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- Table of Contents
Plan COPS5 chromogenic IHC on paraffin sections using an IHC-validated antibody and high-staining tissue controls (HPA tissue IHC). Assess nuclear and cytoplasmic staining separately, and start the catalog antibody at 2 μg/mL (HPA tissue IHC; datasheet M01849-2).
Expected localisation, validated protocols, controls and antibodies — the at-a-glance facts below, then the full design guide.
| Expected localisation | Nuclear and cytoplasmic tissue staining (HPA tissue IHC) | |
| Staining pattern | Nuclear and cytoplasmic staining in cells across tissues (HPA tissue IHC) | |
| Antigen retrieval | EDTA pH 8.0 HIER, heat-mediated (datasheet M01849-2) | |
| 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 paraffin-section fixation consistent across specimens. (selected-SKU IHC image M01849-2) | |
| Caveat | IFIT3 can diminish nuclear localization (UniProt) | |
| Regulation | No intensity regulator annotated (UniProt) | |
| Isoform / epitope | No isoforms annotated; chain spans residues 2–334 (UniProt) |
Compare the catalog antibody’s EDTA pH 8.0 retrieval protocol (datasheet M01849-2) with published COPS5 IHC protocols for paraffin sections (PMC4932188; PMC5722579).
| Sample | Paraffin-embedded human esophageal squamous carcinoma tissue; fixative not specified (datasheet M01849-2) |
| Fixation | Image fixative and duration unreported (datasheet M01849-2); 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 M01849-2); 20 min, 95–100 °C (standard) |
| Peroxidase block | 3% H2O2, 10 min, room temperature (standard) |
| Blocking | 10% goat serum (datasheet M01849-2) |
| Primary antibody | Mouse monoclonal (clone 4G9) anti-COPS5, 2μg/ml (datasheet M01849-2) |
| Primary incubation | Overnight at 4 °C (datasheet M01849-2) |
| Detection | Streptavidin-biotin complex (SABC), DAB chromogen (datasheet M01849-2) |
| Counterstain | Hematoxylin, blue, dehydrate and mount (standard) |
| Expected result | COPS5-positive staining in adipocytes of adipose tissue (HPA tissue IHC: High). HPA tissue profile: Cytoplasmic and nuclear expression in all tissues. No signal in the no-primary control. |
COPS5 is a soluble protein found in the cytosol, nucleus and perinuclear region; it has no transmembrane segment (UniProt Q92905). In tissue sections, expect cytoplasmic and nuclear staining across cell types, including strong staining in the listed HPA high-expression cells (HPA: tissue IHC). HPA rates its tissue pattern Supported, with medium consistency between staining and RNA data (HPA: tissue IHC).
| Nuclear and cytoplasmic staining in adipocytes, glandular cells or hematopoietic cells. | This fits the reported tissue pattern; HPA grades these cell types High in specified tissues (HPA: tissue IHC). Assess staining within cells, while allowing nuclear-to-cytoplasmic balance to vary: both compartments are reported (UniProt Q92905; HPA: tissue IHC). |
| Predominantly sharp cell-surface or extracellular staining, with little intracellular signal. | Treat this as a localization mismatch to investigate, since COPS5 has no transmembrane segment and its reported sites are intracellular (UniProt Q92905). Check whether the pattern follows section edges, deposits or structures outside cells before interpreting it as COPS5 (general IHC practice). |
| Staining is confined to an unexpected population while the expected cells are blank. | A single stained cell type is hard to reconcile with HPA's cytoplasmic and nuclear expression across tissues (HPA: tissue IHC). Consider antibody cross-reactivity or endogenous detection activity; compare morphology and a detection control before assigning the signal to COPS5 (general IHC practice). |
| Haze or granular chromogen covers many structures without clear cell boundaries. | This distribution cannot establish nuclear or cytoplasmic localization (general IHC practice). Review blocking, washes and detection controls for background, then judge whether recognizable cells retain the reported intracellular pattern (HPA: tissue IHC; general IHC practice). |
| No detectable signal in a section containing an HPA High cell type. | A negative result there conflicts with the reported staining, but does not by itself prove COPS5 is absent (HPA: tissue IHC). Check tissue preservation, retrieval and detection performance with appropriate controls before drawing a biological conclusion (general IHC practice). |
| Tissue distribution | HPA reports cytoplasmic and nuclear expression in all tissues and low tissue RNA specificity; its listed High cells include adipocytes, glandular, hematopoietic, respiratory epithelial and glial cells (HPA: tissue IHC). Use the stated cell type within its listed tissue when selecting an expected-positive area. |
| Location and topology | UniProt places COPS5 in cytosol, nucleus and perinuclear cytoplasm, with no transmembrane segment (UniProt Q92905). This supports intracellular interpretation; a membrane-dominant pattern needs independent scrutiny (UniProt Q92905; general IHC practice). |
| Evidence strength | The tissue profile is Supported with medium staining-to-RNA consistency; HPA004845 and CAB004242 are IHC Supported (HPA: tissue IHC; HPA: antibodies). These ratings support comparison with the reported pattern, without making every individual stained structure specific. |
| Processing and fixation evidence | UniProt lists no signal peptide or propeptide and no glycosylation sites (UniProt Q92905). The supplied sources do not report COPS5-specific fixation sensitivity or retrieval conditions; choose and assess retrieval using general IHC controls (general IHC practice). |
| IF/ICC Q&A: should its image match tissue IHC exactly? | No exact match is established: HPA reports enhanced nucleoplasmic localization in ICC-IF images, while tissue IHC reports nuclear and cytoplasmic staining (HPA: subcellular; HPA: tissue IHC). Interpret each result in its own specimen and detection context. |
| Situation | Likely cause | Next action |
|---|---|---|
| Blank staining in an expected-positive area. | A failed retrieval or detection step is possible; the sources give no COPS5-specific retrieval setting (general IHC practice). | Confirm the listed HPA High cell type is present, then check a positive control and the IHC-validated antibody's documented procedure (HPA: tissue IHC; general IHC practice). |
| Uniform brown haze obscures cells. | Nonspecific reagent binding, inadequate washing or endogenous detection activity can produce background (general IHC practice). | Review blocking and wash steps; use an appropriate detection control and score only cell-associated nuclear or cytoplasmic signal (general IHC practice; HPA: tissue IHC). |
| Staining appears only on cell borders or outside cells. | That placement disagrees with COPS5's intracellular locations and lack of a transmembrane segment (UniProt Q92905). | Inspect morphology and deposits, compare a detection control, and re-evaluate intracellular staining before calling the section positive (general IHC practice). |
| Only one unexpected cell population stains. | Cross-reactivity or endogenous detection activity is possible; HPA describes expression across tissues (HPA: tissue IHC; general IHC practice). | Identify the stained cells morphologically and compare expected-positive cells and detection controls; avoid assigning specificity from color alone (HPA: tissue IHC; general IHC practice). |
| Nuclear staining dominates, with faint cytoplasm. | Compartment balance may differ by specimen: UniProt lists both locations, and HPA ICC-IF emphasizes nucleoplasm (UniProt Q92905; HPA: subcellular). | Check whether nuclear signal is cell-associated and whether cytoplasm is discernible; compare tissue IHC controls before rejecting the pattern (HPA: tissue IHC; general IHC practice). |
| Intensity varies between areas of one section. | Cell composition or staining performance may differ across areas (general IHC practice); HPA High calls apply to named cell types in specified tissues (HPA: tissue IHC). | Compare like cell types in intact areas, inspect section quality and controls, and record compartment and intensity separately (HPA: tissue IHC; general IHC practice). |
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 |
|---|---|---|---|---|
| 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 | Glandular cells | High | Protein (IHC) | HPA → |
| Tissue | Cell type | Level | Evidence | Source |
|---|---|---|---|---|
| None in HPA: COPS5 is detected in all 45 scored tissues. Use a no-primary (secondary-only) and an isotype control instead. | ||||
Use compartment-aware controls and consistent section processing to troubleshoot COPS5 staining in paraffin sections (UniProt Q92905 localisation; standard IHC practice).
The catalog shows COPS5 IHC in human tissue and mouse and rat testis, plus IF in T-47D cells (catalog: IHC and IF captions).
M01849-2 has paraffin-section IHC images from human esophageal squamous carcinoma, liver cancer, lung cancer and placenta, plus an IF image from T-47D cells (catalog: M01849-2 image captions). PB9490 has paraffin-section IHC images from human mammary cancer and mouse and rat testis; M01849 has a paraffin-section IHC image from human breast cancer (catalog: PB9490 and M01849 IHC captions).
Which to pick: For tissue IHC across human, mouse and rat samples, choose PB9490: its own captions show paraffin-section staining in all three species, and its listed IHC dilution is 0.5–1 μg/ml (catalog: PB9490 IHC captions and dilution). For IF/ICC, M01849-2 has a fluorescence image in T-47D cells using 5 μg/ml; M01849 lists IF/ICC but has no IF image in this payload (catalog: M01849-2 IF caption; M01849 applications and IF images). M01849 is a rabbit monoclonal IHC option with a human breast cancer paraffin-section image at 1:50; the fixative is unreported in the IHC captions for all three SKUs (catalog: M01849 host, clone and IHC caption; M01849-2, PB9490 and M01849 IHC captions).