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- Table of Contents
Plan SERPINB5 paraffin-section IHC using esophageal squamous cells as a positive control and adipocytes as a negative control (HPA tissue IHC). This guide covers fixation consistency, chromogenic detection, and scoring of the variable cytoplasmic staining pattern (standard IHC practice; HPA tissue IHC).
Expected localisation, validated protocols, controls and antibodies — the at-a-glance facts below, then the full design guide.
| Expected localisation | Cytoplasmic tissue staining (HPA tissue IHC); secreted protein (UniProt) | |
| Staining pattern | Variable cytoplasmic staining, strongest in squamous epithelia (HPA tissue IHC) | |
| Antigen retrieval | EDTA pH 8.0 HIER, heat-mediated (datasheet M03409) | |
| Positive control | Esophagus+4 more · see all | |
| Negative control | Adipose tissue+4 more · see all |
| Fixation | Keep fixation consistent across sections. (standard IHC practice; not target-specific) | |
| Caveat | Secretion may complicate interpretation of cytoplasmic staining (UniProt; HPA tissue IHC) | |
| Regulation | Highest staining in squamous epithelia and gut (HPA tissue IHC) | |
| Isoform / epitope | 2 isoforms; epitope and compartment effects unreported (UniProt) |
The catalog antibody uses heat-mediated EDTA pH 8.0 retrieval (datasheet M03409). Published SERPINB5 IHC methods from 3 articles follow (PMC12921336; PMC10425712; PMC6995195).
| Sample | Paraffin-embedded human tonsil tissue; fixative not specified (datasheet M03409) |
| Fixation | Image fixative and duration unreported (datasheet M03409); 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 M03409); 20 min, 95–100 °C (standard) |
| Peroxidase block | 3% H2O2, 10 min, room temperature (standard) |
| Blocking | 10% goat serum (datasheet M03409) |
| Primary antibody | Mouse monoclonal (clone 7G4E1) anti-SERPINB5, 2 μg/ml (datasheet M03409) |
| Primary incubation | Overnight at 4 °C (datasheet M03409) |
| Detection | HRP-conjugated secondary, DAB chromogen (datasheet M03409) |
| Counterstain | Hematoxylin, blue, dehydrate and mount (standard) |
| Expected result | SERPINB5-positive staining in squamous epithelial cells of esophagus (HPA tissue IHC: High). HPA tissue profile: Cytoplasmic expression with varying intensity in most tissues, most abundant in squamous epithelia and the gastrointestinal tract. No signal in the no-primary control. |
For IHC of paraffin sections, expect predominantly cytoplasmic SERPINB5 staining in epithelial cells, especially esophageal squamous cells, skin basal cells and bladder urothelial cells (HPA: High in each). UniProt describes SERPINB5 as secreted, with no transmembrane segment (UniProt P36952: subcellular location and topology). Treat the tissue pattern as a guide: HPA rates its IHC reliability Enhanced but reports medium agreement with RNA data and pending external verification (HPA: tissue IHC).
| Strong cytoplasmic staining in esophageal squamous cells, skin basal cells or bladder urothelial cells. | This matches the most useful positive tissue examples (HPA: High in these cells; cytoplasmic tissue profile). Compare staining within the named cell population, rather than assigning one score to the whole section (general IHC practice). |
| Predominantly nuclear or sharply membrane-restricted staining, with little cytoplasmic signal. | This departs from the reported tissue IHC pattern (HPA: cytoplasmic tissue profile). Review morphology and controls before calling it specific; UniProt reports a secreted protein without a transmembrane segment, so membrane restriction needs independent support (UniProt P36952: location and topology). |
| Strong staining chiefly in adipocytes, smooth muscle cells or lymph-node germinal-center cells. | Those named populations were not detected in the HPA tissue examples (HPA: adipose tissue, smooth muscle, lymph node). Consider antibody cross-reactivity or endogenous detection activity, then compare with a known-positive epithelial section and appropriate detection controls (general IHC practice). |
| Diffuse color across epithelium, stroma and blank areas, with no clear cell boundaries. | That distribution cannot be read as a cell-specific SERPINB5 pattern (HPA: cytoplasmic tissue profile). Background may arise from detection chemistry, inadequate blocking or excess antibody (general IHC practice); check the negative detection control before scoring. |
| No convincing signal in a section containing esophageal squamous epithelium. | HPA reports High staining in those cells, so this is a failed positive-control result until the staining run is checked (HPA: Esophagus, High). Review tissue preservation, retrieval, antibody and detection steps as general IHC variables; no SERPINB5-specific fixation sensitivity is supplied (general IHC practice). |
| Tissue and cell choice (HPA: tissue IHC) | Esophagus squamous cells, skin basal cells and bladder urothelial cells are High; cervical, tonsillar and vaginal squamous cells are Medium (HPA: tissue IHC). Choose a High example for the run control; a Medium example offers less room to detect a weak run (general IHC practice). |
| Cellular compartment (HPA: tissue IHC; UniProt P36952) | HPA tissue IHC describes cytoplasmic staining; UniProt lists SERPINB5 as secreted and lacking a transmembrane segment (HPA: tissue profile; UniProt P36952: location and topology). The annotations differ in emphasis, so require a convincing tissue and cell pattern before interpreting extracellular color. |
| Evidence strength (HPA: tissue IHC; HPA: antibodies) | HPA calls tissue IHC Enhanced and lists 4 antibodies with Enhanced IHC status, yet describes only medium staining–RNA consistency and pending external verification (HPA: reliability and antibody validation). Use the pattern as a reference, while retaining run controls for each experiment (general IHC practice). |
| Isoforms and modification (UniProt P36952) | UniProt lists 2 isoforms and 4 glycosylation sites, at residues 99, 133, 188 and 361 (UniProt P36952: isoforms and glycosylation). These annotations alone do not identify the antibody epitope or predict a different staining pattern; assess any proposed variant-specific interpretation separately. |
| IF/ICC Q: What pattern should I compare? (HPA: subcellular ICC-IF) | A: HPA reports SERPINB5 mainly in vesicles in ICC-IF, with a supported vesicle location (HPA: subcellular ICC-IF). That is an IF reference, while the paraffin-section IHC comparison remains the HPA cytoplasmic tissue pattern (HPA: tissue IHC). |
| Situation | Likely cause | Next action |
|---|---|---|
| Known-positive esophageal epithelium is blank. | The expected High cell population is missing from the readout (HPA: Esophagus, High); the run or tissue may have failed (general IHC practice). | Confirm the squamous cells are present; review retrieval, antibody dilution and detection against the run controls (general IHC practice). No target-specific retrieval or fixation response is established here. |
| All tissue compartments have a pale, even deposit. | Uniform color obscures the expected cytoplasmic epithelial contrast (HPA: tissue IHC profile); nonspecific detection background is possible (general IHC practice). | Inspect a no-primary detection control, then review blocking, washes and antibody concentration under the standard IHC workflow (general IHC practice). |
| Signal appears mainly in nuclei or along cell borders. | The compartment differs from HPA's cytoplasmic tissue profile; a border-only pattern is also unsupported by UniProt's lack of a transmembrane segment (HPA: tissue IHC; UniProt P36952: topology). | Check section morphology and detection controls, then compare with a known-positive epithelial section before assigning SERPINB5 specificity (general IHC practice; HPA: High epithelial examples). |
| Adipocytes or smooth muscle stain as strongly as the epithelial control. | HPA reports SERPINB5 as not detected in those named cells; cross-reactivity or endogenous detection activity should be considered (HPA: adipose tissue and smooth muscle). | Compare those cells with a High epithelial control and a no-primary control; review blocking and detection chemistry if the controls show color (HPA: High epithelial examples; general IHC practice). |
| A low-expression tissue looks negative. | HPA lists only Low staining in lung alveolar cells and bronchial respiratory cells, so a weak result is hard to distinguish from a missed signal (HPA: Lung and Bronchus, Low). | Judge run performance in a High epithelial example first; interpret the low-level tissue only after its cell type and local background are clear (HPA: High epithelial examples; general IHC practice). |
| IHC looks broadly cytoplasmic, but IF looks punctate. | The two HPA readouts use different pattern descriptions: cytoplasmic tissue IHC and mainly vesicular ICC-IF (HPA: tissue IHC; HPA: subcellular ICC-IF). | Score each assay against its own HPA reference and its own controls; do not require paraffin-section chromogenic staining to resolve individual vesicles (HPA: tissue IHC and subcellular ICC-IF; general IHC practice). |
Comprehensive Human Protein Atlas IHC scoring per tissue (reliability: Enhanced — Medium consistency between antibody staining and RNA expression data. Pending external verification.). 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 |
|---|---|---|---|---|
| Esophagus | Squamous epithelial cells | High | Protein (IHC) | HPA → |
| Skin | Cells in basal layer | High | Protein (IHC) | HPA → |
| Urinary bladder | Urothelial cells | High | Protein (IHC) | HPA → |
| Cervix | Squamous epithelial cells | Medium | Protein (IHC) | HPA → |
| Tonsil | Squamous epithelial cells | Medium | Protein (IHC) | HPA → |
| 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 → |
| Hippocampus | Glial cells | Not detected | Protein (IHC) | HPA → |
Troubleshoot SERPINB5 staining in paraffin sections by checking retrieval, cellular distribution, controls, and scoring against documented tissue patterns.
The catalog shows anti-SERPINB5 IHC images from human paraffin sections and mouse colon, plus an IF/ICC image from A431 cells (catalog image captions).
M03409 has human tonsil and laryngeal squamous cell carcinoma IHC images from paraffin sections (M03409 IHC captions). PB9356 has human colon cancer and mouse colon IHC images from paraffin sections, plus an A431-cell IF/ICC image (PB9356 image captions).
Which to pick: For human tissue IHC, M03409 offers mouse monoclonal clone 7G4E1, with pH 8.0 EDTA retrieval shown in its human tonsil paraffin-section image (catalog: M03409 clone; M03409 IHC caption). Choose PB9356 for IF/ICC or IHC across human and mouse samples: those applications and species are listed, and its own images show A431-cell IF and paraffin-section IHC in both species (catalog: PB9356 applications and reactivity; PB9356 image captions). The fixative is unreported for both IHC images (M03409 and PB9356 IHC captions).