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CLDN1 / Claudin-1 · IHC design guide
Design Immunohistochemistry for CLDN1
Plan CLDN1 IHC on paraffin sections using high-staining kidney Bowman’s capsule, skin granular layer, or tonsil squamous epithelium as positive tissue references (HPA tissue IHC). Assess membranous staining and include a no-primary control (HPA tissue IHC; standard IHC practice).
Evidence assembled Oct 2026 · For research use; verify linked source records and product datasheet before use
CLDN1 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 in tissue (HPA tissue IHC); tight junction (UniProt) | |
| Staining pattern | Membranous staining, most abundant in squamous epithelium (HPA tissue IHC) | |
| Antigen retrieval | EDTA pH 8.0 HIER, heat-mediated (datasheet A01585-2) | |
| Positive control | Kidney+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 | RNA levels may mispredict staining intensity (HPA tissue IHC) | |
| Regulation | No specific expression regulator reported (UniProt) | |
| Isoform / epitope | No annotated isoforms; extracellular vs cytoplasmic epitope matters (UniProt) |
Section 1
Recommended CLDN1 IHC & IF Protocols
The catalog antibody uses EDTA pH 8.0 retrieval (datasheet A01585-2). The published CLDN1 IHC protocols below cover breast, colorectal, mouse colon, and other paraffin sections (PMC1064136; PMC4202803; PMC7571313; PMC12624041).
| Sample | Paraffin-embedded human lung cancer tissue; fixative not specified (datasheet A01585-2) |
| Fixation | Image fixative and duration unreported (datasheet A01585-2); 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 A01585-2); 20 min, 95–100 °C (standard) |
| Peroxidase block | 3% H2O2, 10 min, room temperature (standard) |
| Blocking | 10% goat serum (datasheet A01585-2) |
| Primary antibody | Rabbit anti-CLDN1, 2μg/ml (datasheet A01585-2) |
| Primary incubation | Overnight at 4 °C (datasheet A01585-2) |
| Detection | Streptavidin-biotin complex (SABC), DAB chromogen (datasheet A01585-2) |
| Counterstain | Hematoxylin, blue, dehydrate and mount (standard) |
| Expected result | CLDN1-positive staining in bowman's capsule of kidney (HPA tissue IHC: High). HPA tissue profile: Membranous expression in several tissues, most abundant in squamous epithelium. No signal in the no-primary control. |
💡Decision noteStart with EDTA pH 8.0 heat retrieval for the catalog antibody (datasheet A01585-2). Citrate pH 6.0 is a published alternative to evaluate (PMC4202803; PMC7571313).
Section 2
What Is the Expected CLDN1 Staining Pattern?
CLDN1 is a 4-pass membrane protein found at tight junctions and at the cell membrane; a CLDN1–CD81 complex can also localize basolaterally (UniProt O95832 topology and subcellular location). In paraffin-section IHC, expect membranous staining in selected epithelial cells, especially squamous epithelium (HPA tissue IHC). HPA rates the tissue profile Enhanced, while describing only medium consistency between antibody staining and RNA expression (HPA tissue IHC).
| Crisp staining traces cell borders in skin granular-layer cells, tonsil squamous epithelium, or kidney Bowman's capsule. | This fits the expected membrane-associated pattern in cell types scored High by HPA (HPA tissue IHC; UniProt O95832 subcellular location). Judge the relevant cells and their borders, rather than the overall darkness of the section. |
| Strong nuclear staining dominates, with little discernible staining at epithelial cell borders. | A predominantly nuclear result does not match the annotated cell-membrane and tight-junction location (UniProt O95832 subcellular location). Treat it as suspect, check assay controls, and avoid scoring nuclear colour alone as a CLDN1-positive result (general IHC practice). |
| Prominent staining occurs in adipocytes or bone-marrow hematopoietic cells while expected epithelial borders are faint. | HPA reports CLDN1 as not detected in those specified cell types (HPA tissue IHC). The mismatch raises concern for cross-reactivity or endogenous detection activity; investigate with appropriate controls before attributing it to CLDN1 (general IHC practice). |
| Colour spreads diffusely through tissue, across cell interiors, or through regions without a readable border pattern. | Diffuse colour lacks the compartment specificity expected for CLDN1 (UniProt O95832 subcellular location). Assess background with a control lacking primary antibody and review blocking, washing, and chromogen development (general IHC practice); diffuse signal alone is not evidence of epithelial CLDN1. |
| There is no convincing membrane signal in skin granular-layer cells, tonsil squamous epithelium, or kidney Bowman's capsule. | These are HPA High cell-type examples, so their absence makes the run difficult to interpret (HPA tissue IHC). First confirm tissue identity and assay performance. HPA supplies no CLDN1-specific fixation-sensitivity finding here, so absence cannot be assigned to fixation chemistry from this record. |
💡Expected CLDN1 appearanceCall a convincing positive result when distinct epithelial cell borders stain, strongest in HPA High examples such as skin granular-layer cells or tonsil squamous cells; isolated nuclear colour or diffuse colour without readable borders is suspect (HPA tissue IHC; UniProt O95832 subcellular location; general IHC practice).
| Membrane topology and location | CLDN1 has 4 transmembrane segments, extracellular loops at residues 29–81 and 137–163, and cytoplasmic regions at 1–7, 103–115, and 185–211 (UniProt O95832 topology). Epitope accessibility depends on the antibody epitope and assay conditions; neither is specified here. |
| Tissue and cell-type choice | HPA scores kidney Bowman's capsule, skin granular-layer cells, and tonsil squamous cells High, but breast and bronchus epithelium Medium (HPA tissue IHC). Compare like cell types: UniProt's broad liver and kidney tissue-specificity statement does not identify which liver cells should stain in an IHC section (UniProt O95832 tissue specificity). |
| Strength of pattern evidence | The tissue IHC profile is Enhanced, with medium staining–RNA consistency (HPA tissue IHC). Antibody HPA048319 has Enhanced IHC validation and CAB002602 has Supported IHC validation (HPA antibodies). Those labels support review of the observed pattern; they do not make every stained cell or compartment target-specific. |
| IF/ICC Q&A: what localization is supported? | HPA summarizes the ICC-IF localization as membrane, but lists no main location and no cell lines with ICC-IF images (HPA subcellular). Use membrane localization as the limited cross-application expectation; this record does not establish a cell-line-specific IF pattern or supply an IF protocol. |
| Situation | Likely cause | Next action |
|---|---|---|
| A known-positive epithelial cell type is blank. | The expected High cell-type signal is missing, or the assay may not have worked as intended (HPA tissue IHC; general IHC practice). | Confirm the section contains the named cell type; check positive and detection controls, antibody application, and the assay's antigen-retrieval instructions (general IHC practice). Do not infer CLDN1-specific fixation sensitivity from these sources. |
| Signal appears chiefly nuclear or as broad cytoplasmic colour. | The dominant compartment conflicts with CLDN1's cell-membrane and tight-junction annotation (UniProt O95832 subcellular location). | Check a known-positive epithelial section for readable cell borders, then inspect control staining and detection conditions (general IHC practice). Record the observed compartment separately from a CLDN1-positive membrane score. |
| Unexpected cells stain more strongly than epithelial borders. | Cross-reactivity or endogenous detection activity is possible, especially when cells such as adipocytes or hematopoietic cells stain despite HPA's not-detected calls (HPA tissue IHC; general IHC practice). | Verify cell identity and include a control lacking primary antibody; review blocking and detection reagents if that control retains signal (general IHC practice). Interpret the result against the cell-specific HPA profile. |
| The whole section has diffuse colour. | The result obscures the border pattern expected from CLDN1 localization (UniProt O95832 subcellular location); background from the staining workflow is possible (general IHC practice). | Compare with a control lacking primary antibody and review blocking, wash steps, and chromogen development (general IHC practice). Score only cells whose membrane pattern remains distinguishable from background. |
| A tissue called positive shows mixed or weak staining. | HPA levels refer to specified cells: breast glandular and bronchial respiratory epithelial cells are Medium, while other listed epithelial examples are High (HPA tissue IHC). | Identify and score the relevant cell population rather than the entire tissue. Use HPA's tissue profile as a guide, allowing for its stated medium consistency between antibody staining and RNA expression (HPA tissue IHC). |
Experiment evidence
IHC & IF images showing CLDN1 staining
A01585-2 · IHCIHC analysis of Claudin 1/CLDN1 using anti Claudin 1/CLDN1 antibody (A01585-2). Claudin 1/CLDN1 was detected in paraffin-embedded section of
A01585-2 · IHCIHC analysis of Claudin 1/CLDN1 using anti Claudin 1/CLDN1 antibody (A01585-2). Claudin 1/CLDN1 was detected in paraffin-embedded section of
A01585-2 · IFIF analysis of Claudin 1/CLDN1 using anti-Claudin 1/CLDN1 antibody (A01585-2). Claudin 1/CLDN1 was detected in immunocytochemical section of
M01585-3 · IHCMouse stomach was stained with anti-Claudin 1 rabbit antibody
M01585-3 · IHCRat stomach was stained with anti-Claudin 1 rabbit antibody
M01585-2 · IHCRat stomach tissue was stained with anti-Claudin 1 rabbit Antibody
M01585-2 · IHCRat esophagus tissue was stained with anti-Claudin 1 rabbit Antibody
A01585-1 · IFImmunofluorescence Validation of CLDN1 in HepG2 Cells Immunofluorescent analysis of 4% paraformaldehyde-fixed HepG2 cells labeling CLDN1 wit
HPA · Cerebral cortexHuman Protein Atlas IHC, Cerebral cortex. Source: https://www.proteinatlas.org/ENSG00000163347-CLDN1/tissue/cerebral+cortex#imid_15107034
HPA · ColonHuman Protein Atlas IHC, Colon. Source: https://www.proteinatlas.org/ENSG00000163347-CLDN1/tissue/colon#imid_15106966
HPA · LiverHuman Protein Atlas IHC, Liver. Source: https://www.proteinatlas.org/ENSG00000163347-CLDN1/tissue/liver#imid_15106959
HPA · KidneyHuman Protein Atlas IHC, Kidney. Source: https://www.proteinatlas.org/ENSG00000163347-CLDN1/tissue/kidney#imid_15106960
← swipe / scroll for more images →
Real IHC / IF data behind the staining-pattern expectations in this section.
Sample controls for CLDN1 IHC & IF
🧪Run kidney first: cells of Bowman’s capsule should show CLDN1 staining (HPA: High in kidney Bowman’s capsule). Use adipose tissue adipocytes as the biological negative (HPA: Not detected in adipocytes); on the kidney slide, neighboring unstained cells should lack crisp junctional membrane signal (UniProt O95832: tight-junction and membrane localization).
Positive control tissue: Kidney (Bowman's capsule, HPA High)
Negative control tissue: Adipose tissue (HPA Not detected)
ICC-IF cell lines (HPA subcellular resource): HPA carries no ICC-IF cell line for CLDN1; derive a cell-line control from the positive tissue's cell type (Bowman's capsule) and confirm it by RNA or western blot first.
Technical controls: Include a no-primary, secondary-only control, a rabbit IgG isotype control matched to the primary antibody’s clonality, and CLDN1 knockout material if available (caption: rabbit primary; standard IHC practice). For chromogenic detection, block endogenous peroxidase and check kidney sections for endogenous biotin when using the caption’s avidin–biotin system (caption: SABC with DAB; standard IHC practice).
⚠️Feasibility: A target-specific fixation window or fixation effect is unreported, and the selected A01585-2 paraffin-section caption does not state the fixative (selected-SKU caption). That caption uses heat retrieval in EDTA at pH 8.0, but does not establish whether retrieval is required under other conditions (selected-SKU caption). The supplied evidence does not establish whether frozen sections or IF are easier; with the caption’s SABC detection, endogenous biotin in kidney is a potential staining artefact to check (selected-SKU caption; standard IHC practice).
HPA tissue IHC evidence for CLDN1
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 |
|---|---|---|---|---|
| Kidney | Bowman's capsule | High | Protein (IHC) | HPA → |
| Skin | Cells in granular layer | High | Protein (IHC) | HPA → |
| Tonsil | Squamous epithelial cells | High | Protein (IHC) | HPA → |
| Breast | Glandular cells | Medium | Protein (IHC) | HPA → |
| Bronchus | Respiratory 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 → |
| 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 → |
| Cerebral cortex | Endothelial cells | Not detected | Protein (IHC) | HPA → |
Section 3
Advanced CLDN1 IHC Tips
Troubleshoot CLDN1 staining by checking retrieval, cell-border localisation and cell-type controls before interpreting chromogenic IHC signal.
How should I retrieve CLDN1 in paraffin sections when junctional staining is weak?
Start CLDN1 paraffin-section IHC with heat-mediated retrieval in EDTA at pH 8.0 (datasheet A01585-2). The selected antibody was used after this retrieval on a paraffin-embedded human lung cancer section at 2 μg/ml overnight at 4°C (selected-SKU IHC caption). If staining is weak, compare heating, cooling and section adherence across paired sections before changing retrieval duration (standard IHC practice). Only then test another buffer or pH as a documented fallback while holding antibody concentration and detection constant (standard IHC practice). Judge improvement by distinct cell-border staining, the expected compartment for this tight-junction protein (UniProt O95832 localisation).
Can fixation account for weak CLDN1 staining in these paraffin sections?
The selected paraffin-section caption does not state a fixative, so CLDN1-specific sensitivity to fixation is unknown here (selected-SKU IHC caption). Record each specimen’s fixative and processing history, then compare sections processed together before attributing weak staining to fixation (standard IHC practice). Include a concurrently processed positive epithelial control and apply the stated EDTA pH 8.0 retrieval consistently (datasheet A01585-2; standard IHC practice). If the control stains but the specimen does not, review tissue preservation and cell identity as well as the staining steps (standard IHC practice). Do not infer a fixation effect from the reported tissue staining pattern (HPA tissue IHC).
Which CLDN1 staining pattern should count as convincing in tissue IHC?
Prioritise staining along epithelial cell borders, especially junctional borders, because CLDN1 localises to tight junctions and cell membranes (UniProt O95832 localisation). Basolateral membrane staining can also be biologically plausible where CLDN1 associates with CD81, but assess it against the tissue architecture (UniProt O95832 localisation). The reference tissue profile describes membranous staining most abundant in squamous epithelium, with high signal in skin granular-layer cells and tonsil squamous epithelial cells (HPA tissue IHC). Use those compartments to evaluate an on-slide positive control rather than treating any brown deposit as positive (HPA tissue IHC; standard IHC practice). Predominantly nuclear signal conflicts with the recorded localisation and warrants review of background and antibody controls (UniProt O95832 localisation; standard IHC practice).
How should CLDN1 topology and an unknown epitope guide IHC troubleshooting?
The record lists 4 transmembrane segments and cytoplasmic and extracellular loops, so epitope position could affect access during staining (UniProt O95832 topology; standard IHC practice). The antibody’s recognised epitope is not supplied, so do not assign its staining to a particular loop or terminus (selected-SKU IHC caption). UniProt lists a single chain of 211 amino acids, no annotated isoforms and 0 glycosylation sites; these annotations do not establish antibody specificity (UniProt O95832 processing, isoforms and glycosylation). If signal changes after retrieval, compare paired sections with identical detection and a known positive tissue compartment (standard IHC practice). Interpret discordant compartment staining using morphology and controls, not an assumed epitope location (standard IHC practice).
How can IF help assess an ambiguous CLDN1 IHC pattern?
On the separate IF/ICC guide, multiplex CLDN1 with an independently validated marker for the expected epithelial cell type to test whether cell-border signal belongs to that population (HPA tissue IHC; standard IF practice). Select fluorophores after checking tissue autofluorescence, and favour a spectrally separated, longer-wavelength channel if shorter-wavelength background obscures the border (standard IF practice). Choose permeabilisation only after establishing whether the antibody epitope faces a cytoplasmic or extracellular region; the supplied caption does not identify that epitope (UniProt O95832 topology; selected-SKU IHC caption). Include single-stain and secondary-only controls to assess bleed-through and nonspecific fluorescence (standard IF practice). Do not transfer an IF exposure or staining threshold directly to chromogenic IHC scoring (standard IHC/IF practice).
What should I check when CLDN1 IHC shows diffuse brown background?
Compare the staining with a no-primary control to identify color generated by the detection system or tissue rather than primary-antibody binding (standard IHC practice). The selected section used 10% goat-serum block, a biotinylated secondary antibody, a streptavidin–biotin complex and DAB, so examine each detection step when background rises (selected-SKU IHC caption). Check endogenous peroxidase blocking and, for this biotin-based method, assess endogenous biotin with an appropriate control (selected-SKU IHC caption; standard IHC practice). Wash and titrate the primary on paired sections while preserving the same retrieval and development conditions (standard IHC practice). Retain only anatomically coherent cell-border signal as a candidate CLDN1 pattern (UniProt O95832 localisation; standard IHC practice).
How should I quantify CLDN1 staining across paraffin sections? ⚠ ANSWER MARKED FOR VERIFICATION
Define a viable epithelial region and score membranous staining within it, since the expected CLDN1 compartment is the cell border (UniProt O95832 localisation; standard IHC practice). Report the percentage of positive epithelial cells and, if intensity matters, a membrane H-score using intensity 0–3 multiplied by the percentage at each intensity, yielding 0–300 (standard IHC practice). For spatial comparisons, report positive border area or positive cells per mm² of viable epithelial tissue and state the segmentation rule (standard IHC practice). Normalise to the number or area of eligible epithelial cells, rather than total section area, when specimens differ in stromal content (standard IHC practice). Keep retrieval, staining and image thresholds consistent across the comparison (standard IHC practice).
How can I distinguish true CLDN1 positivity from artefact?
A convincing result follows epithelial cell borders in intact tissue, matching CLDN1’s tight-junction and membrane localisation (UniProt O95832 localisation). High staining in skin granular-layer cells, tonsil squamous epithelium or kidney Bowman’s capsule can support control performance, whereas HPA reports no detection in adipocytes (HPA tissue IHC). Question isolated nuclear color, staining confined to cut edges or necrotic areas, and deposits that ignore cell outlines (UniProt O95832 localisation; standard IHC practice). Check no-primary and detection controls for endogenous enzyme activity or nonspecific chromogen before calling an unusual compartment positive (standard IHC practice). Interpret a negative specimen against its eligible cell population and a concurrently stained positive control (standard IHC practice).
Boster reagents
Best CLDN1 / Claudin-1 IHC Antibodies
Anti-CLDN1 antibodies have IHC images from human lung and rectal cancer, human breast, mouse stomach, and rat stomach and esophagus, plus an IF image from HepG2 cells (catalog image captions).
Real IHC data
Anti-Claudin 1/CLDN1 Antibody
Cat # A01585-2
Real IHC data
Anti-Claudin 1 Rabbit Monoclonal Antibody
Cat # M01585-3
Real IHC data
Anti-Claudin 1 Rabbit Monoclonal Antibody
Cat # M01585-2
Real IF data
Anti-Claudin-1 CLDN1 Antibody
Cat # A01585-1
A01585-2 has IHC images from paraffin sections of human lung and rectal cancer; M01585-3 has IHC images from mouse and rat stomach and human breast (catalog IHC image captions). M01585-2 has IHC images from rat stomach and esophagus, while A01585-1 has an IF image from HepG2 cells (catalog image captions).
Which to pick: For human paraffin-section IHC, choose A01585-2: its own IHC captions document EDTA retrieval at pH 8.0 and antibody at 2 μg/mL; the fixative is unreported (A01585-2 IHC image captions). For IF/ICC, A01585-1 lists both applications and has a 4% paraformaldehyde-fixed HepG2 IF image; A01585-2 also lists IF/ICC (catalog applications; A01585-1 IF image caption). For IHC across human, mouse, and rat, choose monoclonal M01585-3: its catalog lists all three species and an IHC dilution of 1:200–1:1000, with IHC images from each; monoclonal M01585-2 lists the same species but has IHC images only from rat tissues (catalog reactivity, dilution and IHC image captions).
Each figure is that product's own IHC / IF validation image from its datasheet.
References
- UniProt Consortium. UniProt entry O95832 (CLD1_HUMAN, Claudin-1).
- Human Protein Atlas. CLDN1 tissue IHC expression (reliability: Enhanced).
- Human Protein Atlas. CLDN1 subcellular location (ICC-IF): Membrane.
- Human Protein Atlas. CLDN1 antibody validation summary (2 antibodies).
- Claudin-1, -3 and -4 proteins and mRNA expression in benign and malignant breast lesions: a research study. Breast cancer research : BCR 2005 — PMC1064136.
- Claudin-1 Expression Is Elevated in Colorectal Cancer Precursor Lesions Harboring the BRAF V600E Mutation. Translational oncology 2014 — PMC4202803.
- Inhibition of miRNA-29a regulates intestinal barrier function in diarrhea-predominant irritable bowel syndrome by upregulating ZO-1 and CLDN1. Experimental and therapeutic medicine 2020 — PMC7571313.
- PABPC3 drives ovarian cancer metastasis and drug sensitivity by downregulating CLDN1 expression. Cell death & disease 2025 — PMC12624041.
- PubMed PMID:9931503 — UniProt-cited evidence.
- PubMed PMID:10828592 — UniProt-cited evidence.
- PubMed PMID:11071387 — UniProt-cited evidence.
Immunohistochemistry protocol sheet for CLDN1 (Claudin-1). Expected localisation Membranous in tissue (HPA tissue IHC); tight junction (UniProt). Antigen retrieval: EDTA pH 8.0 HIER, heat-mediated (datasheet A01585-2). Validated IHC antibody: A01585-2 at 2μg/ml (the product's own IHC validation image is shown). Controls (HPA): positive Kidney (Bowman's capsule); negative Adipose tissue. IHC-P workflow on paraffin sections; fixative unspecified. Protocol steps: 1. Sample: Paraffin-embedded human lung cancer tissue; fixative not specified (datasheet A01585-2); 2. Fixation: Image fixative and duration unreported (datasheet A01585-2); 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 A01585-2); 20 min, 95–100 °C (standard); 6. Peroxidase block: 3% H2O2, 10 min , room temperature (standard); 7. Blocking: 10% goat serum (datasheet A01585-2); 8. Primary antibody: Rabbit anti-CLDN1, 2μg/ml (datasheet A01585-2); 9. Primary incubation: Overnight at 4 °C (datasheet A01585-2). Watch for: Fixation: Keep fixation consistent across sections (standard IHC practice; not target-specific); Caveat: RNA levels may mispredict staining intensity (HPA tissue IHC); Isoform / epitope: No annotated isoforms; extracellular vs cytoplasmic epitope matters (UniProt); Regulation: No specific expression regulator reported (UniProt). Evidence: UniProt O95832, HPA tissue IHC · Enhanced, HPA ICC-IF · Membrane, Datasheet A01585-2, PMC1064136, PMC4202803. QR code links to https://www.bosterbio.com/bosterbio-gene-info-cards/CLDN1/immunohistochemistry-ihc-guide.