CDK12 / Cyclin-dependent kinase 12 · IHC design guide

Design Immunohistochemistry for CDK12

Plan CDK12 IHC in paraffin sections around general nuclear staining (HPA tissue IHC) and the catalog antibody’s 2–5 μg/ml range (datasheet A03495-1). Breast glandular cells show high staining (HPA tissue IHC) and can serve as a positive control for chromogenic nuclear scoring.

Evidence assembled Oct 2026 · For research use; verify linked source records and product datasheet before use
Immunohistochemistry protocol sheet for CDK12 (IHC for CDK12): expected localisation Nuclear tissue staining; speckles annotated molecularly (HPA tissue IHC; UniProt), antibody A03495-1, validated IHC image, and IHC protocol steps
Printable CDK12 IHC protocol sheet — expected localisation Nuclear tissue staining; speckles annotated molecularly (HPA tissue IHC; UniProt), antibody A03495-1, controls and protocol steps. Open the full CDK12 IHC guide →

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 tissue staining; speckles annotated molecularly (HPA tissue IHC; UniProt)
Staining pattern General nuclear staining across cell types (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 tissue fixation consistent (standard IHC practice; not target-specific)
Caveat Broad nuclear expression limits tissue-negative controls (HPA tissue IHC)
Regulation Widely expressed; regulation unspecified (UniProt)
Isoform / epitope 3 isoforms; check epitope coverage by sequence (UniProt)
Section 1

Recommended CDK12 IHC & IF Protocols

The catalog antibody protocol is accompanied by one published CDK12 IHC protocol for paraffin-embedded gastric tissue (PMC6743279).

Recommended immunohistochemistry (IHC-P) protocol parameters
SampleParaffin-embedded human bladder urothelial carcinoma tissue; fixative not specified (datasheet A03495-1)
FixationImage fixative and duration unreported (datasheet A03495-1); 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 A03495-1); 20 min, 95–100 °C (standard)
Peroxidase block3% H2O2, 10 min, room temperature (standard)
Blocking10% goat serum (datasheet A03495-1)
Primary antibodyRabbit anti-CDK12, 2-5 μg/ml (datasheet A03495-1)
Primary incubationOvernight at 4 °C (datasheet A03495-1)
DetectionHRP-conjugated secondary, DAB chromogen (datasheet A03495-1)
CounterstainHematoxylin, blue, dehydrate and mount (standard)
Expected resultCDK12-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 EDTA pH 8.0 heat-mediated retrieval (datasheet: A03495-1); the published gastric tissue protocol does not report retrieval conditions (PMC6743279).
Section 2

What Is the Expected CDK12 Staining Pattern?

CDK12 should stain nuclei, consistent with its nuclear and nuclear-speckle localization (UniProt Q9NYV4; HPA subcellular). Expect broad expression, including strong staining in the listed glandular, hematopoietic, respiratory epithelial, granular-layer, and neuronal cells (UniProt Q9NYV4: widely expressed; HPA tissue IHC: High). HPA rates the tissue pattern Supported because antibody staining is highly consistent with RNA expression (HPA tissue IHC: Supported). CDK12 has no transmembrane segment (UniProt Q9NYV4 topology).

What am I looking at on my slide?
Distinct nuclear staining in glandular cells of breast, appendix, adrenal gland, or cervix.This fits the reported High staining in those cells (HPA tissue IHC). Judge localization within identifiable cells; broad expression means adjacent positive cell types need not be dismissed (UniProt Q9NYV4: widely expressed; HPA tissue IHC: general nuclear expression).
Strong nuclei in bone-marrow hematopoietic cells, bronchial respiratory epithelium, cerebellar granular-layer cells, or cortical neurons.These are additional reported High patterns (HPA tissue IHC). Nuclear enrichment supports the call (HPA tissue IHC: general nuclear expression); speckles may be easier to resolve by IF than by chromogenic IHC (HPA subcellular; general microscopy practice).
Predominantly cytoplasmic, membranous, or extracellular color with little nuclear signal.This conflicts with the reported nuclear pattern (UniProt Q9NYV4: nucleus and nuclear speckles; HPA tissue IHC: general nuclear expression). Check morphology, counterstain, and detection controls before calling it CDK12; the compartment mismatch alone does not identify the artefact (general IHC practice).
Signal is strongest in an unexpected cell population while reported high-staining cells are faint.Consider cross-reactivity or endogenous detection activity (general IHC practice). HPA reports broad nuclear expression, so an unlisted positive cell type is not automatically false; weigh its compartment, nearby known-positive cells, and controls together (HPA tissue IHC; UniProt Q9NYV4: widely expressed).
Diffuse haze across cells and blank areas, or no stain in a reported high-staining tissue.Haze without nuclear contrast suggests background; absent nuclear signal in a reported positive population raises a failed-staining concern (general IHC practice; HPA tissue IHC: High in listed populations). Neither finding by itself proves that CDK12 is absent from the specimen.
💡Expected CDK12 appearanceCall a positive result when identifiable cells show nuclear enrichment, potentially strong in HPA-listed High populations; diffuse color without nuclear contrast or dominant membrane staining is suspect (HPA tissue IHC; UniProt Q9NYV4 localization; general IHC practice).
How each factor affects the staining
Expected compartmentCDK12 is nuclear and colocalizes with nuclear speckles through interphase (UniProt Q9NYV4); HPA describes general nuclear tissue staining (HPA tissue IHC). Score staining against the nuclear counterstain. In chromogenic sections, visible speckles are helpful but are not required to recognize nuclear enrichment (general microscopy practice).
Choice of reference tissue and cellsHPA lists High staining in specific cells from eight tissues, with no negative or low examples in this payload (HPA tissue IHC). Choose an identified listed population as a positive reference; do not treat an unlisted tissue as a validated negative control or infer that every cell in a listed tissue must stain strongly.
Antibody evidenceHPA008038 is IHC Supported and ICC Enhanced; HPA073305 has ICC Enhanced but no IHC rating in this record (HPA antibodies). Apply the IHC interpretation to an IHC-validated antibody and its controls. The ICC rating does not supply an IHC-P dilution or establish an IHC result for the second antibody.
Molecular variationUniProt lists 3 isoforms and numerous modified residues, including phosphorylation sites (UniProt Q9NYV4). The supplied record gives no antibody epitope or isoform recognition data, so these features cannot explain a specific staining difference or justify changing antigen retrieval.
IF/ICC: what pattern should be expected?HPA reports enhanced nucleoplasmic and nuclear-speckle localization in ICC-IF, with images from Rh30, SiHa, U2OS, A-431, and U-251MG (HPA subcellular). Expect nuclear enrichment with possible speckled detail; this is an IF interpretation, not an IF protocol or evidence that every cell line has identical intensity.
Why is my staining missing, weak or wrong?
SituationLikely causeNext action
Reported high-staining cells show no nuclear signal.The IHC run or tissue may be unsuitable; absence in one section does not establish a CDK12-negative tissue (general IHC practice; HPA tissue IHC: High in listed cells).Verify the intended cell population and tissue preservation, then review the IHC-validated antibody's supplied IHC-P conditions and a positive-control section (general IHC practice). No CDK12-specific retrieval or dilution is provided here.
Stain is mainly cytoplasmic or membranous.The distribution conflicts with nuclear CDK12 localization; nonspecific binding, misread morphology, or detection artefact are possibilities (UniProt Q9NYV4; HPA tissue IHC; general IHC practice).Compare with the nuclear counterstain and a known-positive section; review antibody and detection controls before scoring the signal as CDK12 (general IHC practice).
Whole sections have diffuse color without crisp nuclei.General background can obscure compartment-specific staining (general IHC practice). HPA's general nuclear pattern cannot validate uniform haze as CDK12 (HPA tissue IHC).Inspect the no-primary control and review blocking, washing, chromogen development, and detection settings under the established IHC workflow (general IHC practice).
An unexpected cell population stains more strongly than listed high-staining cells.Cross-reactivity or endogenous detection activity is possible, although CDK12 is widely expressed (general IHC practice; UniProt Q9NYV4). HPA's list is not an exclusion map (HPA tissue IHC).Check whether the signal is nuclear, compare a listed positive population, and use no-primary and detection controls to locate background (HPA tissue IHC; general IHC practice).
A nuclear result lacks obvious speckles in chromogenic sections.Speckles may be below the practical visual resolution of the section and chromogen pattern (general microscopy practice); HPA nevertheless reports nuclear speckles in ICC-IF (HPA subcellular).Score convincing nuclear enrichment in identifiable cells and reserve fine speckle assessment for the separate IF/ICC workflow (HPA tissue IHC; HPA subcellular; general microscopy practice).
Two antibodies or runs give different staining intensity.The record provides antibody validation categories but no shared epitope, dilution, or retrieval comparison (HPA antibodies). Intensity differences therefore have no supported CDK12-specific explanation here.Compare compartments and the same identified reference cells, confirm each antibody's IHC validation, and document run conditions before interpreting a biological difference (HPA antibodies; HPA tissue IHC; general IHC practice).

Sample controls for CDK12 IHC & IF

🧪Run bronchus first and score its respiratory epithelial cells for CDK12 staining (HPA: High in bronchus respiratory epithelial cells). HPA detects CDK12 in all 45 scored tissues, so there is no HPA-supported negative tissue; use no-primary and isotype controls, and treat any unstained adjacent stromal cells as an internal background reference only, not as validated CDK12-negative cells (HPA: no negative rows).
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, a concentration-matched rabbit IgG isotype control for the rabbit catalog antibody, and a CDK12 knockout specimen or a validated immunizing-peptide block as a biological specificity control (caption: rabbit anti-CDK12 A03495-1; standard IHC control practice). Quench endogenous peroxidase and check any inflammatory cells in bronchus for residual chromogen signal (HPA: bronchus respiratory epithelial cells High; standard chromogenic IHC practice).
⚠️Feasibility: A target-specific fixation window and its effect are unreported, and the selected A03495-1 paraffin-section caption does not state the fixative (caption: fixative not stated). Start with heat retrieval in EDTA at pH 8.0 as used in that caption; whether CDK12 staining depends on this retrieval condition is unreported (caption: EDTA pH 8.0 heat retrieval). Frozen sections cannot be judged easier from the supplied evidence; IF/ICC has a nuclear readout in imaged cell lines, while bronchial inflammatory cells can contribute endogenous peroxidase signal in chromogenic IHC (HPA: nucleoplasm and nuclear speckles in ICC-IF; HPA: bronchus respiratory epithelial cells High; 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

TissueCell typeLevelEvidenceSource
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

TissueCell typeLevelEvidenceSource
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 by checking nuclear localisation, retrieval conditions and cell level controls before comparing chromogenic IHC results across sections.

Which retrieval condition should I try first for weak CDK12 staining?
Use heat mediated antigen retrieval in EDTA at pH 8.0 for paraffin sections (datasheet A03495-1). The selected antibody produced CDK12 staining after this retrieval in a paraffin section of human bladder urothelial carcinoma (datasheet A03495-1). If nuclear staining is weak, check that heating and cooling were consistent across sections, then adjust retrieval duration in a small matched series (standard IHC practice). Keep the primary antibody near the documented 2 μg/ml condition while assessing retrieval, so changes remain interpretable (datasheet A03495-1). Compare nuclear signal with background and tissue morphology before extending retrieval further; excessive treatment can damage sections (standard IHC practice).
How should I troubleshoot fixation when CDK12 nuclear staining varies?
The selected image documents a paraffin section but does not state its fixative, so CDK12 sensitivity to particular fixation conditions is unknown (datasheet A03495-1). Record the fixative, fixation duration and tissue processing history for each section, and compare sections processed together before changing antibody conditions (standard IHC practice). If staining differs between batches, repeat the documented EDTA retrieval at pH 8.0 and 2 μg/ml primary concentration on matched sections (datasheet A03495-1). Assess nuclear staining alongside morphology, since damaged tissue can make a fixation or processing problem appear to be altered CDK12 expression (standard IHC practice). Do not infer fixation tolerance from broad tissue expression or nuclear localisation (UniProt Q9NYV4; HPA tissue IHC).
Where should convincing CDK12 staining appear in a tissue section?
Expect predominantly nuclear staining: CDK12 is assigned to the nucleus and nuclear speckles (UniProt Q9NYV4), and tissue IHC shows general nuclear expression (HPA tissue IHC). Chromogenic DAB staining may show a nuclear pattern without resolving individual speckles, so score the compartment that is reliably visible in the section (standard IHC practice). If diffuse cytoplasmic color dominates, inspect counterstain, tissue edges and secondary only controls before calling the pattern CDK12 positive (standard IHC practice; UniProt Q9NYV4 localisation). Compare similar cell populations within the same section rather than assuming equal intensity across all cells (standard IHC practice). Record mixed nuclear and cytoplasmic staining separately for review instead of folding both into a single positive score (standard IHC practice).
Could isoforms or epitope accessibility explain discordant CDK12 staining?
CDK12 has 3 listed isoforms, while the supplied antibody caption does not identify its epitope or establish which isoforms it detects (UniProt Q9NYV4; datasheet A03495-1). Map any available immunogen sequence against the isoforms before interpreting differences between specimens as isoform changes (standard antibody validation practice; UniProt Q9NYV4). CDK12 also has documented modified residues, including phosphorylation sites, but their effect on this antibody’s staining is unestablished (UniProt Q9NYV4; datasheet A03495-1). If staining is discordant, compare matched sections using the documented EDTA pH 8.0 retrieval and examine whether nuclear signal changes with processing (datasheet A03495-1; standard IHC practice). Seek independent epitope or genetic validation before assigning an isoform specific IHC pattern (standard antibody validation practice).
How can I investigate CDK12 localisation with multiplex IF?
Use IF as a separate optimisation: the supplied antibody image documents paraffin section chromogenic IHC, without an IF fixation or permeabilisation condition (datasheet A03495-1). Pair CDK12 with a marker for the expected cell population and a nuclear counterstain, then examine signal within identified nuclei (standard IF practice; UniProt Q9NYV4 localisation). Choose spectrally separated fluorophores after checking tissue autofluorescence in an unstained control, favoring a channel with low background for the weaker signal (standard IF practice). Because CDK12 is nuclear and has no transmembrane segment, optimise permeabilisation to expose its intracellular epitope while preserving nuclear morphology (UniProt Q9NYV4 topology and localisation; standard IF practice). Validate multiplex specificity with single stain and secondary only controls before interpreting apparent nuclear speckles (standard IF practice; HPA subcellular).
What should I check when CDK12 DAB staining is diffuse?
The documented workflow used a goat serum block at 10%, a rabbit primary at 2 μg/ml overnight at 4°C, and DAB detection (datasheet A03495-1). For diffuse color, compare a primary omitted section and check peroxidase blocking, washing, DAB development and primary concentration on matched sections (standard chromogenic IHC practice). Endogenous enzyme activity, excess detection reagent or nonspecific binding can produce color outside nuclei, so use those controls to locate the source (standard chromogenic IHC practice). Because CDK12 is nuclear, widespread cytoplasmic or extracellular deposition warrants scrutiny before scoring it as target signal (UniProt Q9NYV4 localisation; HPA tissue IHC). Keep exposure and development conditions consistent when comparing sections (standard IHC practice).
How should I score CDK12 staining across specimens? ⚠ ANSWER MARKED FOR VERIFICATION
Score CDK12 in defined cell populations and nuclear compartments, consistent with its nuclear localisation and the general nuclear tissue IHC profile (UniProt Q9NYV4; HPA tissue IHC). Record the percentage of positive nuclei and staining intensity, then calculate an H score if intensity categories can be applied consistently (standard IHC quantification practice). If spatial abundance is the question, report positive nuclei per mm² within a specified viable tissue area (standard IHC quantification practice). Normalise cell counts to all evaluable nuclei in that population, or density to the measured area, and apply the same thresholds across batches (standard IHC quantification practice). Exclude necrosis and damaged edges under predefined rules, and retain background control images for threshold review (standard IHC quantification practice).
How do I distinguish true CDK12 positivity from artefact?
A credible positive pattern is nuclear in identifiable viable cells, consistent with CDK12 nuclear localisation and the reported general nuclear tissue IHC pattern (UniProt Q9NYV4; HPA tissue IHC). Broad tissue expression means an unexpected cell population deserves verification, but it does not by itself establish that every cell must stain (UniProt Q9NYV4 tissue specificity; HPA tissue IHC). Treat staining confined to section edges, necrotic areas or structures without interpretable nuclei as suspect, and compare it with morphology and a primary omitted control (standard IHC practice). Peroxidase related color that persists without primary antibody should not be assigned to CDK12 (standard chromogenic IHC practice). Confirm disputed calls on matched sections using the documented EDTA pH 8.0 retrieval (datasheet A03495-1).
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); listed reactivity is Human (catalog: reactivity).

Real IHC data IHC analysis of CDK12 using anti-CDK12 antibody (A03495-1). CDK12 was detected in a paraffin-embedded section of human bladder urothelial carcinoma 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-CDK12 Antibody (A03495-1) 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-CDK12 Antibody ®
Cat # A03495-1

A03495-1 will render with an IHC figure from human bladder urothelial carcinoma; additional IHC captions show human prostate cancer and spleen in paraffin sections (catalog IHC image captions). Its IF/ICC caption shows A549 cells (catalog IF image caption).

Which to pick: Choose A03495-1 for human paraffin-section IHC: its caption documents heat retrieval in EDTA, pH 8.0, and primary antibody at 2 μg/ml (catalog IHC image caption). The same SKU is listed for IF/ICC at 5 μg/ml and has an A549 cell image (catalog applications, dilution, and IF image caption). Cross-species use has no listed validation (catalog: Human reactivity); clonality and the paraffin-section fixative are unreported (catalog payload and IHC image caption).

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

References

  1. UniProt Consortium. UniProt entry Q9NYV4 (CDK12_HUMAN, Cyclin-dependent kinase 12).
  2. Human Protein Atlas. CDK12 tissue IHC expression (reliability: Supported).
  3. Human Protein Atlas. CDK12 subcellular location (ICC-IF): Localized to the nucleoplasm and nuclear speckles..
  4. Human Protein Atlas. CDK12 antibody validation summary (2 antibodies).
  5. CDK12 Loss Promotes Prostate Cancer Development While Exposing Vulnerabilities to Paralog-Based Synthetic Lethality. bioRxiv : the preprint server for biology 2024 — PMC10983964.
  6. CDK12 is a potential biomarker for diagnosis, prognosis and immunomodulation in pan-cancer. Scientific reports 2024 — PMC10951204.
  7. CDK12 loss drives prostate cancer progression, transcription-replication conflicts, and synthetic lethality with paralog CDK13. Cell reports. Medicine 2024 — PMC11513839.
  8. 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.
  9. PubMed PMID:11683387 — UniProt-cited evidence.
  10. PubMed PMID:10048485 — UniProt-cited evidence.
  11. PubMed PMID:12168954 — UniProt-cited evidence.