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PADI2 / Protein-arginine deiminase type-2 · IHC design guide
Design Immunohistochemistry for PADI2
Plan chromogenic PADI2 IHC on paraffin sections using breast glandular cells as a positive reference (HPA tissue IHC). Start with the catalog antibody at 2–5 μg/ml (datasheet A06877) and compare staining with adipocytes, where PADI2 was not detected (HPA tissue IHC).
Evidence assembled Oct 2026 · For research use; verify linked source records and product datasheet before use
PADI2 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 | Predominantly cytoplasmic in tissues (HPA tissue IHC) | |
| Staining pattern | Cytoplasmic staining in glia and breast glandular cells (HPA tissue IHC) | |
| Antigen retrieval | EDTA pH 8.0 HIER, heat-mediated (datasheet A06877) | |
| Positive control | Breast+4 more · see all | |
| Negative control | Adipose tissue+4 more · see all |
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 A06877) | |
| Caveat | Endometrial carcinoma stains; normal stroma is undetected (datasheet A06877; HPA tissue IHC) | |
| Regulation | No staining regulator specified (UniProt) | |
| Isoform / epitope | 2 isoforms; epitope differences are unspecified (UniProt) |
Section 1
Recommended PADI2 IHC & IF Protocols
The catalog antibody’s IHC-P protocol (datasheet A06877) is accompanied by four published PADI2 IHC workflows (PMC10452823; PMC5406534; PMC5352236; PMC13019754).
| Sample | Paraffin-embedded human endometrial carcinoma tissue; fixative not specified (datasheet A06877) |
| Fixation | Image fixative and duration unreported (datasheet A06877); 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 A06877); 20 min, 95–100 °C (standard) |
| Peroxidase block | 3% H2O2, 10 min, room temperature (standard) |
| Blocking | 10% goat serum (datasheet A06877) |
| Primary antibody | Rabbit anti-PADI2, 2-5 μg/ml (datasheet A06877) |
| Primary incubation | Overnight at 4 °C (datasheet A06877) |
| Detection | HRP-conjugated secondary, DAB chromogen (datasheet A06877) |
| Counterstain | Hematoxylin, blue, dehydrate and mount (standard) |
| Expected result | PADI2-positive staining in glandular cells of breast (HPA tissue IHC: High). HPA tissue profile: Cytoplasmic expression in several tissues, including skeletal muscle, salivary gland, breast,large intestine and CNS. No signal in the no-primary control. |
💡Decision noteStart with heat-mediated EDTA pH 8.0 retrieval (datasheet A06877). Citrate retrieval at 95 °C for 10 min is a published alternative (PMC5352236 methods).
Section 2
What Is the Expected PADI2 Staining Pattern?
PADI2 should stain predominantly in the cytoplasm (UniProt Q9Y2J8: cytoplasm; no transmembrane segment). In tissue sections, expect staining in selected cell populations rather than every cell: breast glandular cells and glial cells in several brain regions are reported as High (HPA tissue IHC). HPA rates the tissue staining profile Enhanced, citing high consistency between antibody staining and RNA expression data (HPA tissue IHC).
| Breast glandular cells show distinct cytoplasmic chromogen, with variation among neighboring cell types. | This fits the reported High staining in breast glandular cells (HPA tissue IHC) and cytoplasmic localisation (UniProt Q9Y2J8). Judge the signal in the named cells; a uniformly stained field is not required by the HPA profile. |
| Nuclei dominate the signal, or staining is confined to sharp cell borders with little cytoplasmic signal. | A nuclear dominant pattern conflicts with the UniProt cytoplasmic annotation (UniProt Q9Y2J8). Investigate compartment assignment and staining specificity before scoring it as PADI2. Some cerebellar granular cells are described as cytoplasm/membrane (HPA tissue IHC), so a membrane component there alone is not decisive. |
| Strong chromogen appears mainly in adipocytes instead of the expected positive cells. | Adipocytes are reported as Not detected (HPA tissue IHC). Check whether the signal follows tissue structures or persists in a no-primary control; cross-reactivity or endogenous detection activity are possible explanations (standard IHC practice), not conclusions from HPA. |
| A diffuse haze covers cells, stroma and slide areas without clear cell boundaries. | This cannot be scored as the cell-specific cytoplasmic pattern reported for PADI2 (HPA tissue IHC; UniProt Q9Y2J8). Review blocking, primary concentration, washes and chromogen development as general background checks (standard IHC practice). |
| The expected cell population remains unstained in a tissue selected as a positive control. | First verify that the section contains the relevant cells: breast glandular cells or glial cells in caudate, cerebral cortex or hippocampus are reported as High (HPA tissue IHC). An absent signal then prompts a check of the staining run and antibody performance; HPA does not establish a PADI2-specific fixation effect. |
💡Expected PADI2 appearanceCall a result positive when distinct, predominantly cytoplasmic staining occurs in an expected cell population, such as High-level breast glandular or brain glial cells (HPA tissue IHC; UniProt Q9Y2J8); diffuse field-wide colour or isolated nuclear signal warrants investigation (standard IHC practice).
| Compartment and topology | PADI2 is annotated as cytoplasmic and has no transmembrane segment (UniProt Q9Y2J8). Score cytoplasmic signal first while allowing for the cytoplasm/membrane description of cerebellar granular cells (HPA tissue IHC). |
| Cell type and tissue choice | HPA reports High staining in breast glandular cells, several brain glial populations and rectal endocrine cells, but Not detected in adipocytes (HPA tissue IHC). Compare the named cells within each section rather than treating the whole tissue as uniformly positive. |
| Evidence behind the reference pattern | HPA labels the tissue profile Enhanced and reports one rabbit polyclonal antibody, HPA047735, with Enhanced IHC validation (HPA tissue IHC; HPA antibodies). This supports the reference pattern but does not validate every staining configuration. |
| Protein forms | UniProt lists two isoforms, a 1–665 chain, and no signal peptide, propeptide or annotated glycosylation sites (UniProt Q9Y2J8). These entries do not identify the antibody epitope or predict isoform-specific staining, shedding, or fixation sensitivity. |
| Situation | Likely cause | Next action |
|---|---|---|
| No signal in a breast positive control. | The section may lack evaluable glandular cells, or the staining run may have failed (standard IHC practice); breast glandular cells are reported as High (HPA tissue IHC). | Confirm cell identity and preservation, then check the IHC-validated antibody, detection reagents and a concurrent control under the same run conditions (standard IHC practice). |
| Only nuclei stain strongly. | Nuclear dominant staining is outside the annotated cytoplasmic location (UniProt Q9Y2J8); the source does not establish its cause. | Check morphology and counterstain, review the no-primary control, and reassess antibody concentration and detection background before assigning PADI2 positivity (standard IHC practice). |
| Adipocytes stain while expected positive cells do not. | That distribution opposes HPA's Not detected call for adipocytes and High call for selected positive cells (HPA tissue IHC); nonspecific binding or detection background may contribute (standard IHC practice). | Compare matched positive and no-primary controls, check cell identification, and optimise blocking or antibody concentration if background persists (standard IHC practice). |
| Brown deposit is widespread and obscures cell boundaries. | Diffuse deposit may reflect excess primary or chromogen, inadequate washing, or endogenous peroxidase when using HRP detection (standard IHC practice). | Inspect a no-primary control; then review washes, development time, antibody concentration and the peroxidase-blocking step if HRP is used (standard IHC practice). |
| Two tissues give different fractions of stained cells. | HPA reports different named positive populations and levels: breast glandular cells are High, while bone marrow hematopoietic cells are Medium (HPA tissue IHC). | Score intensity and the fraction of positive cells within the identified population in each tissue; use the corresponding HPA tissue pattern as the comparison (HPA tissue IHC; standard IHC practice). |
| Can an IF/ICC image confirm the compartment call? | HPA lists no main subcellular location or ICC-IF cell-line images for PADI2 (HPA subcellular). | Use the UniProt cytoplasmic annotation and HPA tissue IHC pattern for this section (UniProt Q9Y2J8; HPA tissue IHC). Treat an IF/ICC image as independently assessed evidence, not as HPA image validation. |
Experiment evidence
IHC & IF images showing PADI2 staining
A06877 · IHCIHC analysis of PADI2 using anti-PADI2 antibody (A06877). PADI2 was detected in a paraffin-embedded section of human endometrial carcinoma t
A06877 · IHCIHC analysis of PADI2 using anti-PADI2 antibody (A06877). PADI2 was detected in a paraffin-embedded section of human breast cancer tissue. H
HPA · Cerebral cortexHuman Protein Atlas IHC, Cerebral cortex. Source: https://www.proteinatlas.org/ENSG00000117115-PADI2/tissue/cerebral+cortex#imid_17123231
HPA · Salivary glandHuman Protein Atlas IHC, Salivary gland. Source: https://www.proteinatlas.org/ENSG00000117115-PADI2/tissue/salivary+gland#imid_17123171
HPA · ColonHuman Protein Atlas IHC, Colon. Source: https://www.proteinatlas.org/ENSG00000117115-PADI2/tissue/colon#imid_17123165
HPA · LiverHuman Protein Atlas IHC, Liver. Source: https://www.proteinatlas.org/ENSG00000117115-PADI2/tissue/liver#imid_17123158
← swipe / scroll for more images →
Real IHC / IF data behind the staining-pattern expectations in this section.
Sample controls for PADI2 IHC & IF
🧪Run breast first: glandular cells should stain (HPA: High in breast glandular cells). Use adipose tissue as the negative tissue (HPA: Not detected in adipocytes); on the breast slide, treat unstained non-glandular cells, if present, as a background reference rather than assuming they are PADI2-negative.
Positive control tissue: Breast (Glandular cells, HPA High)
Negative control tissue: Adipose tissue (HPA Not detected)
ICC-IF cell lines (HPA subcellular resource): HPA carries no ICC-IF cell line for PADI2; derive a cell-line control from the positive tissue's cell type (Glandular cells) and confirm it by RNA or western blot first.
Technical controls: Include a no-primary, secondary-only control; a rabbit IgG isotype control matched to the primary antibody’s clonality and concentration; and verified PADI2-knockout tissue as a biological negative (A06877 tissue-IHC caption: rabbit primary antibody). For chromogenic IHC, quench endogenous peroxidase and inspect breast sections for DAB-like signal in blood-rich areas (A06877 tissue-IHC caption: HRP/DAB detection).
⚠️Feasibility: No target-specific fixation window or fixation effect is reported, and the selected A06877 paraffin-section caption does not state the fixative (A06877 tissue-IHC caption). The caption uses heat retrieval in EDTA at pH 8.0, but does not establish that retrieval is required (A06877 tissue-IHC caption). The supplied evidence does not establish whether frozen sections or IF are easier; in breast sections, check that apparent staining is within glandular cells rather than luminal debris or blood-rich areas (HPA: High in breast glandular cells; A06877 tissue-IHC caption: HRP/DAB detection).
HPA tissue IHC evidence for PADI2
Comprehensive Human Protein Atlas IHC scoring per tissue (reliability: Enhanced — High consistency between antibody staining and RNA expression data.). Rows are taken directly from the HPA tissue chart — click any row's HPA link to view the source.
Positive expression · recommended positive controls
| Tissue | Cell type | Level | Evidence | Source |
|---|---|---|---|---|
| Breast | Glandular cells | High | Protein (IHC) | HPA → |
| Caudate | Glial cells | High | Protein (IHC) | HPA → |
| Cerebellum | Granular cells - cytoplasm/membrane | High | Protein (IHC) | HPA → |
| Cerebral cortex | Glial cells | High | Protein (IHC) | HPA → |
| Hippocampus | Glial cells | High | Protein (IHC) | HPA → |
Undetected expression · recommended negative controls
| Tissue | Cell type | Level | Evidence | Source |
|---|---|---|---|---|
| Adipose tissue | Adipocytes | Not detected | Protein (IHC) | HPA → |
| Adrenal gland | Glandular cells | Not detected | Protein (IHC) | HPA → |
| Appendix | Endocrine cells | Not detected | Protein (IHC) | HPA → |
| Bronchus | Respiratory epithelial cells | Not detected | Protein (IHC) | HPA → |
| Cervix | Squamous epithelial cells | Not detected | Protein (IHC) | HPA → |
Section 3
Advanced PADI2 IHC Tips
Troubleshoot PADI2 staining in paraffin sections by checking retrieval, cell type, cytoplasmic localisation, and controls before comparing chromogenic signal across samples.
What retrieval should I try first when PADI2 staining is weak?
Use heat-mediated antigen retrieval in EDTA at pH 8.0 for paraffin-section PADI2 IHC (datasheet A06877). The selected image used that retrieval before incubation with 2 μg/ml primary antibody overnight at 4°C, so keep those conditions together when establishing a reference slide (datasheet A06877). If staining remains weak, compare retrieval duration on adjacent sections while holding detection and exposure to chromogen constant; excessive heating can damage morphology and complicate scoring (standard IHC practice). Judge improvement in expected cytoplasmic staining against matched background and a positive control, rather than treating stronger DAB everywhere as improved PADI2 detection (UniProt Q9Y2J8 subcellular location; standard IHC practice).
How should I troubleshoot fixation when paraffin-section PADI2 staining varies?
The selected PADI2 paraffin-section image does not state a fixative, so target-specific fixation sensitivity is unknown (datasheet A06877). Record each specimen’s fixative and fixation duration, then compare sections processed and stained together; fixation differences can change antigen accessibility and tissue morphology in IHC generally (standard IHC practice). Use the reported EDTA retrieval at pH 8.0 and 2 μg/ml primary incubation as a consistent starting point while examining that variation (datasheet A06877). If a poorly stained section also has damaged morphology, assess processing with a matched control before attributing its low cytoplasmic signal to low PADI2 expression (UniProt Q9Y2J8 subcellular location; standard IHC practice).
Should I score nuclear or membrane staining as PADI2 positive?
Prioritise cytoplasmic staining: PADI2 is annotated as cytoplasmic and has no transmembrane segment (UniProt Q9Y2J8 subcellular location and topology). Tissue IHC reports high signal in breast glandular cells and glial cells in several brain regions, providing cell populations in which to examine that pattern (HPA tissue IHC). A sharp membrane rim or exclusively nuclear DAB signal warrants scrutiny of counterstain, section edges, and nonspecific detection before it enters a positive score (UniProt Q9Y2J8 subcellular location; standard IHC practice). Compare the suspect pattern with a no-primary control and with cytoplasmic signal in a matched positive section; localisation alone cannot establish antibody specificity (standard IHC practice).
Can this IHC result distinguish PADI2 isoforms or reveal epitope masking?
PADI2 has 2 annotated isoforms, but the supplied antibody evidence does not map its epitope or establish isoform selectivity (UniProt Q9Y2J8 isoforms; datasheet A06877). Treat chromogenic signal as PADI2 staining without assigning it to isoform 1 or 2 on morphology alone (UniProt Q9Y2J8 isoforms; standard IHC practice). The record describes one full-length chain, residues 1–665, with no annotated glycosylation sites or modified residues; these annotations do not identify the antibody’s binding site (UniProt Q9Y2J8 processing and PTMs). If staining changes after retrieval, check an independently validated epitope or orthogonal expression evidence before calling the difference isoform-specific (standard IHC practice).
How could IF help check a puzzling PADI2 IHC pattern?
Use IF as a separate follow-up to paraffin-section chromogenic IHC, since the selected antibody evidence here documents IHC and supplies no IF/ICC image (datasheet A06877; HPA subcellular). Multiplex PADI2 with a validated marker for the expected cell population, such as glial cells in a brain section, and include single-label controls to check channel separation (HPA tissue IHC; standard IF practice). Choose a fluorophore whose signal can be distinguished from the specimen’s autofluorescence, and inspect an unstained section before interpreting weak fluorescence (standard IF practice). Because PADI2 is cytoplasmic and lacks a transmembrane segment, assess permeabilisation for access to its cytoplasmic epitope; the precise antibody epitope remains unspecified (UniProt Q9Y2J8 subcellular location and topology; datasheet A06877).
What should I check when DAB background obscures cytoplasmic PADI2?
Begin with a no-primary section to separate secondary or detection-system background from primary-antibody staining (standard IHC practice). The selected paraffin-section example used 10% goat serum blocking, 2 μg/ml rabbit primary overnight at 4°C, and a peroxidase-based DAB readout (datasheet A06877). Include a peroxidase-blocking step and inspect whether precipitate or widespread brown signal persists when primary antibody is omitted; these are general chromogenic IHC checks (standard IHC practice). Adjust blocking, washing, and DAB development using adjacent sections, then accept improvements only if the expected cytoplasmic cell pattern remains visible (UniProt Q9Y2J8 subcellular location; standard IHC practice).
How should I quantify PADI2 staining across paraffin sections? ⚠ ANSWER MARKED FOR VERIFICATION
Define the cell population and region before scoring, then record cytoplasmic PADI2 intensity and the percentage of positive cells (UniProt Q9Y2J8 subcellular location; standard IHC practice). An H-score combines intensity grades with their corresponding positive-cell percentages; use the same thresholds, counterstain, and DAB development settings across the comparison (standard IHC practice). For a cell-rich region, positive-cell density per mm² is another option, provided the measured tissue area and excluded damaged areas are documented (standard IHC practice). Normalise to the number of eligible cells or intact tissue area, and stratify by cell type because HPA reports different expression levels among tissues and cells (HPA tissue IHC; standard IHC practice).
How can I distinguish true PADI2 signal from a staining artefact?
A credible positive has a reproducible cytoplasmic pattern in an appropriate cell population, consistent with PADI2 localisation and reported tissue staining (UniProt Q9Y2J8 subcellular location; HPA tissue IHC). Compare suspect regions with matched controls and nearby intact tissue; edge staining, necrotic material, and signal that ignores cell boundaries can mislead chromogenic scoring (standard IHC practice). Test whether brown signal persists without primary antibody and check peroxidase blocking, since endogenous enzyme activity can contribute to a DAB readout (standard IHC practice). Be cautious when interpreting carcinoma staining against normal endometrium: the selected image shows endometrial carcinoma, while HPA reports PADI2 undetected in normal endometrial stromal cells (datasheet A06877; HPA tissue IHC).
Boster reagents
Best PADI2 / Protein-arginine deiminase type-2 IHC Antibodies
A06877 has real paraffin-section IHC images from human endometrial carcinoma and breast cancer, and mouse and rat spinal cord (catalog IHC image captions). No IF image is supplied (catalog IF images).
Real IHC data
Anti-PADI2 Antibody ®
Cat # A06877
A06877 has paraffin-section IHC images from human endometrial carcinoma and breast cancer, mouse spinal cord, and rat spinal cord (catalog IHC image captions). Its listed applications include IHC, with human, mouse, and rat reactivity (catalog applications and reactivity).
Which to pick: Choose A06877 for paraffin-section tissue IHC; its own image caption documents EDTA retrieval at pH 8.0, a 10% goat-serum block, and 2 μg/ml primary antibody overnight at 4°C (A06877 IHC image caption). It is also the cross-species IHC choice for human, mouse, and rat tissue (A06877 IHC image captions); the fixative is unreported (A06877 IHC image captions). No IF/ICC antibody is supported by this catalog payload because A06877 has no listed IF/ICC application or IF image (catalog applications and IF images).
Each figure is that product's own IHC / IF validation image from its datasheet.
References
- UniProt Consortium. UniProt entry Q9Y2J8 (PADI2_HUMAN, Protein-arginine deiminase type-2).
- Human Protein Atlas. PADI2 tissue IHC expression (reliability: Enhanced).
- Human Protein Atlas. PADI2 subcellular location (ICC-IF): Highest expression in RPTEC/TERT1: 30.6 nTPM.
- Human Protein Atlas. PADI2 antibody validation summary (1 antibodies).
- Peptidylarginine Deiminase Type 2 Predicts Tumor Progression and Poor Prognosis in Patients with Curatively Resected Biliary Tract Cancer. Cancers 2023 — PMC10452823.
- Protein-arginine deiminase 2 suppresses proliferation of colon cancer cells through protein citrullination. Cancer science 2017 — PMC5406534.
- Investigating the expression, effect and tumorigenic pathway of PADI2 in tumors. OncoTargets and therapy 2017 — PMC5352236.
- Inhibition of PADI2-mediated vimentin citrullination alleviates silica-induced pulmonary fibrosis in mice. Particle and fibre toxicology 2026 — PMC13019754.
- PubMed PMID:12392711 — UniProt-cited evidence.
- PubMed PMID:15087120 — UniProt-cited evidence.
- PubMed PMID:10231032 — UniProt-cited evidence.
Immunohistochemistry protocol sheet for PADI2 (Protein-arginine deiminase type-2). Expected localisation Predominantly cytoplasmic in tissues (HPA tissue IHC). Antigen retrieval: EDTA pH 8.0 HIER, heat-mediated (datasheet A06877). Validated IHC antibody: A06877 at 2-5 μg/ml (the product's own IHC validation image is shown). Controls (HPA): positive Breast (Glandular cells); negative Adipose tissue. IHC-P workflow on paraffin sections; fixative unspecified. Protocol steps: 1. Sample: Paraffin-embedded human endometrial carcinoma tissue; fixative not specified (datasheet A06877); 2. Fixation: Image fixative and duration unreported (datasheet A06877); 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 A06877); 20 min, 95–100 °C (standard); 6. Peroxidase block: 3% H2O2, 10 min , room temperature (standard); 7. Blocking: 10% goat serum (datasheet A06877); 8. Primary antibody: Rabbit anti-PADI2, 2-5 μg/ml (datasheet A06877); 9. Primary incubation: Overnight at 4 °C (datasheet A06877). Watch for: Fixation: Matched tissue-IHC evidence does not establish the fixation claim. Validate the specimen-specific method before use. (selected-SKU IHC image A06877); Caveat: Endometrial carcinoma stains; normal stroma is undetected (datasheet A06877; HPA tissue IHC); Isoform / epitope: 2 isoforms; epitope differences are unspecified (UniProt); Regulation: No staining regulator specified (UniProt). Evidence: UniProt Q9Y2J8, HPA tissue IHC · Enhanced, HPA cell-line RNA · Highest expression in RPTEC/TERT1: 30.6 nTPM, Datasheet A06877, PMC10452823, PMC5406534. QR code links to https://www.bosterbio.com/bosterbio-gene-info-cards/PADI2/immunohistochemistry-ihc-guide.