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SLC39A9 / Zinc transporter ZIP9 · IHC design guide
Design Immunohistochemistry for SLC39A9
Plan chromogenic SLC39A9 IHC-P around the general cytoplasmic tissue pattern and the cell types with high staining (HPA tissue IHC). A catalog image of human brain uses 2.5 μg/mL as a starting antibody concentration (datasheet: A13097-2).
Evidence assembled Oct 2026 · For research use; verify linked source records and product datasheet before use
SLC39A9 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 | General cytoplasmic tissue staining (HPA tissue IHC) | |
| Staining pattern | Cytoplasmic staining in glandular, neuronal and endothelial cells (HPA tissue IHC) | |
| Antigen retrieval | Tris-EDTA pH 9.0 HIER, 95–98 °C, 20 min (rule: nuclear antigen) | |
| 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 paraffin sections (standard IHC practice; not target-specific); optimize empirically. | |
| Caveat | Smooth muscle and marrow cells show low staining (HPA tissue IHC) | |
| Regulation | Expression regulation is not specified (UniProt) | |
| Isoform / epitope | 3 isoforms; extracellular versus cytoplasmic epitope access may differ (UniProt) |
Section 1
Recommended SLC39A9 IHC & IF Protocols
Compare the catalog antibody’s IHC-P protocol with two published SLC39A9 tissue protocols (PMC11212825; PMC8977092).
| Sample | Tissue sections; selected-image fixative not specified (standard IHC workflow) |
| Fixation | Image fixative and duration unreported (datasheet A13097-2); 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 Tris-EDTA buffer, pH 9.0, 20 min at 95–98 °C (standard rule: nuclear 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-SLC39A9, 2.5 μg/mL (datasheet A13097-2) |
| 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 | SLC39A9-positive staining in glandular cells of adrenal gland (HPA tissue IHC: High). HPA tissue profile: General cytoplasmic expression. No signal in the no-primary control. |
💡Decision noteStart with Tris-EDTA HIER at pH 9.0, 95–98 °C for 20 min (page retrieval); compare acidic citrate retrieval for ovarian sections (PMC11212825).
Section 2
What Is the Expected SLC39A9 Staining Pattern?
SLC39A9 is an 8-pass membrane protein annotated at the trans-Golgi network, cell membrane and other sites (UniProt Q9NUM3 topology; UniProt Q9NUM3 subcellular). In tissue IHC, expect chiefly cytoplasmic staining, including strong staining in glandular and selected epithelial, neuronal and endothelial cells (HPA: general cytoplasmic expression; HPA: High in listed cell types). HPA rates its tissue staining Approved, meaning antibody staining is consistent with RNA data but awaits external verification (HPA: Approved).
| Cytoplasmic brown signal in adrenal, appendix, breast or duodenal glandular cells. | This fits the reported IHC profile: HPA records High staining in those glandular cells and describes overall expression as cytoplasmic (HPA: High in glandular cells; HPA: general cytoplasmic expression). Compare staining within the relevant cells, rather than treating every cell in the section as an equivalent positive. |
| Signal is confined to extracellular material, with little staining inside the expected cells. | That distribution does not fit the reported cytoplasmic IHC profile or the annotated membrane-associated locations (HPA: general cytoplasmic expression; UniProt Q9NUM3 subcellular). Check section deposits and detection artefacts before interpreting it as SLC39A9. A punctate intracellular pattern alone is not a failure of localisation. |
| Strong staining appears chiefly in smooth muscle or bone marrow hematopoietic cells. | HPA reports Low staining in these cells, so a dominant signal warrants scrutiny (HPA: Low in smooth muscle cells; HPA: Low in hematopoietic cells). Review morphology and background controls for cross-reactivity or endogenous detection activity. Low is not a validated absence of protein. |
| Brown colour spreads across cells, stroma and blank areas without cellular boundaries. | A diffuse deposit cannot be scored as the reported cell-associated cytoplasmic pattern (HPA: general cytoplasmic expression). In routine chromogenic IHC, uneven reagent coverage, insufficient washing or detection background can produce this appearance; assess a no-primary control alongside the section. |
| No cellular signal appears in a section expected to show strong staining. | First verify that the section contains the relevant cells: HPA reports High staining in bronchial respiratory epithelium, cerebellar Purkinje cells and cortical neurons, among others (HPA: High in listed cell types). A blank result may reflect the run or specimen; HPA tissue levels do not establish SLC39A9-specific fixation sensitivity. |
💡Expected SLC39A9 appearanceCall a section positive when identifiable cells show predominantly cytoplasmic brown staining, potentially strong in HPA-listed High cell types; colour spread through extracellular space or blank areas is suspect (HPA: general cytoplasmic expression; HPA: High in listed cell types).
| Which cells serve as comparison points? | HPA records High staining in several glandular populations, bronchial respiratory epithelium, Purkinje cells, cortical neurons and colon endothelial cells (HPA: tissue IHC). Smooth muscle and bone marrow hematopoietic cells are Low comparators, not confirmed negatives (HPA: Low in listed cell types; HPA: no negative tissues listed). |
| How far does the antibody evidence extend? | The tissue IHC antibody HPA007921 is Approved, and HPA reports consistency with RNA data pending external verification (HPA: HPA007921 IHC Approved; HPA: reliability description). This supports an expected pattern, but does not make an unexpected stain specific by itself. |
| What does protein topology tell us? | SLC39A9 has 8 annotated transmembrane segments and no annotated signal peptide or propeptide (UniProt Q9NUM3 topology; UniProt Q9NUM3 processing). Topology supports a membrane-associated interpretation; without an antibody epitope map, it does not specify retrieval conditions or predict whether a given stain will succeed. |
| Do variants or modifications change the call? | UniProt lists 3 isoforms and glycosylation sites at residues 29 and 241 (UniProt Q9NUM3 isoforms; UniProt Q9NUM3 glycosylation). The supplied record does not link those features to this antibody's epitope or to a distinct tissue IHC pattern. |
| IF/ICC: What localisation should I compare? | HPA reports approved endoplasmic reticulum localisation by ICC-IF, while UniProt also annotates Golgi, cell membrane, perinuclear cytoplasm, mitochondrion and nucleus (HPA: subcellular ICC-IF; UniProt Q9NUM3 subcellular). Interpret IF on its own guide page; these records do not establish an IF protocol or require tissue IHC to resolve individual organelles. |
| Situation | Likely cause | Next action |
|---|---|---|
| Expected glandular or epithelial cells remain unstained. | The section may lack intact target cells, or an IHC workflow step may have failed; HPA reports High staining in specific cell populations, not in every field (HPA: tissue IHC). | Confirm cell identity on the counterstain, then check a known staining section and the run controls. Review retrieval, primary incubation and detection as general IHC workflow checks; do not infer SLC39A9-specific fixation failure. |
| Only a fine perinuclear or punctate cytoplasmic pattern is visible. | The recorded tissue pattern is broadly cytoplasmic, and UniProt annotates trans-Golgi and perinuclear locations (HPA: general cytoplasmic expression; UniProt Q9NUM3 subcellular). | Score signal in identifiable cells and compare it with the HPA tissue pattern. Do not reject intracellular puncta solely because the IHC image cannot resolve their organelle. |
| A smooth muscle or marrow field looks more intense than the expected positive cells. | Those cell types are reported Low, so the contrast is discordant with the HPA tissue observations (HPA: Low in smooth muscle cells; HPA: Low in hematopoietic cells). | Check tissue identity and a no-primary control for endogenous or detection signal; review antibody specificity before calling the discordant cells positive. |
| The entire section has brown haze. | Uniform haze obscures the reported cytoplasmic cellular pattern (HPA: general cytoplasmic expression). In chromogenic IHC, nonspecific detection signal or insufficient washing can contribute. | Compare the no-primary control and inspect reagent coverage. Optimize washing or detection conditions as general IHC practice, then reassess identifiable cells. |
| Signal appears only as extracellular deposits. | This location conflicts with HPA's cytoplasmic tissue profile and UniProt's annotated cellular locations (HPA: general cytoplasmic expression; UniProt Q9NUM3 subcellular). | Inspect the section for precipitate or damaged areas, review the detection control, and repeat interpretation in intact cells before assigning SLC39A9 staining. |
| IHC looks cytoplasmic, but an ICC-IF reference looks reticular. | HPA describes tissue IHC broadly as cytoplasmic and its ICC-IF localisation as endoplasmic reticulum; the methods resolve different levels of detail (HPA: tissue IHC profile; HPA: subcellular ICC-IF). | Use the tissue cell-type and cytoplasmic criteria for this IHC readout. Consult the separate IF/ICC guide for fluorescence localisation; do not force a fine organelle assignment from chromogenic tissue IHC. |
Experiment evidence
IHC & IF images showing SLC39A9 staining
A13097-2 · IHCImmunohistochemistry of ZIP9 in human brain tissue with ZIP9 antibody at 2.5 μg/mL.
A13097-2 · IFImmunofluorescence of ZIP9 in human brain tissue with ZIP9 antibody at 20 μg/mL.
HPA · Cerebral cortexHuman Protein Atlas IHC, Cerebral cortex. Source: https://www.proteinatlas.org/ENSG00000029364-SLC39A9/tissue/cerebral+cortex#imid_2740500
HPA · ColonHuman Protein Atlas IHC, Colon. Source: https://www.proteinatlas.org/ENSG00000029364-SLC39A9/tissue/colon#imid_2740442
HPA · LiverHuman Protein Atlas IHC, Liver. Source: https://www.proteinatlas.org/ENSG00000029364-SLC39A9/tissue/liver#imid_2740435
HPA · KidneyHuman Protein Atlas IHC, Kidney. Source: https://www.proteinatlas.org/ENSG00000029364-SLC39A9/tissue/kidney#imid_2740436
HPA · ICC-IF A-431Human Protein Atlas immunofluorescence, A-431, antibody HPA075390; green = SLC39A9, blue = nucleus, red = microtubules.
HPA · ICC-IF A-431Human Protein Atlas immunofluorescence, A-431, antibody HPA075390; green = SLC39A9, blue = nucleus, red = microtubules.
← swipe / scroll for more images →
Real IHC / IF data behind the staining-pattern expectations in this section.
Sample controls for SLC39A9 IHC & IF
🧪Run adrenal gland first and assess its glandular cells, which HPA scores High (HPA: adrenal gland, glandular cells High). HPA detects SLC39A9 in all 45 scored tissues, so use no-primary and isotype controls instead of a negative tissue; any cells considered internally negative should show only background chromogen, but no such cell population is validated by the supplied evidence (HPA: no negative tissue rows).
Positive control tissue: Adrenal gland (Glandular cells, HPA High)
Negative control tissue: None in HPA: SLC39A9 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 SLC39A9 in A-431, A-549, U2OS, with annotated localisation: Endoplasmic reticulum (approved) (HPA subcellular).
Technical controls: Include a no-primary, secondary-only slide and an isotype control matched to the primary antibody’s host species and clonality; confirm specificity with a knockout specimen or peptide block where available (standard IHC practice). For adrenal gland, quench endogenous peroxidase and distinguish native pigment from chromogenic staining (standard IHC practice).
⚠️Feasibility: A target-specific fixation window or fixation effect is unreported, and the selected A13097-2 brain IHC caption does not state a fixative (selected SKU caption: fixative not stated). Test antigen retrieval empirically for paraffin sections; the supplied evidence does not establish that frozen sections or IF are easier (standard IHC practice; HPA: ICC-IF images available). In adrenal sections, native pigment can complicate chromogen interpretation (standard IHC practice).
HPA tissue IHC evidence for SLC39A9
Comprehensive Human Protein Atlas IHC scoring per tissue (reliability: Approved — High consistency between antibody staining and RNA expression data. Pending external verification.). 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 → |
| Breast | Glandular cells | High | Protein (IHC) | HPA → |
| Bronchus | Respiratory epithelial cells | High | Protein (IHC) | HPA → |
| Cerebellum | Purkinje cells | High | Protein (IHC) | HPA → |
Undetected expression · recommended negative controls
| Tissue | Cell type | Level | Evidence | Source |
|---|---|---|---|---|
| None in HPA: SLC39A9 is detected in all 45 scored tissues. Use a no-primary (secondary-only) and an isotype control instead. | ||||
Section 3
Advanced SLC39A9 IHC Tips
Troubleshoot SLC39A9 staining by checking retrieval, compartment pattern, cell identity and controls before comparing chromogenic IHC scores.
How should I retrieve SLC39A9 in paraffin sections when staining is weak?
Start paraffin IHC with Tris-EDTA pH 9.0 heat-induced retrieval at 95–98 °C for 20 min (page retrieval setting). Cool sections in retrieval buffer for 20 min, then compare a matched positive-control section across runs so heating differences are visible (standard IHC practice; HPA: high staining in cerebral cortex neuronal cells). SLC39A9 has 8 transmembrane segments, so weak staining may reflect limited epitope access, although the antibody epitope is unspecified (UniProt Q9NUM3 topology; supplied evidence: no epitope map). If staining remains weak, test citrate pH 6.0 as a fallback on adjacent sections and retain the condition with the best specific pattern and tissue preservation (standard IHC practice).
Can I attribute weak SLC39A9 staining to overfixation?
Target-specific fixation sensitivity is unknown: the selected A13097-2 tissue-IHC caption reports human brain staining at 2.5 µg/mL but gives no fixative or fixation time (A13097-2 caption). Record fixative, time to fixation and duration for each paraffin specimen; compare sections processed together before assigning a fixation effect (standard IHC practice). For a controlled comparison, hold retrieval at Tris-EDTA pH 9.0, 95–98 °C for 20 min while varying only the documented fixation condition (page retrieval setting; standard IHC practice). Assess morphology alongside signal, because tissue damage or staining loss alone cannot establish a SLC39A9-specific fixation mechanism (standard IHC practice; supplied evidence: no fixation comparison).
Which SLC39A9 staining pattern should I accept in chromogenic IHC?
Expect predominantly cytoplasmic staining in tissue IHC, with the cell type considered alongside intensity (HPA tissue IHC: general cytoplasmic expression). A perinuclear or membrane-associated component can be plausible because SLC39A9 is annotated at the trans-Golgi network, cell membrane and perinuclear cytoplasm (UniProt Q9NUM3 subcellular annotation). The subcellular IF record instead identifies the endoplasmic reticulum as its approved main location, so do not demand an identical compartment pattern across assays (HPA subcellular: endoplasmic reticulum approved). Compare stained and control sections at the same magnification, recording discrete cytoplasmic, perinuclear, membrane and nuclear components separately rather than treating every brown deposit as equivalent (standard IHC practice).
Could isoforms or epitope accessibility explain discordant SLC39A9 IHC?
SLC39A9 has 3 annotated isoforms and 8 transmembrane segments, but the supplied antibody evidence does not map its epitope or establish isoform coverage (UniProt Q9NUM3 isoforms and topology; supplied evidence: no epitope map). Two glycosylation sites are annotated at residues 29 and 241; their effect on this antibody’s tissue staining is unknown (UniProt Q9NUM3 glycosylation; supplied evidence: no glycosylation comparison). Check the antibody immunogen and isoform sequences before interpreting a missing compartment or sample as isoform absence (standard antibody-validation practice). If specificity remains uncertain, compare an independent epitope antibody or a genetically depleted control using identical retrieval and detection settings (standard IHC validation practice).
How can IF help resolve SLC39A9 cell identity and compartment?
On the separate IF/ICC guide, pair SLC39A9 with a marker for the expected cell type; Purkinje cells are one tissue-IHC example with high staining (HPA tissue IHC: cerebellar Purkinje cells high). Choose a spectrally separated far-red fluorophore for the weaker signal when tissue autofluorescence overlaps shorter wavelengths, and inspect single-stain controls before assigning colocalisation (standard IF practice). Because the antibody epitope and its membrane-facing side are unspecified, compare permeabilised and unpermeabilised preparations before interpreting absent intracellular signal (supplied evidence: no epitope map; standard IF practice). Interpret an endoplasmic-reticulum-like pattern against compartment controls, since the IF subcellular record lists endoplasmic reticulum as the approved main location (HPA subcellular: endoplasmic reticulum approved).
How do I separate true SLC39A9 signal from chromogenic background?
Run a no-primary control beside each staining batch and compare it with the same counterstain and detection exposure (standard IHC practice). Block endogenous peroxidase before DAB development, then shorten DAB exposure if diffuse brown precipitate obscures cell boundaries (standard chromogenic IHC practice). Titrate the catalog antibody around the documented 2.5 µg/mL human brain image concentration while keeping retrieval and detection fixed; that caption does not establish a universal working concentration (A13097-2 caption; standard IHC optimisation practice). Assess background in low-staining smooth muscle cells alongside higher-staining neuronal or glandular cells, accounting for morphology and run controls before calling a difference specific (HPA tissue IHC: smooth muscle low; cerebral cortex neuronal cells and adrenal gland glandular cells high).
How should I score heterogeneous SLC39A9 staining across paraffin sections? ⚠ ANSWER MARKED FOR VERIFICATION
Define the scored compartment and cell population before measuring signal; HPA describes general cytoplasmic tissue staining and reports different levels across cell types (HPA tissue IHC: profile and cell-level entries). For each region, report the percentage of positive cells and an H-score from 0–300, calculated as the sum of percentage at each intensity grade multiplied by its 0–3 grade (standard IHC scoring practice). Normalise positive-cell counts to the number of eligible cells, or report stained-cell density per mm² of viable tissue when cell counts are impractical (standard histomorphometry practice). Keep retrieval, imaging and thresholds constant, and exclude folds, edges and necrosis by predefined rules (standard IHC quantification practice).
What would make a positive SLC39A9 IHC result convincing?
A convincing result combines cell-associated staining, the expected compartment pattern and a clean no-primary control (standard IHC validation practice; HPA tissue IHC: general cytoplasmic expression). High staining in cerebral cortex neuronal cells or cerebellar Purkinje cells is consistent with the tissue-IHC profile, while smooth muscle cells are reported as low (HPA tissue IHC: listed cell levels). Review strong isolated nuclear-only deposits cautiously: UniProt includes a nuclear annotation, but tissue IHC is described mainly as cytoplasmic (UniProt Q9NUM3 subcellular annotation; HPA tissue IHC: profile). Exclude section-edge staining, necrotic deposits and residual endogenous peroxidase signal before assigning positive cells or comparing scores (standard chromogenic IHC practice).
Boster reagents
Best SLC39A9 / Zinc transporter ZIP9 IHC Antibodies
A13097-2 is an anti-SLC39A9 antibody with IHC-P and IF applications (catalog: applications) and figures showing human brain tissue in both assays (catalog image captions).
Real IHC data
Anti-ZIP9 SLC39A9 Antibody
Cat # A13097-2
A13097-2 has a human brain tissue IHC image at 2.5 μg/mL (catalog IHC image caption). Its IF image shows human brain tissue at 20 μg/mL; Human and Mouse reactivity are listed (catalog IF image caption; catalog: reactivity).
Which to pick: For paraffin-section IHC, choose A13097-2 because IHC-P is listed (catalog: applications); its own IHC image shows human brain tissue, but the fixative is unreported (catalog IHC image caption). For IF, choose A13097-2 based on its human brain tissue IF image; ICC validation is unreported (catalog IF image caption; catalog: applications). For cross-species work, A13097-2 lists Human and Mouse reactivity, while both pictured assays use human tissue; the antibody host is rabbit and no clone is specified (catalog: reactivity, host, clone; catalog image captions).
Each figure is that product's own IHC / IF validation image from its datasheet.
References
- UniProt Consortium. UniProt entry Q9NUM3 (S39A9_HUMAN, Zinc transporter ZIP9).
- Human Protein Atlas. SLC39A9 tissue IHC expression (reliability: Approved).
- Human Protein Atlas. SLC39A9 subcellular location (ICC-IF): Localized to the endoplasmic reticulum..
- Human Protein Atlas. SLC39A9 antibody validation summary (2 antibodies).
- Novel Plasma Membrane Androgen Receptor SLC39A9 Mediates Ovulatory Changes in Cells of the Monkey Ovarian Follicle. Endocrinology 2024 — PMC11212825.
- ZIP9 Is a Druggable Determinant of Sex Differences in Melanoma. Cancer research 2021 — PMC8977092.
- PubMed PMID:12975309 — UniProt-cited evidence.
- PubMed PMID:14702039 — UniProt-cited evidence.
- PubMed PMID:12508121 — UniProt-cited evidence.
Immunohistochemistry protocol sheet for SLC39A9 (Zinc transporter ZIP9). Expected localisation General cytoplasmic tissue staining (HPA tissue IHC). Antigen retrieval: Tris-EDTA pH 9.0 HIER, 95–98 °C, 20 min (rule: nuclear antigen). Validated IHC antibody: A13097-2 at 2.5 μg/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 workflow; specimen preparation unspecified. Protocol steps: 1. Sample: Tissue sections; selected-image fixative not specified (standard IHC workflow); 2. Fixation: Image fixative and duration unreported (datasheet A13097-2); 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 Tris-EDTA buffer, pH 9.0 , 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-SLC39A9, 2.5 μg/mL (datasheet A13097-2); 9. Primary incubation: Overnight at 4 °C (standard). Watch for: Fixation: Keep fixation consistent across paraffin sections (standard IHC practice; not target-specific); optimize empirically.; Caveat: Smooth muscle and marrow cells show low staining (HPA tissue IHC); Isoform / epitope: 3 isoforms; extracellular versus cytoplasmic epitope access may differ (UniProt); Regulation: Expression regulation is not specified (UniProt). Evidence: UniProt Q9NUM3, HPA tissue IHC · Approved, HPA ICC-IF · endoplasmic reticulum., Datasheet A13097-2, PMC11212825, PMC8977092. QR code links to https://www.bosterbio.com/bosterbio-gene-info-cards/SLC39A9/immunohistochemistry-ihc-guide.