This website uses cookies to ensure you get the best experience on our website.
- Table of Contents
NR1D1 / Nuclear receptor subfamily 1 group D member 1 · IHC design guide
Design Immunohistochemistry for NR1D1
Plan paraffin-section NR1D1 IHC with a catalog antibody dilution of 2–5 μg/ml (datasheet A01077-2). Interpret cytoplasmic staining in light of the tissue profile’s uncertain reliability (HPA tissue IHC).
Evidence assembled Oct 2026 · For research use; verify linked source records and product datasheet before use
NR1D1 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 signal across most tissues (HPA tissue IHC) | |
| Antigen retrieval | EDTA pH 8.0 HIER, heat-mediated (datasheet A01077-2) | |
| 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 | Staining has low consistency with RNA data (HPA tissue IHC) | |
| Regulation | Diurnal expression oscillation (UniProt) | |
| Isoform / epitope | No annotated isoforms; one full-length chain (UniProt) |
Section 1
Recommended NR1D1 IHC & IF Protocols
The catalog antibody’s IHC protocol and these four published NR1D1 IHC protocols provide starting conditions for paraffin sections (datasheet A01077-2; PMC6883674; PMC10531686; PMC12339034; PMC5438901).
| Sample | Paraffin-embedded human breast cancer tissue; fixative not specified (datasheet A01077-2) |
| Fixation | Image fixative and duration unreported (datasheet A01077-2); 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 A01077-2); 20 min, 95–100 °C (standard) |
| Peroxidase block | 3% H2O2, 10 min, room temperature (standard) |
| Blocking | 10% goat serum (datasheet A01077-2) |
| Primary antibody | Rabbit anti-NR1D1, 2-5 μg/ml (datasheet A01077-2) |
| Primary incubation | Overnight at 4 °C (datasheet A01077-2) |
| Detection | HRP-conjugated secondary, DAB chromogen (datasheet A01077-2) |
| Counterstain | Hematoxylin, blue, dehydrate and mount (standard) |
| Expected result | NR1D1-positive staining in glandular cells of adrenal gland (HPA tissue IHC: Medium). HPA tissue profile: Cytoplasmic expression most tissues. No signal in the no-primary control. |
💡Decision noteStart with heat-mediated EDTA retrieval at pH 8.0 for the catalog antibody (datasheet A01077-2). Published citrate conditions apply to the antibodies used in those studies (PMC6883674; PMC12339034).
Section 2
What Is the Expected NR1D1 Staining Pattern?
NR1D1 can localize to the nucleus and cytoplasm, with context-dependent distribution (UniProt P20393: subcellular location). In paraffin tissue IHC, HPA reports predominantly cytoplasmic staining across tissues, including medium staining in several glandular and endothelial cell populations (HPA: tissue IHC). Interpret that pattern cautiously: HPA rates its tissue staining Uncertain because antibody staining and RNA expression have low consistency (HPA: tissue IHC reliability). NR1D1 has no transmembrane segment (UniProt P20393: topology).
| Cytoplasmic staining in adrenal, appendix, duodenal or endometrial glandular cells, or colon endothelial cells. | This resembles HPA’s reported medium staining in those cell populations and its predominantly cytoplasmic tissue pattern (HPA: tissue IHC). Record the stained cell type and compartment. The resemblance supports interpretation but does not confirm specificity: the tissue IHC assessment remains Uncertain (HPA: tissue IHC reliability). |
| Nuclear staining, or a prominent membranous or extracellular outline. | Nuclear staining can fit NR1D1 biology; UniProt lists the nucleus, and HPA supports nuclear bodies in ICC-IF (UniProt P20393: subcellular location; HPA: subcellular ICC-IF). A membrane or extracellular outline is less consistent with a protein lacking a transmembrane segment (UniProt P20393: topology). Check controls before calling it artefact (general IHC practice). |
| Strong staining in cells listed by HPA as not detected, such as adipocytes or ovarian stromal cells. | This conflicts with those HPA tissue IHC observations and raises concern for cross-reactivity or endogenous detection activity (HPA: tissue IHC; general IHC practice). It is not decisive by itself: HPA’s tissue assessment is Uncertain, and UniProt reports high expression in adipose tissue without resolving staining in individual adipocytes (HPA: tissue IHC reliability; UniProt P20393: tissue specificity). |
| Diffuse color across tissue structures, with little distinction between cells. | A uniform deposit is difficult to assign to the reported glandular or endothelial populations and may reflect background from the staining workflow (HPA: tissue IHC; general IHC practice). Compare the no-primary control, review blocking and detection steps, and judge any remaining signal by its cellular distribution (general IHC practice). |
| No staining in an adrenal gland or appendix section expected to provide a positive comparison. | HPA reports medium staining in glandular cells in both tissues, so a blank result calls for a workflow and specimen check (HPA: tissue IHC; general IHC practice). A negative section alone does not establish absence of NR1D1: tissue staining is rated Uncertain, and UniProt reports diurnal variation in expression (HPA: tissue IHC reliability; UniProt P20393: tissue specificity). |
💡Expected NR1D1 appearanceFor IHC, a plausible positive is cell-associated cytoplasmic staining of about the reported medium level in HPA-listed glandular or endothelial cells; nuclear signal may also be biologically plausible, whereas a strong membrane outline or diffuse deposit warrants control checks (HPA: tissue IHC; UniProt P20393: subcellular location and topology; general IHC practice).
| IHC compartment versus IF/ICC: what should IF/ICC show? | HPA describes cytoplasmic expression in most tissue IHC samples but supports localization to nuclear bodies in ICC-IF; UniProt lists both nuclear and cytoplasmic locations (HPA: tissue IHC and subcellular ICC-IF; UniProt P20393: subcellular location). Assess the two applications against their respective observations rather than requiring identical patterns. |
| Time and cellular context | UniProt reports predominantly nuclear localization at ZT8 and cytoplasmic localization at ZT20, alongside diurnal expression in the suprachiasmatic nucleus and peripheral tissues (UniProt P20393: subcellular location and tissue specificity). Where collection time is known, keep it with the staining record; these statements do not predict an IHC intensity at a particular time. |
| Confidence in tissue comparisons | HPA rates tissue IHC Uncertain because staining and RNA expression have low consistency; the listed antibody’s IHC status is also Uncertain (HPA: tissue IHC reliability and antibody validation). Treat medium and not-detected entries as observed comparisons, not definitive positive or negative standards. |
| Topology and processing | UniProt lists no transmembrane segment, signal peptide or propeptide, and one chain spanning residues 1–614 (UniProt P20393: topology and processing). This supports scrutiny of an isolated membrane pattern; the supplied record does not establish epitope accessibility or a target-specific retrieval requirement. |
| Situation | Likely cause | Next action |
|---|---|---|
| Expected positive tissue is blank or very faint. | The staining run may have failed, or the section may differ from HPA’s observed medium-staining example (HPA: tissue IHC; general IHC practice). | Check section integrity, retrieval and detection run controls, then compare another HPA-listed medium-staining cell population if available (HPA: tissue IHC; general IHC practice). Do not infer a target-specific retrieval condition from these sources. |
| Signal appears mainly on membranes or outside cells. | An isolated surface pattern is hard to reconcile with NR1D1’s lack of a transmembrane segment (UniProt P20393: topology). | Inspect tissue morphology and no-primary controls; review detection background before scoring the outline as NR1D1 (general IHC practice). Nuclear signal alone should be assessed separately because UniProt also lists nuclear localization (UniProt P20393: subcellular location). |
| The whole section has diffuse chromogenic color. | Nonspecific background or endogenous detection activity can obscure cellular localization (general IHC practice). | Compare a no-primary control and review blocking, washing and detection conditions (general IHC practice). Score only signal that can be assigned to cells and compartments; HPA’s tissue pattern is predominantly cytoplasmic (HPA: tissue IHC). |
| A purported negative cell population stains strongly. | The result differs from HPA’s not-detected observations, but those observations carry an Uncertain reliability rating (HPA: tissue IHC). | Check the exact cell type, no-primary control and nearby tissue morphology before attributing the signal to NR1D1 (general IHC practice). For adipocytes, note the distinction between HPA’s not-detected IHC result and UniProt’s adipose tissue expression statement (HPA: tissue IHC; UniProt P20393: tissue specificity). |
| Nuclear and cytoplasmic proportions differ between specimens. | NR1D1 localization can vary with context and circadian time; UniProt reports nuclear predominance at ZT8 and cytoplasmic localization at ZT20 (UniProt P20393: subcellular location). | Record compartment, cell type and collection time when known, and compare matched specimens and staining runs (general IHC practice). Do not diagnose a technical failure from this difference alone (UniProt P20393: subcellular location). |
| An IHC result differs from an IF/ICC image. | HPA reports a predominantly cytoplasmic tissue IHC profile and supported nuclear-body localization in ICC-IF (HPA: tissue IHC and subcellular ICC-IF). | Interpret each result in its application and cellular context, while retaining HPA’s Uncertain tissue IHC rating (HPA: tissue IHC reliability and subcellular ICC-IF). |
Experiment evidence
IHC & IF images showing NR1D1 staining
A01077-2 · IHCIHC analysis of NR1D1 using anti-NR1D1 antibody (A01077-2). NR1D1 was detected in a paraffin-embedded section of human breast cancer tissue.
A01077-2 · IHCIHC analysis of NR1D1 using anti-NR1D1 antibody (A01077-2). NR1D1 was detected in a paraffin-embedded section of human colon cancer tissue.
HPA · Cerebral cortexHuman Protein Atlas IHC, Cerebral cortex. Source: https://www.proteinatlas.org/ENSG00000126368-NR1D1/tissue/cerebral+cortex#imid_7920416
HPA · ColonHuman Protein Atlas IHC, Colon. Source: https://www.proteinatlas.org/ENSG00000126368-NR1D1/tissue/colon#imid_7919262
HPA · LiverHuman Protein Atlas IHC, Liver. Source: https://www.proteinatlas.org/ENSG00000126368-NR1D1/tissue/liver#imid_7919263
HPA · KidneyHuman Protein Atlas IHC, Kidney. Source: https://www.proteinatlas.org/ENSG00000126368-NR1D1/tissue/kidney#imid_7919272
HPA · ICC-IF HaCaTHuman Protein Atlas immunofluorescence, HaCaT, antibody HPA007935; green = NR1D1, blue = nucleus, red = microtubules.
HPA · ICC-IF HaCaTHuman Protein Atlas immunofluorescence, HaCaT, antibody HPA007935; green = NR1D1, blue = nucleus, red = microtubules.
← swipe / scroll for more images →
Real IHC / IF data behind the staining-pattern expectations in this section.
Sample controls for NR1D1 IHC & IF
🧪Run adrenal gland first: its glandular cells should show medium NR1D1 staining (HPA: adrenal gland, glandular cells, Medium). Use salivary glandular cells as the negative tissue (HPA: salivary gland, glandular cells, Not detected); on the adrenal slide, look for cells outside the glandular compartment that lack specific staining, and verify their negative status rather than assuming it.
Positive control tissue: Adrenal gland (Glandular cells, HPA Medium)
Negative control tissue: Adipose tissue (HPA Not detected)
ICC-IF cell lines (HPA subcellular resource): HPA ICC-IF images show NR1D1 in HaCaT, PC-3, U2OS, with annotated localisation: Nuclear bodies (supported) (HPA subcellular).
Technical controls: Include a no-primary, secondary-only control, a rabbit isotype control matched to the primary antibody’s clonality, and NR1D1-knockout tissue or an antigen-peptide block where available (selected-SKU caption: rabbit primary and anti-rabbit secondary; standard IHC controls). For chromogenic detection, quench endogenous peroxidase and inspect the no-primary adrenal section for intrinsic pigment or background (standard IHC practice).
⚠️Feasibility: No target-specific fixation window or fixation effect is reported, and the selected-SKU paraffin-section caption does not state a fixative (selected-SKU tissue-IHC caption: fixative not stated). The caption uses heat retrieval in EDTA, pH 8.0, but does not establish that retrieval is required for every specimen (selected-SKU tissue-IHC caption). The supplied evidence does not establish that frozen sections or IF are easier; adrenal pigment or background should be checked against the no-primary control (standard IHC practice).
HPA tissue IHC evidence for NR1D1
Comprehensive Human Protein Atlas IHC scoring per tissue (reliability: Uncertain — Low 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 | Medium | Protein (IHC) | HPA → |
| Appendix | Glandular cells | Medium | Protein (IHC) | HPA → |
| Bone marrow | Hematopoietic cells | Medium | Protein (IHC) | HPA → |
| Bronchus | Respiratory epithelial cells | Medium | Protein (IHC) | HPA → |
| Cerebellum | Cells in granular layer | Medium | Protein (IHC) | HPA → |
Undetected expression · recommended negative controls
| Tissue | Cell type | Level | Evidence | Source |
|---|---|---|---|---|
| Adipose tissue | Adipocytes | Not detected | Protein (IHC) | HPA → |
| Breast | Adipocytes | Not detected | Protein (IHC) | HPA → |
| Ovary | Ovarian stroma cells | Not detected | Protein (IHC) | HPA → |
| Salivary gland | Glandular cells | Not detected | Protein (IHC) | HPA → |
| Smooth muscle | Smooth muscle cells | Not detected | Protein (IHC) | HPA → |
Section 3
Advanced NR1D1 IHC Tips
Troubleshoot NR1D1 staining in paraffin sections by checking retrieval, compartment, controls and scoring before interpreting differences between specimens.
How should I optimize retrieval when NR1D1 staining is weak in paraffin sections?
Start with heat-mediated retrieval in EDTA at pH 8.0 for NR1D1 paraffin sections (datasheet A01077-2). The selected tissue image used that retrieval before overnight incubation with 2 μg/ml antibody at 4°C, so keep those conditions together for the first comparison (caption A01077-2). If staining remains weak, compare a longer heating interval or another retrieval buffer on adjacent sections while holding antibody concentration and detection constant (standard IHC practice). Judge improvement by signal in intact cells and stable tissue morphology, and include a no-primary control to reveal retrieval-dependent background (standard IHC practice).
Could fixation explain weak or uneven NR1D1 staining?
NR1D1-specific fixation sensitivity is unknown: the selected paraffin-section caption does not state a fixative (caption A01077-2). Record the actual fixative, fixation duration, specimen thickness and processing history before comparing staining across blocks, because these variables can change antigen accessibility (standard IHC practice). Test adjacent sections with the established EDTA pH 8.0 retrieval and the same antibody concentration, then compare intact regions under identical detection conditions (datasheet A01077-2; standard IHC practice). If staining varies with processing history, report that association as a technical concern rather than claiming a demonstrated NR1D1 fixation effect (standard IHC practice).
Is cytoplasmic NR1D1 staining credible when I expect a nuclear receptor?
NR1D1 is reported in the nucleus and cytoplasm, with predominant nuclear localization at ZT8 and cytoplasmic localization at ZT20 (UniProt P20393). The tissue IHC summary describes cytoplasmic expression in most tissues, but assigns its staining an uncertain reliability rating (HPA tissue IHC). Score nuclear and cytoplasmic signal separately in morphologically intact cells, with the same thresholds and section handling across samples (standard IHC practice). A compartment shift can be biologically plausible, but compare collection timing and cell context before attributing it to circadian regulation; include staining controls because the HPA tissue pattern awaits external verification (UniProt P20393; HPA tissue IHC).
How can I investigate unexpected NR1D1 staining if the antibody epitope is unclear?
The supplied NR1D1 record lists 0 isoforms and a 1–614 chain, so these data offer no alternative isoform to explain distinct staining patterns (UniProt P20393). Its ligand-binding domain spans residues 284–614, and documented modifications include phosphorylation at residues 55 and 59 and acetylation at 191 and 192 (UniProt P20393). Determine the catalog antibody’s immunogen or mapped epitope before proposing epitope masking or modification-dependent recognition, since that information is absent here (standard IHC practice). Compare retrieval conditions and an independent antibody with a documented, different epitope on matched sections; require concordant cellular staining before interpreting discrepancies (standard IHC practice).
How should I investigate an NR1D1 signal with multiplex immunofluorescence?
Use IF as a separate validation experiment, pairing NR1D1 with a marker for the expected cell population in the specimen; endothelial cells and macrophages are documented expression contexts (UniProt P20393). Choose spectrally separated fluorophores and inspect unstained tissue in each channel, selecting a channel with lower autofluorescence for the weaker signal (standard IF practice). NR1D1 has no transmembrane segment and is reported in nuclear bodies, nucleus and cytoplasm, so use permeabilisation that allows antibody access to intracellular epitopes and assess nuclear access explicitly (UniProt P20393; HPA subcellular; standard IF practice). Include single-stain and no-primary controls, then compare compartments without transferring the paraffin-section retrieval conditions to IF (standard IF practice).
What should I change when NR1D1 DAB staining looks diffuse or nonspecific?
First compare stained sections with a no-primary control and examine whether color follows tissue edges, damaged areas or endogenous pigment rather than intact cells (standard IHC practice). The selected paraffin-section image used 10% goat serum blocking, 2 μg/ml primary antibody overnight at 4°C, and peroxidase detection with DAB (caption A01077-2). Add a peroxidase block before DAB development and check the secondary reagent, wash steps and development time if background persists (standard IHC practice). Titrate the primary antibody around the documented starting concentration on matched sections, retaining a condition that preserves cell-associated signal while reducing diffuse color (caption A01077-2; standard IHC practice).
How should I quantify NR1D1 across paraffin sections with mixed nuclear and cytoplasmic staining? ⚠ ANSWER MARKED FOR VERIFICATION
Define eligible cell populations and score nuclear and cytoplasmic NR1D1 separately, since both compartments are reported and tissue staining reliability is uncertain (UniProt P20393; HPA tissue IHC). Within a predefined region, record the percentage of positive eligible cells and an intensity-based H-score, or count positive cells per mm² when cell density varies (standard IHC practice). Normalize cell counts to the area of viable tissue and report the denominator for percentage scores; exclude folds, necrosis and section edges consistently (standard IHC practice). Keep retrieval, antibody concentration, DAB development and scoring thresholds matched across samples, and record collection time when testing circadian differences (datasheet A01077-2; UniProt P20393; standard IHC practice).
How can I distinguish genuine NR1D1 staining from tissue artefacts?
Look for reproducible staining in intact cells and assess nuclear and cytoplasmic compartments separately; both are documented for NR1D1 (UniProt P20393). A nuclear-bodies pattern has independent subcellular support, while the reported cytoplasmic tissue IHC profile carries uncertain reliability because staining and RNA data have low consistency (HPA subcellular; HPA tissue IHC). Question signal restricted to cut edges, necrotic areas or an unexpected cell population, and check pigment or endogenous peroxidase with appropriate control sections (standard IHC practice). Confirm a proposed positive pattern across matched sections and independent evidence before assigning a biological interpretation, especially when specimen collection times differ (UniProt P20393; standard IHC practice).
Boster reagents
Best NR1D1 / Nuclear receptor subfamily 1 group D member 1 IHC Antibodies
The catalog lists human, mouse and rat reactive NR1D1 antibodies for IHC and IF/ICC; the supplied image evidence covers human paraffin section IHC only (catalog applications/reactivity; A01077-2 IHC captions).
Real IHC data
Anti-NR1D1 Antibody ®
Cat # A01077-2
A01077-2 has IHC images from human breast cancer, colon cancer and colon paraffin sections; its listed IHC dilution is 2–5 μg/ml for human samples (A01077-2 IHC captions; catalog dilution). M01077-1 lists IHC and IF/ICC applications and human, mouse and rat reactivity, but has no supplied IHC or IF image (M01077-1 catalog applications/reactivity; image fields).
Which to pick: For tissue IHC, choose A01077-2 when a documented human paraffin section example matters; its captions describe EDTA retrieval at pH 8.0, 2 μg/ml primary antibody and DAB detection, with the fixative unreported (A01077-2 IHC captions). For IF/ICC, M01077-1 is the listed option because it is a rabbit monoclonal with IF/ICC among its applications, although no IF image is supplied (M01077-1 catalog clone/applications; image fields). Both list human, mouse and rat reactivity, but the supplied tissue images document only A01077-2 in human paraffin sections (catalog reactivity; A01077-2 IHC captions).
Each figure is that product's own IHC / IF validation image from its datasheet.
References
- UniProt Consortium. UniProt entry P20393 (NR1D1_HUMAN, Nuclear receptor subfamily 1 group D member 1).
- Human Protein Atlas. NR1D1 tissue IHC expression (reliability: Uncertain).
- Human Protein Atlas. NR1D1 subcellular location (ICC-IF): Localized to the nuclear bodies..
- Human Protein Atlas. NR1D1 antibody validation summary (1 antibodies).
- High expression of NR1D1 is associated with good prognosis in triple-negative breast cancer patients treated with chemotherapy. Breast cancer research : BCR 2019 — PMC6883674.
- Uncovering the Novel Role of NR1D1 in Regulating BNIP3-Mediated Mitophagy in Ulcerative Colitis. International journal of molecular sciences 2023 — PMC10531686.
- Co-regulation of Nr1d1 and Pparα in age-related changes of lipid metabolism and its modulation by calorie restriction. Aging 2025 — PMC12339034.
- Dysregulated circadian rhythm pathway in human osteoarthritis: NR1D1 and BMAL1 suppression alters TGF-β signaling in chondrocytes. Osteoarthritis and cartilage 2017 — PMC5438901.
- PubMed PMID:2539258 — UniProt-cited evidence.
- PubMed PMID:1971514 — UniProt-cited evidence.
- PubMed PMID:15489334 — UniProt-cited evidence.
Immunohistochemistry protocol sheet for NR1D1 (Nuclear receptor subfamily 1 group D member 1). Expected localisation Cytoplasmic tissue staining (HPA tissue IHC). Antigen retrieval: EDTA pH 8.0 HIER, heat-mediated (datasheet A01077-2). Validated IHC antibody: A01077-2 at 2-5 μg/ml (the product's own IHC validation image is shown). Controls (HPA): positive Adrenal gland (Glandular 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 A01077-2); 2. Fixation: Image fixative and duration unreported (datasheet A01077-2); 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 A01077-2); 20 min, 95–100 °C (standard); 6. Peroxidase block: 3% H2O2, 10 min , room temperature (standard); 7. Blocking: 10% goat serum (datasheet A01077-2); 8. Primary antibody: Rabbit anti-NR1D1, 2-5 μg/ml (datasheet A01077-2); 9. Primary incubation: Overnight at 4 °C (datasheet A01077-2). Watch for: Fixation: Keep fixation consistent across sections. (standard IHC practice; not target-specific); Caveat: Staining has low consistency with RNA data (HPA tissue IHC); Isoform / epitope: No annotated isoforms; one full-length chain (UniProt); Regulation: Diurnal expression oscillation (UniProt). Evidence: UniProt P20393, HPA tissue IHC · Uncertain, HPA ICC-IF · nuclear bodies., Datasheet A01077-2, PMC6883674, PMC10531686. QR code links to https://www.bosterbio.com/bosterbio-gene-info-cards/NR1D1/immunohistochemistry-ihc-guide.