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- Table of Contents
Plan paraffin-section SORL1 IHC using cerebellar Purkinje cells as a high-staining reference (HPA tissue IHC). Interpret staining with the predominantly intracellular localization and possible ectodomain shedding in mind (UniProt).
Expected localisation, validated protocols, controls and antibodies — the at-a-glance facts below, then the full design guide.
| Expected localisation | TGN/endosomal localization expected; tissue pattern uncertain (UniProt) | |
| Staining pattern | Purkinje cells: high; compartment unreported (HPA tissue IHC) | |
| Antigen retrieval | EDTA pH 8.0 HIER, heat-mediated (datasheet M01887-2) | |
| Positive control | Cerebellum+4 more · see all | |
| Negative control | Adipose tissue+4 more · see all |
| Fixation | Keep fixation consistent across sections. (standard IHC practice; not target-specific) | |
| Caveat | Shedding can release the extracellular domain (UniProt) | |
| Regulation | Reduced in Alzheimer frontal cortex (UniProt) | |
| Isoform / epitope | No isoforms listed; epitope side matters after shedding (UniProt) |
The catalog antibody protocol uses EDTA pH 8.0 retrieval (datasheet: M01887-2). Published IHC protocols cover human brain (PMC5465543) and interspinous ligament (PMC9019158).
| Sample | Paraffin-embedded mouse brain tissue; fixative not specified (datasheet M01887-2) |
| Fixation | Image fixative and duration unreported (datasheet M01887-2); verify before use. |
| Sectioning | 4–5 µm sections on charged slides (standard) |
| Deparaffinisation | Xylene, graded ethanol series to water (standard) |
| Antigen retrieval | Heat retrieval: EDTA pH 8.0 (datasheet M01887-2); 20 min, 95–100 °C (standard) |
| Peroxidase block | 3% H2O2, 10 min, room temperature (standard) |
| Blocking | 10% goat serum (datasheet M01887-2) |
| Primary antibody | Rabbit monoclonal (clone 22S13) anti-SORL1, 1:50 (datasheet M01887-2) |
| Primary incubation | Overnight at 4 °C (datasheet M01887-2) |
| Detection | HRP-conjugated secondary, DAB chromogen (datasheet M01887-2) |
| Counterstain | Hematoxylin, blue, dehydrate and mount (standard) |
| Expected result | SORL1-positive staining in purkinje cells of cerebellum (HPA tissue IHC: High). HPA tissue profile: plasma protein. No signal in the no-primary control. |
SORL1 should appear mainly intracellular, consistent with its trans-Golgi and endosomal localisation and single transmembrane segment (UniProt Q92673 subcellular location and topology). In paraffin-section IHC, cerebellar Purkinje cells are the clearest supplied positive example, with high staining; cerebral cortex neuropil shows medium staining (HPA: tissue IHC). Treat these as provisional reference patterns because HPA rates the tissue IHC evidence Uncertain (HPA: reliability).
| Purkinje cells stain strongly, with predominantly intracellular signal; cortex neuropil may stain less strongly (HPA: High in Purkinje cells; Medium in cortex neuropil; UniProt Q92673 subcellular location). | This fits the supplied tissue pattern and the receptor’s mainly trans-Golgi and endosomal distribution. Score the named cells or structures rather than treating an entire brain section as uniformly positive (HPA: tissue IHC; UniProt Q92673 subcellular location). |
| A dominant nuclear stain replaces the expected intracellular pattern (UniProt Q92673 subcellular location). | Question the result and check antibody specificity and controls. UniProt reports that a cleaved cytosolic fragment can enter the nucleus, so nuclear signal alone cannot identify full-length SORL1; interpretation depends on the antibody’s epitope (UniProt Q92673 processing and topology). |
| Cells scored as negative by HPA stain as strongly as Purkinje cells, such as adipocytes or spleen red-pulp cells (HPA: Not detected in those cells; High in Purkinje cells). | Investigate cross-reactivity or endogenous detection activity before assigning SORL1 positivity. HPA’s negative calls apply to those specified cell types, and its overall IHC reliability is Uncertain (HPA: tissue IHC and reliability; general IHC practice). |
| Chromogen is diffuse across the section, including areas without a clear cellular pattern (general IHC practice). | This can reflect nonspecific background or detection activity; extracellular staining also requires care because the SORL1 ectodomain can be shed. Use controls and morphology to distinguish these possibilities (general IHC practice; UniProt Q92673 shedding). |
| Purkinje cells show no convincing signal in an otherwise assessable cerebellar section (HPA: High in Purkinje cells). | Check the run and tissue before calling SORL1 absent. The HPA pattern is a useful reference, but its Uncertain reliability means a negative result needs independent support (HPA: tissue IHC and reliability; general IHC practice). |
| Subcellular distribution (UniProt Q92673 subcellular location) | SORL1 is mainly in the trans-Golgi network and endosomes, with lower plasma-membrane abundance. Judge intracellular and surface signals in that context; a membrane-only pattern needs scrutiny (UniProt Q92673 subcellular location). |
| Epitope and processing (UniProt Q92673 topology and processing) | Most of the receptor is lumenal, followed by a transmembrane segment and short cytoplasmic tail. Ectodomain shedding and subsequent cleavage can separate signals from different regions; antibody epitope information is needed to interpret them (UniProt Q92673 topology and processing). |
| Cell-level reference patterns (HPA: tissue IHC) | Use the named cell or structure: Purkinje cells are High, cortex neuropil Medium, and adipocytes Not detected. These entries do not imply uniform staining across their tissues (HPA: tissue IHC). |
| Strength of IHC evidence (HPA: reliability and antibody validation) | HPA calls the tissue IHC profile Uncertain and lists IHC validation as Uncertain for HPA031321 and CAB011500. Treat agreement with its pattern as supportive rather than conclusive (HPA: reliability and antibody validation). |
| Chromogenic detection background (general IHC practice) | Endogenous enzyme activity and nonspecific detection can mimic a positive deposit. Evaluate reagent and tissue controls when staining ignores cell boundaries or appears in an unexpected compartment (general IHC practice). |
| IF/ICC pattern? (HPA: subcellular ICC-IF) | HPA summarises SORL1 as Membrane, Secreted but provides no main location or cell-line ICC-IF images here. This IHC pattern cannot establish an IF/ICC image pattern; consult the separate IF/ICC guide (HPA: subcellular ICC-IF). |
| Situation | Likely cause | Next action |
|---|---|---|
| Purkinje cells are blank (HPA: High in Purkinje cells). | The run may have insufficient detectable signal, or this section may not reproduce HPA’s Uncertain reference pattern (general IHC practice; HPA: reliability). | Verify that the named cells are present, inspect the positive control, then review antigen retrieval, antibody dilution and detection performance using the catalog antibody’s IHC-P instructions (general IHC practice; HPA: tissue IHC). |
| Adipocytes or spleen red-pulp cells show strong deposit (HPA: Not detected in those cells). | Cross-reactivity or endogenous detection activity is possible; a cell-level HPA negative is not proof of complete tissue absence (general IHC practice; HPA: tissue IHC). | Compare a no-primary control and the positive reference cells, then reassess antibody specificity before scoring those cells as SORL1-positive (general IHC practice; HPA: tissue IHC). |
| The whole section has a diffuse brown haze (general IHC practice). | Nonspecific binding, incomplete blocking or detection background can obscure a cellular pattern; extracellular SORL1 ectodomain is also biologically possible (general IHC practice; UniProt Q92673 shedding). | Inspect no-primary and tissue controls, review blocking and wash steps, and score only interpretable cell-associated deposits (general IHC practice). |
| Staining is mainly at cell borders (UniProt Q92673 subcellular location). | Some surface SORL1 is plausible, but UniProt describes the receptor as predominantly intracellular (UniProt Q92673 subcellular location). | Compare intracellular signal and the expected Purkinje-cell pattern; check controls and the antibody epitope before interpreting a membrane-only result (UniProt Q92673 subcellular location; HPA: tissue IHC; general IHC practice). |
| Nuclei stain prominently (UniProt Q92673 processing). | A released C-terminal fragment can localise to nuclei, while nonspecific nuclear staining remains possible (UniProt Q92673 processing; general IHC practice). | Check whether the antibody recognises the cytoplasmic C-terminus, review no-primary controls, and avoid calling nuclear deposit full-length receptor without further validation (UniProt Q92673 topology and processing; general IHC practice). |
| A result conflicts with the HPA tissue pattern (HPA: tissue IHC). | HPA rates this IHC profile Uncertain and notes that secreted variants complicate RNA–protein agreement (HPA: reliability description). | Record the exact cell type and compartment, compare matched controls, and seek independent support before treating either the new stain or the HPA pattern as definitive (HPA: reliability; general IHC practice). |
Comprehensive Human Protein Atlas IHC scoring per tissue (reliability: Uncertain — At least one protein variant secreted, tissue location of RNA and protein might differ and correlation is complex. 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 |
|---|---|---|---|---|
| Cerebellum | Purkinje cells | High | Protein (IHC) | HPA → |
| Adrenal gland | Glandular cells | Medium | Protein (IHC) | HPA → |
| Appendix | Glandular cells | Medium | Protein (IHC) | HPA → |
| Breast | Glandular cells | Medium | Protein (IHC) | HPA → |
| Bronchus | Respiratory epithelial cells | 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 → |
| Liver | Cholangiocytes | Not detected | Protein (IHC) | HPA → |
| Placenta | Decidual cells | Not detected | Protein (IHC) | HPA → |
| Soft tissue | Chondrocytes | Not detected | Protein (IHC) | HPA → |
Troubleshoot SORL1 staining in paraffin sections by checking retrieval, compartment, cell type, and controls before comparing signal intensity (UniProt Q92673; HPA tissue IHC).
Two anti-SORL1 antibodies have IHC images from paraffin sections: mouse and rat brain for both, plus human breast cancer tissue for A01887-1 (catalog IHC captions). A01887-1 also has a human tissue IF image (catalog IF caption).
M01887-2 is listed for IHC in human, mouse and rat; its images show paraffin sections of mouse and rat brain (catalog applications, reactivity and IHC captions). A01887-1 is listed for IHC and IF in human, mouse and rat; its images show IHC in human breast cancer tissue and mouse and rat brain, plus IF in human breast cancer tissue (catalog applications, reactivity and image captions).
Which to pick: For brain tissue IHC, choose M01887-2 if a rabbit monoclonal is preferred; its own captions show paraffin sections of mouse and rat brain, while human reactivity is listed without a human IHC image (catalog clone, reactivity and M01887-2 IHC captions). For IF, choose A01887-1: its IF caption shows a paraffin section of human breast cancer tissue; ICC validation is unreported (catalog applications and A01887-1 IF caption). For IHC across the three listed species, A01887-1 has images for each; both antibodies’ IHC captions describe paraffin sections and leave the fixative unreported (catalog reactivity and IHC captions).