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Plan chromogenic IRF1 IHC on paraffin sections using the catalog antibody at 0.5–1 μg/mL (datasheet A00580-1). Assess nuclear and nucleolar staining against tissue examples, while accounting for medium consistency between antibody staining and RNA expression (HPA tissue IHC).
Expected localisation, validated protocols, controls and antibodies — the at-a-glance facts below, then the full design guide.
| Expected localisation | Nuclear and nucleolar tissue staining (HPA tissue IHC) | |
| Staining pattern | Nuclear and nucleolar; high in placental endothelial cells (HPA tissue IHC) | |
| Antigen retrieval | EDTA pH 8.0 HIER, heat-mediated (datasheet A00580-1) | |
| Positive control | Placenta+4 more · see all | |
| Negative control | Cerebellum+4 more · see all |
| Fixation | Keep fixation consistent across sections (standard IHC practice; not target-specific) | |
| Caveat | Antibody staining and RNA show medium consistency (HPA tissue IHC) | |
| Regulation | Staining intensity varies by tissue cell type (HPA tissue IHC) | |
| Isoform / epitope | No annotated isoforms; one 1–325 chain (UniProt) |
Compare the catalog antibody’s IHC protocol (datasheet A00580-1) with three published IRF1 IHC protocols (PMC4359953; PMC13472745; PMC12799679).
| Sample | Paraffin-embedded human Lung cancer tissue; fixative not specified (datasheet A00580-1) |
| Fixation | Image fixative and duration unreported (datasheet A00580-1); 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 A00580-1); 20 min, 95–100 °C (standard) |
| Peroxidase block | 3% H2O2, 10 min, room temperature (standard) |
| Blocking | 10% goat serum (datasheet A00580-1) |
| Primary antibody | Rabbit anti-IRF1, 0.5-1μg/ml (datasheet A00580-1) |
| Primary incubation | Overnight at 4 °C (datasheet A00580-1) |
| Detection | Streptavidin-biotin complex (SABC), DAB chromogen (datasheet A00580-1) |
| Counterstain | Hematoxylin, blue, dehydrate and mount (standard) |
| Expected result | IRF1-positive staining in endothelial cells of placenta (HPA tissue IHC: High). HPA tissue profile: Nuclear and nucleolar expression in several different tissue types. No signal in the no-primary control. |
IRF1 should appear chiefly in nuclei, sometimes with nucleolar staining, across several tissue types (HPA tissue IHC: Supported). Cytoplasmic signal can also occur (UniProt P10914; HPA ICC-IF). Placental endothelial cells and testicular pachytene spermatocytes are high-staining examples (HPA tissue IHC: High). IRF1 has no transmembrane segment, so a membrane-restricted pattern is unexpected (UniProt P10914 topology).
| Distinct nuclear staining in placental endothelial cells or testicular pachytene spermatocytes. | This matches high-staining cell populations in the tissue survey (HPA tissue IHC: High). Nuclear staining also fits the reported tissue profile (HPA tissue IHC: nuclear and nucleolar). Compare the named cells with surrounding cells; the tissue label alone does not identify every cell as positive (HPA tissue IHC: cell-specific levels). |
| Signal is restricted to cell membranes, or a known-positive population shows cytoplasm without discernible nuclei. | Review the pattern before scoring it as IRF1: the protein has no transmembrane segment (UniProt P10914 topology), while nuclear localisation is expected (HPA tissue IHC). Cytoplasmic localisation is possible (UniProt P10914; HPA ICC-IF), so cytoplasmic signal alone is not proof of artefact. |
| Strong staining appears in a listed non-detected cell population, such as liver cholangiocytes. | This conflicts with that population's surveyed result (HPA tissue IHC: cholangiocytes Not detected). Check morphology and controls for cross-reactivity or endogenous detection activity (standard IHC practice). One unexpected field cannot establish a universal negative result: HPA reports staining at the named cell level (HPA tissue IHC). |
| Brown deposit spreads across the section without clear cellular boundaries or a nuclear pattern. | Treat the diffuse appearance as possible background rather than assigning it to IRF1-positive cells (standard IHC practice). Compare with a detection control and inspect whether the expected nuclei remain distinguishable (standard IHC practice; HPA tissue IHC: nuclear profile). |
| A known high-staining population has no detectable nuclear signal. | First verify the selected cells and control section: placental endothelial cells and pachytene spermatocytes are high in the survey (HPA tissue IHC: High). A blank result may reflect the assay workflow or specimen; the supplied sources do not establish an IRF1-specific fixation sensitivity. |
| Compartment and scoring | Score nuclei in identified cells first because tissue IHC reports nuclear and nucleolar expression (HPA tissue IHC). Cytoplasmic staining can accompany it (UniProt P10914; HPA ICC-IF). An apparent shift in the nuclear-to-cytoplasmic balance needs cautious interpretation: MYD88-associated IRF1 enters nuclei more efficiently (UniProt P10914), but the supplied tissue survey does not measure that interaction. |
| Cell population within a tissue | Choose and score the named population: placental endothelial cells and testicular pachytene spermatocytes are High, while liver cholangiocytes and lymph-node germinal-center cells are Not detected (HPA tissue IHC). A positive or negative whole-tissue label would obscure these cell-specific observations (HPA tissue IHC). |
| RNA and protein readouts | Bone marrow is tissue-enhanced by RNA yet its hematopoietic cells show Low protein staining in this survey (HPA tissue IHC). Use the observed IHC level when choosing a staining reference; RNA enrichment does not set an expected chromogenic intensity (HPA tissue IHC: RNA specificity and protein levels). |
| Evidence strength and antibody choice | The tissue profile is Supported, with medium consistency between staining and RNA data (HPA tissue IHC: reliability). HPA063131 and CAB011662 have Supported IHC status; HPA070953 has no listed IHC status (HPA antibody validation). Those labels support cautious comparison across specimens, not a claim that every cell will stain identically. |
| IF/ICC Q: Should fluorescence reproduce the paraffin-section pattern? | A: Use compartment agreement as a check, not identical tissue intensity: ICC-IF places IRF1 mainly in nucleoplasm with additional cytosol (HPA ICC-IF: approved locations), whereas the tissue IHC profile includes nuclear and nucleolar staining (HPA tissue IHC). This section supplies no IF/ICC protocol option. |
| Situation | Likely cause | Next action |
|---|---|---|
| The positive control has no nuclear staining. | The selected control cells may be absent, or a general retrieval, primary-antibody, or detection step may have failed (standard IHC practice). IRF1-specific retrieval or fixation sensitivity is unreported in the supplied sources. | Confirm that placental endothelial cells or testicular pachytene spermatocytes are present (HPA tissue IHC: High). Then check the IHC-validated antibody's stated IHC-P instructions and run the workflow controls (standard IHC practice). |
| Only membranes carry a crisp chromogenic rim. | Membrane-restricted IRF1 conflicts with its lack of a transmembrane segment and reported nuclear distribution (UniProt P10914 topology; HPA tissue IHC). | Verify the stained structure against morphology and a detection control; score IRF1 only when a compatible cellular pattern is present (standard IHC practice; HPA tissue IHC: nuclear profile). |
| A surveyed non-detected population stains strongly. | Possible cross-reactivity, endogenous detection activity, or mistaken cell identification should be checked (standard IHC practice). For example, liver cholangiocytes were Not detected (HPA tissue IHC). | Reidentify the cells, inspect the detection control, and compare a named high-staining population on a separate control section (standard IHC practice; HPA tissue IHC: High in placental endothelial cells). |
| The entire section has diffuse brown haze. | Diffuse deposit can obscure the compartment needed to interpret IRF1 staining (standard IHC practice; HPA tissue IHC: nuclear profile). It does not establish widespread IRF1 expression. | Inspect reagent-only detection controls and the wash and blocking steps; rescore only cells with interpretable boundaries and nuclei (standard IHC practice). |
| Cytoplasm stains alongside nuclei. | This can be compatible with IRF1: UniProt lists nucleus and cytoplasm, and ICC-IF reports additional cytosol (UniProt P10914; HPA ICC-IF). | Record nuclear and cytoplasmic staining separately, checking that the expected nuclear signal is visible in the relevant cells (standard IHC scoring practice; HPA tissue IHC: nuclear profile). |
| Bone marrow looks faint despite its RNA enrichment. | RNA and protein observations differ here: bone marrow is tissue-enhanced by RNA, while hematopoietic cells are Low by IHC (HPA tissue IHC). | Use a named High IHC population to assess assay performance, then report bone-marrow staining at its observed cellular intensity (HPA tissue IHC: High placental endothelial cells; Low bone-marrow hematopoietic cells). |
Comprehensive Human Protein Atlas IHC scoring per tissue (reliability: Supported — 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 |
|---|---|---|---|---|
| Placenta | Endothelial cells | High | Protein (IHC) | HPA → |
| Testis | Pachytene spermatocytes | High | Protein (IHC) | HPA → |
| Adipose tissue | Adipocytes | Medium | Protein (IHC) | HPA → |
| Adrenal gland | Glandular cells | Medium | Protein (IHC) | HPA → |
| Appendix | Glandular cells | Medium | Protein (IHC) | HPA → |
| Tissue | Cell type | Level | Evidence | Source |
|---|---|---|---|---|
| Cerebellum | Cells in granular layer | Not detected | Protein (IHC) | HPA → |
| Liver | Cholangiocytes | Not detected | Protein (IHC) | HPA → |
| Lymph node | Germinal center cells | Not detected | Protein (IHC) | HPA → |
| Ovary | Ovarian stroma cells | Not detected | Protein (IHC) | HPA → |
| Prostate | Glandular cells | Not detected | Protein (IHC) | HPA → |
Troubleshoot IRF1 staining by checking retrieval, compartment, cell identity and controls before interpreting chromogenic signal in paraffin sections.
Two anti-IRF1 antibodies have IHC images from paraffin sections: human lung cancer and mouse intestine for A00580-1, and rat kidney for M00580 (catalog IHC captions). Both also have cell IF images (catalog IF captions).
A00580-1 will render with IHC data from human lung cancer and mouse intestine paraffin sections; its IF image shows A431 cells (A00580-1 image captions). M00580 will render with IHC data from a rat kidney paraffin section; its IF image shows HeLa cells (M00580 image captions).
Which to pick: For tissue IHC, choose A00580-1 for the pictured human or mouse samples, or M00580 for the pictured rat sample (catalog IHC captions); both captions specify paraffin sections, and neither reports the fixative (catalog IHC captions). For IF/ICC, A00580-1 has an A431 cell image and a stated 2 μg/ml IF dilution, while M00580 is monoclonal and has a HeLa cell image with a stated 1:50–1:100 IF dilution (catalog IF captions; catalog dilution fields; catalog clone field). For broader listed species reactivity, M00580 covers human, mouse and rat, versus human and mouse for A00580-1 (catalog reactivity fields).