JMJD4 / 2-oxoglutarate and iron-dependent oxygenase JMJD4 · IHC design guide

Design Immunohistochemistry for JMJD4

Plan JMJD4 IHC-P around cytoplasmic staining reported in several tissues (HPA tissue IHC). Start with the catalog antibody at 2.5 μg/mL (datasheet: A16245) and assess glandular cells and kidney tubules as high-staining references (HPA tissue IHC).

Evidence assembled Oct 2026 · For research use; verify linked source records and product datasheet before use
Immunohistochemistry protocol sheet for JMJD4 (IHC for JMJD4): expected localisation Cytoplasmic (HPA tissue IHC), antibody A16245, validated IHC image, and IHC protocol steps
Printable JMJD4 IHC protocol sheet — expected localisation Cytoplasmic (HPA tissue IHC), antibody A16245, controls and protocol steps. Open the full JMJD4 IHC guide →

JMJD4 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 (HPA tissue IHC)
Staining pattern Cytoplasmic staining across several 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 ⓘ Adipose tissue+4 more · see all
Important caveats
Reasons your staining may differ from the expected pattern.
Fixation Keep fixation consistent across sections. (standard IHC practice; not target-specific)
Caveat Tissue staining awaits external verification (HPA tissue IHC)
Regulation No tissue-specific regulation annotated (UniProt)
Isoform / epitope 3 isoforms; epitope coverage unspecified (UniProt)
Section 1

Recommended JMJD4 IHC & IF Protocols

The catalog antibody has an IHC protocol; the published JMJD4 protocol below adds details from paired kidney specimens (PMC10439757).

Recommended immunohistochemistry (IHC-P) protocol parameters
SampleTissue sections; selected-image fixative not specified (standard IHC workflow)
FixationImage fixative and duration unreported (datasheet A16245); 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-JMJD4, 2.5 μg/mL (datasheet A16245)
Primary incubationOvernight at 4 °C (standard)
DetectionHRP-polymer secondary, DAB chromogen 5–10 min (standard)
CounterstainHematoxylin, blue, dehydrate and mount (standard)
Expected resultJMJD4-positive staining in glandular cells of adrenal gland (HPA tissue IHC: High). HPA tissue profile: Cytoplasmic 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 antigen retrieval); the published protocol specifies heating without conditions (PMC10439757).
Section 2

What Is the Expected JMJD4 Staining Pattern?

For paraffin-section IHC, expect predominantly cytoplasmic JMJD4 staining in the cell types reported as high by HPA, including kidney tubular cells, lung alveolar cells, heart cardiomyocytes, and glandular cells in several organs (UniProt Q9H9V9: cytoplasm; HPA tissue IHC: High in these cells). JMJD4 has no transmembrane segment (UniProt Q9H9V9: topology). Treat the pattern as provisional: HPA rates its tissue IHC profile Uncertain, pending external verification (HPA: tissue IHC reliability).

What am I looking at on my slide?
Cytoplasmic signal in kidney tubular cells or lung alveolar cells, with discernible cell boundaries.This fits the reported compartment and two reported high-staining cell populations (UniProt Q9H9V9: cytoplasm; HPA tissue IHC: High in kidney tubular and lung alveolar cells). Score signal in the named cells rather than assigning one intensity to the whole section (general IHC practice). The match supports interpretation but does not independently validate antibody specificity (HPA: IHC reliability Uncertain).
Signal is predominantly nuclear or outlines the plasma membrane, with little cytoplasmic staining.For tissue IHC, this conflicts with the reported cytoplasmic pattern and warrants an artefact or specificity check (UniProt Q9H9V9: cytoplasm; HPA: cytoplasmic tissue expression). HPA separately reports mainly plasma-membrane and additional vesicular ICC-IF localization, both uncertain (HPA: subcellular ICC-IF). That discordant IF observation does not establish a membrane-positive tissue IHC pattern.
Strong staining appears in skin keratinocytes or skeletal-muscle myocytes.HPA reports JMJD4 as Not detected in those cell types, so strong signal there is a warning for cross-reactivity or detection-system activity (HPA tissue IHC: Not detected in skin keratinocytes and skeletal-muscle myocytes; general IHC practice). Compare the suspect cells with a reported high-staining population and appropriate staining controls before calling the result JMJD4-specific (HPA tissue IHC: High in selected cells; general IHC practice).
Chromogen covers most of the section, including extracellular spaces or cells expected to be unstained.A widespread deposit obscures the cell-specific pattern needed for interpretation (general IHC practice). Uneven blocking, excessive antibody or detection reagent, and endogenous enzyme activity are general IHC possibilities, not documented JMJD4-specific effects (general IHC practice). HPA's uncertain tissue profile cannot resolve whether broad staining represents target signal (HPA: tissue IHC reliability Uncertain).
No detectable signal appears in kidney tubules or heart cardiomyocytes.Both are reported as High, so a blank result merits checking the staining run before interpreting JMJD4 as absent (HPA tissue IHC: High in kidney tubular cells and heart cardiomyocytes; general IHC practice). Verify that the positive-control section and detection controls worked, then review antibody dilution and retrieval conditions as general IHC variables (general IHC practice). HPA's uncertain reliability limits certainty about any single sample (HPA: tissue IHC reliability Uncertain).
💡Expected JMJD4 appearanceA plausible positive is cytoplasmic staining in a reported high-staining cell population, such as kidney tubular cells or lung alveolar cells; dominant nuclear or broad extracellular staining is suspect, while the expected strength remains provisional because HPA rates the tissue IHC profile Uncertain (UniProt Q9H9V9: cytoplasm; HPA tissue IHC: High in those cells; HPA: IHC reliability Uncertain).
How each factor affects the staining
Tissue and cell selectionHPA reports High staining in kidney tubular cells, heart cardiomyocytes, lung alveolar cells, and several glandular cell populations, but Not detected in skin keratinocytes and skeletal-muscle myocytes (HPA: tissue IHC). These are useful contrasts for reading a section; they are observations from an Uncertain profile, not certified positive and negative controls (HPA: tissue IHC reliability).
Compartment evidence across applicationsUniProt assigns JMJD4 to the cytoplasm, and HPA describes cytoplasmic tissue expression (UniProt Q9H9V9: subcellular location; HPA: tissue IHC). HPA ICC-IF instead lists plasma membrane and vesicles, both uncertain (HPA: subcellular ICC-IF). Read the tissue IHC pattern on its own terms; the ICC-IF result does not define a paraffin-section scoring rule.
Protein features and isoformsJMJD4 has no signal peptide, propeptide, transmembrane segment, or annotated glycosylation site; UniProt lists three isoforms and a JmjC domain at residues 142–301 (UniProt Q9H9V9: processing, topology, glycosylation, isoforms, domains). These annotations do not identify the antibody epitope or establish retrieval requirements or isoform-specific staining.
Strength of antibody evidenceHPA marks tissue IHC reliability Uncertain and lists IHC status as Uncertain for both HPA027260 and HPA052861 (HPA: tissue IHC reliability; HPA: antibody validation). A pattern match is therefore supportive rather than conclusive. Interpret compartment, cell type, and controls together, especially when a slide differs from the reported pattern (general IHC practice).
Why is my staining missing, weak or wrong?
SituationLikely causeNext action
A reported high-staining cell population is blank.The staining run may have failed, or the sample may differ from HPA's observed examples (general IHC practice; HPA tissue IHC: High in selected cells, reliability Uncertain).Check a same-run positive-control section and detection controls, then review retrieval and antibody dilution as general IHC variables (general IHC practice). Do not infer a JMJD4-specific fixation effect; none is established by the supplied UniProt or HPA records.
Predominantly nuclear or sharp membrane-rim staining appears in tissue IHC.The pattern differs from UniProt's cytoplasmic assignment and HPA's cytoplasmic tissue description (UniProt Q9H9V9: cytoplasm; HPA: tissue IHC). HPA's uncertain membrane ICC-IF observation cannot establish its cause in paraffin sections (HPA: subcellular ICC-IF).Review morphology and compartment boundaries, compare a reported high-staining cell population, and inspect control staining before scoring the rim or nuclear signal as JMJD4 (HPA: tissue IHC; general IHC practice).
Strong signal appears in skin keratinocytes or skeletal-muscle myocytes.Those populations are reported Not detected; cross-reactivity or detection-system activity is possible (HPA tissue IHC: Not detected; general IHC practice).Check an appropriate primary-antibody omission control and detection controls, then compare cell-specific staining in a reported high-staining tissue (general IHC practice; HPA tissue IHC: High in selected cells). Treat HPA's negative observations as provisional because its IHC reliability is Uncertain (HPA: tissue IHC reliability).
Diffuse chromogen or extracellular staining obscures cells.Background from antibody concentration, blocking, washing, or endogenous enzyme activity is possible in chromogenic IHC (general IHC practice).Inspect omission and detection controls; adjust blocking, washes, dilution, or endogenous-enzyme quenching according to the detection system (general IHC practice). Reassess whether signal resolves into the reported cytoplasmic, cell-specific pattern (UniProt Q9H9V9: cytoplasm; HPA: tissue IHC).
Two IHC-validated antibodies give different tissue patterns.HPA assigns IHC status Uncertain to both listed antibodies, so agreement with one image alone cannot settle specificity (HPA: HPA027260 and HPA052861 IHC validation; HPA: tissue IHC reliability Uncertain).Compare the same named cell populations and subcellular compartment across sections, using matched staining controls (HPA: tissue IHC; UniProt Q9H9V9: cytoplasm; general IHC practice). Record disagreement rather than averaging it into an apparently definitive JMJD4 score.
IF/ICC shows membrane or vesicular signal. Does that change the IHC expectation?HPA reports mainly plasma-membrane and additional vesicular ICC-IF localization, with both locations marked uncertain (HPA: subcellular ICC-IF). Tissue IHC instead reports cytoplasmic expression (HPA: tissue IHC).Keep the tissue IHC interpretation anchored to the cytoplasmic tissue observation and UniProt localization (HPA: tissue IHC; UniProt Q9H9V9: cytoplasm). Treat the IF/ICC observation as unresolved application-specific evidence; it supplies no paraffin-section protocol or basis for calling a membrane-rim IHC result positive.

Sample controls for JMJD4 IHC & IF

🧪Run kidney first: tubular cells should stain strongly (HPA: High in kidney cells in tubules). Use oral mucosa squamous epithelial cells as the negative tissue (HPA: Not detected); on the kidney slide, any unstained nontubular cells should resemble background in the no-primary control, but the supplied HPA rows do not establish those cells as JMJD4-negative.
Positive control tissue: Adrenal gland (Glandular cells, HPA High)
Negative control tissue: Adipose tissue (HPA Not detected)
ICC-IF cell lines (HPA subcellular resource): HPA ICC-IF images show JMJD4 in A-431, U-251MG, U2OS, with annotated localisation: Plasma membrane (uncertain) (HPA subcellular).
Technical controls: Include a no-primary, secondary-only control; an isotype control matched to the primary antibody’s host species and clonality; and a biological specificity control using JMJD4 knockout material or peptide blocking where applicable (standard IHC practice). In kidney, control endogenous peroxidase activity and, if using avidin–biotin detection, endogenous biotin (standard IHC practice).
⚠️Feasibility: A target-specific fixation window and antigen-retrieval dependency are unreported in the supplied evidence; the fixative is also unreported in the selected A16245 rat spleen IHC caption (caption: 2.5 μg/mL). The evidence does not establish whether frozen sections or IF are easier for JMJD4. Kidney tubules can contain endogenous biotin, which may complicate avidin–biotin detection (standard IHC practice).

HPA tissue IHC evidence for JMJD4

Comprehensive Human Protein Atlas IHC scoring per tissue (reliability: Uncertain — 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

TissueCell typeLevelEvidenceSource
Adrenal gland Glandular cells High Protein (IHC) HPA →
Heart muscle Cardiomyocytes High Protein (IHC) HPA →
Kidney Cells in tubules High Protein (IHC) HPA →
Lung Alveolar cells High Protein (IHC) HPA →
Pancreas Exocrine glandular cells High Protein (IHC) HPA →

Undetected expression · recommended negative controls

TissueCell typeLevelEvidenceSource
Adipose tissue Adipocytes Not detected Protein (IHC) HPA →
Caudate Glial cells Not detected Protein (IHC) HPA →
Hippocampus Glial cells Not detected Protein (IHC) HPA →
Lymph node Germinal center cells Not detected Protein (IHC) HPA →
Oral mucosa Squamous epithelial cells Not detected Protein (IHC) HPA →
Section 3

Advanced JMJD4 IHC Tips

Troubleshoot JMJD4 staining by checking retrieval, controls and cellular distribution before comparing chromogenic signal across paraffin sections.

How should I adjust retrieval when JMJD4 staining is weak in paraffin sections?
Start with citrate buffer at pH 6.0, heated to 95–98 °C for 20 min (page retrieval specification). Compare sections processed together with an identical cooling period, since changes in retrieval can alter both signal and tissue preservation (standard IHC practice). JMJD4 is annotated as cytoplasmic and has no transmembrane segment, but those annotations do not establish how its epitope survives processing (UniProt Q9H9V9). If staining remains weak, test a second retrieval condition on adjacent sections while holding antibody concentration and detection constant, then judge specific cellular staining against background and tissue morphology (standard IHC practice).
Could fixation explain inconsistent JMJD4 staining between specimens?
Target-specific fixation sensitivity is unknown: the selected rat spleen IHC caption reports 2.5 µg/mL antibody but gives no fixative or fixation time (A16245 tissue-IHC caption). Record each specimen’s fixative, fixation duration, processing schedule and section age before comparing its chromogenic signal (standard IHC practice). Test matched material across the available processing conditions, using the same pH 6.0 citrate retrieval and detection run (page retrieval specification; standard IHC practice). If intensity tracks processing history, report that association as a technical limitation until replicate sections and controls establish whether the effect is reproducible (standard IHC practice).
What compartment should count as credible JMJD4 staining?
Use cytoplasmic staining as the initial IHC expectation because JMJD4 is annotated in the cytoplasm (UniProt Q9H9V9), and tissue IHC reports cytoplasmic expression in several tissues (HPA tissue IHC: reliability uncertain). Evaluate membrane-like staining separately: an ICC/IF entry places JMJD4 mainly at the plasma membrane with additional vesicles, but labels both locations uncertain (HPA subcellular: uncertain). Compare signal within identified cells rather than counting a dark tissue border or extracellular deposit as cellular staining (standard IHC practice). If a compartment differs from the cytoplasmic IHC pattern, seek agreement across adjacent sections and an independent antibody or assay before assigning it to JMJD4 (standard IHC practice).
Can the antibody miss a JMJD4 isoform after retrieval?
JMJD4 has 3 listed isoforms, numbered 3, 1 and 2, and its JmjC domain spans residues 142–301 (UniProt Q9H9V9). An isoform claim requires the catalog antibody’s mapped epitope and the relevant isoform sequences; the supplied caption does not identify that epitope (A16245 tissue-IHC caption). Check whether the immunogen region is shared before interpreting a negative cell population as isoform absence (standard antibody validation practice). Keep retrieval and detection identical across comparison sections, and confirm any proposed isoform-specific pattern with an independent assay that distinguishes those isoforms (standard IHC practice).
How can IF help investigate a disputed chromogenic JMJD4 pattern?
Use IF as an orthogonal check of the IHC pattern, pairing JMJD4 with a validated marker for the expected cell type, such as a tubular cell marker when evaluating kidney tubules (HPA tissue IHC: high in kidney tubular cells; standard IF practice). Choose a far-red JMJD4 fluorophore when tissue autofluorescence compromises shorter wavelengths, and inspect single-label controls before interpreting overlap (standard IF practice). For a proposed cytoplasmic epitope, test mild permeabilisation; for a proposed extracellular membrane epitope, compare staining without permeabilisation, since the antibody’s epitope side is unspecified (UniProt Q9H9V9; standard IF practice). Treat membrane or vesicle agreement cautiously because those ICC/IF locations are marked uncertain (HPA subcellular: uncertain).
How do I distinguish JMJD4 signal from chromogenic background?
Run a no-primary control and examine whether diffuse DAB persists after a peroxidase block, for example 3% hydrogen peroxide for 10 min (standard IHC practice). Use an appropriate protein block and compare a small antibody concentration series around the caption’s 2.5 µg/mL reference without treating that image concentration as a universal optimum (A16245 tissue-IHC caption; standard IHC practice). Inspect tissue edges, folds and necrotic regions separately from intact cells, because these areas can produce misleading deposits (standard IHC practice). A convincing result should retain a cellular pattern as background falls and should be reproducible in adjacent sections (standard IHC practice).
How should I score JMJD4 IHC across tissue regions? ⚠ ANSWER MARKED FOR VERIFICATION
Define the cell population and compartment before scoring, then record the percentage of positive cells and an intensity-weighted H-score on a consistent 0–300 scale (standard IHC scoring practice). Normalise each result to the number of eligible, intact cells within the same annotated tissue area; use positive-cell density per mm² only when area-based sampling is appropriate (standard IHC scoring practice). Keep exposure, chromogen development and positivity thresholds consistent across a batch (standard IHC practice). Report uncertain or excluded regions separately, and interpret tissue comparisons cautiously because the available tissue IHC profile is pending external verification (HPA tissue IHC: reliability uncertain).
When is a surprising JMJD4-positive cell likely to be artefactual?
First check whether staining occupies intact cell cytoplasm, the reported tissue IHC pattern, rather than only edges, necrotic material or extracellular deposits (HPA tissue IHC: cytoplasmic expression, reliability uncertain; standard IHC practice). Confirm the cell identity before comparing it with reported high staining in cardiomyocytes or kidney tubular cells and reported absence in adipocytes (HPA tissue IHC: cell-specific observations, reliability uncertain). Recheck the no-primary control and peroxidase block if DAB appears broadly, since endogenous enzyme activity can mimic specific chromogenic staining (standard IHC practice). A novel cell or membrane pattern needs reproducibility and independent validation, especially because the membrane assignment comes from uncertain ICC/IF localisation (HPA subcellular: uncertain).
Boster reagents

Best JMJD4 / 2-oxoglutarate and iron-dependent oxygenase JMJD4 IHC Antibodies

The catalog includes a paraffin-section IHC antibody with a rat spleen image (A16245 application list; A16245 IHC caption) and an IF/ICC antibody with a PC-12 cell image (A16245-1 application list; A16245-1 IF caption).

Real IHC data Immunohistochemistry of JMJD4 in rat spleen tissue with JMJD4 antibody at 2.5 μg/mL.
Anti-JMJD4 Antibody
Cat # A16245
Real IF data Immunofluorescence analysis of PC-12 cells using JMJD4 Rabbit pAb at dilution of 1:100 . Blue: DAPI for nuclear staining.
Anti-JMJD4 Antibody
Cat # A16245-1

A16245 lists IHC-P and IF for human and rat, with a rat spleen IHC image at 2.5 μg/mL (A16245 application and reactivity lists; A16245 IHC caption). A16245-1 lists IF/ICC for human, mouse and rat, with a PC-12 cell IF image at 1:100 (A16245-1 application and reactivity lists; A16245-1 IF caption).

Which to pick: Choose A16245 for tissue IHC: it lists IHC-P and has a rat spleen IHC image; the caption does not report the fixative (A16245 application list; A16245 IHC caption). For IF/ICC, A16245-1 has a PC-12 cell IF image, while A16245 has a rat spleen IF image (A16245-1 IF caption; A16245 IF caption). For human, mouse and rat IF/ICC work, A16245-1 has the broader listed reactivity; both antibodies are rabbit hosted, and the catalog does not specify a clone for either (A16245-1 reactivity, application and host fields; A16245 host field; catalog clone fields).

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

References

  1. UniProt Consortium. UniProt entry Q9H9V9 (JMJD4_HUMAN, 2-oxoglutarate and iron-dependent oxygenase JMJD4).
  2. Human Protein Atlas. JMJD4 tissue IHC expression (reliability: Uncertain).
  3. Human Protein Atlas. JMJD4 subcellular location (ICC-IF): Mainly localized to the plasma membrane. In addition localized to vesicles..
  4. Human Protein Atlas. JMJD4 antibody validation summary (2 antibodies).
  5. High Expression of JMJD4 Is a Potential Diagnostic and Prognostic Marker of Renal Cell Carcinoma. Disease markers 2021 — PMC8720244.
  6. Protein Expression of NEK2, JMJD4, and REST in Clear Cell Renal Cell Carcinoma (ccRCC): Clinical, Pathological, and Prognostic Findings. Iranian journal of pathology 2023 — PMC10439757.
  7. PubMed PMID:14702039 — UniProt-cited evidence.
  8. PubMed PMID:16710414 — UniProt-cited evidence.
  9. PubMed PMID:24486019 — UniProt-cited evidence.