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ATXN1 / Ataxin-1 · IHC design guide
Design Immunohistochemistry for ATXN1
Plan paraffin-section ATXN1 staining around cytoplasmic and nuclear tissue signal (HPA tissue IHC). Use high-staining colon glandular cells or caudate neurons as positive references (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 tissue staining (HPA tissue IHC) | |
| Staining pattern | Across tissues, cells show cytoplasmic and nuclear staining (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 | Matched tissue-IHC evidence does not establish the fixation claim. Validate the specimen-specific method before use. (selected-SKU IHC image M01786-1) | |
| Caveat | Fibroblasts may stain weakly despite broad tissue staining (HPA tissue IHC) | |
| Regulation | Broad expression; variable intensity (HPA tissue IHC) | |
| Isoform / epitope | 1 annotated isoform; no alternate isoform to map (UniProt) |
Section 1
Recommended ATXN1 IHC & IF Protocols
Compare the catalog antibody’s IHC-P protocol (datasheet M01786-1) with published ATXN1 staining of zebrafish heads (PMC2722686) and human cervical tissue arrays (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 a retrieval buffer (PMC5706899).
Section 2
What Is the Expected ATXN1 Staining Pattern?
ATXN1 should stain nuclei and cytoplasm in a range of tissues (HPA tissue IHC; UniProt P54253). Strong examples include glandular cells in colon and appendix, respiratory epithelial cells in bronchus, and neuronal cells in caudate (HPA tissue IHC). ATXN1 has no transmembrane segment (UniProt P54253 topology). HPA rates its tissue IHC profile Approved, with medium consistency between staining and RNA expression (HPA tissue IHC).
| Nuclear staining with cytoplasmic staining in the expected cells. | This fits the reported tissue IHC pattern (HPA tissue IHC). Judge each compartment against surrounding cells and the chosen reference tissue; nuclear staining alone should not be assumed to represent every cell's full pattern (HPA tissue IHC). |
| Staining is confined mainly to cell borders, the extracellular space, or another unexpected compartment. | That distribution does not match the reported nuclear and cytoplasmic locations (HPA tissue IHC; UniProt P54253). Review morphology and controls before scoring it as ATXN1; misplaced chromogen may reflect nonspecific staining or a detection artefact (standard IHC practice). |
| The strongest signal appears in cells other than the expected population. | Compare cell identity with the tissue reference: HPA reports high staining in colon glandular cells and caudate neuronal cells (HPA tissue IHC). A mismatched pattern can suggest cross-reactivity or endogenous detection activity; cell identity alone cannot establish the cause (standard IHC practice). |
| Chromogen forms a broad haze across cells and surrounding tissue. | Poorly bounded signal makes nuclear and cytoplasmic localisation hard to score. Diffuse background can arise from nonspecific binding or detection chemistry (standard IHC practice); it does not reproduce the cell-resolved pattern reported by HPA (HPA tissue IHC). |
| No signal appears in a tissue chosen for its reported high staining. | A blank result in appendix glandular cells or cerebellar granular-layer cells conflicts with the reported high staining (HPA tissue IHC). Check section quality, retrieval, antibody and detection controls before concluding that the specimen lacks ATXN1 (standard IHC practice). |
💡Expected ATXN1 appearanceCall the result positive when identifiable cells show convincing nuclear and cytoplasmic staining, especially in HPA high-staining cell populations (HPA tissue IHC); isolated edge staining or diffuse, cell-independent colour is suspect (standard IHC practice).
| Tissue and cell selection | ATXN1 is widely expressed (UniProt P54253); HPA reports low tissue specificity and high staining in selected epithelial and neuronal populations (HPA tissue IHC). Use those named populations as positive references. HPA lists some stromal, adipose and immune populations as low, not absent (HPA tissue IHC). |
| Compartment | UniProt places ATXN1 in cytoplasm and nucleus, with nuclear USP7 colocalisation (UniProt P54253). HPA tissue IHC also reports both compartments. Neither source supports interpreting a membrane-only pattern as the expected result (UniProt P54253 topology; HPA tissue IHC). |
| IHC evidence strength | The tissue profile is Approved with medium staining–RNA consistency (HPA tissue IHC). HPA008335 is IHC Approved; the supplied antibody record does not label it IHC Enhanced (HPA antibody validation). Treat a matching pattern as supportive, while keeping specimen controls in the interpretation (standard IHC practice). |
| Antigen and antibody context | ATXN1 is reported as one 815-residue chain, with no signal peptide, propeptide or transmembrane segment (UniProt P54253). The supplied sources give no antibody epitope or target-specific fixation sensitivity; they cannot predict an ATXN1 retrieval response or a fixation-driven tissue difference. |
| Can IF/ICC findings guide this IHC readout? | Yes, for compartment context: HPA reports supported nucleoplasm localisation, plus nucleoli and cytosol, in ICC-IF (HPA subcellular). HPA070756 is ICC Supported, while HPA008335 is IHC Approved (HPA antibody validation). These are distinct application records; interpret the paraffin section against tissue IHC. |
| Situation | Likely cause | Next action |
|---|---|---|
| Known high-staining tissue is blank (HPA tissue IHC). | A failed staining run or unsuitable assay conditions are possible; a blank slide alone does not establish absent protein (standard IHC practice). | Check section integrity, a run control, antigen retrieval conditions, primary antibody use and detection reagents (standard IHC practice). Compare the reported high-staining cell population before scoring (HPA tissue IHC). |
| Signal appears at the membrane or extracellularly instead of in cells. | That pattern conflicts with nuclear and cytoplasmic localisation and the absence of a transmembrane segment (HPA tissue IHC; UniProt P54253). Background or cross-reactivity is possible (standard IHC practice). | Inspect morphology and a negative control, then reassess primary antibody and detection specificity before calling the signal ATXN1 (standard IHC practice). |
| Colour persists in the no-primary control. | Primary-independent colour can reflect endogenous detection activity or reagent background (standard IHC practice). | Review the chromogenic detection and blocking steps, and compare control and test sections at the same settings (standard IHC practice). |
| The whole section has diffuse colour. | Nonspecific binding or excess detection signal can obscure cell boundaries (standard IHC practice). | Check blocking, washing, antibody concentration and detection development; score only a resolved cellular pattern (standard IHC practice). |
| Only low-staining populations are visible, or they appear blank. | HPA labels ovarian stroma cells, adipocytes and several immune populations Low; Low does not define a negative control (HPA tissue IHC). | Include a named HPA high-staining population in the run and judge the low-staining cells relative to it (HPA tissue IHC; standard IHC practice). |
| A nuclear pattern looks different from an ICC-IF reference. | HPA ICC-IF resolves nucleoplasm and additional nucleolar and cytosolic locations; tissue IHC describes broader nuclear and cytoplasmic expression (HPA subcellular; HPA tissue IHC). | Score the paraffin section against the tissue IHC cell and compartment pattern; use ICC-IF as supporting location context (HPA tissue IHC; HPA subcellular). |
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 cerebellum first and expect staining in cells of the granular layer (HPA: High in cerebellar granular-layer cells). HPA detects ATXN1 in all 45 scored tissues, so there is no validated negative tissue; use no-primary and isotype controls, and treat cells without DAB signal on the positive slide as a background reference rather than confirmed ATXN1-negative cells (HPA: no negative tissue rows).
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; an isotype control matched to the mouse primary’s immunoglobulin class and concentration; and, if available, ATXN1-knockout material as a biological specificity control (caption: mouse anti-Ataxin 1; standard IHC practice). Block endogenous peroxidase and inspect vascular or blood-cell background in cerebellum before interpreting DAB staining (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 the fixative (caption: fixative not stated). That caption used heat retrieval in EDTA, pH 8.0, but does not establish that retrieval is required; the supplied evidence does not show that frozen sections or IF are easier (caption: EDTA retrieval; HPA: RT-4 and U2OS ICC-IF images). For cerebellar IF, check neuronal autofluorescence before assigning ATXN1 signal (standard IF 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, cellular compartment, background controls and scoring within defined cell populations.
Which retrieval condition should I start with for weak ATXN1 staining in paraffin sections?
Start with heat-mediated EDTA retrieval at pH 8.0 for paraffin sections (datasheet M01786-1). The selected tissue image used this condition before 10% goat serum blocking and 2 μg/ml primary antibody overnight at 4°C (datasheet M01786-1). If staining remains weak, check heating consistency, then vary retrieval duration on serial sections while holding antibody and detection conditions constant (standard IHC practice). Compare nuclear and cytoplasmic recovery because both compartments can contain ATXN1 (HPA tissue IHC; UniProt P54253 subcellular). Inspect morphology and section adhesion after each adjustment, since excessive retrieval can compromise interpretation (standard IHC practice).
How should I assess fixation when ATXN1 staining varies between paraffin sections?
ATXN1-specific fixation sensitivity is unknown: the selected paraffin-section caption does not report its fixative (datasheet M01786-1). Record each specimen’s fixative, fixation interval and processing history before attributing staining differences to ATXN1 biology (standard IHC practice). Compare similarly processed sections in the same run, using the documented EDTA retrieval at pH 8.0 and 2 μg/ml primary incubation as a starting point (datasheet M01786-1). Assess tissue preservation and nuclear detail alongside signal, since poor morphology limits compartment scoring (standard IHC practice). Do not infer a fixation effect from ATXN1 phosphorylation or its lack of a transmembrane segment (UniProt P54253 modified residues; topology).
Should ATXN1 staining be restricted to nuclei in chromogenic IHC?
No: tissue IHC reports both cytoplasmic and nuclear expression across tissues (HPA tissue IHC). UniProt also assigns ATXN1 to cytoplasm and nucleus, while cell imaging supports nucleoplasm as its main location with additional nucleolar and cytosolic signal (UniProt P54253 subcellular; HPA subcellular). Score nuclear and cytoplasmic DAB separately within the same defined cell population, using a counterstain to set nuclear boundaries (standard IHC practice). Compare the pattern with a concurrently stained control section and check whether diffuse signal extends into extracellular space or damaged regions (standard IHC practice). A nuclear-only scoring rule could discard genuine cytoplasmic staining (HPA tissue IHC).
Can an unexpected ATXN1 pattern be explained by isoforms or epitope masking?
The supplied record lists 1 ATXN1 isoform and an AXH domain at residues 562–693 (UniProt P54253 isoforms; domains). It also lists phosphorylated residues, including 82, 88, 238, 253 and 775 (UniProt P54253 modified residues). The catalog caption does not identify the antibody epitope or establish phosphorylation-dependent recognition, so neither mechanism explains a changed staining pattern on this evidence (datasheet M01786-1). Test retrieval and primary concentration on matched serial sections, then compare compartment patterns under identical detection conditions (standard IHC practice). Interpret any epitope explanation only after obtaining direct antibody characterization or an independent specificity control (standard IHC practice).
How should I adapt ATXN1 localisation checks for multiplex IF?
For multiplex IF, pair ATXN1 with a marker identifying the cell population being assessed, such as neuronal cells in caudate or glandular cells in colon (HPA tissue IHC). Choose spectrally separated fluorophores and favor a far-red ATXN1 channel if tissue autofluorescence interferes; include unstained and single-channel controls (standard IF practice). ATXN1 is intracellular and has no transmembrane segment, so permeabilise cells to access nuclear and cytosolic epitopes, then optimise that step for preserved morphology (UniProt P54253 subcellular; topology; standard IF practice). HPA cell images place ATXN1 mainly in nucleoplasm, with additional nucleolar and cytosolic signal (HPA subcellular). Establish IF fixation and antibody conditions independently; the selected paraffin IHC caption reports no IF procedure (datasheet M01786-1).
What should I check when ATXN1 DAB staining looks diffuse or widespread?
First compare a no-primary section with the ATXN1 section to identify detection background, and check that the peroxidase block suppresses endogenous enzyme activity (standard IHC practice). The selected image used 10% goat serum blocking, 2 μg/ml primary antibody overnight at 4°C, and an anti-mouse secondary for 30 minutes at 37°C (datasheet M01786-1). Its chromogen was DAB, so assess whether development time spreads signal beyond cellular boundaries (datasheet M01786-1; standard IHC practice). Examine section edges, folds and damaged areas separately from intact tissue (standard IHC practice). Widespread cellular staining alone is plausible because ATXN1 is broadly expressed, but it still requires compartment and control checks (UniProt P54253 tissue specificity; HPA tissue IHC).
How should I quantify nuclear and cytoplasmic ATXN1 staining across sections? ⚠ ANSWER MARKED FOR VERIFICATION
Define the cell population and viable analysis area before scoring, then report nuclear and cytoplasmic staining separately because tissue IHC shows both patterns (HPA tissue IHC; standard IHC practice). For each compartment, record the percentage of positive cells and intensity on a 0–3 scale; an H-score sums percentage times intensity to give 0–300 (standard IHC practice). If counting stained cells, report density per mm² of viable tissue and state the cell-identification rule (standard IHC practice). Normalise comparisons to the same cell population, section area and staining batch rather than raw DAB-covered area (standard IHC practice). Exclude folds and necrosis consistently, and retain matched controls for batch comparison (standard IHC practice).
How can I distinguish credible ATXN1 staining from tissue artefact?
Credible ATXN1 staining should resolve within cells and can occupy nuclei and cytoplasm; nucleoplasmic enrichment is also supported by cell imaging (HPA tissue IHC; HPA subcellular). Check the relevant cell population: HPA reports high staining in caudate neuronal cells and colon glandular cells, but low staining in adipocytes and soft-tissue fibroblasts (HPA tissue IHC). Do not treat staining at torn edges, folds or necrotic areas as equivalent to intact-cell signal (standard IHC practice). A no-primary control and an effective peroxidase block help identify detection artefacts, including endogenous enzyme signal (standard IHC practice). The selected paraffin image demonstrates staining in human hepatocellular carcinoma but does not establish specificity in every tissue (datasheet M01786-1).
Boster reagents
Best ATXN1 / Ataxin-1 IHC Antibodies
Anti-ATXN1 antibodies have paraffin-section IHC images from human tissues and mouse brain (catalog IHC captions); PB9422 also has an IF image from HepG2 cells (catalog IF caption).
Real IHC data
Anti-Ataxin 1 Antibody ® (monoclonal, 2B13G8)
Cat # M01786-1
Real IHC data
Anti-Ataxin 1/ATXN1 Antibody ®
Cat # PB9422
M01786-1 has IHC images from human hepatocellular carcinoma, laryngeal squamous cell carcinoma, thyroiditis, and mouse brain paraffin sections (M01786-1 IHC captions). PB9422 has IHC images from human colon cancer, mouse brain, and rat brain paraffin sections, plus IF data from HepG2 cells (PB9422 IHC and IF captions).
Which to pick: For tissue IHC, choose M01786-1 when a mouse monoclonal is preferred (catalog: clone 2B13G8); its IHC captions document paraffin sections (M01786-1 IHC captions). Choose PB9422 for IF/ICC because those applications and a HepG2 IF image are documented (PB9422 applications and IF caption). For cross-species IHC, both list human, mouse, and rat reactivity (catalog reactivity), while PB9422 additionally shows IHC images for all three species (PB9422 IHC captions); the fixative is unreported in both products’ 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 tissue staining (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: Matched tissue-IHC evidence does not establish the fixation claim. Validate the specimen-specific method before use. (selected-SKU IHC image M01786-1); Caveat: Fibroblasts may stain weakly despite broad tissue staining (HPA tissue IHC); Isoform / epitope: 1 annotated isoform; no alternate isoform to map (UniProt); Regulation: Broad expression; variable intensity (HPA tissue IHC). 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.