This website uses cookies to ensure you get the best experience on our website.
- Table of Contents
Plan chromogenic IHC for ALYREF in paraffin sections using its widespread nuclear tissue pattern as the staining reference (HPA tissue IHC). The guide covers consistent fixation, antibody incubation, detection and interpretation, with catalog antibody conditions for human tissue (datasheet M03580).
Expected localisation, validated protocols, controls and antibodies — the at-a-glance facts below, then the full design guide.
| Expected localisation | Nuclear staining across tissues (HPA tissue IHC) | |
| Staining pattern | Widespread nuclear staining, including marrow cells (HPA tissue IHC) | |
| Antigen retrieval | EDTA pH 8.0 HIER, heat-mediated (datasheet M03580) | |
| 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 | Ubiquitous staining limits negative tissue controls (HPA tissue IHC) | |
| Regulation | Staining-related regulation unspecified (UniProt) | |
| Isoform / epitope | No annotated isoforms; chain 2–257; epitope unknown (UniProt) |
Compare the catalog antibody’s IHC-P protocol (datasheet: M03580) with published ALYREF staining in hepatocellular carcinoma (PMC9079359) and retinoblastoma (PMC12439426).
| Sample | Paraffin-embedded human lung cancer tissue; fixative not specified (datasheet M03580) |
| Fixation | Image fixative and duration unreported (datasheet M03580); 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 M03580); 20 min, 95–100 °C (standard) |
| Peroxidase block | 3% H2O2, 10 min, room temperature (standard) |
| Blocking | 10% goat serum (datasheet M03580) |
| Primary antibody | Rabbit monoclonal (clone 22A24) anti-ALYREF, 1:50 (datasheet M03580) |
| Primary incubation | Overnight at 4 °C (datasheet M03580) |
| Detection | HRP-conjugated secondary, DAB chromogen (datasheet M03580) |
| Counterstain | Hematoxylin, blue, dehydrate and mount (standard) |
| Expected result | ALYREF-positive staining in adipocytes of adipose tissue (HPA tissue IHC: High). HPA tissue profile: Ubiquitous nuclear expression. No signal in the no-primary control. |
ALYREF should appear predominantly in nuclei across many cell types in paraffin sections (HPA tissue IHC: supported, ubiquitous nuclear expression). High staining is reported in bone marrow hematopoietic cells, adipocytes, glandular cells, respiratory epithelial cells and selected brain cells (HPA tissue IHC). Nuclear speckles and some cytoplasmic transit are biologically plausible (UniProt Q86V81: subcellular location). ALYREF has no transmembrane segment, so a membrane outline is unexpected (UniProt Q86V81: topology).
| Distinct nuclear staining in bone marrow hematopoietic cells, with evaluable unstained background (HPA tissue IHC: High). | This fits the reported ubiquitous nuclear profile and provides a useful known-positive tissue for judging a run (HPA tissue IHC: supported). A brown nuclear signal in IHC does not establish whether individual nuclear speckles are resolved; speckles are an approved ICC-IF location (HPA subcellular). |
| A continuous membrane rim, or cytoplasmic staining that dominates while nuclei remain blank (UniProt Q86V81: topology and location). | Question the result: ALYREF lacks a transmembrane segment and is chiefly nuclear, although cytoplasmic travel with mRNA is reported (UniProt Q86V81: topology and location). Review the counterstain and compare a known-positive section before assigning a biological redistribution (HPA tissue IHC: ubiquitous nuclear expression). |
| Signal appears only in cells outside the reported high-staining groups, while expected nuclei are blank (HPA tissue IHC: High-cell listings). | Consider nonspecific antibody binding or endogenous chromogen activity (general IHC practice). An unlisted cell type is not automatically negative: HPA describes ubiquitous nuclear expression and supplies no negative tissue list (HPA tissue IHC). Assess compartment and controls together. |
| Brown haze covers nuclei and surrounding tissue, obscuring cell boundaries (general IHC practice). | A widespread deposit cannot be scored reliably as ALYREF nuclear staining (HPA tissue IHC: ubiquitous nuclear profile; general IHC practice). Check background in a no-primary control and examine blocking, washes and chromogen development as general IHC variables, without assuming a target-specific cause. |
| No nuclear signal in bone marrow hematopoietic cells or another listed high-staining population (HPA tissue IHC: High). | Treat the run as unresolved before calling the specimen ALYREF-negative (HPA tissue IHC: supported, High). Check that the assay detects its positive control; review antibody suitability, retrieval and detection as general IHC practice. The supplied sources report no ALYREF-specific retrieval or fixation sensitivity. |
| Cell population and intensity | HPA reports High staining in adipocytes, adrenal and appendix glandular cells, bone marrow hematopoietic cells, bronchial respiratory epithelial cells, caudate glial cells and cerebellar granular-layer cells (HPA tissue IHC). These are examples, not a ranked intensity scale or a list of exclusive positives (HPA tissue IHC: ubiquitous nuclear expression). |
| Subcellular distribution | Nuclear and nuclear-speckle localization is reported by UniProt; nucleoplasm and nuclear speckles are approved ICC-IF locations (UniProt Q86V81: location; HPA subcellular). Cytoplasmic travel is reported with mRNA-bound EJC (UniProt Q86V81: location). A chiefly cytoplasmic IHC pattern therefore needs control-based review. |
| IHC antibody evidence | HPA019799 and CAB016281 have Supported IHC status; HPA061282 has no listed IHC status (HPA antibodies). These statuses describe the listed antibodies, so do not transfer them to a different catalog antibody or infer its dilution, epitope or performance (HPA antibodies). |
| IF/ICC Q: What pattern should I expect? | A: Nucleoplasmic signal with nuclear speckles is the approved HPA ICC-IF pattern (HPA subcellular). HPA019799 is ICC Enhanced and HPA061282 ICC Approved (HPA antibodies). This localization guides interpretation only; the supplied record gives no IF/ICC protocol for this section. |
| Retrieval and specimen preparation | The supplied UniProt and HPA records give no ALYREF-specific retrieval condition or fixation effect. If an IHC run fails, review retrieval against the assay's own validated instructions as general IHC practice; do not infer epitope masking from HPA staining levels or UniProt modifications. |
| Situation | Likely cause | Next action |
|---|---|---|
| Known-positive bone marrow nuclei are blank (HPA tissue IHC: High in hematopoietic cells). | An assay or detection failure is possible (general IHC practice); absence alone does not establish biological loss. | Verify the positive control, catalog antibody's IHC-P suitability, retrieval and detection steps (general IHC practice). No ALYREF-specific retrieval setting is supplied. |
| Predominantly cytoplasmic signal replaces the expected nuclear pattern (HPA tissue IHC: ubiquitous nuclear expression). | Some cytoplasmic ALYREF is plausible, but an exclusively cytoplasmic result conflicts with the reported dominant location (UniProt Q86V81: location). | Check nuclear counterstain and compare a listed High population on the same run (general IHC practice; HPA tissue IHC). Avoid scoring cytoplasm alone as confirmation. |
| Membrane outlines stain more clearly than nuclei (UniProt Q86V81: topology and location). | A membrane-dominant pattern is inconsistent with the absence of a transmembrane segment (UniProt Q86V81: topology). | Compare the no-primary control and review nonspecific binding or chromogen deposit (general IHC practice); seek nuclear staining in a known-positive tissue (HPA tissue IHC). |
| Diffuse brown background prevents nuclear scoring (general IHC practice). | Nonspecific binding, endogenous detection activity or excess chromogen development may contribute (general IHC practice); the source record identifies no ALYREF-specific cause. | Inspect a no-primary control, then review blocking, washes and development against the validated IHC workflow (general IHC practice). Score only distinguishable cellular nuclei. |
| Unexpected cells stain while a listed High population remains blank (HPA tissue IHC). | Cross-reactivity or endogenous detection activity is possible (general IHC practice), but HPA's ubiquitous nuclear profile prevents treating unlisted cells as inherently negative (HPA tissue IHC). | Compare cellular localization, morphology and controls; repeat with an independently validated antibody if available (general IHC practice; HPA antibodies: two Supported IHC entries). |
| Nuclei stain, but individual speckles cannot be distinguished in chromogenic IHC (HPA tissue IHC; HPA subcellular). | HPA's speckle assignment comes from ICC-IF, while its tissue IHC summary reports ubiquitous nuclear expression (HPA subcellular; HPA tissue IHC). | Interpret a clear nuclear IHC result at the compartment level (HPA tissue IHC). Use the separate IF/ICC guide when speckle-level localization is the experimental question (HPA subcellular). |
Comprehensive Human Protein Atlas IHC scoring per tissue (reliability: Supported — 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 |
|---|---|---|---|---|
| Adipose tissue | Adipocytes | High | Protein (IHC) | HPA → |
| Adrenal gland | Glandular cells | High | Protein (IHC) | HPA → |
| Appendix | Glandular cells | High | Protein (IHC) | HPA → |
| Bone marrow | Hematopoietic cells | High | Protein (IHC) | HPA → |
| Breast | Adipocytes | High | Protein (IHC) | HPA → |
| Tissue | Cell type | Level | Evidence | Source |
|---|---|---|---|---|
| None in HPA: ALYREF is detected in all 45 scored tissues. Use a no-primary (secondary-only) and an isotype control instead. | ||||
Use nuclear staining as the main readout for ALYREF in paraffin section IHC, while checking retrieval, background and compartment specific controls (HPA: ubiquitous nuclear expression).
Two anti-ALYREF antibodies have IHC images from human paraffin sections (catalog image captions); one also has IF/ICC data from A431 cells (A03580-3 IF image caption). Both list human, mouse and rat reactivity (catalog).
M03580 will render with human lung cancer paraffin-section IHC data; its other IHC captions show human lymphoma, glioma and testis cancer sections (M03580 IHC image captions). A03580-3 will render with human liver cancer paraffin-section IHC data and also has A431 cell IF/ICC data (A03580-3 IHC and IF image captions).
Which to pick: For tissue IHC, choose M03580 if a rabbit monoclonal with several illustrated human paraffin-section samples is useful (M03580 catalog; M03580 IHC image captions); its illustrated protocol used EDTA retrieval at pH 8.0 and a 1:50 primary dilution (M03580 IHC image captions). For IF/ICC, choose A03580-3 because its A431 image documents fluorescence detection at 5 μg/ml (A03580-3 IF image caption). Both list human, mouse and rat reactivity, while their illustrated tissue IHC is human paraffin sections only; neither IHC caption reports the fixative (catalog reactivity; M03580 and A03580-3 IHC image captions).