CDK6 / Cyclin-dependent kinase 6 · IHC design guide

Design Immunohistochemistry for CDK6

Plan chromogenic CDK6 IHC in paraffin sections around the predominantly cytoplasmic, sometimes nuclear tissue pattern (HPA tissue IHC). This guide covers fixation, antibody use, controls and scoring while accounting for variation across cell types (HPA tissue IHC).

Evidence assembled Oct 2026 · For research use; verify linked source records and product datasheet before use
Immunohistochemistry protocol sheet for CDK6 (IHC for CDK6): expected localisation Predominantly cytoplasmic; sometimes nuclear (HPA tissue IHC), antibody PB9995, validated IHC image, and IHC protocol steps
Printable CDK6 IHC protocol sheet — expected localisation Predominantly cytoplasmic; sometimes nuclear (HPA tissue IHC), antibody PB9995, controls and protocol steps. Open the full CDK6 IHC guide →

CDK6 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; sometimes nuclear (HPA tissue IHC)
Staining pattern Several cell types: cytoplasmic, sometimes nuclear (HPA tissue IHC)
Antigen retrieval Citrate pH 6 HIER, heat-mediated (datasheet PB9995)
Positive control ⓘ Duodenum+4 more · see all
Negative control ⓘ Caudate+4 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 varies across cell types and tissues (HPA tissue IHC)
Regulation Reduced in differentiating cells (UniProt)
Isoform / epitope No annotated isoforms; one chain, 1–326 (UniProt)
Section 1

Recommended CDK6 IHC & IF Protocols

Compare the catalog antibody’s IHC-P protocol (datasheet PB9995) with a published CDK6 staining protocol for mouse tumors and human ovarian cancer tissue microarrays (PMC4144705).

Recommended immunohistochemistry (IHC-P) protocol parameters
SampleParaffin-embedded human intestinal cancer tissues; fixative not specified (datasheet PB9995)
FixationImage fixative and duration unreported (datasheet PB9995); verify before use.
Sectioning4–5 µm sections on charged slides (standard)
DeparaffinisationXylene, graded ethanol series to water (standard)
Antigen retrievalHeat retrieval: Citrate pH 6, 20 min (datasheet PB9995)
Peroxidase block3% H2O2, 10 min, room temperature (standard)
Blocking10% goat serum (datasheet PB9995)
Primary antibodyRabbit anti-CDK6, 0.5-1μg/ml recommended; image 2μg/ml (datasheet PB9995)
Primary incubationOvernight at 4 °C (datasheet PB9995)
DetectionStreptavidin-biotin complex (SABC), DAB chromogen (datasheet PB9995)
CounterstainHematoxylin, blue, dehydrate and mount (standard)
Expected resultCDK6-positive staining in paneth cells of duodenum (HPA tissue IHC: High). HPA tissue profile: Cytoplasmic expression in several tissues, which in cases was combined with nuclear expression. Highest expression in bone marrow cells. No signal in the no-primary control.
💡Decision noteStart with heat-mediated citrate retrieval at pH 6 for the catalog antibody (datasheet PB9995); the published excerpt does not specify retrieval (PMC4144705).
Section 2

What Is the Expected CDK6 Staining Pattern?

CDK6 is a nonmembrane protein found in the cytoplasm and nucleus; UniProt also places it at centrosomes during mitosis (UniProt Q00534 topology and subcellular location). In paraffin tissue sections, expect chiefly cytoplasmic staining, sometimes with nuclear staining, in selected cell populations (HPA tissue IHC). HPA rates its tissue IHC evidence “Enhanced,” with medium consistency between staining and RNA data (HPA tissue IHC).

What am I looking at on my slide?
Cytoplasmic staining in duodenal Paneth cells, placental cytotrophoblasts, or small-intestinal enterocytes.This fits HPA's High ratings for those cell populations (HPA tissue IHC). Assess the named cells within intact tissue architecture; a High rating describes those cells, not every cell in the section. Cytoplasmic staining may accompany nuclear staining in some tissues (HPA tissue IHC).
Cytoplasmic staining with nuclear staining in a subset of positive cells.A mixed pattern is plausible: HPA reports cytoplasmic expression that is sometimes combined with nuclear expression, and UniProt lists both compartments (HPA tissue IHC; UniProt Q00534 subcellular location). Nuclear staining alone should be judged against the tissue and antibody controls before calling it specific (general IHC practice).
Predominant cell-surface, extracellular, or uniform acellular color deposit.This does not match the reported tissue pattern or a protein lacking a transmembrane segment and signal peptide (HPA tissue IHC; UniProt Q00534 topology and processing). Consider nonspecific detection or tissue-associated pigment; compare with a no-primary control and tissue morphology (general IHC practice).
Strong color in a population HPA reports as Not detected, such as cardiomyocytes or caudate glial cells.The result conflicts with those cell-specific HPA observations and raises concern for cross-reactivity or endogenous detection activity (HPA tissue IHC; general IHC practice). It does not make the entire heart or caudate a validated negative control; identify the stained cell type before interpreting it.
No staining in the expected positive cells of a control section.Loss of signal in Paneth cells, cytotrophoblasts, or small-intestinal enterocytes conflicts with their High HPA ratings (HPA tissue IHC). Check tissue preservation, primary-antibody application, retrieval, and detection with run controls (general IHC practice). HPA does not establish a CDK6-specific fixation effect.
💡Expected CDK6 appearanceCall positive a cellular, chiefly cytoplasmic chromogenic signal, with possible nuclear signal, in the specified HPA-positive populations; Paneth cells, cytotrophoblasts, and small-intestinal enterocytes are rated High, while widespread extracellular color or staining in HPA Not detected cell populations is suspect (HPA tissue IHC; UniProt Q00534 topology).
How each factor affects the staining
Tissue and cell selectionHPA rates Paneth cells, cytotrophoblasts, and small-intestinal enterocytes High; bone-marrow hematopoietic cells are rated Medium even though the HPA profile describes bone marrow as having the highest expression (HPA tissue IHC). Score named cell populations, not whole organs.
Compartment and cell-cycle contextUniProt lists cytoplasm, nucleus, and centrosome localization during mitosis; HPA tissue IHC chiefly describes cytoplasmic staining, sometimes with nuclear staining (UniProt Q00534 subcellular location; HPA tissue IHC). A rare mitotic focus needs morphology-based review before interpretation.
Protein architecture and processingCDK6 has one listed 1–326 chain, no signal peptide, no transmembrane segment, and no listed isoforms (UniProt Q00534 processing, topology, and isoforms). These features support intracellular interpretation; they do not predict how a particular antibody will behave in paraffin sections.
Antibody evidenceTwo HPA antibodies have Enhanced IHC validation: HPA002637 and CAB004363 (HPA antibodies). That supports the reported tissue pattern but does not prove specificity for every staining condition or specimen; compare localization and controls for the antibody used (general IHC practice).
Why is my staining missing, weak or wrong?
SituationLikely causeNext action
Expected positive cells are blank.The control may lack detectable staining in this run despite High HPA ratings for Paneth cells, cytotrophoblasts, and small-intestinal enterocytes (HPA tissue IHC).Confirm the cell population is present, then review primary-antibody application, retrieval, chromogen development, and a run control (general IHC practice). Do not infer CDK6-specific fixation sensitivity from HPA.
Only nuclei stain strongly.Nuclear CDK6 is possible, but HPA tissue IHC describes chiefly cytoplasmic expression, sometimes combined with nuclear expression (UniProt Q00534 subcellular location; HPA tissue IHC).Compare the same cell population with an HPA-positive tissue and a no-primary control; assess whether the nuclear pattern tracks cell morphology and the antibody's validated pattern (general IHC practice; HPA tissue IHC).
Cardiomyocytes or caudate glial cells stain strongly.Those specific populations are Not detected in HPA tissue IHC; cross-reactivity or endogenous detection activity is possible (HPA tissue IHC; general IHC practice).Verify cell identity and compare no-primary and detection-only controls; adjust blocking or detection as indicated by the control result (general IHC practice). Do not treat every cell in those organs as negative.
Color spreads across stroma or obscures cell borders.Diffuse deposit prevents assessment of the cellular pattern reported by HPA and may reflect background from the detection workflow (HPA tissue IHC; general IHC practice).Inspect no-primary controls, wash and blocking steps, and chromogen development; score only interpretable cellular staining after background is resolved (general IHC practice).
A focal dot or edge signal is mistaken for the dominant pattern.UniProt places CDK6 at centrosomes during mitosis and at the ruffling edge of spreading fibroblasts; HPA tissue IHC chiefly reports cytoplasmic staining (UniProt Q00534 subcellular location; HPA tissue IHC).Check cell morphology and the broader cytoplasmic pattern before scoring a focal signal. HPA reports soft-tissue fibroblasts as Not detected, so the ruffle annotation alone does not establish a positive tissue control (HPA tissue IHC).
Q: Should IF/ICC show the same compartment emphasis as chromogenic tissue IHC?HPA ICC-IF reports mainly nucleoplasmic CDK6 with additional cytosol localization, whereas its tissue IHC profile emphasizes cytoplasm (HPA subcellular ICC-IF; HPA tissue IHC).A: Interpret IF/ICC against its own HPA localization evidence and cell context; do not require its nucleoplasmic emphasis to match every paraffin tissue section (HPA subcellular ICC-IF; HPA tissue IHC).

Sample controls for CDK6 IHC & IF

🧪Run duodenum first and confirm staining in Paneth cells (HPA: High in duodenal Paneth cells). Use heart muscle cardiomyocytes as the negative tissue (HPA: Not detected in cardiomyocytes); on the duodenal slide, score any cells without specific staining as internal background comparators, without assuming a particular neighboring cell type is CDK6-negative.
Positive control tissue: Duodenum (Paneth cells, HPA High)
Negative control tissue: Caudate (HPA Not detected)
ICC-IF cell lines (HPA subcellular resource): HPA ICC-IF images show CDK6 in A-431, U-251MG, U2OS, ASC52telo, hTERT-RPE1 (serum starved), with annotated localisation: Nucleoplasm (supported) (HPA subcellular).
Technical controls: Include a no-primary, secondary-only control; a concentration-matched rabbit IgG isotype control for the rabbit catalog antibody; and, where available, CDK6-knockout tissue or a validated peptide-block control (selected PB9995 tissue-IHC caption: rabbit primary). For duodenal chromogenic IHC, check endogenous peroxidase and biotin background because the selected detection method uses a biotinylated secondary, streptavidin–biotin complex and DAB (selected PB9995 tissue-IHC caption).
⚠️Feasibility: A target-specific fixation window or fixation effect is unreported, and the fixative for the selected paraffin-section example is unreported (selected PB9995 tissue-IHC caption). That example used heat-mediated citrate retrieval at pH 6 for 20 minutes, which provides a starting condition without establishing that retrieval is required in every specimen (selected PB9995 tissue-IHC caption). There is no supplied comparison showing that frozen sections or IF are easier; for IF interpretation, CDK6 signal may be nucleoplasmic with additional cytosolic staining (HPA subcellular: supported nucleoplasm and cytosol).

HPA tissue IHC evidence for CDK6

Comprehensive Human Protein Atlas IHC scoring per tissue (reliability: Enhanced — Medium consistency between antibody staining and RNA expression data.). Rows are taken directly from the HPA tissue chart — click any row's HPA link to view the source.

Positive expression · recommended positive controls

TissueCell typeLevelEvidenceSource
Duodenum Paneth cells High Protein (IHC) HPA →
Placenta Cytotrophoblasts High Protein (IHC) HPA →
Small intestine Enterocytes High Protein (IHC) HPA →
Appendix Enterocytes Medium Protein (IHC) HPA →
Bone marrow Hematopoietic cells Medium Protein (IHC) HPA →

Undetected expression · recommended negative controls

TissueCell typeLevelEvidenceSource
Caudate Glial cells Not detected Protein (IHC) HPA →
Heart muscle Cardiomyocytes Not detected Protein (IHC) HPA →
Hippocampus Glial cells Not detected Protein (IHC) HPA →
Liver Cholangiocytes Not detected Protein (IHC) HPA →
Nasopharynx Basal cells Not detected Protein (IHC) HPA →
Section 3

Advanced CDK6 IHC Tips

Troubleshoot CDK6 staining in paraffin sections using the catalog antibody’s tissue image, reported CDK6 localisation, and cell-specific reference patterns.

Which retrieval conditions should I try first for weak CDK6 staining?
Start with heat-mediated citrate retrieval at pH 6 for 20 minutes on paraffin sections (datasheet PB9995). The selected tissue image pairs that step with 2 μg/mL primary antibody overnight at 4 °C, providing a documented starting combination (datasheet PB9995). If staining is weak, first check heating consistency, section adhesion, and whether the detection reagents worked on a control section (standard IHC practice). Then adjust heating time in small steps while processing control and test sections together; excessive heating can damage morphology and obscure compartment scoring (standard IHC practice). Record retrieval conditions alongside nuclear and cytoplasmic staining because both compartments are reported for CDK6 (HPA tissue IHC; UniProt Q00534 localisation).
Could fixation explain inconsistent CDK6 staining between paraffin blocks?
The selected CDK6 image identifies paraffin-embedded tissue but does not state its fixative, so target-specific fixation sensitivity is unknown (datasheet PB9995 caption). Record each block’s fixative, fixation duration, processing history, and section age before comparing staining intensity (standard IHC practice). Process matched control sections with the same pH 6, 20-minute citrate retrieval and 2 μg/mL primary concentration used in the image (datasheet PB9995). Compare preserved morphology and staining within the same cell type; fixation or processing differences can affect antigen accessibility in chromogenic IHC (standard IHC practice). Neither CDK6’s intracellular localisation nor its annotated phosphorylation sites establishes how this antibody responds to fixation (UniProt Q00534 localisation and modified residues; datasheet PB9995 caption).
Should CDK6 staining be nuclear, cytoplasmic, or both?
Score nuclear and cytoplasmic DAB separately: tissue IHC reports cytoplasmic staining in several tissues, sometimes with nuclear staining (HPA tissue IHC). CDK6 is also annotated in nucleus and cytoplasm, with kinase activity only in the nucleus; centrosomal localisation during mitosis provides context for occasional focal staining (UniProt Q00534 localisation). The supported cell-imaging pattern is mainly nucleoplasmic with additional cytosol (HPA subcellular). Use a counterstain to locate nuclei, then check whether brown signal occupies the expected cellular compartment instead of folds, lumina, or section edges (standard IHC practice). A cytoplasmic-only or nuclear-only result merits control comparison before assigning biological meaning because reported localisation depends on context (HPA tissue IHC; UniProt Q00534 localisation).
Can an isoform or modified epitope explain a changed staining pattern?
The supplied CDK6 record lists 0 isoforms and a single chain spanning residues 1–326; it does not identify this antibody’s epitope (UniProt Q00534; datasheet PB9995 caption). Its protein kinase domain spans residues 13–300, and annotated modified residues include phosphotyrosines 13 and 24 plus phosphothreonines 49 and 70 (UniProt Q00534 domains and modified residues). Those annotations cannot establish whether modification or retrieval alters recognition by the catalog antibody (UniProt Q00534; datasheet PB9995 caption). If staining changes across samples, compare matched retrieval and detection runs, then seek an independently validated antibody with a disclosed epitope if epitope dependence matters (standard IHC practice).
How should I assess CDK6 localisation in a multiplex IF follow-up?
Treat IF/ICC as a separate assay: the selected antibody evidence describes chromogenic staining of paraffin sections, without an IF protocol or stated fixative (datasheet PB9995 caption). Multiplex with a validated marker for the cell population under study and score CDK6 within marker-positive cells; the HPA tissue profile offers examples of CDK6-positive cell types for selecting a relevant comparator (HPA tissue IHC; standard IF practice). Choose spectrally separated fluorophores after checking unstained tissue for autofluorescence, and include single-stain controls for channel bleed-through (standard IF practice). CDK6 has no transmembrane segment and is reported in nucleoplasm and cytosol, so optimise permeabilisation for intracellular access while preserving those compartments (UniProt Q00534 topology; HPA subcellular; standard IF practice).
What should I check when CDK6 DAB staining looks diffuse?
Compare the suspect section with a no-primary control and inspect whether colour persists in the same structures; residual signal implicates the detection workflow rather than the primary antibody (standard IHC practice). The selected image uses a biotinylated secondary, streptavidin–biotin complex, and DAB, so include controls for nonspecific secondary binding and detection background (datasheet PB9995). Apply an appropriate endogenous peroxidase block, maintain thorough washes, and assess endogenous biotin when using this detection chemistry (standard IHC practice). The image used 10% goat serum block and 2 μg/mL primary overnight at 4 °C; these are reference conditions for controlled adjustments (datasheet PB9995). Evaluate diffuse brown haze against nuclear and cytoplasmic cell boundaries (HPA tissue IHC; standard IHC practice).
How should I score heterogeneous CDK6 staining across sections? ⚠ ANSWER MARKED FOR VERIFICATION
Define the cell population and compartment before scoring, since tissue IHC shows cytoplasmic expression with nuclear expression in some cases (HPA tissue IHC). For each compartment, report the percentage of positive cells and intensity, or calculate an H-score from the percentages assigned to intensity categories 0–3 (standard IHC practice). If cell abundance varies, report CDK6-positive cells per mm² and normalise cell-level scores to the number of eligible cells, not the whole-section area (standard IHC practice). Keep retrieval, staining batch, threshold, and sampled regions consistent, and exclude folds and necrotic areas from analysis (standard IHC practice). Report nuclear and cytoplasmic results separately rather than collapsing distinct patterns into one score (HPA tissue IHC; standard IHC practice).
How can I distinguish a credible CDK6 signal from artefact?
A credible result follows identifiable cell boundaries, survives comparison with a no-primary control, and shows plausible nuclear or cytoplasmic localisation (standard IHC practice; HPA tissue IHC). Cell identity matters: high staining is reported in duodenal Paneth cells and placental cytotrophoblasts, whereas caudate glial cells and cardiomyocytes were not detected in the cited tissue profile (HPA tissue IHC). Treat signal confined to section edges, folds, necrosis, or the no-primary control as suspect; assess endogenous peroxidase and biotin-related detection background with the selected DAB workflow (standard IHC practice; datasheet PB9995). HPA rates its tissue staining reliability as Enhanced but reports only medium consistency with RNA expression, so resolve unexpected patterns with independent controls before interpreting them biologically (HPA tissue IHC).
Boster reagents

Best CDK6 / Cyclin-dependent kinase 6 IHC Antibodies

Anti-CDK6 antibodies have IHC images from human intestinal, mammary and lung cancer and tonsil, plus a K562 IF image (catalog captions); listed reactivity includes human, mouse and rat (catalog reactivity).

Real IHC data IHC analysis of Cdk6 using anti-Cdk6 antibody (PB9995). Cdk6 was detected in paraffin-embedded section of human intestinal cancer tissues. Heat mediated antigen retrieval was performed in citrate buffer (pH6, epitope retrieval solution) for 20 mins. The tissue section was blocked with 10% goat serum. The tissue section was then incubated with 2μg/ml rabbit anti-Cdk6 Antibody (PB9995) overnight at 4°C. Biotinylated goat anti-rabbit IgG was used as secondary antibody and incubated for 30 minutes at 37°C. The tissue section was developed using Strepavidin-Biotin-Complex (SABC)(Catalog # SA1022) with DAB as the chromogen.
Anti-Cdk6 Antibody ®
Cat # PB9995
Real IHC data IHC analysis of Cdk6 using anti-Cdk6 antibody (A00358). Cdk6 was detected in paraffin-embedded section of human intestinal cancer tissue. Heat mediated antigen retrieval was performed in citrate buffer (pH6, epitope retrieval solution) for 20 mins. The tissue section was blocked with 10% goat serum. The tissue section was then incubated with 2μg/ml rabbit anti-Cdk6 Antibody (A00358) overnight at 4℃. Biotinylated goat anti-rabbit IgG was used as secondary antibody and incubated for 30 minutes at 37℃. The tissue section was developed using Strepavidin-Biotin-Complex (SABC)(Catalog # SA1022) with DAB as the chromogen.
Anti-Cdk6 Antibody ®
Cat # A00358
Real IHC data Rat colon tonsil was stained with Anti-CDK6 rabbit antibody
Anti-CDK6 Rabbit Monoclonal Antibody
Cat # M00358-2
Real IHC data Immunohistochemical analysis of paraffin-embedded human lung cancer, using CDK6 Antibody.
Anti-CDK6 Rabbit Monoclonal Antibody
Cat # M00358

PB9995 and A00358 show paraffin-section IHC in human intestinal and mammary cancer and tonsil, while M00358-2 shows human tonsil IHC (respective IHC captions). M00358 shows paraffin-section human lung cancer IHC and K562-cell IF (M00358 IHC/IF captions).

Which to pick: For tissue IHC, PB9995 or A00358 have rabbit polyclonal antibodies with human paraffin-section examples using citrate retrieval and DAB; their captions do not report the fixative (PB9995/A00358 catalog entries and IHC captions). For IF/ICC, M00358 is a human-reactive rabbit monoclonal listed for both applications and has a K562 IF image (M00358 catalog entry and IF caption). For cross-species work, A00358 lists human/mouse reactivity and PB9995 lists human/rat reactivity, although their supplied IHC images show human tissue only (A00358/PB9995 catalog entries and IHC captions).

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

References

  1. UniProt Consortium. UniProt entry Q00534 (CDK6_HUMAN, Cyclin-dependent kinase 6).
  2. Human Protein Atlas. CDK6 tissue IHC expression (reliability: Enhanced).
  3. Human Protein Atlas. CDK6 subcellular location (ICC-IF): Mainly localized to the nucleoplasm. In addition localized to the cytosol..
  4. Human Protein Atlas. CDK6 antibody validation summary (2 antibodies).
  5. CDK6 protein expression is associated with disease progression and treatment resistance in multiple myeloma. HemaSphere 2024 — PMC10878183.
  6. Cyclin-dependent kinase 6 (CDK6) is a candidate diagnostic biomarker for early non-small cell lung cancer. Translational cancer research 2020 — PMC8798208.
  7. Expression and Significance of Cyclin-Dependent Protein Kinase 6 in Diffuse Large B-Cell Lymphoma. International journal of general medicine 2022 — PMC9483138.
  8. MiR-506 suppresses proliferation and induces senescence by directly targeting the CDK4/6-FOXM1 axis in ovarian cancer. The Journal of pathology 2014 — PMC4144705.
  9. PubMed PMID:1639063 — UniProt-cited evidence.
  10. PubMed PMID:14702039 — UniProt-cited evidence.
  11. PubMed PMID:12853948 — UniProt-cited evidence.