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NIPBL / Nipped-B-like protein · IHC design guide
Design Immunohistochemistry for NIPBL
Plan NIPBL IHC in paraffin sections around the nuclear staining seen in most tissues (HPA tissue IHC). This guide covers fixation, retrieval, controls and chromogenic scoring, with three isoforms to consider when assessing antibody specificity (UniProt).
Evidence assembled Oct 2026 · For research use; verify linked source records and product datasheet before use
NIPBL 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 | Predominantly nuclear in tissue IHC (HPA tissue IHC) | |
| Staining pattern | Nuclear staining in glandular and trophoblastic cells (HPA tissue IHC) | |
| Antigen retrieval | Tris-EDTA pH 9.0 HIER, heat-mediated (datasheet A01939) | |
| 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 conditions consistent across sections (standard IHC practice; not target-specific) | |
| Caveat | Antibody staining and RNA show medium consistency (HPA tissue IHC) | |
| Regulation | Expression regulation is unreported (UniProt) | |
| Isoform / epitope | Three isoforms; epitope coverage is unspecified (UniProt) |
Section 1
Recommended NIPBL IHC & IF Protocols
The catalog antibody protocol uses heat-mediated Tris-EDTA pH 9.0 retrieval (datasheet: A01939). Published IHC protocols cover lung adenocarcinoma (PMC4438579) and testes (PMC3765518).
| Sample | Paraffin-embedded human tonsil tissue; fixative not specified (datasheet A01939) |
| Fixation | Image fixative and duration unreported (datasheet A01939); verify before use. |
| Sectioning | 4–5 µm sections on charged slides (standard) |
| Deparaffinisation | Xylene, graded ethanol series to water (standard) |
| Antigen retrieval | Heat retrieval: Tris-EDTA pH 9.0 (datasheet A01939); 20 min, 95–100 °C (standard) |
| 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-NIPBL, 1:50 recommended; image 1:200 (datasheet A01939) |
| 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 | NIPBL-positive staining in glandular cells of adrenal gland (HPA tissue IHC: High). HPA tissue profile: Nuclear expression in a majority of the tissues. No signal in the no-primary control. |
💡Decision noteStart with Tris-EDTA pH 9.0 heat retrieval: it matches the catalog antibody protocol (datasheet: A01939) and the detailed lung adenocarcinoma protocol (PMC4438579).
Section 2
What Is the Expected NIPBL Staining Pattern?
NIPBL should appear predominantly in nuclei across many tissues, consistent with its nuclear and chromosome localization and lack of a transmembrane segment (UniProt Q6KC79 topology; HPA: nuclear expression in a majority of tissues). Strong examples include adrenal and thyroid glandular cells, placental trophoblasts, and testicular pachytene spermatocytes (HPA tissue IHC: High). HPA rates the tissue profile Approved, with medium consistency between staining and RNA expression (HPA tissue IHC).
| Distinct nuclear staining in the expected cells, with little signal outside nuclei. | This matches the reported pattern (HPA tissue IHC: nuclear expression in a majority of tissues; UniProt Q6KC79: nucleus and chromosome). Compare intensity within the relevant cell population: HPA reports High staining in placental trophoblasts and Medium staining in skin fibroblasts (HPA tissue IHC). |
| Predominantly cytoplasmic or membrane-like staining in a paraffin section. | Treat this as a localization mismatch requiring validation, since the expected tissue pattern is nuclear (HPA tissue IHC). HPA reports uncertain cytosol and vesicle localization in ICC-IF; that observation alone does not establish a cytoplasmic IHC pattern (HPA subcellular ICC-IF). |
| Strong staining in a cell population reported as not detected. | Check identity and controls before interpreting it as NIPBL: HPA reports no detection in adipocytes, liver cholangiocytes, and splenic red-pulp cells (HPA tissue IHC). Cross-reactivity or endogenous detection activity can produce apparent signal (general IHC practice); an individual HPA observation is not an absolute exclusion rule. |
| Diffuse color across nuclei, cytoplasm, and tissue background. | The distribution does not resolve the predominantly nuclear pattern (HPA tissue IHC). Assess background with a negative detection control, then review blocking, wash stringency, and detection conditions (general chromogenic IHC practice). |
| No nuclear staining in a known-positive comparison section. | A failed positive comparison limits interpretation of the test section. Adrenal glandular cells or placental trophoblasts are High in the HPA tissue profile (HPA tissue IHC). Check section quality, retrieval, antibody conditions, and detection controls as general IHC workflow steps; no NIPBL-specific fixation effect is established here. |
💡Expected NIPBL appearanceCall the result consistent with NIPBL when the expected cells show predominantly nuclear staining—potentially High in placental trophoblasts or thyroid glandular cells (HPA tissue IHC)—while widespread cytoplasmic color or strong signal in HPA not-detected cells prompts a false-positive check (HPA tissue IHC; general IHC practice).
| Cell-level reference | Use the named cell population, not the whole organ, for comparison (HPA tissue IHC). UniProt describes high liver expression, while HPA reports cholangiocytes as Not detected; those statements refer to different levels of observation (UniProt Q6KC79; HPA tissue IHC). |
| Subcellular location | A nuclear readout is supported by both sources (UniProt Q6KC79; HPA tissue IHC). NIPBL has no annotated transmembrane segment, so membrane staining has no support from its reported topology (UniProt Q6KC79 topology). |
| Antibody evidence | HPA040834 is Approved for IHC and Supported for ICC; HPA058239 has Supported ICC status with no IHC status supplied (HPA antibodies). Interpret IHC images using the IHC evidence for the chosen antibody, alongside HPA's medium consistency rating for the tissue profile (HPA tissue IHC). |
| Isoforms and processing | UniProt lists 3 isoforms and one annotated protein chain spanning residues 1–2804, without a signal peptide or propeptide (UniProt Q6KC79). The payload gives no antibody epitope, so isoform coverage cannot be inferred. |
| Retrieval and fixation | Target-specific fixation effects are not established by the supplied assay evidence. Verify with a matched IHC source before attributing a result to fixation. |
| Can IF/ICC clarify a compartment? | HPA supports nucleoplasm as the main ICC-IF location; vesicle and cytosol locations are uncertain (HPA subcellular ICC-IF). Use this as a localization comparison, without treating the uncertain locations as expected chromogenic IHC staining. |
| Situation | Likely cause | Next action |
|---|---|---|
| The positive comparison has no nuclear signal. | The staining run may have failed, or the comparison section may be unsuitable; HPA reports High staining in adrenal glandular cells and placental trophoblasts (HPA tissue IHC). | Check the positive section, retrieval conditions, antibody application, and detection reagents with run controls (general paraffin-IHC practice). Avoid calling the test section negative until the comparison works. |
| Color is mainly cytoplasmic or outlines membranes. | This conflicts with the reported nuclear tissue pattern (HPA tissue IHC; UniProt Q6KC79: nucleus and chromosome). HPA's uncertain cytosol and vesicle ICC-IF observations do not validate that IHC appearance (HPA subcellular ICC-IF). | Confirm compartment boundaries with the counterstain and review the negative detection control; reassess antibody specificity if the mismatch persists (general IHC practice). |
| The entire section has diffuse color. | Diffuse deposition can obscure the expected nuclear pattern (HPA tissue IHC); background from blocking, washes, or detection is a general chromogenic IHC possibility. | Compare a negative detection control and review blocking, wash stringency, and detection time (general IHC practice). Score nuclear staining only where cell boundaries and counterstained nuclei remain interpretable. |
| A reported not-detected cell type stains strongly. | Cross-reactivity or endogenous detection activity is possible (general IHC practice). HPA lists adipocytes and liver cholangiocytes as Not detected, but its tissue profile has medium consistency with RNA data (HPA tissue IHC). | Verify the cell type and compare negative detection and known-positive controls. Treat persistent staining as unresolved until specificity is supported; do not turn an HPA reference level into an absolute biological rule. |
| A section gives mixed signals across cell types. | Cell-specific levels can differ within and between tissues: HPA reports High placental trophoblasts, Medium skin fibroblasts, and Low skeletal myocytes (HPA tissue IHC). | Score the named cells and nuclear compartment separately, using the same staining run for comparisons (general IHC practice). Avoid assigning one expected intensity to every cell in a tissue. |
| An IF/ICC image shows extra cytosolic or vesicular signal. | HPA labels those additional locations uncertain, while nucleoplasm is supported (HPA subcellular ICC-IF). | Use the supported nucleoplasmic signal as the localization reference (HPA subcellular ICC-IF). Assess extra signal with appropriate imaging controls as general IF practice; do not use it to redefine the expected IHC pattern. |
Experiment evidence
IHC & IF images showing NIPBL staining
A01939 · IHCImmunohistochemical analysis of paraffin-embedded human tonsil. 1, Antibody was diluted at 1:200 (4° overnight). 2, Tris-EDTA, pH9.0 was use
HPA · Cerebral cortexHuman Protein Atlas IHC, Cerebral cortex. Source: https://www.proteinatlas.org/ENSG00000164190-NIPBL/tissue/cerebral+cortex#imid_10916899
HPA · ColonHuman Protein Atlas IHC, Colon. Source: https://www.proteinatlas.org/ENSG00000164190-NIPBL/tissue/colon#imid_10916825
HPA · LiverHuman Protein Atlas IHC, Liver. Source: https://www.proteinatlas.org/ENSG00000164190-NIPBL/tissue/liver#imid_10916826
HPA · KidneyHuman Protein Atlas IHC, Kidney. Source: https://www.proteinatlas.org/ENSG00000164190-NIPBL/tissue/kidney#imid_10916835
HPA · ICC-IF A-431Human Protein Atlas immunofluorescence, A-431, antibody HPA040834; green = NIPBL, blue = nucleus, red = microtubules.
HPA · ICC-IF A-431Human Protein Atlas immunofluorescence, A-431, antibody HPA040834; green = NIPBL, blue = nucleus, red = microtubules.
← swipe / scroll for more images →
Real IHC / IF data behind the staining-pattern expectations in this section.
Sample controls for NIPBL IHC & IF
🧪Run placenta first: trophoblastic cells should show nuclear staining (HPA: High in trophoblastic cells; UniProt Q6KC79: nucleus). Use prostate glandular cells as the negative tissue comparator (HPA: Not detected in prostate glandular cells). On the placenta slide, assess background in adjacent cells by looking for counterstain without chromogenic nuclear signal; HPA does not identify a confirmed negative cell type within that slide (HPA: placenta tissue row).
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 NIPBL in A-431, SiHa, U2OS, KOLF2.1J, with annotated localisation: Nucleoplasm (supported) (HPA subcellular).
Technical controls: Include no-primary (secondary-only) and host-species- and clonality-matched isotype controls, plus NIPBL knockout material or a validated peptide block as a biological specificity control (standard IHC practice). Block endogenous peroxidase and inspect blood-rich placental areas for residual chromogen background (standard chromogenic IHC practice).
⚠️Feasibility: A target-specific fixation window is unreported, and the selected A01939 paraffin-section caption does not report a fixative (A01939 tissue-IHC caption). The caption uses Tris-EDTA retrieval at pH 9.0 and a 1:200 primary dilution, but does not establish that retrieval is required (A01939 tissue-IHC caption). The supplied evidence does not compare frozen sections with paraffin IHC or IF/ICC for ease of use; placental blood may complicate chromogenic scoring through endogenous peroxidase background (standard IHC practice).
HPA tissue IHC evidence for NIPBL
Comprehensive Human Protein Atlas IHC scoring per tissue (reliability: Approved — Medium consistency between antibody staining and RNA expression data.). Rows are taken directly from the HPA tissue chart — click any row's HPA link to view the source.
Positive expression · recommended positive controls
| Tissue | Cell type | Level | Evidence | Source |
|---|---|---|---|---|
| Adrenal gland | Glandular cells | High | Protein (IHC) | HPA → |
| Placenta | Trophoblastic cells | High | Protein (IHC) | HPA → |
| Skin | Fibroblasts | Medium | Protein (IHC) | HPA → |
| Stomach | Glandular cells | High | Protein (IHC) | HPA → |
| Testis | Pachytene spermatocytes | High | Protein (IHC) | HPA → |
Undetected expression · recommended negative controls
| Tissue | Cell type | Level | Evidence | Source |
|---|---|---|---|---|
| Adipose tissue | Adipocytes | Not detected | Protein (IHC) | HPA → |
| Liver | Cholangiocytes | Not detected | Protein (IHC) | HPA → |
| Lymph node | Germinal center cells | Not detected | Protein (IHC) | HPA → |
| Parathyroid gland | Glandular cells | Not detected | Protein (IHC) | HPA → |
| Prostate | Glandular cells | Not detected | Protein (IHC) | HPA → |
Section 3
Advanced NIPBL IHC Tips
Use the IHC-validated antibody as a starting point for paraffin-section staining, then assess signal by cell type and nuclear localisation (datasheet A01939; HPA tissue IHC).
What retrieval conditions should I try when NIPBL nuclear staining is weak?
Use heat-mediated Tris-EDTA, pH 9.0, antigen retrieval for paraffin sections (datasheet A01939). The selected tissue-IHC image used this retrieval with the catalog antibody at 1:200, incubated at 4°C overnight (datasheet A01939). If nuclear staining remains weak, compare retrieval duration on adjacent sections while keeping antibody incubation and chromogenic development constant (standard IHC practice). Evaluate signal in identifiable nuclei and check for tissue damage after heating; NIPBL is nuclear and chromosomal, while the HPA tissue profile reports nuclear staining in a majority of tissues (UniProt Q6KC79 subcellular location; HPA tissue IHC).
How should I troubleshoot fixation-related loss of NIPBL staining?
Target-specific fixation sensitivity is unknown: the selected paraffin-section caption does not state its fixative, and the supplied evidence does not establish a NIPBL-specific fixation effect (datasheet A01939). Record each specimen’s fixative, fixation duration and processing history before comparing staining across blocks (standard IHC practice). Apply the stated Tris-EDTA, pH 9.0, retrieval and 1:200 primary-antibody dilution consistently when assessing those differences (datasheet A01939). If a block stains poorly, compare it with a separately processed, morphologically preserved section and interpret any difference as a processing observation, not proof of NIPBL fixation sensitivity (standard IHC practice).
Where should convincing NIPBL staining appear in paraffin sections?
Expect predominantly nuclear staining: NIPBL is annotated in the nucleus and on chromosomes, and HPA reports nuclear expression in a majority of tissues (UniProt Q6KC79 subcellular location; HPA tissue IHC). HPA subcellular imaging supports nucleoplasmic localisation; its additional vesicle and cytosol assignments are uncertain (HPA subcellular). Assess chromogenic signal within intact nuclei against the counterstain, using the catalog antibody’s 1:200 tissue-IHC dilution as the documented starting condition (datasheet A01939; standard IHC practice). Predominantly diffuse cytoplasmic colour without corresponding nuclear signal warrants review of background, morphology and controls before assigning it to NIPBL (HPA subcellular; standard IHC practice).
Could NIPBL isoforms or epitope masking explain inconsistent IHC staining?
NIPBL has 3 annotated isoforms, and the supplied record does not map the catalog antibody’s epitope to any one of them (UniProt Q6KC79 isoforms; datasheet A01939). Therefore, a negative paraffin-section result cannot establish that a particular isoform is absent (UniProt Q6KC79 isoforms; standard IHC interpretation). The protein has no annotated transmembrane segment, and the record lists phosphorylation sites including serines 150 and 162; neither fact establishes antibody recognition of a modified epitope (UniProt Q6KC79 topology and modified residues). Compare adjacent sections under the documented pH 9.0 retrieval condition and consult epitope information if it becomes available (datasheet A01939; standard IHC practice).
How can IF help assess a questionable NIPBL IHC pattern?
Use IF as a localisation cross-check: HPA supports nucleoplasmic NIPBL signal in cell imaging, whereas its vesicle and cytosol assignments are uncertain (HPA subcellular). Multiplex with a marker for the expected cell type, then determine whether NIPBL signal falls within its nuclei; HPA tissue examples include high staining in placental trophoblastic cells (HPA tissue IHC; standard IF practice). Choose fluorophores in channels with low autofluorescence for the specimen and include single-channel controls to identify bleed-through (standard IF practice). Because NIPBL has no transmembrane segment and localises to the nucleus, permeabilise for access to its intracellular epitope, optimising this separately from the documented pH 9.0 tissue-IHC retrieval (UniProt Q6KC79 topology and subcellular location; datasheet A01939; standard IF practice).
How do I reduce diffuse brown background without losing nuclear signal?
First inspect a section processed without primary antibody to identify staining from detection reagents or endogenous peroxidase (standard chromogenic IHC practice). Use a peroxidase block before chromogenic detection and assess whether nonspecific colour falls after appropriate protein blocking and washing; these are general workflow steps, not NIPBL-specific findings (standard chromogenic IHC practice). Keep the documented primary dilution at 1:200 and secondary dilution at 1:200 initially, with the latter incubated for 45 minutes at room temperature (datasheet A01939). Judge changes by preservation of nuclear contrast in intact cells rather than by overall brown intensity (UniProt Q6KC79 subcellular location; standard IHC practice).
How should I quantify NIPBL staining across tissue sections? ⚠ ANSWER MARKED FOR VERIFICATION
Define the cell population and count only morphologically intact nuclei, consistent with the reported nuclear tissue pattern (HPA tissue IHC; standard IHC practice). For intensity scoring, assign nuclear categories 0–3 and calculate an H-score of 0–300; alternatively report the percentage of positive nuclei or positive-cell density per mm² (standard IHC scoring practice). Normalise positive counts to all eligible nuclei in the same defined compartment, or density to the measured tissue area, and keep thresholds and imaging settings consistent (standard IHC quantification practice). Record cell type because HPA reports both high-staining populations and populations with no detected signal, including placental trophoblastic cells and adipocytes, respectively (HPA tissue IHC).
What distinguishes true NIPBL staining from chromogenic artefact?
Prioritise crisp staining within intact nuclei, in keeping with NIPBL’s nuclear and chromosomal annotation and HPA’s predominantly nuclear tissue pattern (UniProt Q6KC79 subcellular location; HPA tissue IHC). Check cell identity: HPA reports high staining in adrenal glandular cells but no detected staining in adipocytes, so a uniform signal across every compartment deserves scrutiny (HPA tissue IHC; standard IHC interpretation). Discount colour concentrated at section edges or in necrotic areas, and investigate signal persisting without primary antibody as possible endogenous-enzyme or detection background (standard chromogenic IHC practice). Treat the selected 1:200 paraffin-section result as evidence for that documented staining setup, not proof that every positive cell is specific (datasheet A01939; standard IHC interpretation).
Boster reagents
Best NIPBL / Nipped-B-like protein IHC Antibodies
A01939 is listed for human and mouse IHC and IF (catalog: applications and reactivity); its supplied image shows IHC on a paraffin-embedded human tonsil section (A01939 IHC caption).
Real IHC data
Anti-Nipped-B-like protein NIPBL Antibody
Cat # A01939
A01939 will render with an IHC image of a paraffin-embedded human tonsil section (A01939 IHC caption). IF is listed as an application, and human and mouse are listed as reactive species; no IF image is supplied (catalog: A01939 applications, reactivity and image captions).
Which to pick: Choose A01939 for paraffin-section tissue IHC because its own image documents that preparation in human tonsil (A01939 IHC caption); the fixative is unreported (A01939 IHC caption). For IF/ICC, A01939 is the only candidate, but IF is listed without a supplied IF image and ICC is not listed (catalog: A01939 applications and image captions). For mouse samples, A01939 lists mouse reactivity, although its supplied IHC image shows human tissue (catalog: A01939 reactivity; A01939 IHC caption).
Each figure is that product's own IHC / IF validation image from its datasheet.
References
- UniProt Consortium. UniProt entry Q6KC79 (NIPBL_HUMAN, Nipped-B-like protein).
- Human Protein Atlas. NIPBL tissue IHC expression (reliability: Approved).
- Human Protein Atlas. NIPBL subcellular location (ICC-IF): Mainly localized to the nucleoplasm. In addition localized to vesicles and cytosol..
- Human Protein Atlas. NIPBL antibody validation summary (2 antibodies).
- Enhanced expression of cohesin loading factor NIPBL confers poor prognosis and chemotherapy resistance in non-small cell lung cancer. Journal of translational medicine 2015 — PMC4438579.
- Cohesin loading factor Nipbl localizes to chromosome axes during mammalian meiotic prophase. Cell division 2013 — PMC3765518.
- NIPBL::NACC1 Fusion Hepatic Carcinoma. The American journal of surgical pathology 2024 — PMC11238093.
- PubMed PMID:15146185 — UniProt-cited evidence.
- PubMed PMID:17974005 — UniProt-cited evidence.
- PubMed PMID:14702039 — UniProt-cited evidence.
Immunohistochemistry protocol sheet for NIPBL (Nipped-B-like protein). Expected localisation Predominantly nuclear in tissue IHC (HPA tissue IHC). Antigen retrieval: Tris-EDTA pH 9.0 HIER, heat-mediated (datasheet A01939). Validated IHC antibody: A01939 at 1:50 recommended; image 1:200 (the product's own IHC validation image is shown). Controls (HPA): positive Adrenal gland (Glandular cells); negative Adipose tissue. IHC workflow; specimen preparation unspecified. Protocol steps: 1. Sample: Paraffin-embedded human tonsil tissue; fixative not specified (datasheet A01939); 2. Fixation: Image fixative and duration unreported (datasheet A01939); 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: Tris-EDTA pH 9.0 (datasheet A01939); 20 min, 95–100 °C (standard); 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-NIPBL, 1:50 recommended; image 1:200 (datasheet A01939); 9. Primary incubation: Overnight at 4 °C (standard). Watch for: Fixation: Keep fixation conditions consistent across sections (standard IHC practice; not target-specific); Caveat: Antibody staining and RNA show medium consistency (HPA tissue IHC); Isoform / epitope: Three isoforms; epitope coverage is unspecified (UniProt); Regulation: Expression regulation is unreported (UniProt). Evidence: UniProt Q6KC79, HPA tissue IHC · Approved, HPA ICC-IF · Mainly localized to the nucleoplasm. In addition localized to…, Datasheet A01939, PMC4438579, PMC3765518. QR code links to https://www.bosterbio.com/bosterbio-gene-info-cards/NIPBL/immunohistochemistry-ihc-guide.