SLC39A6 / Zinc transporter ZIP6 · IHC design guide

Design Immunohistochemistry for SLC39A6

Plan paraffin-section IHC for SLC39A6 with the catalog antibody starting at 2.5 μg/mL (datasheet). Compare the observed cytoplasmic pattern with HPA tissue staining, while considering ZIP6’s membrane localization when interpreting signal (HPA tissue IHC; UniProt).

Evidence assembled Oct 2026 · For research use; verify linked source records and product datasheet before use
Immunohistochemistry protocol sheet for SLC39A6 (IHC for SLC39A6): expected localisation Cytoplasmic staining (HPA tissue IHC); membrane localization expected (UniProt), antibody A05693, validated IHC image, and IHC protocol steps
Printable SLC39A6 IHC protocol sheet — expected localisation Cytoplasmic staining (HPA tissue IHC); membrane localization expected (UniProt), antibody A05693, controls and protocol steps. Open the full SLC39A6 IHC guide →

SLC39A6 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 Cytoplasmic staining (HPA tissue IHC); membrane localization expected (UniProt)
Staining pattern General cytoplasmic staining; nuclear staining in some tissues (HPA tissue IHC)
Antigen retrieval Citrate pH 6.0 HIER, 95–98 °C, 20 min (rule: cytoplasmic / membrane antigen)
Positive control ⓘ Adrenal gland+4 more · see all
Negative control ⓘ Appendix+4 more · see all
Important caveats
Reasons your staining may differ from the expected pattern.
Fixation Keep formalin fixation consistent across sections (standard IHC practice; not target-specific); Matched tissue-IHC evidence does not establish the fixation claim. Validate the specimen-specific method before use. (selected-SKU IHC image A05693)
Caveat Placenta: high expression reported, but trophoblast IHC is absent (UniProt; HPA tissue IHC)
Regulation TCR activation recruits ZIP6 to the synapse (UniProt)
Isoform / epitope 2 isoforms; check whether the epitope is extracellular or cytoplasmic (UniProt)
Section 1

Recommended SLC39A6 IHC & IF Protocols

Compare the catalog antibody’s IHC-P protocol with published SLC39A6 tissue protocols (PMC8505289; PMC4595240; PMC8771636).

Recommended immunohistochemistry (IHC-P) protocol parameters
SampleTissue sections; selected-image fixative not specified (standard IHC workflow)
FixationImage fixative and duration unreported (datasheet A05693); verify before use.
Sectioning4–5 µm sections on charged slides (standard)
DeparaffinisationXylene, graded ethanol series to water (standard)
Antigen retrievalHeat-induced epitope retrieval in citrate buffer, pH 6.0, 20 min at 95–98 °C (standard rule: cytoplasmic / membrane antigen)
Peroxidase block3% H2O2, 10 min, room temperature (standard)
Blocking10% normal serum of the secondary host, 30 min, room temperature (standard)
Primary antibodyRabbit anti-SLC39A6, 2.5 μg/mL (datasheet A05693)
Primary incubationOvernight at 4 °C (standard)
DetectionHRP-polymer secondary, DAB chromogen 5–10 min (standard)
CounterstainHematoxylin, blue, dehydrate and mount (standard)
Expected resultSLC39A6-positive staining in glandular cells of adrenal gland (HPA tissue IHC: High). HPA tissue profile: General cytoplasmic expression. Additional nuclear expression in several tissues. No signal in the no-primary control.
💡Decision noteStart with citrate pH 6.0 HIER at 95–98 °C for 20 min (page retrieval); published alternatives include microwave citrate (PMC8505289) and autoclaved EDTA (PMC4595240).
Section 2

What Is the Expected SLC39A6 Staining Pattern?

SLC39A6 is a six-pass membrane protein found at the cell membrane, including lamellipodia and membrane rafts (UniProt Q13433 topology/localization). In tissue IHC, expect predominantly cytoplasmic staining, with additional nuclear staining in some tissues (HPA: tissue IHC profile). Signal should follow the identified cell population: for example, adrenal glandular cells, fallopian tube non-ciliated cells and nasopharyngeal basal cells stain High (HPA: tissue IHC). HPA rates tissue staining Approved, with medium consistency against RNA data (HPA: reliability).

What am I looking at on my slide?
Cytoplasmic staining in adrenal glandular cells, fallopian tube non-ciliated cells or nasopharyngeal basal cells.This matches HPA's general cytoplasmic profile and its High calls for those cell populations (HPA: tissue IHC). A membrane component is biologically plausible for a six-pass transporter (UniProt Q13433 topology), but HPA's tissue profile does not require a crisp membrane outline in every positive cell.
A membrane rim or polarized membrane signal accompanies cytoplasmic staining.This is compatible with cell membrane localization (UniProt Q13433 localization). Judge it alongside the tissue's named cell type and HPA pattern; membrane signal alone does not validate antibody specificity. UniProt describes apical localization in choroid plexus epithelial cells by similarity, so that detail is an inference, not a demonstrated tissue IHC benchmark (UniProt Q13433 localization).
Strong, exclusively nuclear staining dominates many cells, with little cytoplasmic signal.Treat this as a pattern requiring investigation, since HPA reports general cytoplasmic staining and additional nuclear expression in several tissues (HPA: tissue IHC profile). Nuclear signal alone is therefore not proof of artefact. Compare the affected cell types and controls before assigning a cause; HPA's ICC-IF nucleoplasm call is uncertain (HPA: subcellular).
Staining appears in a cell population that HPA lists as Not detected, such as lung alveolar cells.This conflicts with the stated cell-level IHC observation (HPA: lung alveolar cells, Not detected). Check morphology and detection controls: cross-reactivity or endogenous detection activity are possible general IHC explanations, not established causes for this specimen. A Not detected call is specific to the listed cells and assay, not every cell in the organ.
No signal appears in an expected High population, such as adrenal glandular cells.The result conflicts with an HPA High tissue IHC call (HPA: adrenal glandular cells). First check that the expected cells are present and that the IHC run and counterstain are interpretable; then review antibody and detection conditions (general IHC practice). HPA's Approved rating has medium RNA concordance, so one negative slide cannot establish absent SLC39A6 (HPA: reliability).
💡Expected SLC39A6 appearanceCall a convincing positive when the named cells show cytoplasmic signal, potentially with a membrane component—especially High adrenal glandular, fallopian tube non-ciliated or nasopharyngeal basal cells (HPA: tissue IHC; UniProt Q13433 localization); widespread staining outside those cells or in a listed Not detected population needs controls before it is accepted as specific (HPA: tissue IHC; general IHC practice).
How each factor affects the staining
Cell identity and tissue choiceHPA's calls are cell specific: adrenal glandular, fallopian tube non-ciliated and nasopharyngeal basal cells are High, while lung alveolar and placental trophoblastic cells are Not detected (HPA: tissue IHC). Confirm the scored cell population by morphology; do not generalize a cell-level call to the whole organ (general IHC practice).
Subcellular interpretationSix transmembrane segments and extracellular and cytoplasmic regions support membrane localization (UniProt Q13433 topology). HPA tissue IHC nonetheless describes general cytoplasmic expression with nuclear staining in several tissues (HPA: tissue IHC profile). Record compartments separately when scoring; a membrane-only requirement would discard part of the observed IHC pattern.
Evidence and antibody validationHPA rates tissue IHC Approved with medium consistency between staining and RNA expression (HPA: reliability). HPA042377 is IHC Approved but ICC Uncertain (HPA: antibody validation). These ratings support a cautious tissue IHC reference; they do not establish that every observed compartment or positive cell on a new slide is specific.
Epitope placementSLC39A6 has extracellular and cytoplasmic regions (UniProt Q13433 topology), but the supplied record gives no epitope for the IHC-validated antibody. Antigen retrieval may be optimized as a general paraffin-IHC step (general IHC practice); these sources do not show a target-specific retrieval or fixation effect, so neither can explain a failed stain on its own.
Expression source and tissue discrepancyUniProt reports high expression in placenta, while HPA lists placental trophoblastic cells as Not detected by tissue IHC (UniProt Q13433 tissue specificity; HPA: placenta trophoblastic cells). The statements cover different evidence and cell resolution. Do not make trophoblast a mandatory positive control or infer a fixation effect from the discrepancy.
Why is my staining missing, weak or wrong?
SituationLikely causeNext action
Expected High cells show no chromogenic signal.Possible assay failure or an unrecognized cell population; HPA lists those cells as High but reports only medium RNA concordance (HPA: tissue IHC; HPA: reliability).Check section morphology and the expected cells, then review the IHC-validated antibody, retrieval, detection reagents and a working positive control (general IHC practice). Avoid calling the target absent from this slide alone.
Diffuse color covers cells and surrounding tissue.Nonspecific binding, inadequate blocking or washout, or endogenous detection activity are general IHC possibilities (general IHC practice); HPA's cytoplasmic profile does not establish a cause (HPA: tissue IHC profile).Inspect a no-primary control, blocking and wash steps, and the chromogen or secondary detection controls; score only cell-associated signal after background is resolved (general IHC practice).
Staining is predominantly nuclear across many cell types.HPA allows nuclear expression in several tissues, but its overall tissue profile is cytoplasmic; the ICC-IF nucleoplasm assignment is uncertain (HPA: tissue IHC profile; HPA: subcellular).Compare nuclear and cytoplasmic signal within the specified cell populations, inspect controls, and report the pattern rather than automatically marking all nuclear color positive or artefactual (general IHC practice).
A listed Not detected cell population stains strongly.Possible cross-reactivity, endogenous detection activity or cell misidentification (general IHC practice); the result disagrees with HPA's cell-specific call (HPA: tissue IHC).Recheck morphology and the exact HPA cell designation, then review no-primary and detection controls before assigning specificity (general IHC practice).
Placental trophoblastic cells are negative despite UniProt's high placental expression.HPA reports trophoblastic cells Not detected by IHC, whereas UniProt describes expression at the tissue level (HPA: placenta trophoblastic cells; UniProt Q13433 tissue specificity). The supplied sources do not resolve that difference.Keep the trophoblast result cell specific and select an HPA High cell population to assess assay performance; do not attribute the difference to fixation or retrieval without evidence (HPA: tissue IHC; general IHC practice).
Can the tissue IHC result determine the expected IF/ICC pattern?HPA's ICC-IF summary places SLC39A6 mainly in cytosol (uncertain), additionally in nucleoplasm (uncertain) and plasma membrane (supported); HPA042377 is ICC Uncertain (HPA: subcellular; HPA: antibody validation).Use the separate IF/ICC guide for assay design. Treat the membrane call as supported and the cytosol and nucleoplasm calls as uncertain; do not transfer tissue IHC validation or its chromogenic appearance directly to IF/ICC (HPA: subcellular; HPA: antibody validation).

Sample controls for SLC39A6 IHC & IF

🧪Run fallopian tube first and look for staining in non-ciliated cells (High; HPA: fallopian tube). Use appendix glandular cells as the negative tissue (Not detected; HPA: appendix); on the positive slide, treat adjacent cells without specific staining as internal background comparators, without assuming that any other cell type is biologically negative.
Positive control tissue: Adrenal gland (Glandular cells, HPA High)
Negative control tissue: Appendix (HPA Not detected)
ICC-IF cell lines (HPA subcellular resource): HPA ICC-IF images show SLC39A6 in A-431, U-251MG, U2OS, with annotated localisation: Cytosol (uncertain) (HPA subcellular).
Technical controls: Include a no-primary (secondary-only) control and an isotype control matched to the primary antibody’s host species and immunoglobulin class; use SLC39A6 knockout material as a biological negative where available. For chromogenic IHC, block endogenous peroxidase and check the fallopian tube lumen for deposited chromogen that could be mistaken for cellular staining.
⚠️Feasibility: A target-specific fixation window and antigen-retrieval dependency are unreported in the supplied evidence; the selected A05693 mouse-lung IHC caption also leaves the fixative unreported (catalog caption: A05693). HPA has ICC-IF images for A-431, U-251MG and U2OS (HPA: subcellular), but the supplied evidence does not establish that frozen sections or IF are easier than paraffin IHC. In fallopian tube, score signal within non-ciliated cells and exclude staining confined to luminal debris or ciliary edges (HPA: High in non-ciliated cells; standard IHC scoring practice).

HPA tissue IHC evidence for SLC39A6

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

TissueCell typeLevelEvidenceSource
Adrenal gland Glandular cells High Protein (IHC) HPA →
Endometrium Glandular cells Medium Protein (IHC) HPA →
Fallopian tube Non-ciliated cells High Protein (IHC) HPA →
Nasopharynx Basal cells High Protein (IHC) HPA →
Bronchus Ciliated cells (cell body) Medium Protein (IHC) HPA →

Undetected expression · recommended negative controls

TissueCell typeLevelEvidenceSource
Appendix Glandular cells Not detected Protein (IHC) HPA →
Caudate Glial cells Not detected Protein (IHC) HPA →
Lung Alveolar cells Not detected Protein (IHC) HPA →
Lymph node Germinal center cells Not detected Protein (IHC) HPA →
Ovary Follicle cells Not detected Protein (IHC) HPA →
Section 3

Advanced SLC39A6 IHC Tips

Troubleshoot ZIP6 staining by checking retrieval, cell identity and compartment, then score signal against appropriate tissue controls (UniProt Q13433; HPA tissue IHC).

How should I retrieve ZIP6 in paraffin sections when staining is weak?
Start with citrate pH 6.0 heat-induced retrieval at 95–98 °C for 20 min (page retrieval setting). Let sections cool in retrieval buffer before washing, and keep heating and cooling consistent across comparison slides (standard IHC practice). ZIP6 has an extracellular region spanning residues 29–325 and 6 transmembrane segments, so accessibility may depend on the antibody’s unknown epitope (UniProt Q13433 topology). If signal remains weak, test a different retrieval condition on matched sections alongside the starting condition, recording background and cell-compartment changes (standard IHC practice). Do not attribute improvement to a particular ZIP6 epitope without an epitope map (UniProt Q13433 topology; standard IHC practice).
Could fixation explain weak or patchy ZIP6 staining?
Target-specific ZIP6 sensitivity to fixation is unknown from the supplied evidence; the mouse lung caption gives no fixative (A05693 tissue-IHC caption). Record fixation method, duration and time before fixation for each paraffin specimen, then compare sections processed and stained together (standard IHC practice). If archival samples differ in these variables, treat intensity differences cautiously and include a control section from the same processing batch (standard IHC practice). Keep citrate pH 6.0 retrieval at 95–98 °C for 20 min constant while investigating fixation as a variable (page retrieval setting). Neither the HPA staining pattern nor ZIP6 topology establishes a ZIP6-specific fixation effect (HPA tissue IHC; UniProt Q13433 topology).
Should ZIP6 staining be membranous or cytoplasmic?
Evaluate membrane and cytoplasmic signal separately: UniProt places ZIP6 at the cell membrane, including lamellipodial and apical membranes (UniProt Q13433 subcellular). HPA tissue IHC describes general cytoplasmic staining with additional nuclear staining in several tissues, while its cell-based data support plasma-membrane localisation (HPA tissue IHC; HPA subcellular). The HPA cytosol and nucleoplasm assignments are marked uncertain, so nuclear-only staining deserves closer review (HPA subcellular). Compare the same cell type across matched sections, checking whether apparent membrane signal follows cell borders rather than section folds or edges (standard IHC practice). Record each compartment’s intensity independently instead of combining them into one ZIP6 score (standard IHC practice).
How could epitope position alter ZIP6 staining?
ZIP6 has 2 annotated isoforms, but the supplied antibody caption does not identify its epitope or establish isoform selectivity (UniProt Q13433 isoforms; A05693 tissue-IHC caption). The precursor carries a signal peptide at residues 1–28, and the annotated chain spans 29–755 (UniProt Q13433 processing). Several extracellular regions and cytoplasmic loops flank its 6 transmembrane segments, making epitope position relevant when interpreting accessibility (UniProt Q13433 topology; standard IHC practice). Five glycosylation sites are annotated, including residues 67 and 684, but their effect on this antibody’s staining is unestablished (UniProt Q13433 glycosylation; A05693 tissue-IHC caption). Request an epitope map before claiming isoform-specific or modification-dependent IHC staining (standard IHC practice).
How can I compare ZIP6 fluorescence with chromogenic IHC?
Treat IF as a separate assay and first establish whether its ZIP6 signal agrees with cell identity and compartment findings in chromogenic sections (standard IF and IHC practice). Multiplex with a validated marker for the expected cell type; for example, HPA reports high ZIP6 staining in fallopian-tube non-ciliated cells (HPA tissue IHC; standard IF practice). Choose a far-red fluorophore when tissue autofluorescence interferes with shorter wavelengths, and inspect unstained controls in every acquisition channel (standard IF practice). If the antibody epitope is intracellular, titrate mild permeabilisation; if extracellular, compare with an unpermeabilised condition to preserve localisation (UniProt Q13433 topology; standard IF practice). The supplied caption documents tissue IHC at 5 µg/mL, not an IF protocol (A05693 tissue-IHC caption).
What should I check when ZIP6 staining is widespread?
Check a no-primary control for detection-system background and review tissue edges, folds and damaged areas before assigning widespread color to ZIP6 (standard chromogenic IHC practice). Block endogenous peroxidase before DAB development and use an appropriate protein block; these are general workflow steps, not ZIP6-specific validation (standard chromogenic IHC practice). The A05693 caption reports mouse lung staining at 5 µg/mL, whereas HPA reports no detection in lung alveolar cells (A05693 tissue-IHC caption; HPA tissue IHC). Those observations refer to different evidence sets and do not establish that every lung cell should stain (A05693 tissue-IHC caption; HPA tissue IHC). Compare defined cell populations and a no-primary section before adjusting antibody concentration or detection time (standard IHC practice).
How should I score ZIP6 across paraffin sections? ⚠ ANSWER MARKED FOR VERIFICATION
Define the cell population and membrane, cytoplasmic or nuclear compartment before scoring; mixed compartments can conceal a change in distribution (UniProt Q13433 subcellular; HPA tissue IHC; standard IHC practice). For each compartment, record percent positive cells and intensity grades 0–3, then calculate an H-score on the 0–300 scale (standard IHC scoring practice). Alternatively, report positive-cell density per mm² when cell abundance is the outcome, using a consistent region-of-interest rule (standard IHC scoring practice). Normalise positive-cell counts to all evaluable cells of the specified type, and exclude folds, necrosis and absent tissue from the denominator (standard IHC practice). Keep staining batches, exposure to chromogen and scoring thresholds consistent across groups (standard IHC practice).
How do I distinguish convincing ZIP6 staining from artefact?
Look for reproducible staining in the expected cell population and a plausible compartment, with a clean no-primary control and intact tissue morphology (UniProt Q13433 subcellular; standard IHC practice). HPA reports high staining in adrenal glandular cells and fallopian-tube non-ciliated cells, but no detection in lung alveolar cells (HPA tissue IHC). Its general cytoplasmic and occasional nuclear pattern means nuclear signal alone needs corroboration, while plasma-membrane localisation has supporting cell-based evidence (HPA tissue IHC; HPA subcellular). Be skeptical of signal confined to section edges, necrotic regions or areas retaining endogenous enzyme activity, and repeat those fields on another section (standard chromogenic IHC practice). Do not infer zinc transport activity or EMT from DAB intensity alone (UniProt Q13433 function; standard IHC interpretation).
Boster reagents

Best SLC39A6 / Zinc transporter ZIP6 IHC Antibodies

A05693 is listed for IHC-P and IF in human and mouse (catalog: applications and reactivity), with IHC and IF images from mouse lung tissue (image captions).

Real IHC data Immunohistochemistry of ZIP6 in mouse lung tissue with ZIP6 antibody at 5 μg/mL.
Anti-ZIP6 SLC39A6 Antibody
Cat # A05693

A05693 will render with a mouse lung IHC image at 5 μg/mL (IHC image caption). The catalog also lists IF and shows a mouse lung IF image at 20 μg/mL (catalog: applications; IF image caption).

Which to pick: For paraffin-section tissue IHC, choose A05693 (catalog: IHC-P); its mouse lung IHC image reports 5 μg/mL, while the fixative is unreported (IHC image caption). For IF, choose A05693 (catalog: IF; IF image caption: mouse lung); ICC validation is unreported (catalog: applications). For work across human and mouse samples, A05693 lists both species (catalog: reactivity), though the supplied images show mouse tissue only (IHC and IF image captions); clonality is unreported (catalog: clone).

Each figure is that product's own IHC / IF validation image from its datasheet.

References

  1. UniProt Consortium. UniProt entry Q13433 (S39A6_HUMAN, Zinc transporter ZIP6).
  2. Human Protein Atlas. SLC39A6 tissue IHC expression (reliability: Approved).
  3. Human Protein Atlas. SLC39A6 subcellular location (ICC-IF): Mainly localized to the cytosol. In addition localized to the nucleoplasm and plasma membrane..
  4. Human Protein Atlas. SLC39A6 antibody validation summary (1 antibodies).
  5. Oestrogen-regulated protein SLC39A6: a biomarker of good prognosis in luminal breast cancer. Breast cancer research and treatment 2021 — PMC8505289.
  6. Involvement of SLC39A6 in gastric adenocarcinoma and correlation of the SLC39A6 polymorphism rs1050631 with clinical outcomes after resection. BMC cancer 2019 — PMC6839152.
  7. SLC39A6: a potential target for diagnosis and therapy of esophageal carcinoma. Journal of translational medicine 2015 — PMC4595240.
  8. Role of SLC39A6 in the development and progression of liver cancer. Oncology letters 2022 — PMC8771636.
  9. PubMed PMID:14702039 — UniProt-cited evidence.
  10. PubMed PMID:16177791 — UniProt-cited evidence.
  11. PubMed PMID:15489334 — UniProt-cited evidence.