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- Table of Contents
Plan chromogenic CD3E IHC on paraffin sections using tonsil as a positive control (HPA tissue IHC; datasheet PB9093). Score selective cytoplasmic staining in T cells while considering CD3E's membrane location and activation linked internalization (HPA tissue IHC; UniProt).
Expected localisation, validated protocols, controls and antibodies — the at-a-glance facts below, then the full design guide.
| Expected localisation | T-cell cytoplasm observed; membrane expected (HPA tissue IHC; UniProt) | |
| Staining pattern | Selective cytoplasmic staining in T cells (HPA tissue IHC) | |
| Antigen retrieval | Citrate pH 6 HIER, heat-mediated (datasheet PB9093) | |
| Positive control | Appendix+4 more · see all | |
| Negative control | Adipose tissue+4 more · see all |
| Fixation | Matched tissue-IHC evidence does not establish the fixation claim. Validate the specimen-specific method before use. (selected-SKU IHC image PB9093) | |
| Caveat | Cytoplasmic IHC may differ from membrane expectations (HPA tissue IHC; UniProt) | |
| Regulation | Activation promotes CD3E internalization (UniProt) | |
| Isoform / epitope | 0 isoforms listed; distinguish extracellular from cytoplasmic epitopes (UniProt) |
The catalog antibody’s paraffin IHC protocol uses citrate pH 6 retrieval (datasheet PB9093). Three published CD3E IHC protocols provide additional conditions (PMC4013007; PMC5351587; PMC12529491).
| Sample | Paraffin-embedded human tonsil tissues; fixative not specified (datasheet PB9093) |
| Fixation | Image fixative and duration unreported (datasheet PB9093); 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 PB9093) |
| Peroxidase block | 3% H2O2, 10 min, room temperature (standard) |
| Blocking | 10% goat serum (datasheet PB9093) |
| Primary antibody | Rabbit anti-CD3E, 0.5-1μg/ml (datasheet PB9093) |
| Primary incubation | Overnight at 4 °C (datasheet PB9093) |
| Detection | Streptavidin-biotin complex (SABC), DAB chromogen (datasheet PB9093) |
| Counterstain | Hematoxylin, blue, dehydrate and mount (standard) |
| Expected result | CD3E-positive staining in lymphoid tissue of appendix (HPA tissue IHC: High). HPA tissue profile: Selective cytoplasmic expression in T-cells. No signal in the no-primary control. |
CD3E is a cell-membrane protein with an extracellular segment at residues 23–126 and a cytoplasmic segment at 153–207 (UniProt P07766 topology). In paraffin-section IHC, expect staining in T-cells; HPA describes selective cytoplasmic expression and rates its tissue pattern Enhanced, reflecting high consistency with RNA data (HPA tissue IHC). Interpret that observed cytoplasmic pattern alongside CD3E’s membrane topology rather than requiring a crisp membrane rim in every cell.
| Discrete stained lymphocytes in appendix lymphoid tissue or the non-germinal-center regions of lymph node or tonsil, with little staining in adjacent non-lymphoid cells (HPA tissue IHC). | This fits the reported high staining in those compartments and selective T-cell expression (HPA tissue IHC). Assess the distribution across cells as well as intensity: a convincing result identifies a lymphocyte population rather than coloring an entire tissue compartment (HPA tissue IHC; general IHC interpretation). |
| Predominantly nuclear staining, with no convincing lymphocyte-associated cytoplasmic or membrane signal. | A nuclear-only pattern does not fit the reported IHC profile or membrane topology (HPA tissue IHC; UniProt P07766 topology). Treat it as suspect and compare it with a known-positive section and detection controls before interpreting it as CD3E (general IHC practice). |
| Broad staining of adipocytes or respiratory epithelial cells instead of a selective lymphocyte population. | HPA reports CD3E as not detected in those cell types (HPA tissue IHC: adipocytes; respiratory epithelial cells). Consider antibody cross-reactivity or endogenous detection activity, and check controls; an occasional stained lymphocyte within an otherwise negative tissue has a different interpretation (general IHC practice; HPA tissue IHC). |
| A diffuse wash of chromogen obscures cell boundaries across positive and negative areas. | The distribution cannot establish selective T-cell staining (HPA tissue IHC; general IHC interpretation). Background can arise from detection activity, inadequate blocking, or excessive antibody concentration; inspect a no-primary control and adjust the general IHC workflow before scoring cells (general IHC practice). |
| No stained lymphocytes in appendix lymphoid tissue, lymph node, or tonsil, while the section and counterstain remain visible. | These are reported high-staining sites, so a blank result warrants a technical check (HPA tissue IHC: High). Confirm that lymphocyte-rich areas are present, then review antibody identity, controls, retrieval and detection conditions; their optimal settings are not established by the supplied target evidence (general IHC practice). |
| Which compartment should guide IHC scoring? | UniProt places CD3E at the cell membrane, with a transmembrane segment at 127–152, while HPA describes selective cytoplasmic T-cell staining in tissue IHC (UniProt P07766 topology; HPA tissue IHC). Use the tissue pattern and cell identity together; a perfectly outlined membrane is not required to match the reported IHC appearance. |
| Which tissue areas provide a useful comparison? | HPA reports High staining in appendix lymphoid tissue and non-germinal-center cells of lymph node and tonsil, and Medium staining in bone-marrow hematopoietic cells and splenic red-pulp cells (HPA tissue IHC). Compare like compartments; these levels do not predict uniform intensity across every cell. |
| How strong is the tissue-pattern evidence? | HPA rates the tissue IHC pattern Enhanced and lists five antibodies with Enhanced IHC validation: HPA040957, HPA043955, CAB000010, CAB072863 and CAB072864 (HPA tissue IHC; HPA antibodies). Validation supports the reported pattern but does not replace controls for the antibody and run in use (general IHC practice). |
| Does the record establish an antigen-retrieval condition? | Target-specific fixation effects are not established by the supplied assay evidence. Verify with a matched IHC source before attributing a result to fixation. |
| Can intracellular signal be biologically plausible? | CD3E participates in TCR-CD3 internalization through sequences in its cytosolic region (UniProt P07766 function). That fact and HPA’s cytoplasmic IHC profile support considering intracellular staining in the right cells; they do not make diffuse staining of unrelated cells specific (UniProt P07766; HPA tissue IHC). |
| For IF/ICC, where has CD3E been seen? | HPA reports plasma-membrane and endoplasmic-reticulum localization, with additional Golgi localization, in its ICC-IF subcellular record (HPA subcellular). Those observations answer the localization question for IF/ICC; they are a separate assay record and do not set a paraffin-section IHC protocol or require every tissue cell to show all three compartments. |
| Situation | Likely cause | Next action |
|---|---|---|
| The expected lymphocyte population is weak or absent in a positive section. | The run may have insufficient usable signal, or the examined area may lack the reported positive compartment (HPA tissue IHC; general IHC practice). | First locate appendix lymphoid tissue or an appropriate lymph-node or tonsil region, then check the IHC-validated antibody’s instructions, retrieval, dilution and detection controls (HPA tissue IHC; general IHC practice). Do not infer a CD3E-specific fixation failure from this result. |
| Signal appears only in nuclei. | Nuclear-only localization conflicts with the membrane topology and selective cytoplasmic tissue profile (UniProt P07766 topology; HPA tissue IHC). | Compare a known-positive lymphocyte area with a no-primary control and review detection background before calling the nuclear signal specific (general IHC practice). |
| Adipocytes or respiratory epithelium stain broadly. | Those cell types are listed as not detected by HPA; cross-reactivity or endogenous detection activity is possible (HPA tissue IHC; general IHC practice). | Check a no-primary control and the distribution in a positive lymphoid compartment. If staining persists without primary antibody, review blocking and detection steps; otherwise reassess antibody specificity (general IHC practice). |
| Diffuse chromogen makes individual lymphocytes hard to identify. | Background obscures the selective cell pattern reported for CD3E (HPA tissue IHC). Excess primary antibody or detection background are general possibilities, not established CD3E-specific effects (general IHC practice). | Use a no-primary control, then review blocking, washing, antibody concentration and development time according to the IHC workflow (general IHC practice). Score only cells whose signal remains distinguishable from background. |
| A membrane rim is faint, but discrete lymphocytes show cytoplasmic staining. | HPA’s paraffin-section tissue profile describes selective cytoplasmic T-cell expression despite CD3E’s membrane topology (HPA tissue IHC; UniProt P07766 topology). | Judge cell identity, tissue distribution and control results together; do not reject an otherwise matching IHC pattern solely because the membrane rim is faint (HPA tissue IHC; general IHC interpretation). |
| The negative comparison tissue contains a few stained small cells. | HPA’s not-detected entries refer to specified cell types, such as adipocytes and respiratory epithelial cells, rather than every cell present in the tissue (HPA tissue IHC). | Identify which cells stain and compare their morphology with lymphocytes in a positive section. Use the negative compartment and a no-primary control to assess nonspecific signal (HPA tissue IHC; general 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 | Lymphoid tissue | High | Protein (IHC) | HPA → |
| Lymph node | Non-germinal center cells | High | Protein (IHC) | HPA → |
| Tonsil | Non-germinal center cells | High | Protein (IHC) | HPA → |
| Bone marrow | Hematopoietic cells | Medium | Protein (IHC) | HPA → |
| Spleen | Cells in red pulp | Medium | 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 → |
| Breast | Adipocytes | Not detected | Protein (IHC) | HPA → |
| Bronchus | Respiratory epithelial cells | Not detected | Protein (IHC) | HPA → |
| Caudate | Glial cells | Not detected | Protein (IHC) | HPA → |
Troubleshoot CD3E staining in paraffin sections by checking retrieval, cell distribution, compartment, controls and scoring before interpreting chromogenic signal.
The catalog covers human, mouse, rat, and chicken reactivity (catalog reactivity). The figures show tissue IHC for six antibodies and human tonsil IF for PB9093 (IHC and IF captions).
PB9093 shows human tonsil paraffin IHC (PB9093 IHC caption); M02675-1 shows human appendix paraffin IHC (M02675-1 IHC caption); M02675-2 shows mouse intestine paraffin IHC, although its listed reactivity is human only (M02675-2 IHC caption; catalog reactivity). M02675-10 shows rat spleen IHC (M02675-10 IHC caption); A02675-2 shows human brain paraffin IHC (A02675-2 IHC caption); M02675-3 shows formalin-fixed, paraffin-embedded human tonsil IHC (M02675-3 IHC caption).
Which to pick: For human paraffin IHC, choose PB9093 when a documented starting condition helps: its tonsil image used citrate retrieval at pH 6 and 1 μg/ml primary antibody; the fixative is unreported (PB9093 IHC caption). For IF, PB9093 has human tonsil images; for ICC, M02675-1 lists that application, though its appendix paraffin IHC caption does not report the fixative (PB9093 IF captions; M02675-1 catalog applications and IHC caption). For cross-species IHC, PB9093 has human, mouse, and rat paraffin image captions plus listed chicken reactivity; those captions do not report the fixative (PB9093 IHC captions; catalog reactivity).