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DHX9 / ATP-dependent RNA helicase A · IHC design guide
Design Immunohistochemistry for DHX9
Plan paraffin-section DHX9 IHC around ubiquitous nuclear staining (HPA tissue IHC). This guide covers fixation consistency, the catalog antibody’s 0.5–1 μg/ml IHC dilution (datasheet A02550-1), and nuclear scoring, including the possibility of absent nuclear staining in mitotic cells (UniProt).
Evidence assembled Oct 2026 · For research use; verify linked source records and product datasheet before use
DHX9 Immunohistochemistry Experimental Design Guide
Expected localisation, validated protocols, controls and antibodies — the at-a-glance facts below, then the full design guide.
Must know before staining
| Expected localisation | Ubiquitous nuclear tissue staining (HPA tissue IHC) | |
| Staining pattern | Nuclear staining across 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 |
Important caveats
Reasons your staining may differ from the expected pattern.
| Fixation | Keep fixation consistent across sections (standard IHC practice; not target-specific) | |
| Caveat | Mitotic cells may lack nuclear staining (UniProt) | |
| Regulation | No expression regulator annotated (UniProt) | |
| Isoform / epitope | 2 isoforms; epitope coverage is unspecified (UniProt) |
Section 1
Recommended DHX9 IHC & IF Protocols
The catalog antibody has a datasheet IHC protocol (datasheet A02550-1). The published options below report DHX9 staining in liver cancer tissue arrays and mouse tissue (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. |
💡Decision noteStart with heat retrieval in EDTA pH 8.0 for the catalog antibody (datasheet A02550-1). The published citrate retrieval conditions apply to their respective protocols (PMC8649379; PMC5023453).
Section 2
What Is the Expected DHX9 Staining Pattern?
DHX9 should show predominantly nuclear staining in paraffin sections, consistent with HPA’s supported, ubiquitous nuclear tissue pattern and UniProt’s nucleoplasmic and nucleolar localization (HPA: tissue IHC; UniProt Q08211: subcellular location). Strong signal is reported in glandular cells of several tissues, bone marrow hematopoietic cells, and selected brain cell populations (HPA: High in listed cells). DHX9 has no transmembrane segment (UniProt Q08211: topology).
| Distinct nuclear staining in glandular cells of adrenal gland, appendix, breast, or cervix. | This matches reported high staining in those glandular cells (HPA: tissue IHC). Judge the nuclear pattern within the named cells; HPA’s high category does not specify a chromogen intensity threshold for an individual slide. |
| Nuclear staining in bone marrow hematopoietic cells, caudate or cortical glia, or cerebellar granular-layer cells. | These are additional high-staining cell populations (HPA: tissue IHC). Compare signal with the local tissue architecture and counterstain; variation between cells does not, by itself, overturn the reported ubiquitous nuclear pattern. |
| Cytoplasmic or membrane staining dominates while nuclei lack a clear signal. | That conflicts with the expected tissue IHC pattern (HPA: ubiquitous nuclear expression). UniProt also lists cytoplasmic localization and nuclear shuttling, so a minor cytoplasmic component alone is not proof of artefact (UniProt Q08211: subcellular location). |
| Strong staining appears in a cell population outside the named high-staining populations. | Investigate cross-reactivity or endogenous detection activity before assigning that signal to DHX9 (general IHC practice). The supplied HPA record lists no negative cell populations, so an unlisted cell type cannot be declared DHX9-negative from this evidence. |
| Diffuse haze obscures nuclei, or a known high-staining population has no detectable signal. | Haze makes localization unreliable; absent signal in a listed high-staining population warrants a run-quality check (general IHC practice; HPA: High in listed cells). Neither appearance alone establishes altered DHX9 expression. |
💡Expected DHX9 appearanceCall a result positive when named high-staining cells show clear, predominantly nuclear chromogen above local background; diffuse haze or dominant membrane staining does not establish DHX9 localization (HPA: tissue IHC; UniProt Q08211: subcellular location).
| Compartment and tissue context | HPA reports ubiquitous nuclear tissue expression and high staining in specific listed cell populations (HPA: tissue IHC). Score nuclei in their identified cells rather than treating all chromogen in a section as target signal. |
| Nucleolar and cytoplasmic localization | UniProt lists nucleoplasm, nucleolus, cytoplasm, and nuclear shuttling (UniProt Q08211: subcellular location). HPA’s ICC-IF summary emphasizes nucleoplasm with additional nucleoli; it does not establish an equally prominent cytoplasmic IHC pattern (HPA: subcellular ICC-IF). |
| Antibody validation | Two listed antibodies have Supported IHC status, while the third has no IHC status in this payload (HPA: HPA028050, CAB011819, HPA055684). Apply the validation status to the antibody actually used; ICC support alone is not an IHC validation claim. |
| Isoform recognition | UniProt lists two DHX9 isoforms (UniProt Q08211: isoforms 1 and 2). Their relative tissue staining and the epitopes recognized by these antibodies are not supplied, so an isoform-specific interpretation requires separate antibody information. |
| Detection chemistry | Endogenous activity and nonspecific chromogen deposition can imitate cellular staining (general IHC practice). Detection controls can help distinguish these contributions from primary-antibody-dependent nuclear signal; this is a general workflow consideration, not a DHX9-specific HPA finding. |
| Situation | Likely cause | Next action |
|---|---|---|
| No nuclear signal in a section containing a listed high-staining cell population. | The run may have failed, or the tissue and antibody conditions may be unsuitable (general IHC practice). HPA’s high category predicts a useful comparison population, not guaranteed staining in every preparation (HPA: tissue IHC). | Check tissue integrity and counterstain, then review the IHC-validated antibody’s stated dilution, retrieval, and detection instructions. Repeat with a run control before interpreting the absence as biological. |
| Uniform brown haze makes cell boundaries and nuclei hard to distinguish. | Excess background from antibody, detection chemistry, or inadequate blocking or washing can obscure compartment assignment (general IHC practice). HPA’s reported nuclear pattern cannot validate a diffuse result (HPA: tissue IHC). | Compare the primary-omission control, inspect washing and blocking, and adjust antibody and detection conditions within the antibody’s instructions. Reassess nuclear localization only after background clears. |
| Most apparent signal lies outside nuclei. | The result departs from HPA’s ubiquitous nuclear tissue pattern (HPA: tissue IHC). UniProt permits some cytoplasmic localization, so compartment alone cannot identify the source of the discrepancy (UniProt Q08211: subcellular location). | Review morphology, counterstain alignment, and primary-omission staining. Confirm that the antibody has IHC support; avoid scoring a predominantly membrane or diffuse pattern as the expected positive result. |
| A cell population not listed as high shows strong staining. | Cross-reactivity or endogenous detection activity is possible (general IHC practice). The supplied HPA list has no negative populations, so unexpected staining is a validation question rather than proof of a false positive (HPA: tissue IHC). | Check the cell identity against morphology and compare a primary-omission control. If the signal persists as primary-dependent staining, seek independent antibody or orthogonal evidence before assigning it to DHX9. |
| Punctate deposits or staining at section edges dominate the image. | Localized reagent deposits or uneven staining can resemble discrete signal (general IHC practice). UniProt reports intranuclear foci in particular contexts, but that annotation does not identify edge deposits as DHX9 (UniProt Q08211: subcellular location). | Inspect adjacent tissue and the primary-omission control for the same deposits. Evaluate any true intranuclear puncta only in intact cells with interpretable nuclear morphology. |
| Q: Should an IF/ICC image be expected to match the paraffin IHC slide exactly? | HPA describes mainly nucleoplasmic IF signal with additional nucleolar localization (HPA: subcellular ICC-IF). Its tissue IHC summary reports ubiquitous nuclear expression; the records describe different assay readouts (HPA: tissue IHC; subcellular ICC-IF). | A: Use nucleoplasmic enrichment with possible nucleolar signal as the IF/ICC localization reference (HPA: subcellular ICC-IF). For paraffin IHC, judge nuclear staining in the reported cell populations and assess assay controls separately. |
Experiment evidence
IHC & IF images showing DHX9 staining
A02550-1 · IHCIHC analysis of DHX9 using anti-DHX9 antibody (A02550-1). DHX9 was detected in paraffin-embedded section of human gastric cancer tissue. Hea
A02550-1 · IHCIHC analysis of DHX9 using anti-DHX9 antibody (A02550-1). DHX9 was detected in paraffin-embedded section of human lung cancer tissue. Heat m
A02550-1 · IFIF analysis of DHX9 using anti-DHX9 antibody (A02550-1). DHX9 was detected in immunocytochemical section of U20S cells. Enzyme antigen retri
HPA · Cerebral cortexHuman Protein Atlas IHC, Cerebral cortex. Source: https://www.proteinatlas.org/ENSG00000135829-DHX9/tissue/cerebral+cortex#imid_7057488
HPA · ColonHuman Protein Atlas IHC, Colon. Source: https://www.proteinatlas.org/ENSG00000135829-DHX9/tissue/colon#imid_7057414
HPA · LiverHuman Protein Atlas IHC, Liver. Source: https://www.proteinatlas.org/ENSG00000135829-DHX9/tissue/liver#imid_7057431
HPA · PancreasHuman Protein Atlas IHC, Pancreas. Source: https://www.proteinatlas.org/ENSG00000135829-DHX9/tissue/pancreas#imid_7057382
HPA · ICC-IF A-431Human Protein Atlas immunofluorescence, A-431, antibody CAB011819; green = DHX9, blue = nucleus, red = microtubules.
HPA · ICC-IF A-431Human Protein Atlas immunofluorescence, A-431, antibody CAB011819; green = DHX9, blue = nucleus, red = microtubules.
← swipe / scroll for more images →
Real IHC / IF data behind the staining-pattern expectations in this section.
Sample controls for DHX9 IHC & IF
🧪Run breast tissue first and assess the glandular cells, which HPA scores High for DHX9 (HPA: breast glandular cells). HPA detects DHX9 in all 45 scored tissues and lists no negative tissue, so no-primary and isotype slides carry the negative control; there are no validated DHX9-negative cells within the positive slide, and cells without nuclear staining should be treated as internal background comparators rather than confirmed negatives (HPA: all 45 tissues detected; UniProt Q08211: predominantly nuclear localization).
Positive control tissue: Adrenal gland (Glandular cells, HPA High)
Negative control tissue: None in HPA: DHX9 is detected in all 45 scored tissues. Use a no-primary (secondary-only) and an isotype control instead.
ICC-IF cell lines (HPA subcellular resource): HPA ICC-IF images show DHX9 in A-431, U-251MG, U2OS, with annotated localisation: Nucleoplasm (enhanced) (HPA subcellular).
Technical controls: Include a no-primary, secondary-only slide and a concentration-matched rabbit IgG isotype control for the rabbit primary antibody; use DHX9 knockout material or a validated peptide block as a biological specificity control (selected-SKU caption: rabbit anti-DHX9 primary; standard IHC practice). Quench endogenous peroxidase in breast sections and check endogenous biotin background when using the caption’s streptavidin–biotin detection system (selected-SKU caption: biotinylated secondary and SABC–DAB; standard IHC practice).
⚠️Feasibility: A target-specific fixation window or fixation effect is unreported, and the selected A02550-1 paraffin-section caption does not state the fixative (selected-SKU caption: fixative unreported). The caption uses heat-mediated EDTA retrieval at pH 8.0, which provides a starting condition but does not establish that retrieval is required (selected-SKU caption: EDTA pH 8.0). The supplied evidence does not establish whether frozen sections or IF are easier than paraffin IHC; for breast tissue, assess peroxidase and biotin background alongside the nuclear signal (HPA: breast glandular cells High; selected-SKU caption: SABC–DAB; standard IHC practice).
HPA tissue IHC evidence for DHX9
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.
Positive expression · recommended positive controls
| 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 → |
Undetected expression · recommended negative controls
| 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. | ||||
Section 3
Advanced DHX9 IHC Tips
Troubleshoot DHX9 chromogenic IHC by checking retrieval, nuclear localisation, staining controls and cell-level scoring before interpreting tissue differences.
How should I adjust retrieval when DHX9 nuclear staining is weak?
Start with heat-mediated retrieval in EDTA at pH 8.0, the condition used for the catalog antibody in paraffin sections (datasheet A02550-1). If nuclear staining remains weak, vary heating and cooling conditions while holding the buffer constant, and compare sections processed together (standard IHC practice). Keep the antibody incubation at the documented 1 μg/ml overnight at 4°C during that comparison so retrieval is the main variable (datasheet A02550-1). Judge improvement by sharper nuclear signal with limited background: DHX9 is mainly nucleoplasmic and can also appear in nucleoli (HPA subcellular).
Could fixation explain variable DHX9 staining between paraffin blocks?
Target-specific DHX9 sensitivity to fixation is unknown: the selected paraffin-section caption does not report a fixative (datasheet A02550-1). Record each block’s fixative and fixation duration when available, then compare sections processed with the same EDTA pH 8.0 retrieval and antibody incubation (datasheet A02550-1; standard IHC practice). Underfixation can impair tissue preservation, while excessive fixation can reduce epitope access in IHC generally; neither outcome has been established specifically for DHX9 here (standard IHC practice). Assess nuclear morphology alongside staining, and avoid assigning a block-to-block difference to DHX9 biology until processing differences have been checked (standard IHC practice).
How should I assess DHX9 staining outside the nucleus?
Expect predominantly nucleoplasmic DHX9 staining, with possible nucleolar signal, when reading chromogenic sections (HPA subcellular). Cytoplasmic staining is biologically possible because DHX9 shuttles and has reported cytoplasmic ribonucleoprotein-granule and centrosomal localisation (UniProt Q08211 subcellular location). First confirm that nuclei are identifiable with a counterstain and that the apparent cytoplasmic signal follows cells rather than section edges or deposits (standard IHC practice). Compare the pattern with nearby intact cells and a negative detection control before treating a cytoplasmic shift as biological; chromogenic overlap can obscure compartment boundaries (standard IHC practice).
Can epitope choice explain discordant DHX9 IHC patterns?
DHX9 has 2 annotated isoforms, but the supplied caption does not identify the catalog antibody’s epitope or establish isoform selectivity (UniProt Q08211 isoforms; datasheet A02550-1). The protein has RNA-binding domains, helicase domains and modified residues, so epitope location and accessibility merit checking in the antibody documentation before assigning a staining difference to an isoform (UniProt Q08211 domains and modified residues; standard IHC practice). Compare independently processed sections using the same EDTA pH 8.0 retrieval to assess reproducibility (datasheet A02550-1; standard IHC practice). Without epitope mapping and suitable validation, IHC signal cannot establish which DHX9 isoform is present (standard IHC practice).
How can IF help resolve an ambiguous DHX9 IHC localisation pattern?
Use a separate IF/ICC assay to examine compartment boundaries when chromogenic DHX9 signal is ambiguous; the catalog caption documents paraffin-section IHC, not IF/ICC performance (datasheet A02550-1). Multiplex DHX9 with a marker for the expected cell type and a nuclear counterstain, then inspect whether signal lies in nucleoplasm or nucleoli (HPA subcellular; standard IF practice). Choose fluorophores after checking tissue autofluorescence and include single-channel controls to assess bleed-through (standard IF practice). DHX9 has no transmembrane segment and is predominantly nuclear, so use permeabilisation appropriate for access to an intracellular nuclear epitope, with fixation conditions validated separately for IF/ICC (UniProt Q08211 topology; HPA subcellular; standard IF practice).
What should I check when DAB background obscures DHX9 nuclei?
The documented chromogenic workflow used 10% goat serum, a biotinylated secondary antibody, a streptavidin–biotin complex and DAB (datasheet A02550-1). Check a section without primary antibody to assess secondary and detection-system background, and include a peroxidase block as a general chromogenic IHC step (standard IHC practice). If staining follows tissue edges, folds or deposits, inspect section quality and washing before changing the documented 1 μg/ml primary concentration (datasheet A02550-1; standard IHC practice). Review DAB development against a concurrently processed control because diffuse brown staining can conceal the predominantly nucleoplasmic DHX9 pattern (HPA subcellular; standard IHC practice).
How should I quantify DHX9 staining across tissue sections? ⚠ ANSWER MARKED FOR VERIFICATION
Score DHX9 primarily in identifiable nuclei, since the supported tissue profile is ubiquitous nuclear expression and the main subcellular location is nucleoplasmic (HPA tissue IHC; HPA subcellular). For comparable cell populations, report the percentage of positive nuclei and an H-score based on staining intensity and positive-cell fraction (standard IHC practice). If cell abundance varies across regions, report positive-cell density per mm² alongside the fraction of all evaluable nuclei, using the same area-selection and threshold rules (standard IHC practice). Keep retrieval, DAB development and image-analysis settings consistent, and exclude necrotic or poorly preserved regions before comparing specimens (standard IHC practice).
How can I distinguish true DHX9 staining from artefact?
A credible pattern shows staining in intact nuclei, often nucleoplasmic with possible nucleolar signal, consistent with the supported ubiquitous nuclear tissue profile (HPA subcellular; HPA tissue IHC). Cytoplasmic DHX9 can occur, but a predominantly extracellular, edge-restricted or necrotic pattern needs scrutiny before biological interpretation (UniProt Q08211 subcellular location; standard IHC practice). Compare the suspect area with an adjacent well-preserved area and a section without primary antibody; endogenous peroxidase and detection background can produce DAB signal (standard IHC practice). Interpret differences within defined cell populations because DHX9 is reported across many tissues and cell types, rather than treating a positive section alone as disease-specific evidence (HPA tissue IHC).
Boster reagents
Best DHX9 / ATP-dependent RNA helicase A IHC Antibodies
A02550-1 has DHX9 IHC images from human gastric and lung cancer paraffin sections and IF images from human gastric cancer sections and U20S cells (catalog image captions).
Real IHC data
Anti-RNA Helicase A/DHX9 Antibody ®
Cat # A02550-1
A02550-1 lists IHC and IF for human, mouse and rat, with images documenting human paraffin-section IHC and human tissue and cell IF (catalog applications; catalog reactivity; catalog image captions). M02550 lists IHC and IF and human, mouse and rat reactivity, but has no IHC or IF images in the payload (catalog applications; catalog reactivity; catalog image captions).
Which to pick: Choose A02550-1 for tissue IHC: its own caption documents heat retrieval in EDTA at pH 8.0 and staining at 1 μg/ml on human paraffin sections; the fixative is unreported (A02550-1 IHC image caption). Choose A02550-1 for IF/ICC when an image example matters; its captions document human gastric cancer sections and U20S cells at 2 μg/ml (A02550-1 IF image captions). For mouse or rat work, both SKUs list reactivity, while M02550 is the monoclonal option with no supplied IHC or IF image; validate staining in the intended sample (catalog reactivity; M02550 catalog clone; catalog image captions).
Each figure is that product's own IHC / IF validation image from its datasheet.
References
- UniProt Consortium. UniProt entry Q08211 (DHX9_HUMAN, ATP-dependent RNA helicase A).
- Human Protein Atlas. DHX9 tissue IHC expression (reliability: Supported).
- Human Protein Atlas. DHX9 subcellular location (ICC-IF): Mainly localized to the nucleoplasm. In addition localized to the nucleoli..
- Human Protein Atlas. DHX9 antibody validation summary (3 antibodies).
- Targeting Hepatocellular Carcinoma Growth: Haprolid's Inhibition of AKT Signaling Through DExH-Box Helicase 9 Downregulation. Cancers 2025 — PMC11816161.
- High expression of DHX9 promotes the growth and metastasis of hepatocellular carcinoma. Journal of clinical laboratory analysis 2021 — PMC8649379.
- High Levels of DEAH-Box Helicases Relate to Poor Prognosis and Reduction of DHX9 Improves Radiosensitivity of Hepatocellular Carcinoma. Frontiers in oncology 2022 — PMC9256992.
- Tumor cell survival dependence on the DHX9 DExH-box helicase. Oncogene 2016 — PMC5023453.
- PubMed PMID:8344961 — UniProt-cited evidence.
- PubMed PMID:8690889 — UniProt-cited evidence.
- PubMed PMID:9111062 — UniProt-cited evidence.
Immunohistochemistry protocol sheet for DHX9 (ATP-dependent RNA helicase A). Expected localisation Ubiquitous nuclear tissue staining (HPA tissue IHC). Antigen retrieval: EDTA pH 8.0 HIER, heat-mediated (datasheet A02550-1). Validated IHC antibody: A02550-1 at 0.5-1μg/ml (the product's own IHC validation image is shown). Controls (HPA): positive Adrenal gland (Glandular cells); negative None in HPA (detected in all 45 tissues); use no-primary + isotype controls. IHC-P workflow on paraffin sections; fixative unspecified. Protocol steps: 1. Sample: Paraffin-embedded human gastric cancer tissue; fixative not specified (datasheet A02550-1); 2. Fixation: Image fixative and duration unreported (datasheet A02550-1); verify before use.; 3. Sectioning: 4–5 µm sections on charged slides (standard); 4. Deparaffinisation: Xylene, graded ethanol series to water (standard); 5. Antigen retrieval: Heat retrieval: EDTA pH 8.0 (datasheet A02550-1); 20 min, 95–100 °C (standard); 6. Peroxidase block: 3% H2O2, 10 min , room temperature (standard); 7. Blocking: 10% goat serum (datasheet A02550-1); 8. Primary antibody: Rabbit anti-DHX9, 0.5-1μg/ml (datasheet A02550-1); 9. Primary incubation: Overnight at 4 °C (datasheet A02550-1). Watch for: Fixation: Keep fixation consistent across sections (standard IHC practice; not target-specific); Caveat: Mitotic cells may lack nuclear staining (UniProt); Isoform / epitope: 2 isoforms; epitope coverage is unspecified (UniProt); Regulation: No expression regulator annotated (UniProt). Evidence: UniProt Q08211, HPA tissue IHC · Supported, HPA ICC-IF · Mainly localized to the nucleoplasm. In addition localized to the…, Datasheet A02550-1, PMC11816161, PMC8649379. QR code links to https://www.bosterbio.com/bosterbio-gene-info-cards/DHX9/immunohistochemistry-ihc-guide.