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ARL6 / ADP-ribosylation factor-like protein 6 · IHC design guide
Design Immunohistochemistry for ARL6
Plan ARL6 staining in paraffin sections using ciliated bronchus or fallopian tube as positive controls (HPA tissue IHC) and a 1:50–1:100 antibody starting range (datasheet: IHC). Assess cytoplasmic and ciliary axoneme staining while allowing for medium consistency between staining and RNA expression (HPA tissue IHC).
Evidence assembled Oct 2026 · For research use; verify linked source records and product datasheet before use
ARL6 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 | Mainly cytoplasmic, with ciliary axoneme staining (HPA tissue IHC) | |
| Staining pattern | Ciliated cells show prominent axoneme staining (HPA tissue IHC) | |
| Antigen retrieval | Citrate pH 6.0 HIER, 95–98 °C, 20 min (rule: cytoplasmic / membrane antigen) | |
| Positive control | Bronchus+4 more · see all | |
| Negative control | Adipose tissue+3 more · see all |
Important caveats
Reasons your staining may differ from the expected pattern.
| Fixation | Keep formalin fixation consistent across paraffin sections. (standard IHC practice; not target-specific) | |
| Caveat | Staining and RNA show only medium consistency (HPA tissue IHC) | |
| Regulation | No staining-linked regulation annotated (UniProt) | |
| Isoform / epitope | 2 isoforms; no transmembrane segment; epitope coverage unknown (UniProt; datasheet) |
Section 1
Recommended ARL6 IHC & IF Protocols
The catalog antibody’s IHC-P protocol is followed by one published ARL6 immunohistochemistry protocol (PMC5154108).
| Sample | Paraffin-embedded human prostate tissue; fixative not specified (datasheet A05003) |
| Fixation | Image fixative and duration unreported (datasheet A05003); verify before use. |
| Sectioning | 4–5 µm sections on charged slides (standard) |
| Deparaffinisation | Xylene, graded ethanol series to water (standard) |
| Antigen retrieval | Heat-induced epitope retrieval in citrate buffer, pH 6.0, 20 min at 95–98 °C (standard rule: cytoplasmic / membrane antigen) |
| Peroxidase block | 3% H2O2, 10 min, room temperature (standard) |
| Blocking | 10% normal serum of the secondary host, 30 min, room temperature (standard) |
| Primary antibody | Rabbit anti-ARL6, 1:50-1:100 (datasheet A05003) |
| Primary incubation | Overnight at 4 °C (standard) |
| Detection | HRP-polymer secondary, DAB chromogen 5–10 min (standard) |
| Counterstain | Hematoxylin, blue, dehydrate and mount (standard) |
| Expected result | ARL6-positive staining in ciliated cells (cilia axoneme) of bronchus (HPA tissue IHC: High). HPA tissue profile: Mainly cytoplasmic expression in most tissues, including cilia positivity. No signal in the no-primary control. |
💡Decision noteFor paraffin sections, start with citrate HIER at pH 6.0, 95–98 °C for 20 min (page antigen retrieval).
Section 2
What Is the Expected ARL6 Staining Pattern?
ARL6 is associated with the cilium membrane, axoneme and basal body, including puncta near the axoneme (UniProt Q9H0F7). In tissue IHC, expect mainly cytoplasmic staining across many tissues and cilia positivity in ciliated cells (HPA tissue IHC). HPA rates the tissue staining Approved, with medium consistency between antibody staining and RNA expression; it should guide interpretation without being treated as definitive validation (HPA tissue IHC). ARL6 has no transmembrane segment (UniProt Q9H0F7 topology).
| Apical cilia stain in bronchus, fallopian tube or nasopharynx. | This fits the reported High staining of ciliated cells at the cilia axoneme in all three tissues (HPA tissue IHC). Assess whether signal follows the ciliated border and its cells, rather than treating every brown deposit near the lumen as ARL6 (general IHC practice). |
| Cytoplasmic staining appears in neurons, glands or kidney tubules. | A cytoplasmic pattern is expected in most tissues (HPA tissue IHC). HPA reports High staining in cerebral cortex neuronal cells, duodenal glandular cells and kidney tubule cells (HPA tissue IHC). Record the stained cell population and compartment separately; a positive field alone does not establish that the expected cells carry the signal (general IHC practice). |
| Strong nuclear-only staining replaces the expected cytoplasmic or ciliary pattern. | Treat this as a questionable tissue IHC result because HPA describes mainly cytoplasmic expression with cilia positivity, while UniProt places ARL6 at ciliary structures (HPA tissue IHC; UniProt Q9H0F7). Nucleoplasm is an uncertain additional location in HPA ICC-IF, so that observation does not independently validate a nuclear-only paraffin-section pattern (HPA subcellular ICC-IF). |
| Strong staining dominates cells reported as not detected. | HPA reports ARL6 as Not detected in adipocytes, cervix or prostate glandular cells, and vaginal squamous cells (HPA tissue IHC). Recheck cell identity, morphology and controls before interpreting strong signal there as target expression; cross-reactivity or endogenous chromogen activity are possible technical explanations, not conclusions from HPA (general IHC practice). |
| Diffuse brown haze obscures cell borders, or no signal appears in an expected positive tissue. | Haze that cannot be assigned to cells or cilia is unsuitable for compartment scoring (general IHC practice). Conversely, absent signal in ciliated bronchus, fallopian tube or nasopharynx should prompt a run check because HPA reports High cilia-axoneme staining there (HPA tissue IHC). Neither observation alone proves an ARL6 expression change. |
💡Expected ARL6 appearanceCall a result positive when discernible cytoplasmic staining occurs in the expected cells, with ciliary signal at ciliated borders where present and High staining in HPA's named positive cell populations; isolated nuclear-only signal or diffuse, cell-unassigned brown deposits are questionable (HPA tissue IHC; general IHC practice).
| Ciliary localisation | UniProt places ARL6 at the cilium membrane, axoneme and basal body and describes puncta flanking the axoneme (UniProt Q9H0F7). HPA tissue IHC records cilia-axoneme positivity but does not resolve those puncta in paraffin sections (HPA tissue IHC). Score a visible ciliated border without requiring sub-ciliary detail. |
| Isoforms and epitope coverage | UniProt lists two ARL6 isoforms (UniProt Q9H0F7). The supplied records do not locate the antibody epitope or establish equal detection of both isoforms. A tissue IHC pattern therefore cannot identify which isoform produced the signal. |
| Protein processing and topology | UniProt lists no signal peptide, propeptide or transmembrane segment, and annotates a chain spanning residues 2–186 (UniProt Q9H0F7). These annotations offer no basis to expect a shed extracellular staining pattern or to infer a target-specific antigen-retrieval requirement. |
| Evidence strength and tissue selection | The tissue profile is Approved with medium consistency between staining and RNA expression, while antibody HPA019361 is Approved for IHC (HPA tissue IHC; HPA antibodies). Retina is tissue enhanced at the RNA level, but the supplied tissue IHC examples do not establish a retinal staining pattern (HPA tissue IHC). |
| IF/ICC Q&A | What should IF/ICC show? HPA supports primary-cilium and cilium-tip localisation; it labels microtubules, cytosol and nucleoplasm uncertain (HPA subcellular ICC-IF). The supplied antibody is Supported for ICC (HPA antibodies). These ICC-IF observations do not set a paraffin-section scoring requirement. |
| Situation | Likely cause | Next action |
|---|---|---|
| No ciliary signal in a bronchus, fallopian tube or nasopharynx section. | The missing signal conflicts with High cilia-axoneme staining in the named ciliated cells (HPA tissue IHC); the cause is undetermined. | Confirm that ciliated epithelium is present, then inspect a known-positive control, antibody application, detection and antigen-retrieval records before interpreting the specimen as negative (general IHC practice). |
| All cells show similar diffuse brown staining. | A cell-independent pattern is inconsistent with assigning HPA's specified cell and cilia staining (HPA tissue IHC); background or chromogen deposition may be involved (general IHC practice). | Review the negative control, blocking and wash steps, and exposure to detection reagents; score only signal that can be assigned to cells or cilia (general IHC practice). |
| A nuclear-only pattern dominates an otherwise readable section. | It diverges from mainly cytoplasmic tissue IHC (HPA tissue IHC). HPA's nucleoplasm entry comes from ICC-IF and is uncertain (HPA subcellular ICC-IF). | Compare the run with a positive tissue control and the expected cytoplasmic or ciliary compartments; do not score nuclear signal alone as confirmation of ARL6 (general IHC practice). |
| Strong staining appears in adipocytes or vaginal squamous cells. | Those cell types are reported Not detected (HPA tissue IHC). Misassigned cells, antibody cross-reactivity or endogenous detection activity may explain the discrepancy (general IHC practice). | Verify morphology and compare a negative control with a named HPA-positive tissue from the same run before reporting an unexpected positive (HPA tissue IHC; general IHC practice). |
| An apical brown line is visible, but individual cilia are unclear. | Section orientation or limited morphological resolution can prevent confident compartment assignment (general IHC practice); HPA's positive call is specifically for ciliated cells at the cilia axoneme (HPA tissue IHC). | Inspect adjacent well-oriented epithelium and its counterstain. Record the finding as apical staining unless cilia can be identified; avoid claiming resolved axonemal puncta (general IHC practice; UniProt Q9H0F7). |
| A negative specimen is being compared with retina RNA enrichment. | HPA reports tissue-enhanced RNA in retina but supplies no retinal IHC result in this record (HPA tissue IHC). RNA enrichment alone does not specify the paraffin-section staining pattern. | Use the named High IHC tissues to check assay performance and report the retinal observation separately, without assigning an expected retinal intensity from the RNA category (HPA tissue IHC; general IHC practice). |
Experiment evidence
IHC & IF images showing ARL6 staining
A05003 · IHCImmunohistochemistry of paraffin-embedded human prostate using ARL6 antibody at dilution of 1:100 .Perform microwave antigen retrieval with
A05003 · IHCImmunohistochemistry of paraffin-embedded human colon using ARL6 antibody at dilution of 1:100 .Perform microwave antigen retrieval with 10
HPA · Cerebral cortexHuman Protein Atlas IHC, Cerebral cortex. Source: https://www.proteinatlas.org/ENSG00000113966-ARL6/tissue/cerebral+cortex#imid_5111300
HPA · ColonHuman Protein Atlas IHC, Colon. Source: https://www.proteinatlas.org/ENSG00000113966-ARL6/tissue/colon#imid_5111234
HPA · LiverHuman Protein Atlas IHC, Liver. Source: https://www.proteinatlas.org/ENSG00000113966-ARL6/tissue/liver#imid_5111235
HPA · KidneyHuman Protein Atlas IHC, Kidney. Source: https://www.proteinatlas.org/ENSG00000113966-ARL6/tissue/kidney#imid_5111220
HPA · ICC-IF U2OSHuman Protein Atlas immunofluorescence, U2OS, antibody HPA019361; green = ARL6, blue = nucleus, red = microtubules.
HPA · ICC-IF U2OSHuman Protein Atlas immunofluorescence, U2OS, antibody HPA019361; green = ARL6, blue = nucleus, red = microtubules.
← swipe / scroll for more images →
Real IHC / IF data behind the staining-pattern expectations in this section.
Sample controls for ARL6 IHC & IF
🧪Run bronchus first: ciliated cells should show ciliary axonemal staining (HPA: High in bronchial ciliated cells). Use adipose tissue as a negative comparator (HPA: Not detected in adipocytes); on the bronchus slide, neighboring cells without cilia should lack an axonemal staining pattern, even if they show other staining.
Positive control tissue: Bronchus (Ciliated cells (cilia axoneme), HPA High)
Negative control tissue: Adipose tissue (HPA Not detected)
ICC-IF cell lines (HPA subcellular resource): HPA ICC-IF images show ARL6 in U2OS, ASC52telo, RPTEC/TERT1, hTERT-RPE1 (serum starved), with annotated localisation: Microtubules (uncertain), Primary cilium (supported) (HPA subcellular).
Technical controls: Include no-primary (secondary-only) and host-species- and clonality-matched isotype controls, plus an ARL6 knockout specimen or a peptide-block control if suitable material is available (standard IHC practice). Block endogenous peroxidase for chromogenic detection in bronchus, and assess endogenous biotin if using a biotin-based detection system (standard IHC practice).
⚠️Feasibility: A target-specific fixation window and fixation effect are unreported in the supplied evidence; the selected A05003 paraffin-section caption does not state a fixative (A05003 tissue-IHC caption). That caption uses microwave retrieval in 10 mM PBS, pH 7.2, with antibody at 1:100 on prostate, so retrieval dependence in bronchus remains unreported (A05003 tissue-IHC caption). IF may help resolve ciliary puncta (UniProt Q9H0F7: puncta flanking the axoneme; HPA: supported primary-cilium localization), while bronchial cilia require care in scoring because the expected signal occupies a narrow axonemal structure (HPA: High in ciliated-cell cilia axoneme); the supplied evidence does not establish that frozen sections are easier.
HPA tissue IHC evidence for ARL6
Comprehensive Human Protein Atlas IHC scoring per tissue (reliability: Approved — 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.
Positive expression · recommended positive controls
| Tissue | Cell type | Level | Evidence | Source |
|---|---|---|---|---|
| Bronchus | Ciliated cells (cilia axoneme) | High | Protein (IHC) | HPA → |
| Cerebral cortex | Neuronal cells | High | Protein (IHC) | HPA → |
| Duodenum | Glandular cells | High | Protein (IHC) | HPA → |
| Fallopian tube | Ciliated cells (cilia axoneme) | High | Protein (IHC) | HPA → |
| Kidney | Cells in tubules | High | Protein (IHC) | HPA → |
Undetected expression · recommended negative controls
| Tissue | Cell type | Level | Evidence | Source |
|---|---|---|---|---|
| Adipose tissue | Adipocytes | Not detected | Protein (IHC) | HPA → |
| Cervix | Glandular cells | Not detected | Protein (IHC) | HPA → |
| Prostate | Glandular cells | Not detected | Protein (IHC) | HPA → |
| Vagina | Squamous epithelial cells | Not detected | Protein (IHC) | HPA → |
Section 3
Advanced ARL6 IHC Tips
Troubleshoot ARL6 staining in paraffin sections by checking retrieval, compartment, tissue context and controls before comparing signal between samples.
How should I adjust retrieval when ARL6 staining is weak in paraffin sections?
Start with citrate buffer at pH 6.0, heated to 95–98 °C for 20 minutes, then cool sections before staining (page retrieval setting). If signal remains weak, test microwave retrieval in 10 mM PBS at pH 7.2 on adjacent sections; that condition accompanies the A05003 paraffin prostate image at 1:100 (A05003 image caption). Keep antibody dilution, detection time and section thickness constant while comparing retrieval conditions (standard IHC practice). Judge improvement by cleaner staining in the expected ciliary or cytoplasmic compartment, alongside a matched no-primary control, rather than by stronger color alone (HPA tissue IHC; UniProt Q9H0F7 localisation; standard IHC practice).
Could fixation explain inconsistent ARL6 staining across paraffin blocks?
ARL6-specific sensitivity to fixation is unknown from the supplied evidence; the A05003 prostate caption identifies paraffin embedding but does not state a fixative (A05003 image caption). Record each block’s fixative, fixation duration and processing history before attributing a difference to the antibody (standard IHC practice). Compare adjacent sections from blocks with known handling using one retrieval condition, one antibody dilution and the same chromogen development time (standard IHC practice). Include a reproducibly staining control section in each run, then assess whether the discrepancy follows block handling or persists across comparable samples (standard IHC practice).
Which ARL6 staining patterns should I expect in tissue sections?
Assess cilia, their bases and cytoplasm separately: ARL6 is assigned to the cilium membrane, axoneme and basal body, with puncta flanking the axoneme (UniProt Q9H0F7 localisation). HPA reports mainly cytoplasmic tissue staining with cilia positivity, including high staining of bronchial ciliated-cell axonemes (HPA tissue IHC). Inspect the apical border at high magnification and compare any discrete signal with an adjacent section stained for a ciliary marker (standard IHC practice). Because ARL6 has no annotated transmembrane segment, avoid interpreting a continuous plasma-membrane outline alone as proof of specific ARL6 staining (UniProt Q9H0F7 topology; standard IHC practice).
Can this IHC assay distinguish the two ARL6 isoforms?
UniProt lists 2 isoforms of ARL6, but the supplied A05003 caption does not map the antibody epitope or establish isoform discrimination (UniProt Q9H0F7 isoforms; A05003 image caption). Request the immunogen sequence and check which isoforms contain that region before making an isoform-specific claim (standard IHC practice). Compare staining after pH 6.0 citrate retrieval with a matched control section, since epitope accessibility can depend on processing and retrieval (page retrieval setting; standard IHC practice). Report the result as ARL6 immunoreactivity unless epitope mapping and an isoform-specific control support a narrower interpretation (standard IHC practice).
How can IF help check whether an IHC ciliary signal is ARL6?
On a separate IF preparation, multiplex ARL6 with a ciliary marker and a marker identifying the expected cell type; inspect whether signals occupy the same cilia or basal regions (UniProt Q9H0F7 localisation; standard IF practice). Choose fluorophores after checking tissue autofluorescence and reserve a spectrally separated channel for the weaker signal (standard IF practice). Match permeabilisation to the mapped epitope: access to a cytoplasmic-facing epitope may require permeabilisation, while an exposed extracellular epitope can be assessed without it (standard IF practice). The supplied evidence does not map this antibody’s epitope, so optimise permeabilisation with appropriate controls and do not transfer the A05003 paraffin retrieval condition directly to IF (A05003 image caption; standard IF practice).
What should I change if ARL6 DAB staining is diffuse or widespread?
First compare a no-primary section and inspect whether color follows tissue edges, folds or damaged areas rather than cilia or cytoplasm (HPA tissue IHC; standard IHC practice). For peroxidase-based detection, include a peroxidase block and evaluate endogenous enzyme signal in the no-primary control (standard IHC practice). Titrate the primary antibody and shorten chromogen development while keeping retrieval and detection reagents constant across comparison sections (standard IHC practice). The A05003 prostate image used 1:100, but HPA reports glandular prostate cells as not detected, so staining in that compartment needs particularly careful control-based interpretation (A05003 image caption; HPA tissue IHC).
How should I quantify ARL6 staining without conflating cilia and cytoplasm? ⚠ ANSWER MARKED FOR VERIFICATION
Define the compartment and eligible cell population before scoring, and score ciliary or basal signal separately from cytoplasmic signal (UniProt Q9H0F7 localisation; HPA tissue IHC). For cytoplasm, report the percentage of positive eligible cells and an H-score based on staining intensity; use identical thresholds across slides (standard IHC practice). For discrete ciliary profiles, report positive profiles per mm² or per counted ciliated cell, normalised to the sampled tissue area or eligible cell count (standard IHC practice). Exclude folds, edges and necrotic regions consistently, and document section thickness, retrieval and chromogen timing for every comparison (standard IHC practice).
When is ARL6 staining convincing rather than an artefact?
Favor signal in cilia, their basal region or cytoplasm when it recurs in anatomically comparable sections and is absent from the no-primary control (UniProt Q9H0F7 localisation; HPA tissue IHC; standard IHC practice). Bronchial ciliated-cell axonemes are reported as high, whereas prostate glandular cells are reported as not detected in HPA tissue IHC (HPA tissue IHC). Treat isolated nuclear-only color, edge staining, necrotic deposits and residual endogenous peroxidase as reasons to investigate specificity before scoring (standard IHC practice). The A05003 prostate image demonstrates staining under its reported conditions, but does not by itself resolve that disagreement with HPA’s prostate assessment (A05003 image caption; HPA tissue IHC).
Boster reagents
Best ARL6 / ADP-ribosylation factor-like protein 6 IHC Antibodies
Anti-ARL6 A05003 has real paraffin-section IHC images from human prostate, colon and liver-damage samples (A05003 image captions); catalog reactivity covers human and mouse (A05003 catalog).
Real IHC data
Anti-ARL6 Antibody
Cat # A05003
A05003 is listed for IHC and reacts with human and mouse samples (A05003 catalog). Its IHC images show paraffin-embedded human prostate, colon and liver-damage samples stained at 1:100 (A05003 image captions).
Which to pick: Choose A05003 for tissue IHC in paraffin sections; its captions document those sections and microwave retrieval in 10 mM PBS, pH 7.2, while the fixative is unreported (A05003 image captions). For cross-species work, A05003 lists human and mouse reactivity, but its supplied IHC images show human samples only (A05003 catalog; A05003 image captions). No IF/ICC application or IF image is supplied for A05003, so this payload does not support an IF/ICC recommendation (A05003 catalog).
Each figure is that product's own IHC / IF validation image from its datasheet.
References
- UniProt Consortium. UniProt entry Q9H0F7 (ARL6_HUMAN, ADP-ribosylation factor-like protein 6).
- Human Protein Atlas. ARL6 tissue IHC expression (reliability: Approved).
- Human Protein Atlas. ARL6 subcellular location (ICC-IF): Mainly localized to the microtubules and primary cilium. In addition localized to the nucleoplasm, cytosol and primary cilium tip..
- Human Protein Atlas. ARL6 antibody validation summary (1 antibodies).
- Small GTPase Arl6 controls RH30 rhabdomyosarcoma cell growth through ciliogenesis and Hedgehog signaling. Cell & bioscience 2016 — PMC5154108.
- Identification and functional analysis of the vision-specific BBS3 (ARL6) long isoform. PLoS genetics 2010 — PMC2841623.
- PubMed PMID:11230166 — UniProt-cited evidence.
- PubMed PMID:14702039 — UniProt-cited evidence.
- PubMed PMID:16641997 — UniProt-cited evidence.
Immunohistochemistry protocol sheet for ARL6 (ADP-ribosylation factor-like protein 6). Expected localisation Mainly cytoplasmic, with ciliary axoneme staining (HPA tissue IHC). Antigen retrieval: Citrate pH 6.0 HIER, 95–98 °C, 20 min (rule: cytoplasmic / membrane antigen). Validated IHC antibody: A05003 at 1:50-1:100 (the product's own IHC validation image is shown). Controls (HPA): positive Bronchus (Ciliated cells (cilia axoneme)); negative Adipose tissue. IHC workflow; specimen preparation unspecified. Protocol steps: 1. Sample: Paraffin-embedded human prostate tissue; fixative not specified (datasheet A05003); 2. Fixation: Image fixative and duration unreported (datasheet A05003); 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-induced epitope retrieval in citrate buffer, pH 6.0 , 20 min at 95–98 °C…; 6. Peroxidase block: 3% H2O2, 10 min , room temperature (standard); 7. Blocking: 10% normal serum of the secondary host, 30 min , room temperature (standard); 8. Primary antibody: Rabbit anti-ARL6, 1:50-1:100 (datasheet A05003); 9. Primary incubation: Overnight at 4 °C (standard). Watch for: Fixation: Keep formalin fixation consistent across paraffin sections. (standard IHC practice; not target-specific); Caveat: Staining and RNA show only medium consistency (HPA tissue IHC); Isoform / epitope: 2 isoforms; no transmembrane segment; epitope coverage unknown (UniProt; datasheet); Regulation: No staining-linked regulation annotated (UniProt). Evidence: UniProt Q9H0F7, HPA tissue IHC · Approved, HPA ICC-IF · Mainly localized to the microtubules and primary cilium. In addition…, Datasheet A05003, PMC5154108. QR code links to https://www.bosterbio.com/bosterbio-gene-info-cards/ARL6/immunohistochemistry-ihc-guide.