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- Table of Contents
Plan DHX9 paraffin-section IHC around broadly nuclear tissue staining (HPA tissue IHC). Start the IHC-validated antibody at 0.5–1 μg/mL (datasheet A02550-1), then assess nuclear staining across cell types.
Expected localisation, validated protocols, controls and antibodies — the at-a-glance facts below, then the full design guide.
| Expected localisation | Predominantly nuclear in tissue (HPA tissue IHC) | |
| Staining pattern | Nuclear staining across many tissue cell types (HPA tissue IHC) | |
| Antigen retrieval | EDTA pH 8.0 HIER, heat-mediated (datasheet A02550-1) | |
| Positive control | Adrenal gland+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 | Nucleocytoplasmic shuttling may add cytoplasmic signal (UniProt) | |
| Regulation | Low tissue specificity (HPA tissue RNA) | |
| Isoform / epitope | 2 isoforms; antibody epitope coverage is unknown (UniProt) |
The catalog antibody has a datasheet IHC-P protocol (datasheet A02550-1). The published options below cover hepatocellular carcinoma tissue microarrays and mouse paraffin sections (PMC11816161; PMC8649379; PMC5023453).
| Sample | Paraffin-embedded human gastric cancer tissue; fixative not specified (datasheet A02550-1) |
| Fixation | Image fixative and duration unreported (datasheet A02550-1); 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 A02550-1); 20 min, 95–100 °C (standard) |
| Peroxidase block | 3% H2O2, 10 min, room temperature (standard) |
| Blocking | 10% goat serum (datasheet A02550-1) |
| Primary antibody | Rabbit anti-DHX9, 0.5-1μg/ml (datasheet A02550-1) |
| Primary incubation | Overnight at 4 °C (datasheet A02550-1) |
| Detection | Streptavidin-biotin complex (SABC), DAB chromogen (datasheet A02550-1) |
| Counterstain | Hematoxylin, blue, dehydrate and mount (standard) |
| Expected result | DHX9-positive staining in glandular cells of adrenal gland (HPA tissue IHC: High). HPA tissue profile: Ubiquitous nuclear expression. No signal in the no-primary control. |
DHX9 should appear predominantly in nuclei across many cell types in paraffin tissue sections (HPA tissue IHC: ubiquitous nuclear expression; Supported reliability). Strong staining is documented in adrenal, appendix, breast and cervical glandular cells, bone marrow hematopoietic cells, and selected brain cells (HPA tissue IHC: High). A membrane rim is not expected for this protein (UniProt Q08211: no transmembrane segment).
| Crisp nuclear chromogen in the expected cells, with little signal over empty spaces or tissue edges. | This fits the reported ubiquitous nuclear tissue pattern; compare intensity within the same section, since HPA lists High staining in selected cell populations rather than a universal intensity threshold (HPA tissue IHC: ubiquitous nuclear expression; High in listed cells). |
| Signal is predominantly cytoplasmic, membranous or extracellular, while nuclei remain pale. | Check for a staining artefact or nonspecific binding before calling this DHX9: HPA tissue IHC reports a nuclear pattern (HPA tissue IHC: ubiquitous nuclear expression). Cytoplasmic DHX9 is biologically possible, so cytoplasmic signal alone does not prove an artefact (UniProt Q08211: cytoplasmic localization and nucleocytoplasmic shuttling). |
| Strong colour marks a cell population other than the one expected to stain strongly in a selected tissue. | Review morphology and cell identity first. HPA identifies High staining in specified populations, but its ubiquitous nuclear profile does not make neighboring cells true negatives (HPA tissue IHC: High in listed cells; ubiquitous nuclear expression). A mismatch concentrated over debris, vessels or cell borders warrants checks for cross-reactivity or endogenous detection activity (general IHC practice). |
| A diffuse haze covers nuclei, cytoplasm and cell-free areas, obscuring cell boundaries. | Do not score the haze as DHX9 expression: it prevents assessment of the nuclear pattern reported by HPA (HPA tissue IHC: ubiquitous nuclear expression). Inspect a reagent control and adjust blocking, washes or chromogen development according to the detection system (general IHC practice). |
| No convincing nuclear colour appears in a well-preserved, documented High-staining cell population. | Treat the result as an unresolved assay failure before interpreting the sample as DHX9-negative (HPA tissue IHC: High in listed cells). Check that nuclei are identifiable with counterstain, then verify the primary antibody, detection reagents and a parallel positive section (general IHC practice). |
| Which tissue and cells provide an interpretable positive comparison? | Use a documented High population, such as appendix glandular cells or bone marrow hematopoietic cells, and identify that population morphologically (HPA tissue IHC: High). HPA lists no negative tissue in this payload; an unstained unrelated cell population is not an established DHX9-negative control (HPA tissue IHC: negative list empty; ubiquitous nuclear expression). |
| How strongly is the tissue pattern validated? | The tissue profile is Supported because antibody staining is highly consistent with RNA expression (HPA tissue IHC: reliability Supported). HPA028050 and CAB011819 have Supported IHC status; HPA055684 has no IHC status in the supplied list (HPA antibodies: IHC statuses). These labels support pattern comparison, not an exact intensity cutoff. |
| What does protein location predict? | Expect nuclear staining in routine tissue assessment, while allowing biologically plausible nucleolar or cytoplasmic signal in context (HPA tissue IHC: ubiquitous nuclear expression; UniProt Q08211: nucleus, nucleolus and cytoplasm). Do not infer that every cytoplasmic deposit is specific from localization alone (general IHC practice). |
| Do protein topology or processing predict a surface pattern? | A surface-only outline has no support from the supplied topology: DHX9 has no transmembrane segment or signal peptide, and its annotated chain spans residues 1–1270 (UniProt Q08211: topology and processing). These annotations do not establish how fixation or antigen retrieval affects this antibody. |
| What should IF/ICC show? | Predominant nucleoplasmic fluorescence, with additional nucleolar staining, matches the cell-image profile (HPA subcellular ICC-IF: nucleoplasm enhanced; nucleoli supported). HPA lists images from A-431, U-251MG and U2OS; these observations inform localization but do not supply an IF/ICC protocol here (HPA subcellular ICC-IF: imaged cell lines). |
| Can the supplied evidence specify antigen retrieval? | No retrieval condition or target-specific fixation sensitivity is supplied by UniProt or HPA. If nuclear signal is weak, compare retrieval conditions with matched positive sections while keeping other variables stable (general IHC practice); do not interpret the HPA High label as evidence for a particular retrieval treatment. |
| Situation | Likely cause | Next action |
|---|---|---|
| Nuclei are blank in both the study section and a documented High population. | The run may have failed at primary incubation, retrieval or detection; the HPA High label alone cannot identify the failed step (HPA tissue IHC: High in listed cells; general IHC practice). | Confirm section integrity and counterstain, reagent order, antibody suitability for IHC and detection performance on a parallel positive section (general IHC practice). |
| Nuclear signal is present but too faint to score confidently. | A weak run may reflect assay conditions or low signal in that population; HPA does not assign the same intensity to every cell (HPA tissue IHC: High in listed cells; ubiquitous nuclear expression). | Compare with a documented High cell population; optimize retrieval or primary-antibody concentration with matched sections, using the antibody's actual IHC instructions when available (general IHC practice). |
| Colour is mainly cytoplasmic or outlines cell membranes. | This departs from the HPA tissue pattern, although UniProt also records cytoplasmic localization; membrane localization lacks support from topology (HPA tissue IHC: ubiquitous nuclear expression; UniProt Q08211: cytoplasm, no transmembrane segment). | Check nuclear counterstain and morphology, then compare a positive section and reagent control before assigning the signal to DHX9 (general IHC practice). |
| Diffuse colour persists outside cells or across the whole section. | Background from binding or detection can hide the expected nuclear pattern (general IHC practice; HPA tissue IHC: ubiquitous nuclear expression). | Inspect a control lacking primary antibody; improve blocking or washing and reduce excessive chromogen development as indicated by the control (general IHC practice). |
| An unexpected cell population dominates the stain. | Cell misidentification, cross-reactivity or endogenous detection activity are possible; ubiquitous nuclear expression means adjacent cells cannot automatically serve as negative references (general IHC practice; HPA tissue IHC: ubiquitous nuclear expression). | Recheck morphology against the HPA High population, then examine a reagent control and a separately validated IHC antibody if available (HPA tissue IHC: High; HPA antibodies: Supported IHC for HPA028050 and CAB011819). |
| Only part of a section stains, or edge staining exceeds the center. | Uneven reagent coverage or section handling may create a spatial gradient unrelated to the reported cell pattern (general IHC practice; HPA tissue IHC: ubiquitous nuclear expression). | Check section adhesion, full reagent coverage and incubation consistency; repeat with a parallel documented High section before comparing biological intensity (general IHC practice; HPA tissue IHC: High in listed cells). |
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 |
|---|---|---|---|---|
| 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 → |
| Caudate | Glial cells | High | Protein (IHC) | HPA → |
| Tissue | Cell type | Level | Evidence | Source |
|---|---|---|---|---|
| None in HPA: DHX9 is detected in all 45 scored tissues. Use a no-primary (secondary-only) and an isotype control instead. | ||||
Troubleshoot DHX9 staining in paraffin sections by checking retrieval, nuclear localisation, controls, and scoring before interpreting cytoplasmic signal.
A02550-1 has IHC images from human gastric and lung cancer paraffin sections and IF images from human gastric cancer sections and U20S cells (catalog image captions).
A02550-1 is the only SKU with a rendering card; its IHC images show human gastric and lung cancer paraffin sections (catalog IHC image captions). Its IF images show human gastric cancer paraffin sections and U20S cells (catalog IF image captions).
Which to pick: Choose A02550-1 for tissue IHC: its own captions document paraffin sections, EDTA retrieval at pH 8.0, and 1 μg/ml primary antibody; the fixative is unreported (A02550-1 IHC image captions). For IF/ICC, A02550-1 has image evidence at 2 μg/ml in human gastric cancer sections and U20S cells, while M02550 lists IF/ICC without an image caption (catalog IF image captions; M02550 applications and image fields). Both list human, mouse, and rat reactivity, but the documented IHC images are human only; M02550 is monoclonal, while A02550-1 is polyclonal (catalog reactivity, clone, description, and IHC image captions).