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- Table of Contents
Plan CLDN3 paraffin-section IHC around membranous staining in gastrointestinal and glandular tissues (HPA tissue IHC). The catalog antibody has an IHC range of 2–5 μg/mL (datasheet A04393-5); breast glandular cells are a positive control and adipocytes a negative control (HPA tissue IHC).
Expected localisation, validated protocols, controls and antibodies — the at-a-glance facts below, then the full design guide.
| Expected localisation | Membranous tissue staining (HPA tissue IHC) | |
| Staining pattern | Membranous staining in gastrointestinal and glandular tissues (HPA tissue IHC) | |
| Antigen retrieval | EDTA pH 8.0 HIER, heat-mediated (datasheet A04393-5) | |
| Positive control | Appendix+4 more · see all | |
| Negative control | Adipose tissue+4 more · see all |
| Fixation | Keep fixation consistent across paraffin sections (standard IHC practice; not target-specific) | |
| Caveat | Staining varies by cell type within tissues (HPA tissue IHC) | |
| Regulation | Expression regulation not annotated (UniProt) | |
| Isoform / epitope | No annotated isoforms; extracellular loops and cytoplasmic tail differ in epitope location (UniProt) |
The catalog antibody protocol uses EDTA pH 8.0 retrieval (datasheet A04393-5). The following published IHC protocols cover breast, intestinal and lung tissue (PMC1064136; PMC13073207; PMC12790956; PMC6631579).
| Sample | Paraffin-embedded human renal clear cell carcinoma tissue; fixative not specified (datasheet A04393-5) |
| Fixation | Image fixative and duration unreported (datasheet A04393-5); 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 A04393-5); 20 min, 95–100 °C (standard) |
| Peroxidase block | 3% H2O2, 10 min, room temperature (standard) |
| Blocking | 10% goat serum (datasheet A04393-5) |
| Primary antibody | Rabbit anti-CLDN3, 2-5μg/ml (datasheet A04393-5) |
| Primary incubation | Overnight at 4 °C (datasheet A04393-5) |
| Detection | Streptavidin-biotin complex (SABC), DAB chromogen (datasheet A04393-5) |
| Counterstain | Hematoxylin, blue, dehydrate and mount (standard) |
| Expected result | CLDN3-positive staining in endocrine cells of appendix (HPA tissue IHC: High). HPA tissue profile: Membranous expression in several tissues, including gastrointestinal tract and glandular tissues. No signal in the no-primary control. |
CLDN3 is a four-pass membrane protein of tight junctions, so expect junctional membrane staining in the cell types where tissue IHC detects it (UniProt O15551 topology; HPA tissue IHC). HPA reports high staining in selected intestinal endocrine cells and glandular cells, with an Enhanced tissue IHC reliability rating based on agreement between antibody staining and RNA expression (HPA tissue IHC).
| Crisp membrane staining outlines contacts between the expected cells, such as breast glandular cells or colon endocrine cells (HPA tissue IHC). | This fits CLDN3 localisation at tight junctions and the cell membrane (UniProt O15551 subcellular location). Score the named cell population and its junctional pattern together; an adjacent cell population need not share the same staining level (HPA tissue IHC). |
| Strong nuclear staining or broad cytoplasmic staining dominates while junctional borders are indistinct. | That compartment pattern does not match the annotated tight-junction and membrane location (UniProt O15551 subcellular location). Treat it as suspect staining; compare with a no-primary control and reassess antibody and detection conditions before scoring it as CLDN3 (standard IHC practice). |
| Adipocytes, cardiomyocytes or esophageal squamous cells stain strongly (HPA: Not detected in those cell types). | Those results conflict with the listed HPA tissue IHC observations, though they do not prove the cause. Check whether the signal persists without primary antibody; persistent color suggests endogenous detection activity, while primary-dependent staining calls for specificity review (standard IHC practice). |
| Color spreads across stroma, empty spaces or many cell types without clear membrane borders. | A diffuse pattern is difficult to reconcile with CLDN3's junctional membrane localisation (UniProt O15551 subcellular location). Compare tissue morphology and a no-primary control, then review blocking, washes and detection background (standard IHC practice). |
| No junctional signal appears in breast glandular cells or colon endocrine cells on an otherwise interpretable section (HPA: High in those cells). | A negative result in an HPA high-staining cell population warrants a run-level check, but HPA does not establish how fixation affects CLDN3. Verify the positive-control tissue, antibody validation, retrieval and detection workflow before interpreting the specimen as negative (HPA tissue IHC; standard IHC practice). |
| Membrane topology | CLDN3 has four transmembrane segments and both extracellular and cytoplasmic regions (UniProt O15551 topology). The antibody epitope is unspecified here, so topology alone cannot select a retrieval condition or predict access to that epitope. |
| Cell population and tissue | HPA reports High staining in appendix, colon and duodenum endocrine cells and in several glandular populations; it reports Not detected in specified adipocytes and cardiomyocytes (HPA tissue IHC). Interpret staining against the named cells, not an entire organ. |
| IHC evidence | The HPA tissue IHC reliability rating is Enhanced, reflecting consistency between antibody staining and RNA expression (HPA tissue IHC). HPA014361 has an Enhanced IHC validation status (HPA antibodies). These support the reported pattern but do not establish target-specific fixation sensitivity. |
| IF/ICC Q: Where should CLDN3 appear? | A: At cell junctions; HPA calls that location supported and lists images from MCF-7 and U2OS (HPA subcellular ICC-IF). HPA014361 is ICC Approved (HPA antibodies). Use this as a localisation check; no IF/ICC protocol is supplied here. |
| Situation | Likely cause | Next action |
|---|---|---|
| Expected positive cells show no signal. | The run may have failed, or the specimen may differ from HPA's observed staining; the result alone cannot distinguish these explanations (HPA tissue IHC; standard IHC practice). | Include a section containing an HPA High cell population, then verify antibody use, retrieval and chromogenic detection steps (HPA tissue IHC; standard IHC practice). |
| Nuclear or broad cytoplasmic color outweighs membrane borders. | The location conflicts with CLDN3's annotated junctional membrane localisation; staining identity remains unresolved (UniProt O15551 subcellular location). | Compare a no-primary control and tissue morphology; adjust background controls or reassess the primary antibody before assigning a CLDN3 score (standard IHC practice). |
| Unexpected color appears in HPA Not detected cells. | For example, staining in adipocytes conflicts with HPA's reported result; cross-reactivity or endogenous detection activity is possible, not established (HPA: Not detected in adipocytes; standard IHC practice). | Run a no-primary control. If using HRP detection, check endogenous-peroxidase blocking; investigate primary-dependent color with antibody controls (standard IHC practice). |
| The entire section has diffuse brown background. | Widespread color without junctional boundaries is unlike the annotated location; nonspecific binding or detection background may contribute (UniProt O15551 subcellular location; standard IHC practice). | Inspect the no-primary control, then review blocking, wash steps and detector exposure while retaining an HPA High positive cell population for comparison (standard IHC practice; HPA tissue IHC). |
| Only some cells in a tissue stain. | HPA assigns levels to named cell types: colon endocrine cells are High, for example; that does not establish equal staining across every colonic cell (HPA tissue IHC). | Identify the stained cells on the counterstained section and compare their compartment and intensity with the relevant HPA cell-type entry (HPA tissue IHC; standard IHC practice). |
| A result changes after changing retrieval conditions. | Retrieval can alter IHC staining in general, but the supplied UniProt and HPA records do not establish a CLDN3-specific retrieval or fixation response (standard IHC practice; UniProt O15551; HPA tissue IHC). | Compare conditions on the same HPA High positive cell population with matched controls; record which condition preserves interpretable junctional staining (HPA tissue IHC; standard IHC practice). |
Comprehensive Human Protein Atlas IHC scoring per tissue (reliability: Enhanced — 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.
| Tissue | Cell type | Level | Evidence | Source |
|---|---|---|---|---|
| Appendix | Endocrine cells | High | Protein (IHC) | HPA → |
| Breast | Glandular cells | High | Protein (IHC) | HPA → |
| Colon | Endocrine cells | High | Protein (IHC) | HPA → |
| Duodenum | Endocrine cells | High | Protein (IHC) | HPA → |
| Endometrium | Glandular cells | High | Protein (IHC) | HPA → |
| Tissue | Cell type | Level | Evidence | Source |
|---|---|---|---|---|
| Adipose tissue | Adipocytes | Not detected | Protein (IHC) | HPA → |
| Adrenal gland | Glandular cells | Not detected | Protein (IHC) | HPA → |
| Bone marrow | Hematopoietic cells | Not detected | Protein (IHC) | HPA → |
| Caudate | Glial cells | Not detected | Protein (IHC) | HPA → |
| Cerebellum | Cells in granular layer | Not detected | Protein (IHC) | HPA → |
Use membrane pattern, cell identity and matched controls to troubleshoot CLDN3 staining in paraffin sections.
Human-reactive anti-CLDN3 antibodies have IHC images from paraffin-embedded tumor sections and IF images from MCF-7 cells or a paraffin-embedded lung tumor section (catalog reactivity and image captions).
A04393-5 shows IHC in human renal clear cell carcinoma and IF/ICC in MCF-7 cells; M04393-2 shows IHC in human colorectal adenocarcinoma and IF in human lung adenocarcinoma (respective image captions). A04393-3 shows IHC in human pancreatic cancer and IF/ICC in MCF-7 cells (A04393-3 image captions).
Which to pick: For tissue IHC, choose the sample match: A04393-5 for human renal clear cell carcinoma (A04393-5 IHC caption), M04393-2 for human colorectal adenocarcinoma (M04393-2 IHC caption), or A04393-3 for human pancreatic cancer (A04393-3 IHC caption); all three captions describe paraffin sections with EDTA retrieval at pH 8.0, but do not report the fixative (respective IHC captions). For IF/ICC, A04393-5 and A04393-3 list both applications and show MCF-7 cell images; the mouse monoclonal M04393-2 lists IF and shows paraffin-section IF in human lung adenocarcinoma (catalog applications, host and clone; respective IF captions). None has documented nonhuman reactivity, so there is no supported cross-species pick (catalog reactivity: Human only).