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- Table of Contents
Plan paraffin-section NRF1 IHC around the nuclear staining reported in most tissues (HPA tissue IHC). This guide pairs catalog antibody conditions with tissue controls and flags the medium consistency between staining and RNA expression (datasheet A01129-2; HPA tissue IHC).
Expected localisation, validated protocols, controls and antibodies — the at-a-glance facts below, then the full design guide.
| Expected localisation | Nuclear staining in most tissues (HPA tissue IHC) | |
| Staining pattern | Nuclear signal in cells across most tissues (HPA tissue IHC) | |
| Antigen retrieval | Citrate pH 6 HIER, heat-mediated (datasheet A01129-2) | |
| Positive control | Adrenal gland+4 more · see all | |
| Negative control | Adipose tissue+4 more · see all |
| Fixation | Keep fixation consistent across sections (standard IHC practice; not target-specific); assess its effect empirically. | |
| Caveat | Skeletal muscle is strongest in UniProt, yet myocytes are undetected by IHC (UniProt; HPA tissue IHC) | |
| Regulation | Broad expression, strongest in skeletal muscle (UniProt) | |
| Isoform / epitope | 4 isoforms; antibody epitope coverage is unspecified (UniProt) |
The catalog antibody’s IHC-P protocol is accompanied by a published nuclear respiratory factor 1 protocol using breast cancer tissue microarrays (PMC5774493).
| Sample | Paraffin-embedded human ovary cancer tissue; fixative not specified (datasheet A01129-2) |
| Fixation | Image fixative and duration unreported (datasheet A01129-2); verify before use. |
| Sectioning | 4–5 µm sections on charged slides (standard) |
| Deparaffinisation | Xylene, graded ethanol series to water (standard) |
| Antigen retrieval | Heat retrieval: Citrate pH 6, 20 min (datasheet A01129-2) |
| Peroxidase block | 3% H2O2, 10 min, room temperature (standard) |
| Blocking | 10% goat serum (datasheet A01129-2) |
| Primary antibody | Rabbit anti-NRF1, 0.5-1μg/ml (datasheet A01129-2) |
| Primary incubation | Overnight at 4 °C (datasheet A01129-2) |
| Detection | Streptavidin-biotin complex (SABC), DAB chromogen (datasheet A01129-2) |
| Counterstain | Hematoxylin, blue, dehydrate and mount (standard) |
| Expected result | NRF1-positive staining in glandular cells of adrenal gland (HPA tissue IHC: Medium). HPA tissue profile: Nuclear expression in most tissues. No signal in the no-primary control. |
NRF1 is a nuclear transcription factor with no transmembrane segment (UniProt Q16656: subcellular location, topology). In paraffin sections, expect nuclear staining in many cell types, including glandular cells in colon and breast and glial cells in cerebral cortex (HPA tissue IHC: Medium). HPA describes nuclear expression in most tissues, but rates its tissue IHC evidence Approved, with medium agreement between staining and RNA data and external verification pending (HPA tissue IHC).
| Nuclear staining in colon glandular cells, with little signal outside nuclei. | This matches the expected compartment and an observed positive cell population (UniProt Q16656: Nucleus; HPA tissue IHC: colon glandular cells, Medium). Judge the nuclear pattern within the tissue architecture, rather than treating every cell on the section as an equivalent positive control. |
| Strong, predominantly membranous staining, with nuclei largely unstained. | A membrane dominant pattern conflicts with NRF1's annotated nuclear location and absence of a transmembrane segment (UniProt Q16656: location, topology). Treat it as suspect until the nuclear pattern is reproduced with appropriate controls; the pattern alone cannot identify the source of artefact. |
| Staining is confined to skeletal myocytes, while an included known positive cell population is unstained. | Do not infer a convincing positive result from the myocyte signal alone. HPA reports skeletal myocytes as Not detected, despite UniProt describing strongest expression in skeletal muscle (HPA tissue IHC; UniProt Q16656: tissue specificity). The sources disagree on this tissue, so it is a poor sole positive control. |
| Brown color appears broadly across nuclei, cytoplasm, and tissue spaces. | A diffuse deposit obscures the expected nuclear distribution (UniProt Q16656: Nucleus). Assess background with a no primary control and inspect tissue morphology (general IHC practice). Cytoplasmic color by itself is inconclusive because HPA notes an additional, uncertain cytosolic location in ICC-IF (HPA subcellular). |
| No nuclear signal in colon glandular cells on an otherwise interpretable section. | This is unexpected for a population reported at Medium staining, though HPA's Approved tissue pattern remains pending external verification (HPA tissue IHC: colon; reliability). Check the assay and specimen before calling NRF1 absent; one negative section cannot resolve technical failure versus biological variation. |
| Which compartment should lead interpretation? | Nuclear staining should dominate in tissue IHC (HPA tissue IHC: nuclear expression in most tissues; UniProt Q16656: Nucleus). A weak cytoplasmic component should be interpreted cautiously: ICC-IF lists cytosol as an additional location with uncertain support (HPA subcellular). |
| Which tissue can serve as a positive comparator? | Colon and breast glandular cells and cerebral cortex glial cells have reported Medium staining (HPA tissue IHC). Choose a comparator whose relevant cells are identifiable on the section; HPA's tissue assessment is Approved with external verification pending (HPA tissue IHC: reliability). |
| Which apparent negative needs special care? | Skeletal myocytes are Not detected by HPA tissue IHC, while UniProt calls skeletal muscle the site of strongest expression (HPA tissue IHC: skeletal muscle; UniProt Q16656: tissue specificity). Record this discrepancy rather than using skeletal muscle alone to accept or reject an assay. |
| How strong is the pattern evidence? | The reported tissue profile is Approved, with medium agreement between antibody staining and RNA expression and external verification pending (HPA tissue IHC: reliability). The listed antibody, HPA029329, is Approved for IHC (HPA antibodies); that status supports use of its pattern as a guide, not proof that every stained structure contains NRF1. |
| What should IF/ICC show? | Expect mainly nucleoplasmic signal; additional cytosolic localisation is uncertain (HPA subcellular: ICC-IF). This is a localisation cross-check only: the primary application here is chromogenic IHC on paraffin sections. |
| Situation | Likely cause | Next action |
|---|---|---|
| No nuclear staining in a known positive comparator. | The readout may have failed, or the selected section may differ from the reported HPA pattern; a single absence does not distinguish those possibilities (HPA tissue IHC: Approved, external verification pending). | Confirm that the comparator contains the expected cell population, inspect morphology, and check the IHC run controls and general retrieval and detection steps (general IHC practice). Repeat before interpreting the specimen as NRF1 negative. |
| Membrane dominant staining replaces the expected nuclear pattern. | The location conflicts with nuclear NRF1 and its lack of a transmembrane segment (UniProt Q16656: location, topology); the image alone cannot assign a specific artefact. | Compare a known positive tissue and a no primary control on the same run, then review primary antibody and detection settings (general IHC practice). Require a reproducible nuclear pattern before scoring positivity. |
| An HPA Not detected cell population stains strongly. | The staining may reflect cross-reactivity or detection background, although HPA's tissue assessment has medium consistency and awaits external verification (HPA tissue IHC: negative populations, reliability). | Check the precise cell identity and compartment, then compare a reported positive population and no primary control (general IHC practice). Do not label the unexpected cell population NRF1 positive from color alone. |
| Brown deposits spread through tissue spaces or obscure cell borders. | Diffuse chromogen can make compartment scoring unreliable (general IHC practice). If the detection system uses peroxidase, endogenous enzyme activity is one possible contributor (general IHC practice). | Inspect a no primary control; if it also develops color, review blocking and detection controls for the system used (general IHC practice). Reassess nuclear staining only after background permits cell level interpretation. |
| Only skeletal muscle is available as a putative positive control. | The sources conflict: HPA reports myocytes Not detected, while UniProt reports strongest expression in skeletal muscle (HPA tissue IHC; UniProt Q16656: tissue specificity). | Use an HPA reported positive cell population, such as colon glandular cells, for the assay comparator when available (HPA tissue IHC: colon, Medium). Document the skeletal muscle result separately rather than using it as the sole pass or fail criterion. |
| Weak cytoplasmic color accompanies otherwise clear nuclear staining. | HPA reports cytosol as an additional but uncertain ICC-IF location, while its tissue IHC profile is nuclear (HPA subcellular; HPA tissue IHC: profile). | Score the interpretable nuclear component and document the cytoplasmic component separately (general IHC practice). Compare background controls before assigning biological meaning to the weaker extra compartment. |
Comprehensive Human Protein Atlas IHC scoring per tissue (reliability: Approved — 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 |
|---|---|---|---|---|
| Adrenal gland | Glandular cells | Medium | Protein (IHC) | HPA → |
| Appendix | Glandular cells | Medium | Protein (IHC) | HPA → |
| Breast | Glandular cells | Medium | Protein (IHC) | HPA → |
| Caudate | Glial cells | Medium | Protein (IHC) | HPA → |
| Cerebellum | Cells in granular layer | 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 → |
| Esophagus | Squamous epithelial cells | Not detected | Protein (IHC) | HPA → |
| Liver | Cholangiocytes | Not detected | Protein (IHC) | HPA → |
| Salivary gland | Glandular cells | Not detected | Protein (IHC) | HPA → |
Troubleshoot chromogenic NRF1 IHC in paraffin sections by checking retrieval, nuclear localisation, controls and cell-specific scoring (datasheet A01129-2; UniProt Q16656; HPA tissue IHC).
The catalog shows NRF1 IHC in human, mouse and rat tissues (catalog IHC captions), IF in MCF7 cells (M01129-1 IF caption), and ICC in A549 cells (PA1948 ICC caption).
A01129-2 has paraffin-section IHC images from human ovary cancer, mouse intestine and spleen, and rat heart (A01129-2 IHC captions); M01129-1 has human cancer tissue IHC images and an MCF7 IF image (M01129-1 image captions). M01129 has paraffin-section IHC images from human cancers (M01129 IHC captions); PA1948 has IHC images from human mammary and intestinal cancers and rat intestine, plus an A549 ICC image (PA1948 image captions).
Which to pick: For human tissue IHC, M01129 offers a rabbit monoclonal antibody with a paraffin-section image using EDTA retrieval (M01129 catalog entry and IHC caption); PA1948 offers human and rat IHC images (PA1948 IHC captions). For IF/ICC, choose M01129-1 when an IF application and MCF7 IF image are needed (M01129-1 catalog entry and IF caption). For cross-species tissue IHC, A01129-2 has human, mouse and rat paraffin-section images (A01129-2 IHC captions); the fixative is unreported in the IHC captions for all four SKUs (A01129-2, M01129-1, M01129 and PA1948 IHC captions).