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CDK12 / Cyclin-dependent kinase 12 · IHC design guide
Design Immunohistochemistry for CDK12
Plan chromogenic CDK12 IHC in paraffin sections around the general nuclear tissue pattern (HPA tissue IHC) and the catalog antibody’s 2–5 μg/ml IHC range (datasheet A03495-1). Breast glandular cells provide a high-staining reference for interpreting nuclear signal (HPA tissue IHC).
Evidence assembled Oct 2026 · For research use; verify linked source records and product datasheet before use
CDK12 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 staining in tissue (HPA tissue IHC) | |
| Staining pattern | General nuclear staining across tissues (HPA tissue IHC) | |
| Antigen retrieval | EDTA pH 8.0 HIER, heat-mediated (datasheet A03495-1) | |
| Positive control | Adrenal gland+4 more · see all | |
| Negative control | None in HPA (detected in all 45 tissues); use no-primary + isotype controls |
Important caveats
Reasons your staining may differ from the expected pattern.
| Fixation | Keep fixation consistent across paraffin sections (standard IHC practice; not target-specific) | |
| Caveat | High staining in varied cell types complicates scoring (HPA tissue IHC) | |
| Regulation | Widely expressed; regulation not stated (UniProt) | |
| Isoform / epitope | 3 isoforms; epitope coverage unreported (UniProt) |
Section 1
Recommended CDK12 IHC & IF Protocols
The catalog antibody’s IHC-P protocol is accompanied by a published CDK12 IHC protocol for gastric tissue microarrays (PMC6743279).
| Sample | Paraffin-embedded human bladder urothelial carcinoma tissue; fixative not specified (datasheet A03495-1) |
| Fixation | Image fixative and duration unreported (datasheet A03495-1); 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 A03495-1); 20 min, 95–100 °C (standard) |
| Peroxidase block | 3% H2O2, 10 min, room temperature (standard) |
| Blocking | 10% goat serum (datasheet A03495-1) |
| Primary antibody | Rabbit anti-CDK12, 2-5 μg/ml (datasheet A03495-1) |
| Primary incubation | Overnight at 4 °C (datasheet A03495-1) |
| Detection | HRP-conjugated secondary, DAB chromogen (datasheet A03495-1) |
| Counterstain | Hematoxylin, blue, dehydrate and mount (standard) |
| Expected result | CDK12-positive staining in glandular cells of adrenal gland (HPA tissue IHC: High). HPA tissue profile: General nuclear expression. No signal in the no-primary control. |
💡Decision noteStart with heat-mediated EDTA pH 8.0 retrieval (datasheet A03495-1). The published gastric IHC excerpt does not specify retrieval (PMC6743279).
Section 2
What Is the Expected CDK12 Staining Pattern?
CDK12 should give predominantly nuclear staining, consistent with its nuclear and nuclear-speckle localisation and lack of a transmembrane segment (UniProt Q9NYV4). Expect staining across multiple tissues rather than in one restricted population (UniProt Q9NYV4: widely expressed; HPA: low tissue specificity). HPA reports high staining in breast glandular cells, bone-marrow hematopoietic cells and cerebral-cortex neurons, with a supported tissue-IHC profile showing general nuclear expression (HPA: tissue IHC).
| Clear nuclear staining in breast glandular cells, with limited staining outside nuclei. | This fits the reported high glandular-cell staining and general nuclear profile (HPA: breast; HPA: tissue IHC). Compare signal with adjacent cells and the no-primary control before scoring intensity (standard IHC practice). |
| Predominantly cytoplasmic or membrane-edge staining, while nuclei remain unstained. | That conflicts with CDK12 localisation to the nucleus and nuclear speckles and its lack of a transmembrane segment (UniProt Q9NYV4). Check detection controls and antibody specificity before calling the pattern positive (standard IHC practice). |
| Breast staining is confined to non-glandular cells, with no glandular nuclear signal. | The distribution misses an HPA-reported high-staining population (HPA: breast glandular cells). Cross-reactivity or endogenous detection activity is possible (standard IHC practice); HPA's list does not establish that other breast cells are CDK12-negative. |
| A diffuse chromogenic haze covers nuclei and surrounding tissue. | The haze obscures the nuclear pattern expected for CDK12 (HPA: general nuclear expression; UniProt Q9NYV4: nucleus). Review background in the no-primary control and adjust blocking, detection or washing as indicated (standard IHC practice). |
| No nuclear signal appears in an otherwise interpretable breast or bone-marrow section. | Both contain HPA-reported high-staining populations (HPA: breast glandular cells; HPA: bone-marrow hematopoietic cells). A negative run warrants checking tissue preservation, retrieval and reagent performance; it alone does not establish absent CDK12 (standard IHC practice). |
💡Expected CDK12 appearanceCall a section positive when identifiable cells show clear nuclear staining, such as high staining in breast glandular cells (HPA: breast; HPA: general nuclear expression); isolated cytoplasmic colour or diffuse haze does not match the expected compartment (UniProt Q9NYV4: nucleus; standard IHC practice).
| Subcellular compartment | CDK12 localises to the nucleus and nuclear speckles, including speckles throughout interphase (UniProt Q9NYV4). Score nuclear signal in identifiable cells; the chromogenic tissue profile is described as general nuclear expression (HPA: tissue IHC). |
| Tissue and cell selection | HPA reports high staining in adrenal and breast glandular cells, bone-marrow hematopoietic cells, and cerebral-cortex neurons (HPA: tissue IHC). These are useful positive-reference populations; no HPA negative tissue is supplied. |
| Strength of pattern evidence | The tissue-IHC profile is Supported, with high consistency between staining and RNA expression (HPA: tissue IHC). HPA008038 has Supported IHC status; HPA073305 has no supplied IHC status (HPA: antibodies). Validation does not replace run controls (standard IHC practice). |
| Isoforms and modified residues | Three isoforms and 38 modified residues are listed (UniProt Q9NYV4). Their effect on this assay cannot be inferred because the supplied evidence gives no antibody epitope; avoid assigning an altered pattern to an isoform or phosphorylation state. |
| Retrieval and detection | Assess retrieval and detection with a documented positive tissue and run controls (standard IHC practice; HPA: high staining in breast glandular cells). Target-specific fixation sensitivity and an optimal retrieval condition are unreported in the supplied evidence. |
| IF/ICC: what localisation should I expect? | Nucleoplasm and nuclear speckles are enhanced locations in the HPA ICC-IF record (HPA: subcellular). That observation supports compartment interpretation; the IHC-P assessment comes from the tissue-IHC record (HPA: tissue IHC). |
| Situation | Likely cause | Next action |
|---|---|---|
| The positive-reference section has no nuclear colour. | The run may have failed at retrieval, primary incubation or detection (standard IHC practice); breast glandular cells are reported as high staining (HPA: breast). | Check reagent steps and controls, then compare the section with a documented high-staining tissue; do not score absence from this failed reference (standard IHC practice; HPA: tissue IHC). |
| Colour appears mainly in cytoplasm or at cell borders. | The compartment disagrees with nuclear CDK12 localisation (UniProt Q9NYV4) and the HPA general nuclear IHC profile (HPA: tissue IHC). | Inspect the no-primary control and repeat with appropriate detection controls before interpreting the signal as CDK12 (standard IHC practice). |
| Bone marrow shows widespread colour that is hard to assign to nuclei. | Hematopoietic cells have high reported CDK12 staining (HPA: bone marrow), while endogenous activity can contribute chromogenic background, depending on detection chemistry (standard IHC practice). | Compare a no-primary control and assess nuclei against the counterstain; address endogenous enzyme activity if the detection system uses that enzyme (standard IHC practice). |
| The whole section has a diffuse haze. | Background from blocking, washing or detection can hide cell boundaries and nuclei (standard IHC practice); CDK12 is expected to stain nuclei (HPA: tissue IHC). | Use the no-primary control to locate the background source, then adjust blocking, washing or detection as indicated (standard IHC practice). |
| Only non-glandular breast cells stain. | This omits a reported high-staining population (HPA: breast glandular cells); cross-reactivity or endogenous detection activity remains possible (standard IHC practice). | Confirm cell identity and nuclear localisation, inspect controls, and repeat with an IHC-supported antibody if needed (standard IHC practice; HPA: HPA008038 IHC Supported). |
| Nuclear signal is visible but difficult to score consistently. | CDK12 is widely expressed (UniProt Q9NYV4), and HPA describes general nuclear expression across tissues (HPA: tissue IHC). | Define the cell population and a consistent nuclear scoring threshold using the same counterstain and positive-reference section throughout the run (standard IHC practice). |
Experiment evidence
IHC & IF images showing CDK12 staining
A03495-1 · IHCIHC analysis of CDK12 using anti-CDK12 antibody (A03495-1). CDK12 was detected in a paraffin-embedded section of human bladder urothelial ca
A03495-1 · IHCIHC analysis of CDK12 using anti-CDK12 antibody (A03495-1). CDK12 was detected in a paraffin-embedded section of human prostate cancer tissu
A03495-1 · IFIF analysis of CDK12 using anti-CDK12 antibody (A03495-1) and anti-Beta Tubulin antibody (M01857-3). CDK12 was detected in immunocytochemica
HPA · Cerebral cortexHuman Protein Atlas IHC, Cerebral cortex. Source: https://www.proteinatlas.org/ENSG00000167258-CDK12/tissue/cerebral+cortex#imid_2381808
HPA · ColonHuman Protein Atlas IHC, Colon. Source: https://www.proteinatlas.org/ENSG00000167258-CDK12/tissue/colon#imid_2381750
HPA · LiverHuman Protein Atlas IHC, Liver. Source: https://www.proteinatlas.org/ENSG00000167258-CDK12/tissue/liver#imid_2381751
HPA · PancreasHuman Protein Atlas IHC, Pancreas. Source: https://www.proteinatlas.org/ENSG00000167258-CDK12/tissue/pancreas#imid_2381686
HPA · ICC-IF Rh30Human Protein Atlas immunofluorescence, Rh30, antibody HPA073305; green = CDK12, blue = nucleus, red = microtubules.
HPA · ICC-IF Rh30Human Protein Atlas immunofluorescence, Rh30, antibody HPA073305; green = CDK12, blue = nucleus, red = microtubules.
← swipe / scroll for more images →
Real IHC / IF data behind the staining-pattern expectations in this section.
Sample controls for CDK12 IHC & IF
🧪Run breast first and assess CDK12 staining in its glandular cells (HPA: High in breast glandular cells). HPA detects CDK12 in all 45 scored tissues, so there is no HPA negative tissue; use no-primary and isotype controls, and treat cells without specific nuclear DAB staining on the positive slide as internal background references rather than a presumed CDK12-negative cell type (HPA: no negative rows; UniProt: nuclear localization).
Positive control tissue: Adrenal gland (Glandular cells, HPA High)
Negative control tissue: None in HPA: CDK12 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 CDK12 in Rh30, SiHa, U2OS, A-431, U-251MG, with annotated localisation: Nucleoplasm (enhanced), Nuclear speckles (enhanced) (HPA subcellular).
Technical controls: Include a no-primary, secondary-only section and a rabbit IgG isotype control matched to the primary antibody’s clonality, alongside a CDK12 knockout specimen if available (caption: rabbit anti-CDK12; standard IHC practice). Block endogenous peroxidase before HRP/DAB detection, particularly around blood-containing areas of the breast section (caption: HRP/DAB detection; standard IHC practice).
⚠️Feasibility: A target-specific fixation window or fixation effect is unreported, and the selected A03495-1 paraffin-section caption does not state its fixative (caption: fixative unreported). That caption uses heat retrieval in EDTA at pH 8.0, but it does not establish that retrieval is required for every specimen; frozen-section ease is unreported (caption: EDTA retrieval; standard IHC practice). IF/ICC can help assess the expected nucleoplasmic and nuclear-speckle pattern, while endogenous peroxidase can add background to chromogenic breast sections (HPA: nucleoplasm and nuclear speckles; standard IHC practice).
HPA tissue IHC evidence for CDK12
Comprehensive Human Protein Atlas IHC scoring per tissue (reliability: Supported — 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 |
|---|---|---|---|---|
| Adrenal gland | Glandular cells | High | Protein (IHC) | HPA → |
| Appendix | Glandular cells | High | Protein (IHC) | HPA → |
| Bone marrow | Hematopoietic cells | High | Protein (IHC) | HPA → |
| Breast | Glandular cells | High | Protein (IHC) | HPA → |
| Bronchus | Respiratory epithelial cells | High | Protein (IHC) | HPA → |
Undetected expression · recommended negative controls
| Tissue | Cell type | Level | Evidence | Source |
|---|---|---|---|---|
| None in HPA: CDK12 is detected in all 45 scored tissues. Use a no-primary (secondary-only) and an isotype control instead. | ||||
Section 3
Advanced CDK12 IHC Tips
Troubleshoot CDK12 staining in paraffin sections by checking retrieval, nuclear localisation, controls and scoring before interpreting differences between samples.
What retrieval conditions should I start with for CDK12 in paraffin sections?
Start with heat-mediated retrieval in EDTA buffer at pH 8.0 (datasheet A03495-1). The selected paraffin-section example then used 10% goat serum blocking, 2 μg/ml primary antibody overnight at 4°C, and peroxidase detection with DAB (datasheet A03495-1). If nuclear staining is weak, first check that heating and cooling were consistent across sections; only then compare an alternative retrieval condition against the EDTA reference, keeping detection settings fixed (standard IHC practice). Judge improvement by clearer nuclear signal with low background, since CDK12 is reported in the nucleus and nuclear speckles (UniProt Q9NYV4).
How should I investigate weak CDK12 staining when fixation history varies?
Record the fixative, fixation duration and tissue-processing history for each section before comparing staining (standard IHC practice). Target-specific CDK12 sensitivity to fixation is unknown here: the selected paraffin-section caption does not state a fixative, so its successful staining cannot establish an optimal fixation condition (datasheet A03495-1). Compare sections with documented, matched processing using EDTA at pH 8.0 and the same antibody and detection settings, then assess nuclear signal and background together (datasheet A03495-1; standard IHC practice). Include a consistently processed reference section across runs to distinguish processing variation from a change in staining performance (standard IHC practice).
How can I decide whether a CDK12 staining pattern is plausible?
Assess CDK12 primarily within nuclei: UniProt places it in the nucleus and nuclear speckles, while HPA reports general nuclear tissue staining (UniProt Q9NYV4; HPA tissue IHC). The selected paraffin-section example demonstrates staining in human bladder urothelial carcinoma, but its caption does not define a diagnostic subcellular pattern (datasheet A03495-1). Compare DAB signal with the counterstained nuclei and score nuclear and cytoplasmic compartments separately, using identical exposure and scoring rules across sections (standard IHC practice). Predominantly extracellular or diffuse cytoplasmic staining deserves a control review before being assigned to CDK12, because those patterns conflict with its reported location (UniProt Q9NYV4; standard IHC practice).
Could isoform or epitope differences explain inconsistent CDK12 staining?
CDK12 has 3 reported isoforms and a protein kinase domain spanning residues 727–1020 (UniProt Q9NYV4). Its record also lists multiple modified residues, but the supplied antibody caption does not identify an epitope or show that any modification changes IHC binding (UniProt Q9NYV4; datasheet A03495-1). Check the antibody’s documented immunogen or epitope before comparing its staining with another reagent, and avoid assigning an isoform from DAB intensity alone (standard IHC practice). If patterns disagree, compare validated antibodies and a suitable specificity control on matched sections, while keeping retrieval at EDTA pH 8.0 for the catalog antibody (datasheet A03495-1; standard IHC practice).
How should I investigate CDK12 localisation by multiplex IF alongside this IHC result?
Use this as a separate IF assessment: HPA reports CDK12 in the nucleoplasm and nuclear speckles and lists ICC/IF images, while the selected antibody caption documents paraffin-section IHC only (HPA subcellular; datasheet A03495-1). Pair CDK12 with a marker for the cell population under study and a nuclear counterstain, then assess colocalisation within individual nuclei rather than comparing fields by eye (standard IF practice). Choose 2 well-separated fluorophore channels and check unstained tissue for autofluorescence before setting thresholds (standard IF practice). Because CDK12 is nuclear and lacks a transmembrane segment, validate permeabilisation that permits nuclear antibody access; the supplied evidence gives no IF-specific fixation or permeabilisation condition for this antibody (UniProt Q9NYV4; standard IF practice).
What should I check when CDK12 DAB staining obscures nuclei?
First inspect a no-primary control to distinguish antibody-associated staining from chromogen or detection background (standard IHC practice). The selected example used 10% goat serum blocking, 2 μg/ml primary antibody overnight at 4°C, a peroxidase-conjugated secondary for 30 minutes at 37°C, and DAB (datasheet A03495-1). If background persists, verify the peroxidase block, antibody dilution, wash quality and DAB development time on matched sections, changing one condition at a time (standard IHC practice). Prefer conditions that preserve interpretable nuclear staining, consistent with reported CDK12 localisation, while reducing signal in the no-primary control (UniProt Q9NYV4; standard IHC practice).
How should I quantify CDK12 staining across paraffin sections? ⚠ ANSWER MARKED FOR VERIFICATION
Define the cell population and regions to score before examining group labels, and exclude folds, necrosis and poorly preserved areas using the same rules throughout (standard IHC practice). For nuclear CDK12, report either the percentage of positive nuclei with an intensity-based H-score, or positive-nucleus density per mm² when cell abundance itself matters (UniProt Q9NYV4; standard IHC practice). Normalize intensity-based results to the number of evaluable nuclei in the specified population, and normalize density to analyzed tissue area (standard IHC practice). Keep retrieval, DAB development, counterstain and scoring thresholds consistent, and include a shared reference section when comparing staining runs (standard IHC practice).
When should an apparent CDK12-positive area be treated as artefact?
A credible result should show staining associated with intact nuclei in the evaluated cells, consistent with CDK12’s nuclear and speckle localisation and HPA’s general nuclear tissue pattern (UniProt Q9NYV4; HPA tissue IHC). Review cytoplasmic or extracellular deposits, section-edge enhancement and signal over necrotic tissue as possible artefacts before scoring them (standard IHC practice). Check a no-primary control and the peroxidase-blocking step when DAB appears in unexpected structures, because endogenous enzyme activity can contribute to chromogenic background (standard IHC practice). Interpret differences only among comparable, well-preserved cell populations processed and scored under the same conditions (standard IHC practice).
Boster reagents
Best CDK12 / Cyclin-dependent kinase 12 IHC Antibodies
A03495-1 has IHC data from human paraffin sections and IF/ICC data from A549 cells (catalog image captions; datasheet: Human reactivity).
Real IHC data
Anti-CDK12 Antibody ®
Cat # A03495-1
A03495-1 will render with its own IHC figure from human bladder urothelial carcinoma; its other IHC captions show human prostate cancer and spleen paraffin sections (catalog IHC image captions). The same SKU has IF/ICC data from A549 cells (catalog IF image caption; datasheet: IF/ICC applications).
Which to pick: For human tissue IHC, choose A03495-1: its IHC caption documents a paraffin section with EDTA retrieval at pH 8.0, while the fixative is unreported (catalog IHC image caption). For IF/ICC, A03495-1 has an A549 cell image and a listed concentration of 5 μg/ml; its host is rabbit and clonality is unreported (catalog IF image caption; datasheet: IF/ICC application, host, clone). No cross-species choice is supported because A03495-1 lists Human reactivity only (datasheet: reactivity).
Each figure is that product's own IHC / IF validation image from its datasheet.
References
- UniProt Consortium. UniProt entry Q9NYV4 (CDK12_HUMAN, Cyclin-dependent kinase 12).
- Human Protein Atlas. CDK12 tissue IHC expression (reliability: Supported).
- Human Protein Atlas. CDK12 subcellular location (ICC-IF): Localized to the nucleoplasm and nuclear speckles..
- Human Protein Atlas. CDK12 antibody validation summary (2 antibodies).
- CDK12 Loss Promotes Prostate Cancer Development While Exposing Vulnerabilities to Paralog-Based Synthetic Lethality. bioRxiv : the preprint server for biology 2024 — PMC10983964.
- CDK12 is a potential biomarker for diagnosis, prognosis and immunomodulation in pan-cancer. Scientific reports 2024 — PMC10951204.
- CDK12 loss drives prostate cancer progression, transcription-replication conflicts, and synthetic lethality with paralog CDK13. Cell reports. Medicine 2024 — PMC11513839.
- Expression pattern of CDK12 protein in gastric cancer and its positive correlation with CD8(+) cell density and CCL12 expression. International journal of medical sciences 2019 — PMC6743279.
- PubMed PMID:11683387 — UniProt-cited evidence.
- PubMed PMID:10048485 — UniProt-cited evidence.
- PubMed PMID:12168954 — UniProt-cited evidence.
Immunohistochemistry protocol sheet for CDK12 (Cyclin-dependent kinase 12). Expected localisation Nuclear staining in tissue (HPA tissue IHC). Antigen retrieval: EDTA pH 8.0 HIER, heat-mediated (datasheet A03495-1). Validated IHC antibody: A03495-1 at 2-5 μg/ml (the product's own IHC validation image is shown). Controls (HPA): positive Adrenal gland (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 bladder urothelial carcinoma tissue; fixative not specified (datasheet A03495-1); 2. Fixation: Image fixative and duration unreported (datasheet A03495-1); 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 A03495-1); 20 min, 95–100 °C (standard); 6. Peroxidase block: 3% H2O2, 10 min , room temperature (standard); 7. Blocking: 10% goat serum (datasheet A03495-1); 8. Primary antibody: Rabbit anti-CDK12, 2-5 μg/ml (datasheet A03495-1); 9. Primary incubation: Overnight at 4 °C (datasheet A03495-1). Watch for: Fixation: Keep fixation consistent across paraffin sections (standard IHC practice; not target-specific); Caveat: High staining in varied cell types complicates scoring (HPA tissue IHC); Isoform / epitope: 3 isoforms; epitope coverage unreported (UniProt); Regulation: Widely expressed; regulation not stated (UniProt). Evidence: UniProt Q9NYV4, HPA tissue IHC · Supported, HPA ICC-IF · nucleoplasm and nuclear speckles., Datasheet A03495-1, PMC6743279. QR code links to https://www.bosterbio.com/bosterbio-gene-info-cards/CDK12/immunohistochemistry-ihc-guide.