PRDM2 / PR domain zinc finger protein 2 · IHC design guide

Design Immunohistochemistry for PRDM2

Plan PRDM2 paraffin IHC with the catalog antibody at 2–5 μg/ml (datasheet: A03223-2). Use high-staining brain neuronal cells as a reference (HPA tissue IHC), and score nuclear and cytoplasmic staining separately (HPA tissue IHC; standard IHC practice).

Evidence assembled Oct 2026 · For research use; verify linked source records and product datasheet before use
Immunohistochemistry protocol sheet for PRDM2 (IHC for PRDM2): expected localisation Nuclear and cytoplasmic staining in most tissues (HPA tissue IHC), antibody A03223-2, validated IHC image, and IHC protocol steps
Printable PRDM2 IHC protocol sheet — expected localisation Nuclear and cytoplasmic staining in most tissues (HPA tissue IHC), antibody A03223-2, controls and protocol steps. Open the full PRDM2 IHC guide →

PRDM2 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 Nuclear and cytoplasmic staining in most tissues (HPA tissue IHC)
Staining pattern Most tissues show nuclear and cytoplasmic cell staining (HPA tissue IHC)
Antigen retrieval EDTA pH 8.0 HIER, heat-mediated (datasheet A03223-2)
Positive control ⓘ Caudate+4 more · see all
Negative control ⓘ Ovary+3 more · see all
Important caveats
Reasons your staining may differ from the expected pattern.
Fixation Keep fixation conditions consistent across sections. (standard IHC practice; not target-specific)
Caveat Staining and RNA expression show low consistency (HPA tissue IHC)
Regulation Isoform 1 exceeds isoform 3 in testis (UniProt)
Isoform / epitope 5 isoforms; epitope coverage is undetermined (UniProt)
Section 1

Recommended PRDM2 IHC & IF Protocols

The catalog antibody uses heat-mediated EDTA pH 8.0 retrieval (datasheet A03223-2). The published lung tumor IHC protocol below adds a tissue-specific example (PMC12327139: IHC methods).

Recommended immunohistochemistry (IHC-P) protocol parameters
SampleParaffin-embedded human rectum adenocarcinoma tissue; fixative not specified (datasheet A03223-2)
FixationImage fixative and duration unreported (datasheet A03223-2); 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 A03223-2); 20 min, 95–100 °C (standard)
Peroxidase block3% H2O2, 10 min, room temperature (standard)
Blocking10% goat serum (datasheet A03223-2)
Primary antibodyRabbit anti-PRDM2, 2-5 μg/ml (datasheet A03223-2)
Primary incubationOvernight at 4 °C (datasheet A03223-2)
DetectionHRP-conjugated secondary, DAB chromogen (datasheet A03223-2)
CounterstainHematoxylin, blue, dehydrate and mount (standard)
Expected resultPRDM2-positive staining in neuronal cells of caudate (HPA tissue IHC: High). HPA tissue profile: Nuclear and cytoplasmic expression in most tissues. No signal in the no-primary control.
💡Decision noteStart with heat-mediated EDTA pH 8.0 retrieval for the catalog antibody (datasheet A03223-2). The published protocol does not specify retrieval (PMC12327139: IHC methods).
Section 2

What Is the Expected PRDM2 Staining Pattern?

PRDM2 is a nuclear protein with no transmembrane segment (UniProt Q13029). In tissue IHC, HPA reports nuclear and cytoplasmic staining in most tissues, with high staining in neurons of the caudate, cerebral cortex and hippocampus (HPA tissue IHC). Use these cells as reference positives while allowing for tissue dependent intensity. HPA rates the tissue staining Approved but reports low consistency between antibody staining and RNA expression (HPA tissue IHC).

What am I looking at on my slide?
Neuronal nuclei stain strongly in caudate, cerebral cortex or hippocampus, with some cytoplasmic staining.This fits the highest listed tissue IHC signals and HPA’s nuclear and cytoplasmic profile (HPA tissue IHC: High in neuronal cells; nuclear and cytoplasmic expression). Interpret the nuclear component alongside PRDM2’s nuclear localization (UniProt Q13029), while keeping HPA’s low staining–RNA consistency in mind (HPA tissue IHC).
Adrenal or breast glandular cells, or kidney tubular cells, show moderate staining.Medium staining in these specific cell populations is consistent with the tissue observations (HPA tissue IHC: Medium in adrenal and breast glandular cells and kidney tubular cells). Compare the cell type and compartment as well as intensity; a medium result here need not resemble the high neuronal examples (HPA tissue IHC).
A sharp membrane rim dominates, or staining appears mainly in a cell population outside the listed pattern.A membrane dominant pattern conflicts with the reported nuclear and cytoplasmic tissue profile and lack of a transmembrane segment (HPA tissue IHC; UniProt Q13029 topology). Staining in an unexpected cell type warrants checks for cross reactivity or endogenous detection activity; HPA’s tissue list is a guide, not proof that every unlisted cell is negative (HPA tissue IHC).
Diffuse color covers cells and surrounding tissue without a clear cellular pattern.Treat this as background until the detection controls separate tissue staining from reagent or endogenous activity (general IHC practice). It cannot be assigned to PRDM2 merely because cytoplasmic expression is reported (HPA tissue IHC: nuclear and cytoplasmic expression). Check whether recognizable nuclei and the expected neuronal cell population remain distinguishable (HPA tissue IHC: High in neuronal cells).
No staining appears in neuronal cells of a caudate, cerebral cortex or hippocampus section.This disagrees with the listed high staining observations (HPA tissue IHC: High in neuronal cells). First check section quality, retrieval, primary antibody use and detection with appropriate controls (general IHC practice). A single blank section does not establish absent PRDM2, particularly given the reported low consistency between antibody staining and RNA expression (HPA tissue IHC).
💡Expected PRDM2 appearanceCall an IHC result supportive when neuronal cells show strong nuclear staining, with possible cytoplasmic signal, in caudate, cerebral cortex or hippocampus (HPA tissue IHC: High; nuclear and cytoplasmic expression; UniProt Q13029: nucleus); a dominant membrane rim or uniform noncellular color is suspect (UniProt Q13029 topology; general IHC practice).
How each factor affects the staining
Tissue and cell selection (HPA tissue IHC)Caudate, cerebral cortex and hippocampus neuronal cells are listed High; adrenal and breast glandular cells and kidney tubular cells are Medium (HPA tissue IHC). Ovarian stroma, splenic red pulp, thyroid glandular cells and vaginal squamous cells are listed Not detected in their specified populations (HPA tissue IHC).
Strength of tissue evidence (HPA tissue IHC; HPA antibody validation)The tissue profile is Approved, and antibody HPA005809 is IHC Approved, but the tissue report flags low consistency between staining and RNA expression (HPA tissue IHC; HPA antibodies). Treat a matching pattern as supportive evidence and investigate discordant specimens with controls rather than treating either readout as definitive.
Antigen retrieval in paraffin sections (general IHC practice)If a reference positive section is weak, review the established IHC-P retrieval and detection conditions before interpreting it as biologically negative (general IHC practice). The supplied UniProt and HPA records do not report PRDM2 specific retrieval or fixation sensitivity; no retrieval condition or target specific effect can be inferred from them.
Isoforms and antibody epitope (UniProt Q13029)UniProt lists five PRDM2 isoforms and says isoform 1 is expressed in testis at a much higher level than isoform 3 (UniProt Q13029). Antibody epitope coverage is not supplied, so a staining difference cannot be assigned to an isoform without independent epitope information. UniProt lists no signal peptide or propeptide and one chain spanning residues 1–1718 (UniProt Q13029).
What should IF/ICC show? (HPA subcellular; HPA antibodies)HPA reports nucleoplasm as Supported and Golgi apparatus as Approved in ICC-IF, with images from A-431, U-251MG and U2OS; antibody HPA005809 is ICC Supported (HPA subcellular; HPA antibodies). These ICC-IF observations help interpret compartment patterns but do not supply an IF/ICC protocol or establish that every tissue IHC section will show a distinct Golgi signal.
Why is my staining missing, weak or wrong?
SituationLikely causeNext action
The chosen positive section has weak or absent neuronal staining.The result conflicts with listed High neuronal staining in caudate, cerebral cortex and hippocampus (HPA tissue IHC); an IHC workflow failure is possible (general IHC practice).Confirm the intended neuronal population, then review section quality, antigen retrieval, primary antibody application and detection controls (general IHC practice). Do not infer PRDM2 specific fixation sensitivity from the supplied records.
A sharp membrane outline is the dominant staining pattern.A membrane dominant pattern does not fit nuclear PRDM2 without a transmembrane segment or HPA’s nuclear and cytoplasmic tissue profile (UniProt Q13029; HPA tissue IHC).Recheck cell boundaries and counterstain, compare the same run with a reference positive section, and inspect primary omitted controls for detection background (general IHC practice). Treat a persistent membrane only pattern as unconfirmed.
Unexpected cells stain as strongly as, or more strongly than, the expected population.Cross reactivity or endogenous detection activity may contribute (general IHC practice); HPA’s Approved tissue profile has low staining–RNA consistency (HPA tissue IHC).Locate staining within the unexpected cells, compare with the specified HPA cell populations, and run appropriate primary omitted and detection controls (general IHC practice; HPA tissue IHC). Do not assign specificity from intensity alone.
Color is diffuse across tissue or appears outside cells.Background from blocking, washing or the detection system can obscure a cellular pattern (general IHC practice). Cytoplasmic staining is reported for PRDM2, but a noncellular haze is not that pattern (HPA tissue IHC).Use a primary omitted control, review blocking and washes, and, where relevant to the chosen chromogen system, assess endogenous enzyme activity (general IHC practice). Score only interpretable cellular staining.
A presumed negative tissue contains stained cells.HPA’s Not detected calls apply to named populations, such as ovarian stroma cells or splenic red pulp cells, rather than every cell in the whole organ (HPA tissue IHC).Identify the stained cell population before calling the control discordant. If the named population stains, check primary omitted and detection controls, then interpret the finding in light of HPA’s low staining–RNA consistency (general IHC practice; HPA tissue IHC).
ICC-IF shows a Golgi pattern while tissue IHC is read mainly as nuclear and cytoplasmic.HPA reports Golgi apparatus as Approved and nucleoplasm as Supported in ICC-IF, while its tissue IHC summary is nuclear and cytoplasmic (HPA subcellular; HPA tissue IHC).Keep the application and specimen type attached to each observation. Assess tissue IHC against its reported cell populations and compartments; use the ICC-IF localization as context, without requiring a visible Golgi pattern in paraffin sections (HPA tissue IHC; HPA subcellular).

Sample controls for PRDM2 IHC & IF

🧪Run caudate first: neuronal cells have High PRDM2 staining (HPA: High in caudate neuronal cells). Use ovarian stroma as a negative tissue comparator (HPA: Not detected in ovarian stroma cells); within the caudate slide, assess unstained cells as background comparators, but HPA does not identify a cell type there as definitively negative.
Positive control tissue: Caudate (Neuronal cells, HPA High)
Negative control tissue: Ovary (HPA Not detected)
ICC-IF cell lines (HPA subcellular resource): HPA ICC-IF images show PRDM2 in A-431, U-251MG, U2OS, with annotated localisation: Nucleoplasm (supported), Golgi apparatus (approved) (HPA subcellular).
Technical controls: Include a no-primary, secondary-only control; a rabbit IgG isotype control matched to the primary antibody’s clonality; and a PRDM2 knockout specimen or validated peptide-block control (caption: rabbit anti-PRDM2 antibody). Quench endogenous peroxidase for DAB IHC; for IF, assess neuronal autofluorescence with a no-primary control (HPA: High in caudate neuronal cells).
⚠️Feasibility: A target-specific fixation window or fixation effect is unreported, and the selected A03223-2 tissue-IHC caption does not state the fixative (selected-SKU caption: fixative not stated). Paraffin IHC has a reported heat-retrieval condition, EDTA at pH 8.0, with primary antibody at 2 μg/ml overnight at 4°C (selected-SKU tissue-IHC caption). Is IF/ICC easier than paraffin IHC? The supplied evidence does not establish that, or that frozen sections are easier; HPA reports ICC-IF images and nucleoplasmic plus Golgi localization, so score those compartments separately if using IF (HPA: subcellular summary and ICC-IF cell lines).

HPA tissue IHC evidence for PRDM2

Comprehensive Human Protein Atlas IHC scoring per tissue (reliability: Approved — Low 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 →
Cerebral cortex Neuronal cells High Protein (IHC) HPA →
Hippocampus Neuronal cells High Protein (IHC) HPA →
Adrenal gland Glandular cells Medium Protein (IHC) HPA →
Breast Glandular cells Medium Protein (IHC) HPA →

Undetected expression · recommended negative controls

TissueCell typeLevelEvidenceSource
Ovary Ovarian stroma cells Not detected Protein (IHC) HPA →
Spleen Cells in red pulp Not detected Protein (IHC) HPA →
Thyroid gland Glandular cells Not detected Protein (IHC) HPA →
Vagina Squamous epithelial cells Not detected Protein (IHC) HPA →
Section 3

Advanced PRDM2 IHC Tips

Use the catalog antibody’s paraffin section IHC example as the starting point, and interpret compartmental staining alongside controls and the reported tissue profile.

What retrieval should I start with for PRDM2 in paraffin sections?
Use heat-mediated EDTA retrieval at pH 8.0 for PRDM2 paraffin sections (datasheet A03223-2). The selected example used that buffer before applying 2 μg/ml primary antibody overnight at 4°C, but it does not report a heating time (datasheet A03223-2). If staining is weak, vary heating duration on adjacent sections while keeping detection and exposure to DAB comparable (standard IHC practice). Include a no-primary control to distinguish weak antigen staining from detection background (standard IHC practice). Record retrieval conditions for each run so a change in nuclear signal can be traced to processing (standard IHC practice).
How should I handle fixation when PRDM2 staining is weak?
PRDM2-specific fixation sensitivity is unknown: the selected paraffin section caption does not state its fixative (datasheet A03223-2). Record each specimen’s fixative, fixation duration and processing history before comparing staining across blocks (standard IHC practice). When material permits, compare similarly processed sections with the same pH 8.0 EDTA retrieval and 2 μg/ml primary concentration used in the selected example (datasheet A03223-2). Evaluate nuclear signal and tissue preservation together, since poor morphology makes cell-level scoring unreliable (UniProt Q13029 localisation; standard IHC practice). Do not assign a fixation effect to PRDM2 from staining differences alone without matched processing controls (standard IHC practice).
Should PRDM2 staining be nuclear or cytoplasmic in tissue IHC?
Prioritise interpretable nuclear staining because PRDM2 is annotated as nuclear (UniProt Q13029 localisation). HPA reports nuclear and cytoplasmic staining in most tissues, while its subcellular data place PRDM2 in the nucleoplasm and Golgi apparatus (HPA tissue IHC; HPA subcellular). Score nuclear and cytoplasmic compartments separately rather than combining them into one positive call (standard IHC practice). Compare cellular staining with a no-primary control and with the same compartment in an adjacent section (standard IHC practice). Treat an exclusively cytoplasmic pattern cautiously, particularly because HPA reports low consistency between antibody staining and RNA expression (HPA tissue IHC).
Can this IHC stain distinguish PRDM2 isoforms or a modified epitope?
Do not assign an isoform from this stain without an epitope map or isoform-specific validation for the antibody (standard IHC practice). PRDM2 has 5 annotated isoforms and a SET domain spanning residues 28–141 (UniProt Q13029 isoforms; UniProt Q13029 domains). Isoform 1 is reported at a much higher level than isoform 3 in testis, but that expression difference does not establish what this antibody detects (UniProt Q13029 tissue specificity; standard IHC practice). Annotated phosphoserines include residues 421 and 643, yet their effect on this IHC epitope is unknown (UniProt Q13029 modified residues). Document antibody epitope information before interpreting compartment or tissue differences as isoform-specific staining (standard IHC practice).
How can I check PRDM2 localisation by IF alongside cell-type markers?
For a separate IF assay, multiplex PRDM2 with a validated neuronal marker when examining the neuronal populations reported as high in caudate, cerebral cortex and hippocampus (HPA tissue IHC; standard IF practice). Choose spectrally separated fluorophores and place the weaker channel away from prominent tissue autofluorescence, checking unstained tissue and single-stain controls (standard IF practice). Permeabilise for intracellular epitopes, since PRDM2 is nuclear and has no transmembrane segment; optimise the treatment against morphology and background (UniProt Q13029 localisation; UniProt Q13029 topology; standard IF practice). HPA reports nucleoplasmic and Golgi localisation in cell imaging, which can guide compartment checks without establishing tissue IF performance for this antibody (HPA subcellular). Keep IF conclusions separate from the catalog antibody’s chromogenic paraffin section result (datasheet A03223-2; standard IF practice).
How do I reduce diffuse or patchy PRDM2 DAB background?
Start by checking a no-primary section for secondary reagent, endogenous peroxidase and chromogen background (standard IHC practice). The selected PRDM2 example used 10% goat serum blocking, 2 μg/ml rabbit primary overnight at 4°C, and a peroxidase-conjugated secondary for 30 minutes at 37°C (datasheet A03223-2). Apply an appropriate peroxidase block before HRP and DAB detection, and wash thoroughly between reagents (standard chromogenic IHC practice). Compare background inside tissue with bare-slide regions and section edges before changing antibody concentration (standard IHC practice). Shorten chromogen development or adjust blocking only after confirming that the nuclear signal remains interpretable (UniProt Q13029 localisation; standard IHC practice).
What is a defensible way to quantify PRDM2 IHC across specimens? ⚠ ANSWER MARKED FOR VERIFICATION
Define the cell population and compartment before scoring, with nuclear PRDM2 as a prespecified readout (UniProt Q13029 localisation; standard IHC practice). Report the percentage of positive cells and staining intensity, or combine them as an H-score using the same thresholds across sections (standard IHC practice). If cell abundance varies, report positive cells per mm² alongside total eligible cells or tissue area so density has a denominator (standard IHC practice). Analyse comparable regions and exclude folds, necrosis and section edges using rules set before scoring (standard IHC practice). Keep cytoplasmic measurements separate because HPA describes both nuclear and cytoplasmic tissue staining and low consistency with RNA expression (HPA tissue IHC).
How can I separate plausible PRDM2 positivity from staining artefacts?
A reproducible nuclear signal in intact cells is consistent with PRDM2’s annotated nuclear localisation (UniProt Q13029 localisation; standard IHC practice). HPA reports high staining in neuronal cells of caudate, cerebral cortex and hippocampus, providing named populations for comparison rather than proof that every positive cell is specific (HPA tissue IHC). Inspect any dominant cytoplasmic signal alongside compartment controls because HPA also reports cytoplasmic tissue staining and Golgi localisation in cell imaging (HPA tissue IHC; HPA subcellular). Discount edge-enhanced staining, necrotic regions and signal reproduced on a no-primary slide, including endogenous peroxidase signal (standard IHC practice). Interpret discordant patterns cautiously because HPA rates consistency between antibody staining and RNA expression as low (HPA tissue IHC).
Boster reagents

Best PRDM2 / PR domain zinc finger protein 2 IHC Antibodies

A03223-2 has IHC images from human rectum adenocarcinoma, human testicular seminoma, and mouse and rat testis paraffin sections (catalog IHC captions). Its IF/ICC image uses U2OS cells (catalog IF caption).

Real IHC data IHC analysis of PRDM2 using anti-PRDM2 antibody (A03223-2). PRDM2 was detected in a paraffin-embedded section of human rectum adenocarcinoma 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-PRDM2 Antibody (A03223-2) 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-PRDM2 Antibody ®
Cat # A03223-2

A03223-2 is listed for IHC and shown on paraffin sections of human rectum adenocarcinoma, human testicular seminoma, mouse testis, and rat testis (catalog applications; A03223-2 IHC captions). A03223-2 is also listed for IF/ICC and shown in U2OS cells (catalog applications; A03223-2 IF caption).

Which to pick: For tissue IHC, choose A03223-2 for paraffin sections; its listed concentration is 2–5 μg/ml, and its IHC images used 2 μg/ml after EDTA retrieval at pH 8.0 (catalog dilution; A03223-2 IHC captions). For IF/ICC, the same SKU has a U2OS cell image using 5 μg/ml (A03223-2 IF caption). For cross-species IHC, A03223-2 has human, mouse, and rat paraffin-section images; its host is rabbit, clonality is unreported, and the IHC captions do not report a fixative (catalog entry; A03223-2 IHC captions).

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

References

  1. UniProt Consortium. UniProt entry Q13029 (PRDM2_HUMAN, PR domain zinc finger protein 2).
  2. Human Protein Atlas. PRDM2 tissue IHC expression (reliability: Approved).
  3. Human Protein Atlas. PRDM2 subcellular location (ICC-IF): Localized to the nucleoplasm and the Golgi apparatus..
  4. Human Protein Atlas. PRDM2 antibody validation summary (1 antibodies).
  5. The methylation profiles of PRDM promoters in non-small cell lung cancer. OncoTargets and therapy 2018 — PMC5973400.
  6. MiRNA-153 attenuates progression of non-small cell lung cancer through targeting positive regulatory/SET domain 2. African health sciences 2024 — PMC12327139.
  7. Dissection of gastric homeostasis in vivo facilitates permanent capture of isthmus-like stem cells in vitro. Nature cell biology 2023 — PMC13528691.
  8. Lower PRDM2 expression is associated with dopamine-agonist resistance and tumor recurrence in prolactinomas. BMC cancer 2015 — PMC4407330.
  9. PubMed PMID:7538672 — UniProt-cited evidence.
  10. PubMed PMID:9006946 — UniProt-cited evidence.
  11. PubMed PMID:17974005 — UniProt-cited evidence.