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- Table of Contents
Plan paraffin-section NRF1 IHC around the nuclear staining reported in most tissues (HPA tissue IHC). Use the tissue profile to select comparison sections and interpret the skeletal muscle discrepancy (HPA tissue IHC; UniProt).
Expected localisation, validated protocols, controls and antibodies — the at-a-glance facts below, then the full design guide.
| Expected localisation | Nuclear in most tissues (HPA tissue IHC) | |
| Staining pattern | Nuclear staining across most tissue cell types (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 compared paraffin sections. (selected-SKU IHC image A01129-2) | |
| Caveat | Skeletal myocytes were not detected despite reported strong muscle expression (HPA tissue IHC; UniProt) | |
| Regulation | Low tissue specificity (HPA tissue RNA) | |
| Isoform / epitope | Four isoforms; check whether the epitope is shared (UniProt) |
Compare the catalog antibody’s IHC-P protocol with a published NRF1 protocol for 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: nucleus, topology). In paraffin-section IHC, expect predominantly nuclear staining across many tissues, including glandular cells in colon, duodenum and breast and glial cells in cerebral cortex (HPA: tissue IHC). HPA rates the tissue staining Approved, with medium consistency against RNA data and external verification pending (HPA: tissue IHC reliability).
| Predominantly nuclear staining of colon or duodenum glandular cells, or cerebral cortex glial cells, at a medium level (HPA: tissue IHC). | This matches the observed cell types and intensity in those tissues (HPA: tissue IHC) and the expected nuclear compartment (UniProt Q16656: nucleus). Compare nuclei with adjacent cells on the same section; the tissue pattern is Approved but awaits external verification (HPA: tissue IHC reliability). |
| Strong staining is confined to cytoplasm, with little or no nuclear signal (HPA: nucleoplasm is the supported ICC-IF location). | Treat a cytoplasm-dominant IHC result as a localisation mismatch and investigate possible artefact (UniProt Q16656: nucleus; HPA: subcellular ICC-IF). HPA also reports cytosol in ICC-IF, but labels that additional location uncertain; it does not establish cytoplasm-only paraffin IHC as the expected pattern (HPA: subcellular ICC-IF). |
| Prominent staining appears in skeletal-muscle myocytes or adipocytes (HPA: both cell types not detected by tissue IHC). | Check cell identity and controls before assigning the signal to NRF1; cross-reactivity or endogenous detection activity is possible (general IHC practice). UniProt reports strongest expression in skeletal muscle at the tissue level, while HPA reports myocytes not detected by IHC, so this discrepancy alone cannot validate or disprove a stain (UniProt Q16656: tissue specificity; HPA: skeletal-muscle IHC). |
| Diffuse color covers nuclei and surrounding tissue without a clear cellular boundary (general IHC practice). | An indistinct deposit is difficult to score as NRF1-positive nuclear staining (UniProt Q16656: nucleus; general IHC practice). Assess background with an appropriate negative control and review blocking, washes and chromogenic detection conditions (general IHC practice); HPA's tissue profile does not identify the cause of diffuse background (HPA: tissue IHC). |
| No nuclear signal appears in colon glandular cells despite intact tissue morphology (HPA: colon glandular cells medium by IHC). | A missing signal in this HPA-observed cell population warrants a run-level check before calling the specimen NRF1-negative (HPA: colon tissue IHC; general IHC practice). The HPA rating is Approved with medium RNA–staining consistency, so one negative result cannot by itself establish absence of NRF1 (HPA: tissue IHC reliability). |
| Tissue and cell choice (HPA: tissue IHC) | HPA reports medium staining in several glandular populations and brain glial cells, low staining in lung macrophages, and no detected staining in adipocytes or skeletal-muscle myocytes (HPA: tissue IHC). Choose comparison areas by cell type, since a tissue-wide label can hide differences among its cells (general IHC practice). |
| Antibody evidence (HPA: HPA029329 IHC Approved) | HPA lists HPA029329 as IHC Approved and the tissue profile as Approved, with medium agreement between staining and RNA expression and external verification pending (HPA: antibody validation; HPA: tissue IHC reliability). Interpret a discordant slide with that evidence limit in mind; no IHC-Enhanced status is supplied (HPA: antibody validation). |
| Isoforms and modifications (UniProt Q16656) | UniProt lists four NRF1 isoforms and five example CK2 phosphoserine sites, but the supplied record gives no antibody epitope or isoform coverage (UniProt Q16656: isoforms, modified residues). These annotations alone cannot predict which isoforms a stain detects or whether modification changes IHC signal (UniProt Q16656; general IHC interpretation). |
| Does IF/ICC show the same compartment? (HPA: subcellular ICC-IF) | In ICC-IF, HPA supports nucleoplasm as the main location and labels additional cytosol localisation uncertain; images are listed for A-431 and U-251MG (HPA: subcellular ICC-IF). This supports a nuclear localisation check, while the paraffin-section tissue and intensity expectations come from HPA tissue IHC (HPA: tissue IHC). |
| Situation | Likely cause | Next action |
|---|---|---|
| Known HPA-positive cells lack nuclear color (HPA: colon glandular cells medium by IHC). | A run or detection failure is possible; a single blank section cannot identify its cause (general IHC practice). | Confirm the positive-control section, then review antigen retrieval, antibody dilution, detection reagents and counterstain visibility (general IHC practice). No NRF1-specific retrieval condition or dilution is supplied (HPA: supplied IHC record). |
| Cytoplasmic signal overwhelms nuclear signal (UniProt Q16656: nucleus). | The stain conflicts with the supported main localisation; HPA's extra cytosol ICC-IF location is uncertain (HPA: subcellular ICC-IF). | Compare nuclear detail and background controls, then reassess staining specificity (general IHC practice). Do not use the uncertain ICC-IF cytosol observation to accept cytoplasm-only IHC (HPA: subcellular ICC-IF). |
| Strong signal appears in adipocytes or skeletal-muscle myocytes (HPA: not detected by IHC). | Cell identification, cross-reactivity or endogenous detection activity may explain unexpected color (general IHC practice). | Verify the stained cell type and inspect appropriate negative and detection controls (general IHC practice). Keep the UniProt skeletal-muscle expression statement distinct from HPA's myocyte IHC observation (UniProt Q16656: tissue specificity; HPA: skeletal-muscle IHC). |
| Diffuse chromogen obscures nuclei (general IHC practice). | Background from blocking, washes or detection chemistry is possible (general IHC practice). | Review negative-control staining and the blocking, wash and chromogen steps before scoring nuclear signal (general IHC practice). HPA's NRF1 profile does not establish a target-specific background mechanism (HPA: tissue IHC). |
| A low-staining tissue gives an equivocal result (HPA: lung macrophages low by IHC). | A weak HPA-observed signal can be difficult to separate from background on a single slide (HPA: tissue IHC; general IHC practice). | Compare the same cell population with a medium-staining tissue area and the run's negative control (HPA: tissue IHC; general IHC practice). Avoid treating an equivocal macrophage result alone as proof of absence (HPA: lung macrophages low by IHC). |
| The IHC pattern disagrees with ICC-IF images (HPA: tissue IHC; HPA: subcellular ICC-IF). | The records describe different preparations, and HPA labels the ICC-IF cytosol location uncertain (HPA: subcellular ICC-IF). | Score paraffin tissue against HPA's observed cell types and nuclear tissue profile; use ICC-IF to inform the supported main compartment (HPA: tissue IHC; HPA: subcellular ICC-IF). |
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 NRF1 staining in paraffin sections by checking nuclear localisation, retrieval, controls and cell type before comparing signal intensity (UniProt Q16656; HPA tissue IHC).
The catalog shows NRF1 staining in paraffin sections from human, mouse and rat tissues, plus IF in human MCF7 cells and ICC in A549 cells (catalog image captions).
A01129-2 has IHC images of human ovary cancer, mouse intestine and spleen, and rat heart; M01129-1 has human rectal, lung, mammary and testis cancer IHC images plus MCF7 IF (catalog image captions). M01129 has human bladder, breast, clear cell renal cell carcinoma and colon cancer IHC images; PA1948 has human mammary and intestinal cancer and rat intestine IHC images plus A549 ICC (catalog image captions).
Which to pick: For paraffin tissue IHC, choose rabbit monoclonal M01129 if its documented EDTA retrieval at pH 8.0 and 1:50 dilution suit the assay (M01129 IHC image caption; catalog: clone ADGI-14). For IF/ICC, choose mouse monoclonal M01129-1: its MCF7 IF image uses 2 μg/ml, and IF and ICC are listed applications (M01129-1 IF image caption; catalog: clone 2G4 and applications). For IHC across species, A01129-2 has paraffin images from human, mouse and rat with citrate retrieval at pH 6; the captions do not report the fixative (A01129-2 IHC image captions).