This website uses cookies to ensure you get the best experience on our website.
- Table of Contents
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).
Expected localisation, validated protocols, controls and antibodies — the at-a-glance facts below, then the full design guide.
| 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 |
| 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) |
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).
| Sample | Paraffin-embedded human intestinal cancer tissues; fixative not specified (datasheet PB9995) |
| Fixation | Image fixative and duration unreported (datasheet PB9995); verify before use. |
| Sectioning | 4–5 µm sections on charged slides (standard) |
| Deparaffinisation | Xylene, graded ethanol series to water (standard) |
| Antigen retrieval | Heat retrieval: Citrate pH 6, 20 min (datasheet PB9995) |
| Peroxidase block | 3% H2O2, 10 min, room temperature (standard) |
| Blocking | 10% goat serum (datasheet PB9995) |
| Primary antibody | Rabbit anti-CDK6, 0.5-1μg/ml recommended; image 2μg/ml (datasheet PB9995) |
| Primary incubation | Overnight at 4 °C (datasheet PB9995) |
| Detection | Streptavidin-biotin complex (SABC), DAB chromogen (datasheet PB9995) |
| Counterstain | Hematoxylin, blue, dehydrate and mount (standard) |
| Expected result | CDK6-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. |
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).
| 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. |
| Tissue and cell selection | HPA 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 context | UniProt 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 processing | CDK6 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 evidence | Two 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). |
| Situation | Likely cause | Next 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). |
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.
| Tissue | Cell type | Level | Evidence | Source |
|---|---|---|---|---|
| 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 → |
| Tissue | Cell type | Level | Evidence | Source |
|---|---|---|---|---|
| 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 → |
Troubleshoot CDK6 staining in paraffin sections using the catalog antibody’s tissue image, reported CDK6 localisation, and cell-specific reference patterns.
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).
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).