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NDE1 / Nuclear distribution protein nudE homolog 1 · IHC design guide
Design Immunohistochemistry for NDE1
Plan chromogenic NDE1 IHC in paraffin sections with the catalog antibody at 2–5 μg/ml (datasheet A03656-2). Use the reported cytoplasmic tissue pattern to guide scoring, while accounting for low consistency between antibody staining and RNA expression (HPA tissue IHC).
Evidence assembled Oct 2026 · For research use; verify linked source records and product datasheet before use
NDE1 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 tissue staining (HPA tissue IHC) | |
| Staining pattern | Cytoplasmic staining in several tissues, strongest in lymphoid tissues (HPA tissue IHC) | |
| Antigen retrieval | EDTA pH 8.0 HIER, heat-mediated (datasheet A03656-2) | |
| Positive control | Caudate+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 paraffin-section fixation consistent (standard IHC practice; not target-specific) | |
| Caveat | Antibody staining has low consistency with RNA expression (HPA tissue IHC) | |
| Regulation | Expressed in developing neuroepithelium (UniProt) | |
| Isoform / epitope | 2 isoforms; epitope coverage needs checking (UniProt) |
Section 1
Recommended NDE1 IHC & IF Protocols
The catalog antibody has an IHC-P protocol (datasheet: A03656-2). One published mouse brain IHC protocol provides a comparison (PMC4048543).
| Sample | Paraffin-embedded human breast cancer tissue; fixative not specified (datasheet A03656-2) |
| Fixation | Image fixative and duration unreported (datasheet A03656-2); verify before use. |
| Sectioning | 4–5 µm sections on charged slides (standard) |
| Deparaffinisation | Xylene, graded ethanol series to water (standard) |
| Antigen retrieval | Heat retrieval: EDTA pH 8.0 (datasheet A03656-2); 20 min, 95–100 °C (standard) |
| Peroxidase block | 3% H2O2, 10 min, room temperature (standard) |
| Blocking | 10% goat serum (datasheet A03656-2) |
| Primary antibody | Rabbit anti-NDE1, 2-5μg/ml (datasheet A03656-2) |
| Primary incubation | Overnight at 4 °C (datasheet A03656-2) |
| Detection | Streptavidin-biotin complex (SABC), DAB chromogen (datasheet A03656-2) |
| Counterstain | Hematoxylin, blue, dehydrate and mount (standard) |
| Expected result | NDE1-positive staining in neuronal cells of caudate (HPA tissue IHC: Medium). HPA tissue profile: Cytoplasmic expression in several tissues, most abundant in lymphoid tissues. No signal in the no-primary control. |
💡Decision noteStart with heat-mediated EDTA retrieval at pH 8.0 for the catalog antibody (datasheet: A03656-2). The published mouse brain protocol used citrate at pH 6.0 (PMC4048543).
Section 2
What Is the Expected NDE1 Staining Pattern?
NDE1 is mainly cytoplasmic and cytoskeletal, with cell cycle dependent localization to centrosomes, spindle and cleavage furrow (UniProt Q9NXR1 localization). In paraffin tissue sections, expect cytoplasmic staining in selected cells, including neuronal cells, duodenal glandular cells and kidney tubule cells (HPA tissue IHC: Medium). Interpret cautiously: the HPA tissue assessment is Approved but reports low consistency between staining and RNA expression (HPA tissue IHC: reliability).
| Cytoplasmic chromogen in neuronal cells of cerebral cortex, hippocampus or caudate. | This fits the reported Medium staining in those cell populations (HPA tissue IHC). Score the named cells and their cytoplasm; staining elsewhere in the section does not establish the same pattern (HPA tissue IHC; standard IHC practice). |
| Cytoplasmic staining in duodenal glandular cells or kidney tubule cells. | Both are reported at Medium intensity (HPA tissue IHC). Compare the relevant cell population with adjacent tissue and controls when judging whether chromogen is cell associated (standard IHC practice). |
| Predominantly nuclear or continuous cell surface staining, without a cytoplasmic pattern. | Treat this as a localization mismatch requiring investigation, rather than confirmed NDE1: UniProt places NDE1 at cytoskeletal and cell division structures and reports no transmembrane segment (UniProt Q9NXR1 localization and topology). |
| Staining concentrated in adipocytes or bronchial respiratory epithelium. | Those cells are reported as Not detected (HPA tissue IHC). Reproducible staining there warrants checks for cross reactivity or endogenous detection activity (standard IHC practice); the HPA result alone does not prove its cause. |
| Diffuse chromogen across tissue, or no cell associated signal in a reported positive population. | Diffuse color is difficult to assign to NDE1 positive cells (standard IHC practice). Absence in cerebral cortical neurons, for example, conflicts with the reported Medium pattern, but HPA notes staining and RNA inconsistency (HPA tissue IHC). |
💡Expected NDE1 appearanceA credible positive is cell associated cytoplasmic staining of roughly Medium intensity in the listed neuronal, duodenal glandular or kidney tubule cells (HPA tissue IHC); diffuse color, dominant nuclear staining or strong staining in reported negative cells warrants investigation (UniProt Q9NXR1 localization; HPA tissue IHC; standard IHC practice).
| Tissue and cell choice | HPA reports Medium staining in selected neuronal, duodenal glandular and kidney tubule cells, but Not detected in several other populations (HPA tissue IHC). Record the cell type, since a whole section can contain more than one staining pattern (standard IHC practice). |
| Strength of tissue evidence | The tissue assessment is Approved, with low consistency between antibody staining and RNA expression and a splice or transcript discrepancy caution (HPA tissue IHC: reliability). HPA024075 is IHC Approved; the supplied status does not say Enhanced (HPA antibodies). |
| Cell cycle and subcellular pattern | UniProt describes centrosome localization in interphase and S phase, partial spindle association during mitosis, kinetochore associated microtubule ends in metaphase and anaphase, and the cleavage furrow during cytokinesis (UniProt Q9NXR1 localization). These structures need not be obvious in every paraffin section (standard IHC practice). |
| Topology and processing | NDE1 has no transmembrane segment, signal sequence or propeptide, and its annotated chain spans residues 1–335 (UniProt Q9NXR1 topology and processing). Its reported association with cytoplasmic vesicles does not make a uniform cell surface rim the expected IHC result (UniProt Q9NXR1 localization). |
| Isoforms and epitope | Two isoforms are listed, but the supplied record gives no antibody epitope or isoform coverage (UniProt Q9NXR1 isoforms; HPA antibodies). If a result depends on isoform detection, check documented immunogen coverage before assigning a negative stain to lack of NDE1 (standard IHC practice). |
| IF/ICC Q&A: Is there an HPA image based location to compare? | No. HPA supplies no main ICC IF location and no cell lines with ICC IF images, while noting cell cycle correlated transcript variation (HPA subcellular). Use the separate IF/ICC guide for that application; the tissue IHC pattern does not validate an IF/ICC image (HPA tissue IHC; HPA subcellular). |
| Situation | Likely cause | Next action |
|---|---|---|
| No chromogen in reported positive neuronal, duodenal or kidney cells. | The result conflicts with HPA's Medium staining report, but the supplied evidence does not identify a target specific fixation or retrieval failure (HPA tissue IHC). | Check a known positive section, primary antibody coverage, detection reagents and the recorded retrieval conditions using routine IHC controls (standard IHC practice). Interpret persistent absence with HPA's low consistency caveat (HPA tissue IHC). |
| Color appears throughout the section without clear cell boundaries. | Diffuse color can arise from background detection or inadequately controlled staining steps (standard IHC practice); the supplied NDE1 sources do not assign a target specific cause. | Compare a no primary control, inspect washes and blocking, and judge whether signal remains localized to the reported cell populations (standard IHC practice; HPA tissue IHC). |
| Reported negative cells show strong staining. | HPA reports adipocytes and bronchial respiratory epithelial cells as Not detected (HPA tissue IHC); cross reactivity or endogenous detection activity are possible explanations (standard IHC practice). | Review no primary and detection controls, then compare a reported positive cell population on a separately processed section before calling the signal NDE1 (standard IHC practice; HPA tissue IHC). |
| Signal is mainly nuclear or forms a continuous membrane rim. | That distribution conflicts with the principal cytoskeletal and cytoplasmic localization and absent transmembrane segment (UniProt Q9NXR1 localization and topology). It is a warning sign, not proof of a particular artefact. | Check counterstain boundaries and a no primary control; assess whether any cell associated cytoplasmic pattern matches the HPA tissue observations (standard IHC practice; HPA tissue IHC). |
| Different positive tissues have unequal staining intensity. | HPA reports selected cell populations at Medium, others at Low or Not detected, and describes cytoplasmic expression in several tissues as most abundant in lymphoid tissues (HPA tissue IHC). | Score each named cell population against its own HPA observation; do not use a single intensity threshold for every tissue (HPA tissue IHC; standard IHC practice). |
| A negative result is attributed to fixation or a specific NDE1 isoform. | No target specific fixation effect or antibody epitope is supplied; UniProt lists 2 isoforms (UniProt Q9NXR1 isoforms; HPA antibodies). | Record processing and retrieval conditions, verify documented epitope coverage where available, and keep the explanation provisional until controlled comparison supports it (standard IHC practice). |
Experiment evidence
IHC & IF images showing NDE1 staining
A03656-2 · IHCIHC analysis of NDE1 using anti-NDE1 antibody (A03656-2). NDE1 was detected in a paraffin-embedded section of human breast cancer tissue. He
A03656-2 · IHCIHC analysis of NDE1 using anti-NDE1 antibody (A03656-2). NDE1 was detected in a paraffin-embedded section of human lung cancer tissue. Heat
HPA · Cerebral cortexHuman Protein Atlas IHC, Cerebral cortex. Source: https://www.proteinatlas.org/ENSG00000072864-NDE1/tissue/cerebral+cortex#imid_6103856
HPA · ColonHuman Protein Atlas IHC, Colon. Source: https://www.proteinatlas.org/ENSG00000072864-NDE1/tissue/colon#imid_6103782
HPA · LiverHuman Protein Atlas IHC, Liver. Source: https://www.proteinatlas.org/ENSG00000072864-NDE1/tissue/liver#imid_6103783
HPA · KidneyHuman Protein Atlas IHC, Kidney. Source: https://www.proteinatlas.org/ENSG00000072864-NDE1/tissue/kidney#imid_6103784
← swipe / scroll for more images →
Real IHC / IF data behind the staining-pattern expectations in this section.
Sample controls for NDE1 IHC & IF
🧪Run cerebral cortex first and expect staining in neuronal cells at a medium level (HPA: cerebral cortex, neuronal cells Medium). Use adipose tissue as the negative, with adipocytes expected to lack staining (HPA: adipose tissue, adipocytes Not detected); on the cortex slide, use non-neuronal cells as internal background comparators only where they lack specific staining, because their NDE1 status is unreported in the supplied HPA rows.
Positive control tissue: Caudate (Neuronal cells, HPA Medium)
Negative control tissue: Adipose tissue (HPA Not detected)
ICC-IF cell lines (HPA subcellular resource): HPA carries no ICC-IF cell line for NDE1; derive a cell-line control from the positive tissue's cell type (Neuronal cells) and confirm it by RNA or western blot first.
Technical controls: Include a no-primary, secondary-only control and a concentration-matched rabbit IgG isotype control (selected-SKU caption: rabbit anti-NDE1 primary); use NDE1 knockout material as a biological negative where available. For chromogenic detection, quench endogenous peroxidase and check for endogenous biotin signal when using the caption’s streptavidin–biotin detection system (selected-SKU caption: SABC with DAB).
⚠️Feasibility: A target-specific fixation window or fixation effect is unreported, and the selected-SKU paraffin-section caption does not state a fixative (selected-SKU caption: fixative not stated). Heat-mediated retrieval in EDTA at pH 8.0 is documented, but retrieval dependence is unreported (selected-SKU caption: EDTA retrieval, pH 8.0). There is no supplied evidence that frozen sections or IF are easier; if assessing cortex by IF, account for possible lipofuscin autofluorescence (standard IF practice).
HPA tissue IHC evidence for NDE1
Comprehensive Human Protein Atlas IHC scoring per tissue (reliability: Approved — Low consistency between antibody staining and RNA expression data. Caution, Splice and/or transcript discrepancy exists.). 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 |
|---|---|---|---|---|
| Caudate | Neuronal cells | Medium | Protein (IHC) | HPA → |
| Cerebral cortex | Neuronal cells | Medium | Protein (IHC) | HPA → |
| Duodenum | Glandular cells | Medium | Protein (IHC) | HPA → |
| Hippocampus | Neuronal cells | Medium | Protein (IHC) | HPA → |
| Kidney | Cells in tubules | Medium | Protein (IHC) | HPA → |
Undetected expression · recommended negative controls
| Tissue | Cell type | Level | Evidence | Source |
|---|---|---|---|---|
| Adipose tissue | Adipocytes | Not detected | Protein (IHC) | HPA → |
| Adrenal gland | Glandular cells | Not detected | Protein (IHC) | HPA → |
| Bone marrow | Hematopoietic cells | Not detected | Protein (IHC) | HPA → |
| Breast | Adipocytes | Not detected | Protein (IHC) | HPA → |
| Bronchus | Respiratory epithelial cells | Not detected | Protein (IHC) | HPA → |
Section 3
Advanced NDE1 IHC Tips
Troubleshoot NDE1 staining in paraffin sections by checking retrieval, cellular distribution, controls, and scoring against the available IHC evidence.
Which retrieval condition should I use when NDE1 staining is weak in paraffin sections?
Start with heat-mediated EDTA retrieval at pH 8.0 for paraffin sections stained with A03656-2 (datasheet A03656-2). The selected tissue-IHC example used this condition before incubation with 2 μg/ml primary antibody overnight at 4°C (caption A03656-2). If staining is weak, check complete deparaffinisation and compare retrieval heating times on adjacent sections while keeping detection conditions constant (standard IHC practice). Include a matched section without primary antibody to reveal retrieval-associated background (standard IHC practice). Record the heating time and method, because the caption supplies a buffer and pH but no retrieval duration (caption A03656-2).
How should I troubleshoot fixation-related loss of NDE1 staining?
Target-specific sensitivity of NDE1 to fixative type or fixation duration is unknown from the supplied evidence (caption A03656-2). The selected image shows paraffin-embedded tissue, but its fixative is unreported (caption A03656-2). Record the fixative and duration for each specimen, then compare similarly processed sections using the documented EDTA retrieval at pH 8.0 (standard IHC practice; datasheet A03656-2). If signal differs between batches, compare a shared positive-control section in each run before attributing the difference to NDE1 abundance (standard IHC practice). Avoid assigning a fixation effect from tissue staining patterns alone; processing and biological variation both need evaluation (standard IHC practice).
Where should convincing NDE1 staining appear in chromogenic tissue sections?
Assess cellular staining against NDE1's reported cytoskeletal and centrosomal localisation, with spindle, kinetochore, and cleavage-furrow association depending on cell-cycle stage (UniProt Q9NXR1 localisation). HPA reports broadly cytoplasmic tissue staining, with its strongest profile in lymphoid tissues (HPA tissue IHC). A diffuse cytoplasmic signal can therefore be plausible, whereas a small centrosomal focus may be difficult to resolve with chromogenic tissue IHC (HPA tissue IHC; UniProt Q9NXR1 localisation; standard IHC practice). Compare morphology and counterstain on the same section before calling puncta or mitotic figures positive (standard IHC practice). Do not require every cell to show a spindle pattern, because spindle association is mitosis-dependent (UniProt Q9NXR1 localisation).
Could isoforms or epitope changes explain inconsistent NDE1 staining?
NDE1 has 2 reported isoforms, but the supplied caption does not map A03656-2 to an epitope or establish isoform coverage (UniProt Q9NXR1 isoforms; caption A03656-2). Ask whether the antibody's documented immunogen overlaps a region shared by both isoforms before interpreting staining differences as isoform expression (standard IHC practice). Several NDE1 residues are annotated as phosphorylated, including positions 211, 215, and 228, but their effect on this antibody's binding is unreported (UniProt Q9NXR1 modified residues; caption A03656-2). Compare serial sections and processing controls when staining varies, and seek epitope-specific validation before assigning the change to a modification (standard IHC practice).
How can I check an NDE1 IHC pattern using multiplex immunofluorescence?
Use an independently validated marker for the expected cell type, such as a neuronal-cell marker when checking a neuronal population, alongside NDE1 (HPA tissue IHC; standard IF practice). Choose a spectrally separated fluorophore, preferably a far-red channel if the tissue shows strong shorter-wavelength autofluorescence, and image single-label controls first (standard IF practice). NDE1 lacks a transmembrane segment and is reported at intracellular cytoskeletal and centrosomal sites, so use a permeabilisation condition that exposes intracellular epitopes (UniProt Q9NXR1 topology and localisation; standard IF practice). Optimise permeabilisation on matched samples, since the supplied paraffin-section caption does not establish an IF fixation or permeabilisation condition (caption A03656-2).
What should I check when NDE1 DAB staining looks diffuse or excessive?
Compare the test section with a no-primary control to identify signal from secondary reagents, tissue pigment, or endogenous enzyme activity (standard IHC practice). The selected example uses a biotinylated secondary, streptavidin-biotin complex, and DAB, so include an appropriate detection-only control if diffuse deposits appear (caption A03656-2; standard IHC practice). Apply a peroxidase block for a peroxidase-based DAB workflow and check the detection system's required controls; these are general workflow steps, not evidence of NDE1-specific behaviour (standard IHC practice). The caption reports 10% goat serum blocking and 2 μg/ml primary antibody overnight at 4°C; compare that documented condition before increasing antibody concentration (caption A03656-2).
How should I score NDE1 staining across tissue sections? ⚠ ANSWER MARKED FOR VERIFICATION
Define the cell population and cytoplasmic scoring compartment before reviewing the slides, since HPA reports cytoplasmic tissue staining (HPA tissue IHC; standard IHC practice). For intensity-based analysis, report an H-score from 0–300 using the percentages of cells at intensity levels 0–3, or report the percentage of positive cells with a fixed threshold (standard IHC practice). For spatial analysis, count positive cells per mm² of viable tissue and normalise to the number or area of eligible cells in each section (standard IHC practice). Keep retrieval, detection, exposure to DAB, and counterstaining consistent across the comparison, and score controls alongside study sections (standard IHC practice).
How can I distinguish true NDE1 staining from tissue artefact?
A plausible result places signal in intact cells with cytoplasmic or cell-cycle-related patterns consistent with reported NDE1 localisation (HPA tissue IHC; UniProt Q9NXR1 localisation). Be cautious with staining restricted to section edges, necrotic areas, or sites that also stain in the no-primary control (standard IHC practice). Check the cell identity: HPA reports medium neuronal-cell staining in cerebral cortex but does not detect staining in breast adipocytes (HPA tissue IHC). HPA labels its tissue evidence Approved while warning of low agreement with RNA expression and possible splice or transcript discrepancy, so treat unexpected positives as requiring independent validation (HPA tissue IHC).
Boster reagents
Best NDE1 / Nuclear distribution protein nudE homolog 1 IHC Antibodies
A03656-2 has real IHC data from paraffin-embedded human breast and lung cancer sections (catalog IHC captions). No IF data are supplied (catalog IF images).
Real IHC data
Anti-NDE1 Antibody ®
Cat # A03656-2
A03656-2 is a rabbit anti-NDE1 antibody listed for human IHC (catalog host, reactivity, applications). Its IHC captions show staining of paraffin-embedded human breast and lung cancer sections (catalog IHC captions).
Which to pick: Choose A03656-2 for human tissue IHC: its captions document EDTA pH 8.0 retrieval and 2 μg/ml primary antibody on paraffin sections; the fixative is unreported (catalog IHC captions). No IF/ICC choice is supported because A03656-2 has no listed IF/ICC application or IF image (catalog applications, IF images). No cross-species choice is supported because A03656-2 lists human reactivity only (catalog reactivity).
Each figure is that product's own IHC / IF validation image from its datasheet.
References
- UniProt Consortium. UniProt entry Q9NXR1 (NDE1_HUMAN, Nuclear distribution protein nudE homolog 1).
- Human Protein Atlas. NDE1 tissue IHC expression (reliability: Approved).
- Human Protein Atlas. NDE1 subcellular location (ICC-IF): Variation in transcript expression is correlated to the cell cycle..
- Human Protein Atlas. NDE1 antibody validation summary (1 antibodies).
- The expression and roles of Nde1 and Ndel1 in the adult mammalian central nervous system. Neuroscience 2014 — PMC4048543.
- Neuropathology of 16p13.11 deletion in epilepsy. PloS one 2012 — PMC3327721.
- NDE1 positively regulates oligodendrocyte morphological differentiation. Scientific reports 2018 — PMC5955916.
- PubMed PMID:14702039 — UniProt-cited evidence.
- PubMed PMID:15616553 — UniProt-cited evidence.
- PubMed PMID:15489334 — UniProt-cited evidence.
Immunohistochemistry protocol sheet for NDE1 (Nuclear distribution protein nudE homolog 1). Expected localisation Cytoplasmic tissue staining (HPA tissue IHC). Antigen retrieval: EDTA pH 8.0 HIER, heat-mediated (datasheet A03656-2). Validated IHC antibody: A03656-2 at 2-5μg/ml (the product's own IHC validation image is shown). Controls (HPA): positive Caudate (Neuronal cells); negative Adipose tissue. IHC-P workflow on paraffin sections; fixative unspecified. Protocol steps: 1. Sample: Paraffin-embedded human breast cancer tissue; fixative not specified (datasheet A03656-2); 2. Fixation: Image fixative and duration unreported (datasheet A03656-2); 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 retrieval: EDTA pH 8.0 (datasheet A03656-2); 20 min, 95–100 °C (standard); 6. Peroxidase block: 3% H2O2, 10 min , room temperature (standard); 7. Blocking: 10% goat serum (datasheet A03656-2); 8. Primary antibody: Rabbit anti-NDE1, 2-5μg/ml (datasheet A03656-2); 9. Primary incubation: Overnight at 4 °C (datasheet A03656-2). Watch for: Fixation: Keep paraffin-section fixation consistent (standard IHC practice; not target-specific); Caveat: Antibody staining has low consistency with RNA expression (HPA tissue IHC); Isoform / epitope: 2 isoforms; epitope coverage needs checking (UniProt); Regulation: Expressed in developing neuroepithelium (UniProt). Evidence: UniProt Q9NXR1, HPA tissue IHC · Approved, HPA cell-line RNA · Variation in transcript expression is correlated to the cell cycle., Datasheet A03656-2, PMC4048543. QR code links to https://www.bosterbio.com/bosterbio-gene-info-cards/NDE1/immunohistochemistry-ihc-guide.