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- Table of Contents
Plan IRF7 paraffin IHC around nuclear staining in most tissues and distinct expression in lymphatic organs (HPA tissue IHC). The IHC-validated antibody has a 2–5 μg/ml range and a documented spleen example (datasheet A00115-3); assess nuclear enrichment in light of activation state (UniProt).
Expected localisation, validated protocols, controls and antibodies — the at-a-glance facts below, then the full design guide.
| Expected localisation | Nuclear in tissue IHC (HPA tissue IHC); cytoplasm possible (UniProt) | |
| Staining pattern | Nuclear staining in most tissues, distinct in lymphatic organs (HPA tissue IHC) | |
| Antigen retrieval | EDTA pH 8.0 HIER, heat-mediated (datasheet A00115-3) | |
| Positive control | Adipose tissue+4 more · see all | |
| Negative control | None in HPA (detected in all 45 tissues); use no-primary + isotype controls |
| Fixation | Keep fixation consistent across sections. (standard IHC practice; not target-specific) | |
| Caveat | Resting cells may retain cytoplasmic IRF7 (UniProt) | |
| Regulation | Viral/TLR cues enrich nuclear signal (UniProt) | |
| Isoform / epitope | 4 isoforms (A–D); verify epitope coverage (UniProt) |
The catalog antibody’s IHC-P protocol (datasheet A00115-3) is accompanied by published IRF7 IHC protocols for gallbladder carcinoma, mouse striatum, and psoriatic skin (PMC6423323; PMC11759022; PMC10876010).
| Sample | Paraffin-embedded human spleen tissue; fixative not specified (datasheet A00115-3) |
| Fixation | Image fixative and duration unreported (datasheet A00115-3); 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 A00115-3); 20 min, 95–100 °C (standard) |
| Peroxidase block | 3% H2O2, 10 min, room temperature (standard) |
| Blocking | 10% goat serum (datasheet A00115-3) |
| Primary antibody | Rabbit anti-IRF7, 2-5 μg/ml (datasheet A00115-3) |
| Primary incubation | Overnight at 4 °C (datasheet A00115-3) |
| Detection | HRP-conjugated secondary, DAB chromogen (datasheet A00115-3) |
| Counterstain | Hematoxylin, blue, dehydrate and mount (standard) |
| Expected result | IRF7-positive staining in adipocytes of adipose tissue (HPA tissue IHC: High). HPA tissue profile: Nuclear expression in most tissues, distinct expression in lymphatic organs. No signal in the no-primary control. |
IRF7 is nuclear and cytoplasmic, with active phosphorylated IRF7 accumulating in nuclei (UniProt Q92985). Expect predominantly nuclear staining across tissues, with distinct expression in lymphatic organs (HPA tissue IHC). Bone marrow hematopoietic cells and several epithelial and other cell populations show high staining (HPA tissue IHC). IRF7 has no transmembrane segment (UniProt Q92985 topology). HPA rates its tissue IHC profile Approved, with medium consistency between staining and RNA data (HPA tissue IHC).
| Nuclear signal in bone marrow hematopoietic cells, with some cytoplasmic signal. | This fits high staining in those cells (HPA: bone marrow) and the reported nuclear and cytoplasmic locations (UniProt Q92985). Score nuclei and cytoplasm separately; cytoplasmic staining alone does not establish activation (UniProt Q92985 function). |
| Predominant staining outlines cell membranes or appears outside cells. | That distribution conflicts with the reported nuclear and cytoplasmic locations and absence of a transmembrane segment (UniProt Q92985). Review morphology and background before assigning it to IRF7; compartment mismatch alone does not identify the artefact (general IHC practice). |
| Strong, widespread staining in prostate glandular cells. | Those cells are reported at low staining level (HPA: prostate glandular cells). Compare them with an HPA high cell population on the same run; unexpected intensity can suggest cross-reactivity or endogenous detection activity, but does not prove either (general IHC practice). |
| Diffuse brown color spans cells and surrounding tissue without clear nuclear boundaries. | The pattern is difficult to reconcile with nuclear expression in most tissues (HPA tissue IHC). Treat it as possible background; examine the counterstain, reagent controls and tissue morphology before scoring cells as positive (general IHC practice). |
| No staining in a section expected to contain bone marrow hematopoietic cells. | HPA reports high staining in that population (HPA: bone marrow), so absence of signal calls for a run check. Confirm the cells are present and review controls and detection steps before interpreting the result as low IRF7 (general IHC practice). |
| Activation state (UniProt Q92985 function) | Inactive IRF7 can reside in cytoplasm; phosphorylation promotes dimerization and nuclear accumulation (UniProt Q92985). Nuclear staining is compatible with that biology, but a routine total-IRF7 stain cannot by itself establish phosphorylation (general IHC interpretation). |
| Tissue and cell distribution (HPA tissue IHC) | HPA describes nuclear expression in most tissues and distinct expression in lymphatic organs (HPA tissue IHC). Its listed high populations include bone marrow hematopoietic cells, bronchial respiratory epithelium and colon glandular cells (HPA tissue IHC); prostate glandular cells are low (HPA tissue IHC). |
| Antibody evidence (HPA antibodies; HPA tissue IHC) | HPA052757 and CAB017694 are each Approved for IHC (HPA antibodies). The overall tissue profile has medium consistency between antibody staining and RNA expression (HPA tissue IHC), so an unexpected result merits validation rather than an automatic biological conclusion (general IHC practice). |
| Isoforms and processing (UniProt Q92985) | Four isoforms, A–D, are listed (UniProt Q92985). The record identifies no signal peptide or propeptide and gives the annotated chain as residues 1–503 (UniProt Q92985). Isoform detection by a particular antibody cannot be inferred without its epitope information (general IHC interpretation). |
| Detection background (general chromogenic IHC practice) | Endogenous enzyme activity or nonspecific reagent binding can produce color independent of the primary antibody (general chromogenic IHC practice). Interpret unexpected staining with suitable reagent controls and cell morphology; neither source establishes a target-specific background mechanism for IRF7. |
| ICC/IF comparison (HPA subcellular; HPA antibodies) | HPA ICC/IF supports nucleoplasm as the main location and cytosol as an additional location (HPA subcellular). HPA052757 is Supported for ICC, while CAB017694 has no listed ICC status (HPA antibodies). ICC/IF localisation can inform compartment review, but does not replace section-based IHC assessment (general practice). |
| Situation | Likely cause | Next action |
|---|---|---|
| High bone marrow hematopoietic cells appear unstained (HPA: bone marrow). | The section may lack the expected cells, or the IHC run may have failed (general IHC practice). The supplied sources do not establish an IRF7-specific fixation sensitivity. | Verify cell identity and section quality, then inspect the run's positive control and primary-antibody and detection steps (general IHC practice). Avoid changing retrieval on the assumption of a documented IRF7 fixation effect. |
| Signal is mainly membranous or extracellular (slide observation). | This conflicts with IRF7's nuclear and cytoplasmic locations and lack of a transmembrane segment (UniProt Q92985); nonspecific staining is possible (general IHC practice). | Recheck cellular boundaries and counterstain; compare the suspect pattern with a reagent control and a section showing expected nuclear staining (general IHC practice; HPA tissue IHC). |
| Prostate glandular cells stain as strongly as an HPA high population (HPA tissue IHC). | HPA lists prostate glandular cells as low (HPA tissue IHC). Cross-reactivity or endogenous detection activity is possible, though the mismatch alone cannot distinguish them (general IHC practice). | Check reagent controls and compare staining across identified cell types (general IHC practice). Record the discrepancy rather than treating prostate intensity as an established IRF7 reference (HPA tissue IHC). |
| Brown color is diffuse and obscures nuclei (slide observation). | Diffuse color can reflect background or excessive detection signal (general chromogenic IHC practice); it cannot be scored reliably against HPA's predominantly nuclear tissue pattern (HPA tissue IHC). | Inspect a no-primary control, counterstain and detection conditions, then repeat scoring only where cell boundaries and nuclei are readable (general chromogenic IHC practice). |
| Cytoplasmic staining appears without a clear nuclear shift (slide observation). | IRF7 can be cytoplasmic, while its active phosphorylated form accumulates in nuclei (UniProt Q92985). A static total-IRF7 image does not establish the signaling state (general IHC interpretation). | Report nuclear and cytoplasmic staining separately and avoid calling activation from localization alone (UniProt Q92985; general IHC interpretation). |
| IHC and an ICC/IF image seem to disagree on compartment (slide observation). | HPA supports nucleoplasm and cytosol in ICC/IF, while tissue IHC reports nuclear expression in most tissues (HPA subcellular; HPA tissue IHC). Preparation and cell context should be reviewed before interpreting the difference (general practice). | Compare identifiable compartments within each preparation and check the antibody's application status: HPA052757 is IHC Approved and ICC Supported; CAB017694 is IHC Approved with no listed ICC status (HPA antibodies). |
Comprehensive Human Protein Atlas IHC scoring per tissue (reliability: Approved — 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.
| Tissue | Cell type | Level | Evidence | Source |
|---|---|---|---|---|
| Adipose tissue | Adipocytes | High | Protein (IHC) | HPA → |
| Bone marrow | Hematopoietic cells | High | Protein (IHC) | HPA → |
| Bronchus | Respiratory epithelial cells | High | Protein (IHC) | HPA → |
| Cerebellum | Cells in granular layer | High | Protein (IHC) | HPA → |
| Cerebral cortex | Glial cells | High | Protein (IHC) | HPA → |
| Tissue | Cell type | Level | Evidence | Source |
|---|---|---|---|---|
| None in HPA: IRF7 is detected in all 45 scored tissues. Use a no-primary (secondary-only) and an isotype control instead. | ||||
Troubleshoot IRF7 staining in paraffin sections by checking retrieval, cell compartment, assay controls and how positive cells are scored.
Both anti-IRF7 antibodies have human paraffin-section IHC images (catalog image captions); M00115 also lists ICC/IF and mouse and rat reactivity (catalog applications/reactivity).
A00115-3 lists human IHC and shows staining in a paraffin-embedded human spleen section (A00115-3 catalog applications/reactivity and image caption). M00115 lists human, mouse and rat IHC and ICC/IF; its IHC image shows a paraffin-embedded human pancreas section (M00115 catalog applications/reactivity and image caption).
Which to pick: Choose A00115-3 for human tissue IHC when its documented processing is useful: EDTA retrieval at pH 8.0, 10% goat serum blocking, and 2 μg/ml primary antibody overnight at 4°C (A00115-3 image caption). Choose the rabbit monoclonal M00115 for ICC/IF or mouse and rat reactivity; its listed IHC and IF dilutions are each 1:50, while its own IHC image documents only a paraffin-embedded human pancreas section (M00115 catalog host/clone, applications/reactivity, dilution fields and image caption). The fixative is unreported for both illustrated sections (A00115-3 and M00115 image captions).