This website uses cookies to ensure you get the best experience on our website.
- Table of Contents
CDH6 / Cadherin-6 · IHC design guide
Design Immunohistochemistry for CDH6
Plan chromogenic CDH6 IHC in paraffin sections using kidney tubular cells as a high staining reference (HPA tissue IHC). Assess membrane and cytoplasmic signal against colon glandular cells, where CDH6 was not detected (HPA tissue IHC).
Evidence assembled Oct 2026 · For research use; verify linked source records and product datasheet before use
CDH6 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 | Membranous and cytoplasmic in tissues (HPA tissue IHC) | |
| Staining pattern | Kidney tubular cells show strong membrane and cytoplasmic staining (HPA tissue IHC) | |
| Antigen retrieval | EDTA pH 8.0 HIER, heat-mediated (datasheet A06353-1) | |
| Positive control | Gallbladder+4 more · see all | |
| Negative control | Adipose tissue+4 more · see all |
Important caveats
Reasons your staining may differ from the expected pattern.
| Fixation | Keep fixation consistent across sections. (standard IHC practice; not target-specific) | |
| Caveat | Cytoplasmic signal can complicate membrane scoring (HPA tissue IHC) | |
| Regulation | Expression regulation not specified (UniProt) | |
| Isoform / epitope | 2 isoforms; check whether the epitope is extracellular or cytoplasmic (UniProt) |
Section 1
Recommended CDH6 IHC & IF Protocols
The catalog antibody protocol uses EDTA pH 8.0 heat retrieval (datasheet A06353-1). The published options below report CDH6 staining conditions for lung cancer, thyroid cancer and reproductive tract sections (PMC13601855; PMC3772092; PMC5342521).
| Sample | Paraffin-embedded human ovarian cancer tissue; fixative not specified (datasheet A06353-1) |
| Fixation | Image fixative and duration unreported (datasheet A06353-1); 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 A06353-1); 20 min, 95–100 °C (standard) |
| Peroxidase block | 3% H2O2, 10 min, room temperature (standard) |
| Blocking | 10% goat serum (datasheet A06353-1) |
| Primary antibody | Rabbit anti-CDH6, 2-5μg/ml (datasheet A06353-1) |
| Primary incubation | Overnight at 4 °C (datasheet A06353-1) |
| Detection | Streptavidin-biotin complex (SABC), DAB chromogen (datasheet A06353-1) |
| Counterstain | Hematoxylin, blue, dehydrate and mount (standard) |
| Expected result | CDH6-positive staining in glandular cells of gallbladder (HPA tissue IHC: High). HPA tissue profile: Membranous and cytoplasmic expression in several tissues, including kidney. No signal in the no-primary control. |
💡Decision noteStart with EDTA pH 8.0 heat retrieval for the catalog antibody (datasheet A06353-1). The cited excerpts do not specify retrieval conditions for their antibodies (PMC13601855; PMC3772092; PMC5342521).
Section 2
What Is the Expected CDH6 Staining Pattern?
CDH6 is a cell-membrane protein with one transmembrane segment and an extracellular region (UniProt P55285 topology). In paraffin-section IHC, expect membranous staining, sometimes with cytoplasmic staining, in the cell types HPA reports: especially kidney tubule cells and gallbladder glandular cells, both High (HPA tissue IHC). Interpret weaker or absent staining by tissue and cell type; HPA rates its tissue profile Enhanced, with medium consistency between staining and RNA data (HPA tissue IHC).
| Kidney tubule cells or gallbladder glandular cells show clear membranous staining, with some cytoplasmic signal. | This fits HPA's High staining in those cells and its reported membranous and cytoplasmic tissue profile (HPA tissue IHC). Judge the relevant cells rather than the whole section: nearby cells need not share their intensity. Membrane localisation also agrees with CDH6 topology (UniProt P55285 topology). |
| The strongest signal is nuclear, or uniformly fills cells without a discernible membrane pattern. | That distribution does not match UniProt's cell-membrane annotation or HPA's tissue profile (UniProt P55285; HPA tissue IHC). Treat it as suspect rather than calling it CDH6 positive; review morphology, negative controls and chromogen background before scoring (general IHC practice). |
| Strong staining appears mainly in cells that HPA reports as Not detected, such as colon glandular cells. | This conflicts with that cell-level reference pattern (HPA: Not detected in colon glandular cells). Consider antibody cross-reactivity or endogenous detection activity, especially if signal also appears in a no-primary control (general IHC practice). An unexpected result warrants controls; HPA's reference profile is not proof that every specimen must be negative. |
| Color spreads across the section, including cell-free areas, and obscures cell borders. | Diffuse deposit is difficult to assign to CDH6-expressing cells and does not establish the reported membranous pattern (HPA tissue IHC). Check no-primary and detection controls, washing and blocking before interpreting intensity (general IHC practice). Avoid scoring diffuse background as cytoplasmic positivity merely because HPA also reports cytoplasmic staining. |
| Kidney tubule cells show no convincing signal while controls and tissue morphology are assessable. | This is unexpected against HPA's High kidney-tubule observation (HPA tissue IHC), but one negative section does not prove absent CDH6. Review antibody suitability, reagent performance and the chosen staining conditions with a positive control (general IHC practice). HPA reports medium staining–RNA consistency, so describe unresolved discrepancies rather than assigning a biological cause (HPA tissue IHC). |
💡Expected CDH6 appearanceCall a result positive when identifiable kidney tubule cells or gallbladder glandular cells show clear, predominantly membranous staining, potentially with cytoplasmic signal, consistent with their High HPA levels; nuclear-only or diffuse cell-free color is suspect (HPA tissue IHC; UniProt P55285 topology; general IHC practice).
| Compartment and epitope context | CDH6 has an extracellular region at residues 54–615, a transmembrane segment at 616–636 and a cytoplasmic region at 637–790 (UniProt P55285 topology). These positions support a membrane expectation. The supplied record gives no antibody epitope, so it cannot predict which region this antibody detects or specify retrieval conditions. |
| Cell-type context | HPA reports High staining in kidney tubule and gallbladder glandular cells; Medium staining in cerebellar Purkinje and cerebral-cortex neuronal cells (HPA tissue IHC). It reports Not detected in several other specified cell types, including colon glandular cells (HPA tissue IHC). Choose comparison cells by the annotated cell type, not the organ name alone. |
| Strength of the reference pattern | HPA labels the tissue IHC profile Enhanced while describing medium consistency between antibody staining and RNA expression (HPA tissue IHC). Its observed levels are useful expectations, not guaranteed intensities for every paraffin section. Record staining location and cell type alongside intensity when comparing a specimen with the reference (general IHC practice). |
| Antibody evidence | HPA lists Enhanced IHC status for HPA007047 and CAB025274, and Approved IHC status for HPA007456 (HPA antibodies). Those statuses belong to the listed antibodies; they do not validate an unspecified catalog antibody. Confirm the IHC status of the antibody actually used before transferring confidence to a result. |
| IF/ICC Q: What localisation is expected? | A: HPA reports CDH6 mainly at the plasma membrane and cell junctions in ICC-IF, with both locations supported (HPA subcellular). That finding provides a compartment comparison for fluorescence images; it is not a paraffin-IHC protocol or a reason to expect identical appearance across the two applications. |
| Situation | Likely cause | Next action |
|---|---|---|
| A kidney section is blank or barely stained. | The result conflicts with High staining in kidney tubule cells (HPA tissue IHC); the supplied sources do not identify why this section is negative. | Verify that tubule cells are present and assess a positive control, antibody suitability and reagent performance (general IHC practice). Record the discrepancy if controls pass; do not infer CDH6 absence from technical failure alone. |
| Signal is strongest in nuclei rather than at cell borders. | Nuclear dominance conflicts with the cell-membrane annotation and HPA's membranous tissue profile (UniProt P55285; HPA tissue IHC). | Inspect the no-primary control, detection background and tissue morphology (general IHC practice). Withhold a CDH6-positive call until an interpretable cell-associated pattern is present. |
| Unexpected cells stain strongly, including colon glandular cells. | HPA reports colon glandular cells as Not detected (HPA tissue IHC); cross-reactivity or endogenous detection activity is possible (general IHC practice). | Compare the unexpected cells with a no-primary control and a documented positive tissue; review antibody validation for the reagent used (general IHC practice; HPA antibodies). |
| Diffuse color obscures the expected membrane pattern. | Background can prevent cell-level localisation and scoring (general IHC practice); HPA's cytoplasmic profile does not establish that cell-free color is CDH6 (HPA tissue IHC). | Review blocking, washing and detection controls, then repeat or adjust the general IHC workflow as needed (general IHC practice). Score only interpretable cells. |
| Staining is present but weaker than in a kidney reference. | HPA reports different levels across cell types, including High kidney tubules and Medium Purkinje cells (HPA tissue IHC); intensity also needs a controlled comparison (general IHC practice). | First confirm the same annotated cell type and assess staining location, control performance and scoring consistency (HPA tissue IHC; general IHC practice). Do not treat every weaker signal as technical failure. |
| Fluorescence shows junctional signal that looks different from chromogenic IHC. | HPA supports plasma-membrane and cell-junction localisation in ICC-IF, while its tissue IHC profile includes membranous and cytoplasmic staining (HPA subcellular; HPA tissue IHC). | Interpret each application against its own HPA localisation evidence and controls (HPA subcellular; HPA tissue IHC; general IHC practice). Use the separate IF/ICC guide for its workflow. |
Experiment evidence
IHC & IF images showing CDH6 staining
A06353-1 · IHCIHC analysis of K Cadherin/CDH6 using anti-K Cadherin/CDH6 antibody (A06353-1). K Cadherin/CDH6 was detected in paraffin-embedded section of
HPA · Cerebral cortexHuman Protein Atlas IHC, Cerebral cortex. Source: https://www.proteinatlas.org/ENSG00000113361-CDH6/tissue/cerebral+cortex#imid_6568856
HPA · CerebellumHuman Protein Atlas IHC, Cerebellum. Source: https://www.proteinatlas.org/ENSG00000113361-CDH6/tissue/cerebellum#imid_6568859
HPA · ColonHuman Protein Atlas IHC, Colon. Source: https://www.proteinatlas.org/ENSG00000113361-CDH6/tissue/colon#imid_6568790
HPA · LiverHuman Protein Atlas IHC, Liver. Source: https://www.proteinatlas.org/ENSG00000113361-CDH6/tissue/liver#imid_6568791
HPA · ICC-IF EFO-21Human Protein Atlas immunofluorescence, EFO-21, antibody HPA007403; green = CDH6, blue = nucleus, red = microtubules.
HPA · ICC-IF EFO-21Human Protein Atlas immunofluorescence, EFO-21, antibody HPA007403; green = CDH6, blue = nucleus, red = microtubules.
← swipe / scroll for more images →
Real IHC / IF data behind the staining-pattern expectations in this section.
Sample controls for CDH6 IHC & IF
🧪Run kidney first: tubular cells should stain strongly (HPA: High in kidney cells in tubules). Use adipose tissue as the negative tissue (HPA: Not detected in adipocytes); on the kidney slide, cells without a discernible junctional signal should remain at background, but the supplied HPA rows do not establish a specific internal cell type as negative.
Positive control tissue: Gallbladder (Glandular cells, HPA High)
Negative control tissue: Adipose tissue (HPA Not detected)
ICC-IF cell lines (HPA subcellular resource): HPA ICC-IF images show CDH6 in EFO-21, HAP1, U2OS, with annotated localisation: Plasma membrane (supported), Cell Junctions (supported) (HPA subcellular).
Technical controls: Include no-primary (secondary-only) and concentration-matched rabbit IgG isotype controls (selected-SKU caption: rabbit primary), plus a CDH6 knockout biological negative if available (standard IHC practice). Quench endogenous peroxidase and block endogenous biotin in kidney sections when using the caption’s biotin-based, DAB detection system (selected-SKU caption: biotinylated secondary, SABC and DAB; standard IHC practice).
⚠️Feasibility: A target-specific fixation window or fixation effect is unreported, and the selected-SKU paraffin-section caption does not state the fixative (selected-SKU caption: fixative unreported). Heat retrieval in EDTA at pH 8.0 is documented for that IHC example, but the evidence does not establish whether frozen sections or IF are easier (selected-SKU caption: heat-mediated EDTA retrieval; HPA: ICC-IF images in EFO-21, HAP1 and U2OS). Assess junctional membrane staining in kidney tubules and check biotin-related background when using SABC detection (UniProt P55285: cell membrane; HPA: plasma membrane and cell junctions; selected-SKU caption: SABC detection; standard IHC practice).
HPA tissue IHC evidence for CDH6
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
| Tissue | Cell type | Level | Evidence | Source |
|---|---|---|---|---|
| Gallbladder | Glandular cells | High | Protein (IHC) | HPA → |
| Kidney | Cells in tubules | High | Protein (IHC) | HPA → |
| Cerebellum | Purkinje cells | Medium | Protein (IHC) | HPA → |
| Cerebral cortex | Neuronal cells | Medium | Protein (IHC) | HPA → |
| Cervix | Squamous epithelial cells | Medium | Protein (IHC) | HPA → |
Undetected expression · recommended negative controls
| Tissue | Cell type | Level | Evidence | Source |
|---|---|---|---|---|
| Adipose tissue | Adipocytes | Not detected | Protein (IHC) | HPA → |
| Appendix | Glandular cells | Not detected | Protein (IHC) | HPA → |
| Bone marrow | Hematopoietic cells | Not detected | Protein (IHC) | HPA → |
| Breast | Adipocytes | Not detected | Protein (IHC) | HPA → |
| Colon | Glandular cells | Not detected | Protein (IHC) | HPA → |
Section 3
Advanced CDH6 IHC Tips
Troubleshoot CDH6 staining in paraffin sections by checking retrieval, compartment, cell type, and controls before comparing signal intensity (standard IHC practice).
Which retrieval conditions should I start with for CDH6 IHC?
Start with heat-mediated retrieval in EDTA at pH 8.0 for paraffin sections (datasheet A06353-1). The selected tissue-IHC example used that retrieval before 10% goat serum blocking and 2 μg/ml primary antibody overnight at 4°C (datasheet A06353-1). If staining is weak, adjust heating duration within the retrieval system’s recommended range while keeping buffer and pH fixed, then compare sections from the same block (standard IHC practice). Check that junctional or membrane staining improves without a parallel rise in diffuse background; CDH6 is a membrane protein with an extracellular region spanning residues 54–615 (UniProt P55285 topology).
Could fixation explain weak or patchy CDH6 staining?
Target-specific sensitivity of CDH6 to fixation is unknown from the supplied evidence (datasheet A06353-1: fixative not stated). The selected image documents a paraffin-embedded ovarian cancer section, but its caption does not identify a fixative or fixation time (datasheet A06353-1). Record the fixative and processing history for each specimen, and compare similarly processed sections before changing antibody concentration or retrieval conditions (standard IHC practice). If a section stains unevenly, inspect folds, tissue thickness, and damaged edges alongside the staining pattern; these can affect interpretation independently of CDH6 expression (standard IHC practice).
Where should convincing CDH6 staining appear in a tissue section?
Prioritise cell-border and junctional staining because CDH6 is a cell-membrane protein, with its transmembrane segment at residues 616–636 (UniProt P55285 topology). Plasma membrane and cell junctions are supported locations in cell imaging, while tissue IHC reports both membranous and cytoplasmic expression (HPA subcellular; HPA tissue IHC). Cytoplasmic signal can therefore be recorded, but score it separately from membrane signal rather than treating the patterns as equivalent (HPA tissue IHC; standard IHC practice). For a tissue reference, kidney tubule cells show high staining in the supplied profile; compare the relevant cell borders rather than the whole section’s average colour (HPA: High in kidney tubule cells).
How should an unknown antibody epitope affect CDH6 interpretation?
CDH6 has 2 annotated isoforms, but the supplied antibody caption does not specify which isoform or epitope the reagent recognises (UniProt P55285 isoforms; datasheet A06353-1). The mature chain spans residues 54–790, with an extracellular region at 54–615 and a cytoplasmic region at 637–790 (UniProt P55285 processing and topology). CDH6 also has annotated glycosylation and phosphorylation sites; their effect on this antibody’s IHC staining is not established by the supplied evidence (UniProt P55285 modifications; datasheet A06353-1). Document the reagent and retrieval conditions, and avoid assigning an absent stain to a particular isoform or modification without epitope-specific validation (standard IHC practice).
How can I check a CDH6 pattern by multiplex IF?
Pair CDH6 with a marker identifying the cell population being examined, and assess whether its signal outlines those cells at contacts (HPA subcellular: plasma membrane and cell junctions; standard IF practice). Choose a fluorophore whose signal can be distinguished from the specimen’s autofluorescence, using an unstained section and single-colour controls to assess bleed-through (standard IF practice). If the antibody epitope is extracellular, start without permeabilisation; if it is cytoplasmic, use controlled permeabilisation, because CDH6 spans the membrane and the supplied caption does not locate this antibody’s epitope (UniProt P55285 topology; datasheet A06353-1). Compare the IF pattern with chromogenic membrane and cytoplasmic compartments, without assuming identical signal intensity across detection methods (HPA tissue IHC; standard IF practice).
What should I change when CDH6 IHC has diffuse background?
First compare the stained section with a no-primary control to locate background from detection reagents rather than the primary antibody (standard IHC practice). The selected example used 10% goat serum blocking, a biotinylated secondary, a streptavidin-biotin complex, and DAB detection (datasheet A06353-1). Check blocking, washing, and primary concentration against that documented workflow, and evaluate endogenous peroxidase or biotin signal where relevant to the detection system (datasheet A06353-1; standard IHC practice). Treat diffuse colour outside identifiable cells cautiously, since supported CDH6 localisation includes plasma membrane and cell junctions, although tissue IHC also reports cytoplasmic staining (HPA subcellular; HPA tissue IHC).
How should I quantify heterogeneous CDH6 staining? ⚠ ANSWER MARKED FOR VERIFICATION
Define the cell population and compartment before scoring, because CDH6 staining may be membranous or cytoplasmic across tissues (HPA tissue IHC). For chromogenic sections, report the percentage of positive cells and a compartment-specific H-score based on staining intensity; keep the scoring rule fixed across specimens (standard IHC practice). Where cell abundance varies, normalise positive-cell counts to the number of eligible cells, or report positive-cell density per mm² of viable tissue with the sampled area stated (standard IHC practice). Exclude folds, necrosis, and damaged edges using the same criteria in every specimen, and retain separate membrane and cytoplasmic results for interpretation (standard IHC practice; HPA tissue IHC).
How do I distinguish true CDH6 positivity from staining artefact?
Give greatest weight to reproducible cell-border or junctional signal in an appropriate cell population, consistent with CDH6 membrane topology and supported cell-imaging localisation (UniProt P55285 topology; HPA subcellular). Kidney tubule cells provide a high-staining reference, whereas colon glandular cells are listed as not detected in the supplied tissue profile (HPA: High in kidney tubule cells; HPA: Not detected in colon glandular cells). Investigate staining restricted to section edges, necrotic areas, or the wrong cell population before calling it positive (standard IHC practice). A no-primary control can reveal endogenous enzyme or detection-system colour, while cytoplasmic signal should be documented separately because tissue IHC does report that compartment (standard IHC practice; HPA tissue IHC).
Boster reagents
Best CDH6 / Cadherin-6 IHC Antibodies
The IHC-validated anti-CDH6 antibody has an image from a human ovarian cancer paraffin section (A06353-1 image caption); catalog reactivity includes Human, Mouse, and Rat (catalog: A06353-1).
Real IHC data
Anti-K Cadherin/CDH6 Antibody ®
Cat # A06353-1
The rendered card is A06353-1, which lists IHC and Human reactivity (catalog: A06353-1). Its IHC image shows staining in a paraffin section of human ovarian cancer tissue (A06353-1 image caption).
Which to pick: For tissue IHC, choose A06353-1: its image documents a human ovarian cancer paraffin section, but does not report the fixative (A06353-1 image caption). For IF, consider A06353, a polyclonal antibody with IF listed as an application; ICC is not listed and no IF image is supplied (catalog: A06353). For cross-species planning, both SKUs list Human, Mouse, and Rat reactivity, while the supplied IHC image documents Human tissue only (catalog: A06353 and A06353-1; A06353-1 image caption).
Each figure is that product's own IHC / IF validation image from its datasheet.
References
- UniProt Consortium. UniProt entry P55285 (CADH6_HUMAN, Cadherin-6).
- Human Protein Atlas. CDH6 tissue IHC expression (reliability: Enhanced).
- Human Protein Atlas. CDH6 subcellular location (ICC-IF): Mainly localized to the plasma membrane and cell junctions..
- Human Protein Atlas. CDH6 antibody validation summary (4 antibodies).
- NRF2-CDH6-CEBPD axis suppresses ferroptosis and drives cisplatin resistance in non-small cell lung cancer. Journal of cell communication and signaling 2026 — PMC13601855.
- Cadherin 6 is a new RUNX2 target in TGF-β signalling pathway. PloS one 2013 — PMC3772092.
- Synaptic cell adhesion molecule Cdh6 identifies a class of sensory neurons with novel functions in colonic motility. bioRxiv : the preprint server for biology 2024 — PMC11326146.
- Cadherin-6 type 2, K-cadherin (CDH6) is regulated by mutant p53 in the fallopian tube but is not expressed in the ovarian surface. Oncotarget 2016 — PMC5342521.
- PubMed PMID:7743525 — UniProt-cited evidence.
- PubMed PMID:14702039 — UniProt-cited evidence.
- PubMed PMID:15489334 — UniProt-cited evidence.
Immunohistochemistry protocol sheet for CDH6 (Cadherin-6). Expected localisation Membranous and cytoplasmic in tissues (HPA tissue IHC). Antigen retrieval: EDTA pH 8.0 HIER, heat-mediated (datasheet A06353-1). Validated IHC antibody: A06353-1 at 2-5μg/ml (the product's own IHC validation image is shown). Controls (HPA): positive Gallbladder (Glandular cells); negative Adipose tissue. IHC-P workflow on paraffin sections; fixative unspecified. Protocol steps: 1. Sample: Paraffin-embedded human ovarian cancer tissue; fixative not specified (datasheet A06353-1); 2. Fixation: Image fixative and duration unreported (datasheet A06353-1); 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 A06353-1); 20 min, 95–100 °C (standard); 6. Peroxidase block: 3% H2O2, 10 min , room temperature (standard); 7. Blocking: 10% goat serum (datasheet A06353-1); 8. Primary antibody: Rabbit anti-CDH6, 2-5μg/ml (datasheet A06353-1); 9. Primary incubation: Overnight at 4 °C (datasheet A06353-1). Watch for: Fixation: Keep fixation consistent across sections. (standard IHC practice; not target-specific); Caveat: Cytoplasmic signal can complicate membrane scoring (HPA tissue IHC); Isoform / epitope: 2 isoforms; check whether the epitope is extracellular or cytoplasmic (UniProt); Regulation: Expression regulation not specified (UniProt). Evidence: UniProt P55285, HPA tissue IHC · Enhanced, HPA ICC-IF · Mainly localized to the plasma membrane and cell junctions., Datasheet A06353-1, PMC13601855, PMC3772092. QR code links to https://www.bosterbio.com/bosterbio-gene-info-cards/CDH6/immunohistochemistry-ihc-guide.