ATXN2 / Ataxin-2 · IHC design guide

Design Immunohistochemistry for ATXN2

Plan chromogenic ATXN2 IHC on paraffin sections using cytoplasmic CNS staining as a reference (HPA tissue IHC). This guide pairs high-staining neuronal examples with cell types where staining was undetected (HPA tissue IHC) and flags the 5 documented isoforms for epitope review (UniProt).

Evidence assembled Oct 2026 · For research use; verify linked source records and product datasheet before use
Immunohistochemistry protocol sheet for ATXN2 (IHC for ATXN2): expected localisation Cytoplasmic; most abundant in CNS (HPA tissue IHC), antibody PA2098, validated IHC image, and IHC protocol steps
Printable ATXN2 IHC protocol sheet — expected localisation Cytoplasmic; most abundant in CNS (HPA tissue IHC), antibody PA2098, controls and protocol steps. Open the full ATXN2 IHC guide →

ATXN2 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; most abundant in CNS (HPA tissue IHC)
Staining pattern Neuronal cytoplasm and cerebellar granular-layer processes (HPA tissue IHC)
Antigen retrieval EDTA pH 8.0 HIER, heat-mediated (datasheet PA2098)
Positive control ⓘ Caudate+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 sections. (standard IHC practice; not target-specific)
Caveat Staining shows medium consistency with RNA expression (HPA tissue IHC)
Regulation Isoform abundance varies in the CNS (UniProt)
Isoform / epitope 5 isoforms; check antibody epitope coverage (UniProt)
Section 1

Recommended ATXN2 IHC & IF Protocols

The catalog antibody uses EDTA pH 8.0 heat retrieval (datasheet PA2098). The published protocols below describe ATXN2 staining in brain sections (PMC7594343; PMC13076406).

Recommended immunohistochemistry (IHC-P) protocol parameters
SampleParaffin-embedded human breast cancer tissue; fixative not specified (datasheet PA2098)
FixationImage fixative and duration unreported (datasheet PA2098); verify before use.
Sectioning4–5 µm sections on charged slides (standard)
DeparaffinisationXylene, graded ethanol series to water (standard)
Antigen retrievalHeat retrieval: EDTA pH 8.0 (datasheet PA2098); 20 min, 95–100 °C (standard)
Peroxidase block3% H2O2, 10 min, room temperature (standard)
Blocking10% goat serum (datasheet PA2098)
Primary antibodyRabbit anti-ATXN2, 2-5 μg/ml (datasheet PA2098)
Primary incubationOvernight at 4 °C (datasheet PA2098)
DetectionHRP-conjugated secondary, DAB chromogen (datasheet PA2098)
CounterstainHematoxylin, blue, dehydrate and mount (standard)
Expected resultATXN2-positive staining in neuronal cells of caudate (HPA tissue IHC: High). HPA tissue profile: Cytoplasmic expression in several tissues, most abundant in CNS. No signal in the no-primary control.
💡Decision noteStart with EDTA pH 8.0 heat retrieval for the catalog antibody (datasheet PA2098). The published glioma protocol uses pH 6.0 autoclave retrieval (PMC13076406).
Section 2

What Is the Expected ATXN2 Staining Pattern?

ATXN2 should appear mainly in the cytoplasm of stained cells (UniProt Q99700: cytoplasm; HPA: cytoplasmic tissue expression). Strong IHC staining is reported in neuronal cells of the caudate and cerebral cortex, cerebellar granular-layer processes, and selected non-neural cells (HPA: High in each). ATXN2 has no transmembrane segment, so a membrane-only pattern would be unexpected (UniProt Q99700: topology). HPA rates the tissue profile Enhanced, with medium consistency between staining and RNA data (HPA: reliability).

What am I looking at on my slide?
Clear cytoplasmic staining in caudate or cerebral-cortex neurons, with recognizable tissue structure.This matches ATXN2 localisation and reported High neuronal staining (UniProt Q99700: cytoplasm; HPA: High in caudate and cerebral-cortex neuronal cells). Compare cells within the section before assigning an overall tissue score (general IHC practice).
Predominantly nuclear or sharply membrane-only staining, without a convincing cytoplasmic component.That compartment is inconsistent with the supplied localisation evidence (UniProt Q99700: cytoplasm and no transmembrane segment; HPA: cytoplasmic expression). Treat it as suspect and check staining controls and morphology before scoring (general IHC practice).
Strong staining in a cell population reported as not detected, while expected positive cells are weak.For example, strong adipocyte or skeletal-myocyte staining conflicts with those cell-specific observations (HPA: Not detected in adipocytes and skeletal myocytes). Check cell identification, antibody specificity, and endogenous chromogen activity (general IHC practice).
Diffuse color across stroma, empty spaces, and multiple cell compartments, obscuring cell borders.This is poor evidence for the reported cell-associated cytoplasmic pattern (HPA: cytoplasmic expression). Review no-primary and detection controls, blocking, washing, and chromogen development (general IHC practice); do not score background as ATXN2.
No detectable staining in caudate neurons or another documented High population.A blank known-positive control makes a negative study section hard to interpret (HPA: High in caudate neuronal cells; general IHC practice). Verify tissue identity and assay performance before calling the study section negative; HPA tissue levels are observations, not guarantees for every specimen.
💡Expected ATXN2 appearanceCall positive when staining is mainly cytoplasmic and clearly cell-associated in an expected population, such as High-staining caudate neurons; isolated nuclear, membrane-only, or diffuse background color is suspect (UniProt Q99700: cytoplasm and topology; HPA: High in caudate neuronal cells; general IHC practice).
How each factor affects the staining
Compartment and topologyCytoplasmic staining is expected, and ATXN2 lacks a transmembrane segment (UniProt Q99700: subcellular location and topology). The protein's EGFR-trafficking function does not by itself establish a membrane IHC pattern (UniProt Q99700: function).
Cell-specific tissue expressionHPA reports High staining in lung macrophages, gallbladder glandular cells, and nasopharyngeal basal cells, alongside CNS populations (HPA: tissue IHC). Low or Not detected calls apply to the named cells, not automatically to every cell in that tissue (HPA: tissue IHC).
Isoforms and tissue selectionUniProt lists 5 isoforms; isoform 1 predominates in brain and spinal cord, while isoform 4 is more abundant in cerebellum (UniProt Q99700: isoforms and tissue specificity). The supplied evidence does not map this assay's epitope to an isoform.
Strength of reference patternHPA calls the tissue profile Enhanced but reports medium consistency between antibody staining and RNA expression (HPA: reliability). Its listed IHC antibodies HPA018295, HPA020339, and HPA021146 each have Enhanced validation (HPA: antibodies); this does not validate every antibody or specimen.
IF/ICC cross-check: where should signal appear?Expect cytosolic signal in an appropriately validated IF/ICC assay (HPA: Cytosol, approved). HPA018295 has Enhanced ICC validation (HPA: antibodies). That subcellular observation supports compartment interpretation; it is not an IHC intensity standard.
Why is my staining missing, weak or wrong?
SituationLikely causeNext action
Positive-control neurons are blank.The expected population may be absent from the section, or the staining workflow may have failed (HPA: High in caudate neuronal cells; general IHC practice).Confirm the cell population on the counterstained section; check the antibody's IHC instructions, reagent integrity, retrieval, and detection controls (general IHC practice). Target-specific fixation sensitivity is unreported in the supplied evidence.
Every cell looks strongly positive.Widespread color can reflect background or overdeveloped chromogen rather than the cell-specific HPA pattern (HPA: tissue IHC; general IHC practice).Compare a no-primary control, inspect unstained spaces, and review blocking, washing, antibody concentration, and development time (general IHC practice). Score only interpretable cell-associated signal.
Staining appears mainly nuclear.A nuclear-dominant result conflicts with the reported cytoplasmic localisation (UniProt Q99700: cytoplasm; HPA: cytoplasmic expression).Recheck cellular boundaries and counterstain, then compare positive and no-primary controls; repeat with an IHC-validated antibody if the pattern persists (general IHC practice; HPA: IHC antibody validation).
Adipocytes or skeletal myocytes stain strongly.Those populations are reported Not detected by HPA; misidentified cells, cross-reactivity, or endogenous detection activity are possible explanations (HPA: adipocytes and skeletal myocytes; general IHC practice).Verify the stained cell type, inspect detection-only controls, and compare a documented positive population on the same run (general IHC practice; HPA: High in caudate neuronal cells).
Skeletal muscle looks negative despite a UniProt expression entry.UniProt reports expression in skeletal muscle, whereas HPA reports myocytes Not detected by tissue IHC (UniProt Q99700: tissue specificity; HPA: skeletal-muscle myocytes). These statements describe different measurements.Do not use skeletal myocytes alone as the positive control; include a documented High IHC population and report the cell type and assay context (HPA: tissue IHC; general IHC practice).
Only some cells in a mixed tissue stain.The HPA calls are cell-specific: lung macrophages are High, while other lung cell populations are not characterized by this payload (HPA: High in lung macrophages).Identify cells by morphology and score each relevant population separately; avoid extending a macrophage result to the whole tissue (HPA: lung macrophages; general IHC practice).

Sample controls for ATXN2 IHC & IF

🧪Run caudate first and look for staining in neuronal cells (HPA: High in caudate neuronal cells). Use adipose tissue as the negative tissue, focusing on adipocytes (HPA: Not detected in adipocytes); on the caudate slide, use adjacent non-neuronal cells as an internal background reference, without assuming they are ATXN2-negative.
Positive control tissue: Caudate (Neuronal cells, HPA High)
Negative control tissue: Adipose tissue (HPA Not detected)
ICC-IF cell lines (HPA subcellular resource): HPA ICC-IF images show ATXN2 in A-431, U-251MG, U2OS, hTERT-RPE1 (serum starved), U2OS, siRNA 1 (10x), U2OS, siRNA 1 (40x), U2OS, siRNA 2 (10x), U2OS, siRNA 2 (40x), U2OS, scrambled (10x), U2OS, scrambled (40x), with annotated localisation: Cytosol (approved) (HPA subcellular).
Technical controls: Include a no-primary, secondary-only control and a concentration-matched rabbit IgG isotype control for the rabbit catalog antibody (caption: rabbit anti-ATXN2 PA2098; standard IHC practice). Add ATXN2 knockout tissue or a validated immunizing-peptide block as a biological specificity control, and block endogenous peroxidase before chromogenic detection in caudate sections (standard IHC practice).
⚠️Feasibility: A target-specific fixation window and fixation effect are unreported in the supplied evidence; the selected PA2098 tissue-IHC caption does not state a fixative (caption: fixative unreported). Heat-mediated EDTA retrieval at pH 8.0 is a starting condition for paraffin IHC, though the reported example used breast cancer tissue rather than caudate (caption: EDTA pH 8.0 retrieval). The supplied evidence does not establish whether frozen sections or IF are easier; assess pigment and background when scoring caudate staining (HPA: High in caudate neuronal cells; standard IHC practice).

HPA tissue IHC evidence for ATXN2

Comprehensive Human Protein Atlas IHC scoring per tissue (reliability: Enhanced — 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

TissueCell typeLevelEvidenceSource
Caudate Neuronal cells High Protein (IHC) HPA →
Cerebellum Processes in granular layer High Protein (IHC) HPA →
Cerebral cortex Neuronal cells High Protein (IHC) HPA →
Gallbladder Glandular cells High Protein (IHC) HPA →
Lung Macrophages High Protein (IHC) HPA →

Undetected expression · recommended negative controls

TissueCell typeLevelEvidenceSource
Adipose tissue Adipocytes Not detected Protein (IHC) HPA →
Cervix Squamous epithelial cells Not detected Protein (IHC) HPA →
Ovary Follicle cells Not detected Protein (IHC) HPA →
Skeletal muscle Myocytes Not detected Protein (IHC) HPA →
Spleen Cells in red pulp Not detected Protein (IHC) HPA →
Section 3

Advanced ATXN2 IHC Tips

Use compartment, cell type and matched controls to assess ATXN2 staining in paraffin sections; interpret weak signals alongside retrieval and detection conditions.

Which retrieval condition should I start with for ATXN2 in paraffin sections?
Start with heat-mediated retrieval in EDTA at pH 8.0 for paraffin sections (datasheet PA2098). This condition accompanies ATXN2 detection with 2 μg/ml primary antibody overnight at 4°C (PA2098 tissue-IHC caption). Include a documented positive section and a no-primary control in the same run to assess weak DAB staining (standard IHC practice). If staining remains weak, compare an alternative retrieval condition on serial sections while keeping antibody and development conditions fixed (standard IHC practice). Judge any gain against tissue damage and the expected cytoplasmic pattern (standard IHC practice; UniProt Q99700: cytoplasm).
How can I troubleshoot fixation-related loss of ATXN2 staining?
ATXN2-specific sensitivity to fixation is unknown: the selected paraffin-section caption does not state a fixative (PA2098 tissue-IHC caption). Record the fixative, fixation duration and section-processing history for each specimen before comparing staining (standard IHC practice). Test adjacent sections with EDTA retrieval at pH 8.0 and the same antibody concentration to limit avoidable variation (datasheet PA2098; standard IHC practice). A positive control processed alongside the sample can reveal a run-level failure, although it cannot establish that the sample's antigen was preserved (standard IHC practice). Interpret signal together with morphology, since damaged or poorly preserved tissue complicates cytoplasmic scoring (standard IHC practice; UniProt Q99700: cytoplasm).
What ATXN2 staining pattern is credible in tissue IHC?
Expect predominantly cytoplasmic staining: ATXN2 is assigned to the cytoplasm, with no transmembrane segment (UniProt Q99700: subcellular location and topology). Tissue IHC reports cytoplasmic expression in several tissues, most abundant in the CNS (HPA tissue IHC profile). Caudate and cerebral cortex neuronal cells show high staining, while cerebellar granular-layer processes are also high (HPA tissue IHC: positive cells). Compare signal within the relevant cell population on a matched positive section rather than treating all tissue compartments alike (standard IHC practice). Predominantly nuclear or sharply membranous DAB warrants review of morphology, controls and nonspecific staining before assignment to ATXN2 (UniProt Q99700: cytoplasm; standard IHC practice).
Could an ATXN2 isoform or modified epitope explain uneven staining?
ATXN2 has 5 listed isoforms, and isoform abundance differs by region: isoform 1 predominates in brain and spinal cord, while isoform 4 is more abundant in cerebellum (UniProt Q99700: isoforms and tissue specificity). Its Sm domain spans residues 267–344, and multiple phosphorylation sites are annotated (UniProt Q99700: domains and modified residues). The supplied antibody evidence does not map the recognized epitope, so these features alone cannot establish isoform coverage or modification sensitivity (PA2098 tissue-IHC caption; UniProt Q99700). Compare similarly processed regions and document staining differences without assigning them to a particular isoform (standard IHC practice). Confirm any isoform-specific claim with independent epitope or isoform evidence (standard IHC practice).
How should IF help assess a questionable ATXN2 IHC pattern?
Use IF as a complementary localisation check for cytosolic ATXN2, which is the approved subcellular location (HPA subcellular: cytosol). Multiplex with a validated marker for the expected cell type; neuronal cells are strongly stained in caudate and cerebral cortex IHC (HPA tissue IHC: positive cells; standard IF practice). Choose a fluorophore channel with low specimen autofluorescence and inspect single-channel images and no-primary controls before interpreting overlap (standard IF practice). Because ATXN2 is cytosolic and has no transmembrane segment, assess whether permeabilisation permits intracellular antibody access (HPA subcellular: cytosol; UniProt Q99700: topology; standard IF practice). Treat IF colocalisation as supporting evidence, then score the chromogenic IHC section on its own morphology and controls (standard IHC/IF practice).
What should I check when ATXN2 DAB staining is diffuse?
First compare the stained section with a no-primary control to identify background from secondary detection or chromogen development (standard IHC practice). The documented tissue example used 10% goat serum blocking, a peroxidase-conjugated secondary for 30 minutes at 37°C, and DAB (PA2098 tissue-IHC caption). Review blocking, washes and primary-antibody concentration together; the documented primary concentration was 2 μg/ml (PA2098 tissue-IHC caption; standard IHC practice). Include a peroxidase-blocking step and inspect control sections for endogenous enzyme signal before calling diffuse DAB specific (standard chromogenic IHC practice). Credible ATXN2 staining should resolve within cytoplasm and fit the specimen's cell morphology (UniProt Q99700: cytoplasm; standard IHC practice).
How should I score ATXN2 staining across tissue sections? ⚠ ANSWER MARKED FOR VERIFICATION
Define the cell population and compartment before scoring; ATXN2 is cytoplasmic, and staining varies across tissue cell types (UniProt Q99700: subcellular location; HPA tissue IHC). For a specified population, record the percentage of positive cells and staining intensity, then calculate an H-score from 0–300 if an intensity-weighted measure is needed (standard IHC scoring practice). For cellular processes or mixed regions, report positive area or density per mm² with a consistent region-of-interest rule (standard image-analysis practice). Normalize counts to eligible cells or measured tissue area, and compare sections processed in the same staining batch (standard IHC practice). Keep neuronal and non-neuronal populations separate when evaluating CNS specimens (HPA tissue IHC: neuronal staining; standard IHC practice).
How can I distinguish true ATXN2 staining from artefact?
A convincing signal follows cytoplasmic cell morphology and appears in an appropriate cell population, such as caudate neurons or lung macrophages (UniProt Q99700: cytoplasm; HPA tissue IHC: high in caudate neuronal cells and lung macrophages). Check a documented positive section and a no-primary section in the same run before interpreting faint DAB (standard IHC practice). Predominantly nuclear or membrane-edge signal conflicts with the reported cytosolic location and needs closer review (HPA subcellular: cytosol; standard IHC practice). Exclude section-edge accentuation, necrotic regions and endogenous peroxidase staining from the scored area (standard chromogenic IHC practice). Treat a negative result cautiously because HPA reports medium consistency between antibody staining and RNA expression (HPA tissue IHC: reliability description).
Boster reagents

Best ATXN2 / Ataxin-2 IHC Antibodies

Three anti-ATXN2 antibodies have IHC images from human paraffin sections; PA2098 also has mouse and rat brain IHC and IF images (catalog image captions).

Real IHC data IHC analysis of ATXN2 using anti-ATXN2 antibody (PA2098). ATXN2 was detected in a paraffin-embedded section of human breast cancer tissue. Heat mediated antigen retrieval was performed in EDTA buffer (pH 8.0, epitope retrieval solution). The tissue section was blocked with 10% goat serum. The tissue section was then incubated with 2 μg/ml rabbit anti-ATXN2 Antibody (PA2098) overnight at 4°C. Peroxidase Conjugated Goat Anti-rabbit IgG was used as secondary antibody and incubated for 30 minutes at 37°C. The tissue section was developed using HRP Conjugated Rabbit IgG Super Vision Assay Kit (Catalog # SV0002) with DAB as the chromogen.
Anti-ATX2/ATXN2 Antibody ®
Cat # PA2098
Real IHC data IHC analysis of SCA2/ATXN2 using anti-SCA2/ATXN2 antibody (A01915). SCA2/ATXN2 was detected in a paraffin-embedded section of human thyroiditis tissue. Heat mediated antigen retrieval was performed in EDTA buffer (pH 8.0, epitope retrieval solution). The tissue section was blocked with 10% goat serum. The tissue section was then incubated with 2 μg/ml rabbit anti-SCA2/ATXN2 Antibody (A01915) overnight at 4°C. Peroxidase Conjugated Goat Anti-rabbit IgG was used as secondary antibody and incubated for 30 minutes at 37°C. The tissue section was developed using HRP Conjugated Rabbit IgG Super Vision Assay Kit (Catalog # SV0002) with DAB as the chromogen.
Anti-SCA2/ATXN2 Antibody ®
Cat # A01915
Real IHC data IHC analysis of ATX2/ATXN2 using anti-ATX2/ATXN2 antibody (PB9483). ATX2/ATXN2 was detected in a paraffin-embedded section of human breast cancer tissue. Heat mediated antigen retrieval was performed in EDTA buffer (pH 8.0, epitope retrieval solution). The tissue section was blocked with 10% goat serum. The tissue section was then incubated with 2 μg/ml rabbit anti-ATX2/ATXN2 Antibody (PB9483) overnight at 4°C. Peroxidase Conjugated Goat Anti-rabbit IgG was used as secondary antibody and incubated for 30 minutes at 37°C. The tissue section was developed using HRP Conjugated Rabbit IgG Super Vision Assay Kit (Catalog # SV0002) with DAB as the chromogen.
Anti-ATX2/ATXN2 Antibody ®
Cat # PB9483

A01915 has human thyroiditis, colorectal adenocarcinoma, tonsil and breast cancer IHC images; PB9483 has human breast cancer, colonic adenoma cancer, glioma and placenta IHC images (A01915 and PB9483 image captions). PA2098 has human breast and rectal cancer plus mouse and rat brain IHC images, and mouse and rat brain IF images (PA2098 image captions).

Which to pick: Choose PA2098 for cross-species tissue IHC or mouse and rat IF; ICC is listed as an application, but the supplied ICC evidence contains no image (PA2098 applications, reactivity and image captions). For human tissue IHC, A01915 is a polyclonal option with human IHC images, while PB9483 has human IHC images; its listed mouse and rat reactivity is not demonstrated by the supplied IHC images (A01915 dilution data and image captions; PB9483 reactivity and image captions). Each SKU’s own IHC caption describes paraffin sections, EDTA retrieval at pH 8.0 and primary antibody at 2 μg/ml; the fixative is unreported (PA2098, A01915 and PB9483 IHC image captions).

Each figure is that product's own IHC / IF validation image from its datasheet.

References

  1. UniProt Consortium. UniProt entry Q99700 (ATX2_HUMAN, Ataxin-2).
  2. Human Protein Atlas. ATXN2 tissue IHC expression (reliability: Enhanced).
  3. Human Protein Atlas. ATXN2 subcellular location (ICC-IF): Localized to the cytosol..
  4. Human Protein Atlas. ATXN2 antibody validation summary (3 antibodies).
  5. Intracellular dynamics of Ataxin-2 in the human brains with normal and frontotemporal lobar degeneration with TDP-43 inclusions. Acta neuropathologica communications 2020 — PMC7594343.
  6. Ataxin-2 as a candidate blood biomarker for estimating disease status in cases of suspected glioblastoma recurrence. Brain tumor pathology 2026 — PMC13076406.
  7. Atxn2 Knockout and CAG42-Knock-in Cerebellum Shows Similarly Dysregulated Expression in Calcium Homeostasis Pathway. Cerebellum (London, England) 2017 — PMC5243904.
  8. ATXN2-CAG42 sequesters PABPC1 into insolubility and induces FBXW8 in cerebellum of old ataxic knock-in mice. PLoS genetics 2012 — PMC3431311.
  9. PubMed PMID:8896555 — UniProt-cited evidence.
  10. PubMed PMID:8896556 — UniProt-cited evidence.
  11. PubMed PMID:14702039 — UniProt-cited evidence.