoplasm, with supported nucleolar and cytosolic localization in ICC-IF (HPA: subcellular). This supports a localization cross-check; HPA070756 has Supported ICC status (HPA: antibodies). |
| Situation | Likely cause | Next action |
|---|---|---|
| Known High reference cells show no chromogenic signal. | A failed staining run or unsuitable section is possible; HPA reports High staining in colon glandular cells (HPA: tissue IHC). | Confirm tissue identity and morphology, then review the run's positive control, antibody incubation, detection, and retrieval settings (standard IHC practice). |
| Nuclear staining is absent but cytoplasmic staining is clear. | HPA reports both compartments in tissue; relative intensity can vary by cell and section (HPA: tissue IHC). | Compare intact reference cells and counterstain; check nuclear detail before calling the result discordant (standard IHC practice). |
| Signal appears only at cell borders. | A surface-only pattern conflicts with reported localization and lack of a transmembrane segment (HPA: tissue IHC; UniProt P54253 topology). | Inspect staining controls and antibody specificity; avoid scoring the border pattern as expected ATXN1. |
| Low reference cells stain more strongly than expected. | HPA rates ovarian stromal cells and soft-tissue fibroblasts Low; unrelated binding or detection activity is possible (HPA: tissue IHC; standard IHC practice). | Check cell identity, compare a High reference population, and use appropriate negative detection controls (standard IHC practice). |
| Brown precipitate obscures nuclei and cell boundaries. | Excess detection signal or inadequate washing can obscure localization (standard IHC practice). | Review detection time, washes, and counterstain; score only cells whose compartments remain identifiable (standard IHC practice). |
| Staining differs across sections or antibodies. | The HPA tissue IHC profile has medium consistency with RNA, and HPA008335 is Approved rather than Enhanced (HPA: reliability; HPA: antibodies). | Compare matched cell types and controls across runs; treat a discordant pattern as unresolved until independently checked. |
Experiment evidence
IHC & IF images showing ATXN1 staining
M01786-1 · IHCIHC analysis of Ataxin 1 using anti-Ataxin 1 antibody (M01786-1). Ataxin 1 was detected in a paraffin-embedded section of human hepatocellul
M01786-1 · IHCIHC analysis of Ataxin 1 using anti-Ataxin 1 antibody (M01786-1). Ataxin 1 was detected in a paraffin-embedded section of human laryngeal sq
PB9422 · IHCIHC analysis of Ataxin 1 using anti-Ataxin 1 antibody (PB9422). Ataxin 1 was detected in a paraffin-embedded section of human colon cancer t
PB9422 · IHCIHC analysis of Ataxin 1 using anti-Ataxin 1 antibody (PB9422). Ataxin 1 was detected in a paraffin-embedded section of mouse brain tissue.
PB9422 · IFIF analysis of Ataxin 1 using anti-Ataxin 1 antibody (PB9422). Ataxin 1 was detected in immunocytochemical section of HepG2 cells. Enzyme an
HPA · Cerebral cortexHuman Protein Atlas IHC, Cerebral cortex. Source: https://www.proteinatlas.org/ENSG00000124788-ATXN1/tissue/cerebral+cortex#imid_2505668
HPA · ColonHuman Protein Atlas IHC, Colon. Source: https://www.proteinatlas.org/ENSG00000124788-ATXN1/tissue/colon#imid_2505602
HPA · LiverHuman Protein Atlas IHC, Liver. Source: https://www.proteinatlas.org/ENSG00000124788-ATXN1/tissue/liver#imid_2505603
HPA · KidneyHuman Protein Atlas IHC, Kidney. Source: https://www.proteinatlas.org/ENSG00000124788-ATXN1/tissue/kidney#imid_2505588
HPA · ICC-IF RT-4Human Protein Atlas immunofluorescence, RT-4, antibody HPA070756; green = ATXN1, blue = nucleus, red = microtubules.
HPA · ICC-IF RT-4Human Protein Atlas immunofluorescence, RT-4, antibody HPA070756; green = ATXN1, blue = nucleus, red = microtubules.
← swipe / scroll for more images →
Real IHC / IF data behind the staining-pattern expectations in this section.
Sample controls for ATXN1 IHC & IF
🧪Run appendix first and score its glandular cells, which show High ATXN1 staining (HPA: appendix glandular cells, High). HPA detects ATXN1 in all 45 scored tissues, so there is no documented negative tissue; use no-primary and isotype slides for background, and treat unstained neighboring cells as a within-slide reference rather than proven ATXN1-negative cells (HPA: no negative rows; standard IHC practice).
Positive control tissue: Appendix (Glandular cells, HPA High)
Negative control tissue: None in HPA: ATXN1 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 ATXN1 in RT-4, U2OS, with annotated localisation: Nucleoplasm (supported) (HPA subcellular).
Technical controls: Include a no-primary (secondary-only) slide, a mouse IgG isotype control matched to the primary's subclass and concentration, and ATXN1-knockout material if available as a biological specificity control (catalog caption: mouse primary; standard IHC practice). For DAB detection in appendix, quench endogenous peroxidase and check inflammatory areas for background staining (catalog caption: HRP/DAB detection; standard IHC practice).
⚠️Feasibility: A target-specific fixation window or fixation effect is unreported, and the selected M01786-1 paraffin-section caption does not state a fixative (catalog caption: fixative not stated). That caption uses heat-mediated EDTA pH 8.0 retrieval and 2 μg/ml primary overnight at 4°C; these are starting conditions, not proof that retrieval is required (catalog caption). No supplied evidence shows frozen sections or IF are easier; HPA ICC-IF images in RT-4 and U2OS support a separate localization readout, while endogenous peroxidase in appendix inflammatory areas may produce DAB background (HPA: ICC-IF cell lines; standard IHC practice).
HPA tissue IHC evidence for ATXN1
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 |
|---|---|---|---|---|
| Appendix | Glandular cells | High | Protein (IHC) | HPA → |
| Breast | Glandular cells | High | Protein (IHC) | HPA → |
| Bronchus | Respiratory epithelial cells | High | Protein (IHC) | HPA → |
| Caudate | Neuronal cells | High | Protein (IHC) | HPA → |
| Cerebellum | Cells in granular layer | High | Protein (IHC) | HPA → |
Undetected expression · recommended negative controls
| Tissue | Cell type | Level | Evidence | Source |
|---|---|---|---|---|
| None in HPA: ATXN1 is detected in all 45 scored tissues. Use a no-primary (secondary-only) and an isotype control instead. | ||||
Section 3
Advanced ATXN1 IHC Tips
Troubleshoot ATXN1 staining in paraffin sections by checking retrieval, tissue processing, intracellular localisation and scoring before interpreting a chromogenic signal.
Where should I start when ATXN1 staining is weak after antigen retrieval?
Start with heat-mediated retrieval in EDTA at pH 8.0 for paraffin sections (datasheet M01786-1). In the documented tissue example, a 10% goat-serum block preceded 2 μg/ml primary antibody overnight at 4°C (caption M01786-1). Keep section thickness, heating, cooling and detection conditions consistent across test slides so retrieval changes can be judged fairly (standard IHC practice). If signal remains weak, compare a small retrieval time series while monitoring tissue integrity; treat other buffers or pH values as fallbacks (standard IHC practice). Score nuclear and cytoplasmic staining separately because both compartments are reported for ATXN1 (UniProt P54253; HPA tissue IHC).
How should I investigate weak ATXN1 staining when fixation details are missing?
The selected paraffin-section caption does not state a fixative, so target-specific fixation sensitivity cannot be established from it (caption M01786-1). Record the actual fixative, fixation duration, section age and storage conditions for each specimen before comparing staining intensity (standard IHC practice). Run differently processed sections through the same EDTA pH 8.0 retrieval and detection run to isolate processing differences (datasheet M01786-1; standard IHC practice). Evaluate morphology alongside signal, since poor tissue preservation can make nuclear and cytoplasmic assignments unreliable (standard IHC practice). HPA tissue staining and ATXN1 topology or phosphorylation do not establish a fixation effect for this antibody (HPA tissue IHC; UniProt P54253).
Is cytoplasmic ATXN1 staining credible when nuclear staining is expected?
Yes, ATXN1 is annotated in both nucleus and cytoplasm, while HPA tissue IHC reports both compartments across tissues (UniProt P54253; HPA tissue IHC). HPA cell imaging places its main signal in the nucleoplasm, with additional nucleolar and cytosolic signal (HPA subcellular). Score nuclear and cytoplasmic chromogen separately using a counterstain that preserves nuclear boundaries, then compare matched cells and sections (standard IHC practice). Treat diffuse staining that obscures cell borders cautiously, particularly if nearby structures show the same colour without cellular definition (standard IHC practice). A membrane-restricted pattern is unexpected because ATXN1 has no transmembrane segment (UniProt P54253 topology).
Could an isoform or hidden epitope explain inconsistent ATXN1 staining?
The supplied record lists one ATXN1 isoform, so isoform switching is not an established explanation for discrepant staining here (UniProt P54253). The antibody epitope is unspecified; do not assume it lies within the AXH domain at residues 562–693 (UniProt P54253; caption M01786-1). ATXN1 has documented phosphoserines, including residues 82 and 775, but their effect on this antibody's binding is unknown (UniProt P54253). Compare retrieval and primary-antibody conditions on matched sections before assigning an epitope-based cause (datasheet M01786-1; standard IHC practice). If specificity remains uncertain, use an independently validated epitope or genetic control where available and interpret divergent compartment patterns cautiously (standard IHC practice).
How can IF help check cell identity and compartment assignments from ATXN1 IHC?
Use a separate IF experiment to compare ATXN1 with a marker of the expected cell type, such as a neuronal marker in caudate, where neuronal staining is high (HPA tissue IHC). Choose spectrally separated fluorophores and inspect an unstained section before selecting channels, because tissue autofluorescence can mimic a dim signal (standard IF practice). Include a nuclear counterstain and use permeabilisation appropriate for intracellular nuclear and cytosolic epitopes; ATXN1 has no transmembrane segment (HPA subcellular; UniProt P54253 topology). HPA imaging supports nucleoplasmic, nucleolar and cytosolic localisation, which can guide comparison with chromogenic compartment scores (HPA subcellular). Establish IF fixation and antibody conditions independently because the selected IHC caption supplies no IF fixation evidence (caption M01786-1).
What should I adjust when ATXN1 chromogen stains nearly every structure?
First compare a no-primary control with the test section to identify detection background before changing the ATXN1 antibody concentration (standard IHC practice). The documented example uses 10% goat serum, 2 μg/ml primary antibody overnight at 4°C, and a peroxidase-based DAB readout (caption M01786-1). For a peroxidase workflow, include an endogenous-peroxidase block and optimise washing and DAB development on matched sections (standard IHC practice). Widespread staining alone does not prove artefact: ATXN1 is widely expressed, and HPA reports cytoplasmic and nuclear staining across tissues (UniProt P54253; HPA tissue IHC). Prioritise cellular localisation and control-slide behaviour over overall colour intensity when judging specificity (standard IHC practice).
How should I score ATXN1 IHC across tissues with different cellular composition? ⚠ ANSWER MARKED FOR VERIFICATION
Define the cell population and compartment before scoring, since HPA reports high ATXN1 staining in several glandular and neuronal populations (HPA tissue IHC). For each compartment, report the percentage of positive target cells and an intensity-weighted H-score using a consistent scoring rubric (standard IHC practice). If spatial cell abundance matters, report positive-cell density per mm² of viable, annotated tissue and state the counted area (standard IHC practice). Normalise percentages and H-scores to eligible cells of the same type, while excluding folds, necrosis and section edges by preset rules (standard IHC practice). Keep retrieval, detection exposure and scoring thresholds consistent across sections; record them alongside the results (standard IHC practice).
Which ATXN1 staining patterns are convincing, and which suggest artefact?
A convincing pattern has defined nuclear or cytoplasmic signal in identifiable cells, consistent with UniProt localisation and HPA tissue IHC (UniProt P54253; HPA tissue IHC). Nuclear enrichment is plausible because HPA cell imaging identifies the nucleoplasm as the main location, with additional nucleolar and cytosolic signal (HPA subcellular). Check cell identity against the sampled tissue: HPA reports high staining in caudate neuronal cells and low staining in adipocytes (HPA tissue IHC). Treat membrane-only staining, edge-heavy colour, necrotic staining or signal in the no-primary control as reasons to investigate artefact (UniProt P54253 topology; standard IHC practice). Review endogenous peroxidase blocking and DAB development before interpreting diffuse brown signal as ATXN1 expression (standard IHC practice).
Boster reagents
Best ATXN1 / Ataxin-1 IHC Antibodies
The catalog shows ATXN1 staining in human paraffin sections, mouse and rat brain paraffin sections, and HepG2 cells by IF/ICC (catalog IHC/IF captions).
Real IHC data
Anti-Ataxin 1 Antibody ® (monoclonal, 2B13G8)
Cat # M01786-1
Real IHC data
Anti-Ataxin 1/ATXN1 Antibody ®
Cat # PB9422
M01786-1 is a mouse monoclonal antibody with IHC examples in human hepatocellular carcinoma, laryngeal squamous cell carcinoma, thyroiditis, and mouse brain paraffin sections (M01786-1 catalog and IHC captions). PB9422 is a rabbit antibody with IHC examples in human colon cancer, mouse brain, and rat brain paraffin sections, plus an IF/ICC example in HepG2 cells (PB9422 catalog and IHC/IF captions).
Which to pick: For paraffin-section IHC, choose M01786-1 if a mouse monoclonal is preferred; its IHC captions show staining in human and mouse sections (M01786-1 catalog and IHC captions). Choose PB9422 for IF/ICC in HepG2 cells or for IHC with examples across human, mouse, and rat tissues (PB9422 catalog and IHC/IF captions). Neither SKU’s IHC captions report the fixative (M01786-1 and PB9422 IHC captions).
Each figure is that product's own IHC / IF validation image from its datasheet.
References
- UniProt Consortium. UniProt entry P54253 (ATX1_HUMAN, Ataxin-1).
- Human Protein Atlas. ATXN1 tissue IHC expression (reliability: Approved).
- Human Protein Atlas. ATXN1 subcellular location (ICC-IF): Mainly localized to the nucleoplasm. In addition localized to the nucleoli and cytosol..
- Human Protein Atlas. ATXN1 antibody validation summary (2 antibodies).
- Characterization of the zebrafish atxn1/axh gene family. Journal of neurogenetics 2009 — PMC2722686.
- Pre-ataxic loss of intrinsic plasticity and motor learning in a mouse model of SCA1. Brain : a journal of neurology 2023 — PMC10232256.
- Ataxin-1 is involved in tumorigenesis of cervical cancer cells via the EGFR-RAS-MAPK signaling pathway. Oncotarget 2017 — PMC5706899.
- HMGB1 facilitates repair of mitochondrial DNA damage and extends the lifespan of mutant ataxin-1 knock-in mice. EMBO molecular medicine 2015 — PMC4309669.
- PubMed PMID:7951322 — UniProt-cited evidence.
- PubMed PMID:14574404 — UniProt-cited evidence.
- PubMed PMID:15489334 — UniProt-cited evidence.
Immunohistochemistry protocol sheet for ATXN1 (Ataxin-1). Expected localisation Cytoplasmic and nuclear staining across tissues (HPA tissue IHC). Antigen retrieval: EDTA pH 8.0 HIER, heat-mediated (datasheet M01786-1). Validated IHC antibody: M01786-1 at 2 μg/ml (the product's own IHC validation image is shown). Controls (HPA): positive Appendix (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 hepatocellular carcinoma tissue; fixative not specified (datasheet M01786-1); 2. Fixation: Image fixative and duration unreported (datasheet M01786-1); 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: EDTA pH 8.0 (datasheet M01786-1); 20 min, 95–100 °C (standard); 6. Peroxidase block: 3% H2O2, 10 min , room temperature (standard); 7. Blocking: 10% goat serum (datasheet M01786-1); 8. Primary antibody: Mouse monoclonal (clone 2B13G8) anti-ATXN1, 2 μg/ml (datasheet M01786-1); 9. Primary incubation: Overnight at 4 °C (datasheet M01786-1). Watch for: Fixation: Keep fixation consistent across paraffin sections. (standard IHC practice; not target-specific); Caveat: Staining and RNA show medium consistency (HPA tissue IHC); Isoform / epitope: One isoform with a full-length chain (UniProt); Regulation: Widely expressed throughout the body (UniProt). Evidence: UniProt P54253, HPA tissue IHC · Approved, HPA ICC-IF · Mainly localized to the nucleoplasm. In addition localized to the…, Datasheet M01786-1, PMC2722686, PMC5706899. QR code links to https://www.bosterbio.com/bosterbio-gene-info-cards/ATXN1/immunohistochemistry-ihc-guide.