FUBP1 / Far upstream element-binding protein 1 · IHC design guide

Design Immunohistochemistry for FUBP1

Plan FUBP1 paraffin-section IHC around the widespread nuclear staining reported in tissue (HPA tissue IHC). This guide covers fixation consistency, antibody dilution, chromogenic detection and interpretation of nuclear staining.

Evidence assembled Oct 2026 · For research use; verify linked source records and product datasheet before use
Immunohistochemistry protocol sheet for FUBP1 (IHC for FUBP1): expected localisation Nuclear staining in tissue (HPA tissue IHC), antibody M03126, validated IHC image, and IHC protocol steps
Printable FUBP1 IHC protocol sheet — expected localisation Nuclear staining in tissue (HPA tissue IHC), antibody M03126, controls and protocol steps. Open the full FUBP1 IHC guide →

FUBP1 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 Nuclear staining in tissue (HPA tissue IHC)
Staining pattern Nuclear staining across many cell types (HPA tissue IHC)
Antigen retrieval EDTA pH 8.0 HIER, heat-mediated (datasheet M03126)
Positive control ⓘ Adipose tissue+4 more · see all
Negative control ⓘ None in HPA (detected in all 45 tissues); use no-primary + isotype controls
Important caveats
Reasons your staining may differ from the expected pattern.
Fixation Keep fixation consistent across sections. (standard IHC practice; not target-specific)
Caveat Ubiquitous staining limits negative tissue controls (HPA tissue IHC)
Regulation Low tissue specificity (HPA tissue RNA)
Isoform / epitope 2 isoforms; epitope coverage is unresolved (UniProt)
Section 1

Recommended FUBP1 IHC & IF Protocols

The catalog antibody’s IHC-P protocol (datasheet M03126) is followed by published FUBP1 staining procedures for murine cell preparations (PMC5447289) and human paraffin sections (PMC10725354; PMC8902172).

Recommended immunohistochemistry (IHC-P) protocol parameters
SampleParaffin-embedded human breast cancer tissue; fixative not specified (datasheet M03126)
FixationImage fixative and duration unreported (datasheet M03126); verify before use.
Sectioning4–5 µm sections on charged slides (standard)
DeparaffinisationXylene, graded ethanol series to water (standard)
Antigen retrievalHeat retrieval: EDTA pH 8.0 (datasheet M03126); 20 min, 95–100 °C (standard)
Peroxidase block3% H2O2, 10 min, room temperature (standard)
Blocking10% goat serum (datasheet M03126)
Primary antibodyRabbit monoclonal (clone AHC-6) anti-FUBP1, 1:50 (datasheet M03126)
Primary incubationOvernight at 4 °C (datasheet M03126)
DetectionHRP-conjugated secondary, DAB chromogen (datasheet M03126)
CounterstainHematoxylin, blue, dehydrate and mount (standard)
Expected resultFUBP1-positive staining in adipocytes of adipose tissue (HPA tissue IHC: High). HPA tissue profile: Ubiquitous nuclear expression. No signal in the no-primary control.
💡Decision noteStart with heat-mediated EDTA pH 8.0 retrieval (datasheet M03126); a pancreatic FFPE study also used microwave EDTA retrieval (PMC10725354).
Section 2

What Is the Expected FUBP1 Staining Pattern?

FUBP1 should appear predominantly in nuclei (UniProt Q96AE4: nucleus), with nucleoplasmic localisation also observed by ICC-IF (HPA subcellular: nucleoplasm). Tissue IHC describes ubiquitous nuclear expression and high staining in several listed cell populations (HPA tissue IHC: Supported; medium consistency with RNA). FUBP1 has no transmembrane segment, so a membrane pattern is unexpected (UniProt Q96AE4: topology).

What am I looking at on my slide?
Many cell nuclei stain across the section, including the expected cells in the tissue examined.This fits the reported ubiquitous nuclear pattern (HPA tissue IHC). High staining is reported in adipocytes, glandular cells, hematopoietic cells, respiratory epithelial cells and specified brain cell populations (HPA tissue IHC: High in listed cells). Compare nuclei within the same section; do not require identical intensity in every cell.
Cytoplasm or cell borders stain more strongly than nuclei.A dominant extranuclear pattern conflicts with the nuclear tissue profile and nucleoplasmic ICC-IF localisation (HPA tissue IHC; HPA subcellular). Treat it as a possible artefact or off-target signal, then inspect morphology and detection controls before interpreting it as FUBP1.
Only an unexpected cell population stains while expected nuclei remain blank.Consider cross-reactivity or endogenous detection activity (general IHC practice). Cell identity alone cannot prove either cause: HPA reports ubiquitous nuclear expression and low RNA tissue specificity (HPA tissue IHC). Recheck compartment, controls and the expected positive cells before assigning specificity.
Colour covers tissue broadly, including spaces between cells, with poorly defined nuclei.This does not provide convincing nuclear localisation (HPA tissue IHC: ubiquitous nuclear expression). Diffuse background can arise from nonspecific reagent binding or detection activity (general IHC practice). Judge the result against a no-primary control and look for discrete nuclear signal above background.
No nuclei stain in a tissue and cell population listed as high.For example, HPA reports high staining in bone marrow hematopoietic cells and breast glandular cells (HPA tissue IHC). Absence of signal warrants a technical check, but does not alone establish loss of FUBP1: HPA rates tissue IHC Supported, with medium antibody–RNA consistency (HPA tissue IHC).
💡Expected FUBP1 appearanceCall a result consistent with FUBP1 when cell nuclei show distinct, potentially high chromogenic staining in the listed positive populations (HPA tissue IHC: ubiquitous nuclear expression; High in listed cells); dominant membrane, cytoplasmic or acellular colour is suspect (UniProt Q96AE4: nucleus and no transmembrane segment; general IHC practice).
How each factor affects the staining
Expected compartmentNuclear tissue staining is the main reference pattern (UniProt Q96AE4: nucleus; HPA tissue IHC). Nucleoplasmic ICC-IF localisation supports the compartment, but IF/ICC has its own guide and does not supply an IHC protocol here (HPA subcellular).
Distribution across tissuesHPA describes ubiquitous nuclear expression and low RNA tissue specificity (HPA tissue IHC). The supplied high examples are positive comparators, while the absence of negative examples gives no evidence for a deliberately negative tissue control (HPA tissue IHC: positive list; negative list empty).
Antibody evidenceThe listed antibody HPA006149 has Supported IHC and Enhanced ICC validation (HPA antibodies). Those ratings apply to that antibody and assay; they do not establish identical staining with another antibody or turn an ICC-IF image into paraffin-section validation.
Protein formsUniProt records two isoforms and a chain spanning residues 2–644 (UniProt Q96AE4: isoforms; processing). Without an epitope map for the antibody used, the record cannot establish whether both isoforms are detected or whether a particular modified residue affects staining.
Membrane and secretion contextNo transmembrane segment, signal peptide or propeptide is recorded (UniProt Q96AE4: topology; processing). These annotations support prioritising intracellular nuclear signal; they do not identify an epitope or predict the outcome of antigen retrieval in a particular specimen.
Why is my staining missing, weak or wrong?
SituationLikely causeNext action
Known positive tissue shows no nuclear colour.The staining run may have failed, or the antibody conditions may be unsuitable (general IHC practice); HPA's high cell-level examples provide comparators (HPA tissue IHC).Check that the expected cells are present, then review the IHC-validated antibody instructions, retrieval and detection steps; compare with a concurrently stained positive section (general IHC practice).
Nuclei are weak while the entire section is faint.Low overall signal may reflect insufficient detection or an unsuitable antibody concentration (general IHC practice). A weak result alone cannot establish low FUBP1 expression in a listed high population (HPA tissue IHC).Review reagent performance, dilution and chromogen development using the antibody's IHC instructions and a positive control (general IHC practice). Score cells only when nuclear colour is distinguishable from background.
Strong diffuse colour obscures nuclei.Nonspecific binding or endogenous detection activity may contribute (general IHC practice); this appearance conflicts with the nuclear reference pattern (HPA tissue IHC).Inspect a no-primary control, then review blocking, washes and detection chemistry (general IHC practice). Reassess the slide only after discrete nuclear staining can be separated from diffuse colour.
Cell borders or cytoplasm dominate the stain.The compartment is inconsistent with nuclear FUBP1 and its lack of a transmembrane segment (UniProt Q96AE4: nucleus; topology). Off-target signal or a staining artefact is possible.Compare with the no-primary control and a positive section; check whether any nuclei retain a distinct signal before calling the pattern FUBP1 (general IHC practice; HPA tissue IHC: nuclear expression).
Only one cell population stains in an otherwise blank section.Selective off-target staining or endogenous activity is possible (general IHC practice), but HPA's ubiquitous nuclear profile does not define any supplied cell population as negative (HPA tissue IHC).Confirm cell identity and nuclear localisation, inspect controls, and compare expected positive cells in the same section (general IHC practice; HPA tissue IHC). Avoid declaring other cells truly negative from this slide alone.
ICC-IF images and paraffin IHC appear different.They are different assays: HPA reports nucleoplasmic ICC-IF localisation and tissue IHC nuclear expression, with separate validation ratings for HPA006149 (HPA subcellular; HPA antibodies).Compare compartment and assay-specific controls before judging agreement (general IHC practice). Use the separate IF/ICC guide for fluorescence workflow; do not use ICC-IF validation as a paraffin IHC protocol.

Sample controls for FUBP1 IHC & IF

🧪Run breast first and assess nuclear staining in its glandular cells (HPA: High in breast glandular cells; UniProt Q96AE4: nucleus). HPA detects FUBP1 in all 45 scored tissues, so use no-primary and isotype controls in place of a negative tissue; cells without nuclear chromogen on the positive slide should show counterstain only, but no cell type there is established as FUBP1-negative (HPA: no negative tissue rows; standard IHC practice).
Positive control tissue: Adipose tissue (Adipocytes, HPA High)
Negative control tissue: None in HPA: FUBP1 is detected in all 45 scored tissues. Use a no-primary (secondary-only) and an isotype control instead.
ICC-IF cell lines (HPA subcellular resource): HPA ICC-IF images show FUBP1 in A-431, U-251MG, U2OS, U2OS, siRNA 1 (10x), U2OS, siRNA 1 (40x), U2OS, siRNA 2 (10x), U2OS, siRNA 2 (40x), U2OS, scrambled (10x), U2OS, scrambled (40x), with annotated localisation: Nucleoplasm (enhanced) (HPA subcellular).
Technical controls: Include a no-primary, secondary-only control, a rabbit IgG isotype control matched to the primary antibody, and FUBP1-knockout material as a biological specificity control (caption: rabbit anti-FUBP1 M03126; standard IHC practice). Quench endogenous peroxidase and inspect the breast section for background chromogen before scoring nuclear signal (caption: peroxidase detection with DAB; standard IHC practice).
⚠️Feasibility: The selected paraffin-section caption reports heat retrieval in EDTA at pH 8.0, a 1:50 primary dilution overnight at 4°C, and DAB detection; its fixative is unreported (caption: M03126). A target-specific fixation window or fixation effect is unreported, and the supplied evidence does not establish whether frozen sections or IF are easier than paraffin IHC (caption: M03126; HPA: ICC-IF images available). In breast sections, glandular nuclear staining must be distinguished from peroxidase background (HPA: High in breast glandular cells; UniProt Q96AE4: nucleus; standard IHC practice).

HPA tissue IHC evidence for FUBP1

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

TissueCell typeLevelEvidenceSource
Adipose tissue Adipocytes High Protein (IHC) HPA →
Adrenal gland Glandular cells High Protein (IHC) HPA →
Appendix Glandular cells High Protein (IHC) HPA →
Bone marrow Hematopoietic cells High Protein (IHC) HPA →
Breast Glandular cells High Protein (IHC) HPA →

Undetected expression · recommended negative controls

TissueCell typeLevelEvidenceSource
None in HPA: FUBP1 is detected in all 45 scored tissues. Use a no-primary (secondary-only) and an isotype control instead.
Section 3

Advanced FUBP1 IHC Tips

Use the documented M03126 tissue staining conditions as the IHC starting point, then judge signal against FUBP1’s expected nuclear localisation.

Which retrieval conditions should I start with for FUBP1 IHC?
Start with heat-mediated antigen retrieval in EDTA at pH 8.0 (datasheet M03126). The M03126 paraffin-section image pairs that retrieval with a 1:50 primary dilution and overnight incubation at 4°C (datasheet M03126); keep those conditions documented while assessing retrieval. Judge improvement by nuclear staining, because FUBP1 is nuclear (UniProt Q96AE4) and its tissue profile is ubiquitously nuclear (HPA tissue IHC). If staining is weak, compare a second retrieval condition on matched sections, checking whether stronger signal also raises background (standard IHC practice). Record heating duration and cooling conditions so that a retrieval change can be distinguished from a detection change (standard IHC practice).
How should I troubleshoot fixation-dependent loss of FUBP1 staining?
Target-specific fixation sensitivity is unknown: the M03126 tissue caption identifies a paraffin section but does not state its fixative (datasheet M03126). For a new specimen series, record fixative, fixation duration and processing conditions, and compare matched sections before changing antibody concentration (standard IHC practice). Keep EDTA retrieval at pH 8.0 constant during that comparison (datasheet M03126). Score nuclear signal and tissue preservation together, since damaged morphology makes compartment assignment unreliable (standard IHC practice; UniProt Q96AE4: nucleus). Do not infer a preferred fixative from the reported nuclear tissue pattern (HPA tissue IHC) or FUBP1’s modified residues (UniProt Q96AE4).
What staining pattern is credible for FUBP1 in paraffin sections?
Prioritise staining within morphologically intact nuclei: FUBP1 is annotated as nuclear (UniProt Q96AE4), and tissue IHC describes ubiquitous nuclear expression (HPA tissue IHC). Use a nuclear counterstain to check whether DAB signal occupies nuclei rather than adjacent cytoplasm or extracellular material (standard IHC practice). Strong staining is reported in breast glandular cells and bone marrow hematopoietic cells (HPA tissue IHC), but compare like cell types within each section. A broad distribution across nuclei is plausible; the tissue staining has Supported reliability with medium agreement between staining and RNA data (HPA tissue IHC). Review focal cytoplasmic or edge staining against negative controls before assigning it to FUBP1 (standard IHC practice).
Could isoforms or epitope masking explain discordant FUBP1 IHC?
FUBP1 has 2 annotated isoforms and 4 KH domains (UniProt Q96AE4), so establish which sequence the catalog antibody recognises before comparing staining across specimens. The supplied M03126 caption does not define its epitope or isoform coverage (datasheet M03126); staining differences alone cannot identify an isoform. FUBP1 also has annotated modified residues, including phosphoserines at positions 52, 55 and 140 (UniProt Q96AE4), but their effect on this antibody is unreported. If staining conflicts with expectation, compare a second antibody with a documented, distinct epitope and retain matched retrieval and scoring conditions (standard IHC practice). Interpret agreement as supporting target assignment, while recording each antibody’s stated isoform coverage (standard IHC practice).
How can IF help assess an ambiguous FUBP1 IHC pattern?
Use IF as a separate localisation check when chromogenic IHC makes the nuclear boundary hard to judge (standard IHC/IF practice). FUBP1 is nuclear, with nucleoplasmic localisation reported in subcellular imaging (UniProt Q96AE4; HPA subcellular). For multiplexing, pair FUBP1 with a marker of the expected cell type and a nuclear counterstain, then check signal within the marked cells (standard IF practice). Select a fluorophore channel with low tissue autofluorescence and inspect unstained tissue in that channel before interpreting signal (standard IF practice). Because FUBP1 is not a membrane-spanning protein (UniProt Q96AE4 topology), permeabilisation must allow antibody access to the nuclear epitope; verify access against an appropriate control (standard IF practice).
What should I adjust when FUBP1 DAB staining is diffuse?
First locate the background: true FUBP1 signal should be predominantly nuclear (UniProt Q96AE4; HPA tissue IHC). The M03126 image used 10% goat serum blocking, a 1:50 rabbit primary overnight at 4°C, and a peroxidase-linked secondary for 30 minutes at 37°C (datasheet M03126). Use a no-primary section to assess secondary or chromogen background, and include a peroxidase block when using DAB (standard chromogenic IHC practice). If diffuse signal persists, compare primary concentrations on matched sections while keeping retrieval and development time fixed (standard IHC practice). Review section edges and damaged regions separately, since local artefacts can inflate apparent positivity (standard IHC practice).
How should I score FUBP1 staining across heterogeneous sections? ⚠ ANSWER MARKED FOR VERIFICATION
Define the cell population and analysis region before scoring, then count nuclear staining because FUBP1 is nuclear (UniProt Q96AE4; HPA tissue IHC). An H-score combines the percentage of cells at each intensity with intensity; alternatively, report % positive nuclei or positive-nucleus density per mm² (standard IHC scoring practice). Normalise each result to eligible, intact nuclei or viable tissue area, as appropriate to the chosen measure (standard IHC scoring practice). Keep counterstain, image acquisition and positivity thresholds consistent across the comparison (standard IHC practice). Report the staining distribution alongside the score, because HPA describes ubiquitous nuclear expression and Supported tissue staining with medium RNA agreement (HPA tissue IHC).
When is apparent FUBP1 positivity likely to be artefactual?
Treat crisp signal in intact nuclei as more credible than isolated cytoplasmic or extracellular deposits, given FUBP1’s nuclear localisation (UniProt Q96AE4; HPA tissue IHC). Check that positive profiles belong to the cell population being scored; staining in another cell population cannot establish positivity for the intended cells (standard IHC interpretation practice). Compare section edges, folds and necrotic areas with preserved interior tissue before accepting focal staining (standard IHC practice). A no-primary control and adequate peroxidase block help identify detection background and endogenous enzyme activity in DAB IHC (standard chromogenic IHC practice). If compartment and controls agree, interpret the result with the tissue profile’s Supported reliability and medium RNA agreement in mind (HPA tissue IHC).
Boster reagents

Best FUBP1 / Far upstream element-binding protein 1 IHC Antibodies

Anti-FUBP1 IHC images cover human breast and colon cancer, mouse spleen and thymus, and rat thymus (catalog IHC captions). IF/ICC data show U2OS cells (A03126-2 IF caption).

Real IHC data IHC analysis of FUBP1 using anti-FUBP1 antibody (M03126). FUBP1 was detected in a paraffin-embedded section of human breast cancer tissue. Heat mediated antigen retrieval was performed in EDTA buffer (pH 8.0, epitope retrieval solution). The tissue section was blocked with 10% goat serum. The tissue section was then incubated with 1:50 rabbit anti-FUBP1 Antibody (M03126) overnight at 4°C. Peroxidase Conjugated Goat Anti-rabbit IgG was used as secondary antibody and incubated for 30 minutes at 37°C. The tissue section was developed using HRP Conjugated Rabbit IgG Super Vision Assay Kit (Catalog # SV0002) with DAB as the chromogen.
Anti-FUBP1 Rabbit Monoclonal Antibody
Cat # M03126
Real IHC data IHC analysis of FUBP1 using anti-FUBP1 antibody (A03126-2). FUBP1 was detected in a paraffin-embedded section of mouse spleen tissue. Heat mediated antigen retrieval was performed in EDTA buffer (pH 8.0, epitope retrieval solution). The tissue section was blocked with 10% goat serum. The tissue section was then incubated with 2 μg/ml rabbit anti-FUBP1 Antibody (A03126-2) overnight at 4°C. Peroxidase Conjugated Goat Anti-rabbit IgG was used as secondary antibody and incubated for 30 minutes at 37°C. The tissue section was developed using HRP Conjugated Rabbit IgG Super Vision Assay Kit (Catalog # SV0002) with DAB as the chromogen.
Anti-FUBP1 Antibody ®
Cat # A03126-2

M03126 has IHC images from paraffin sections of human breast and colon cancer, mouse thymus, and rat thymus (M03126 IHC captions). A03126-2 has IHC images from paraffin sections of mouse spleen and human breast and colon cancer, plus IF/ICC data from U2OS cells (A03126-2 IHC and IF captions).

Which to pick: For tissue IHC across the pictured species, choose monoclonal M03126: its paraffin-section captions show human, mouse, and rat samples at 1:50 (M03126 catalog; M03126 IHC captions). For IF/ICC, choose A03126-2, which has a U2OS cell image at 5 μg/ml; M03126 lists IF/ICC as applications but has no IF image in this payload (A03126-2 IF caption; M03126 catalog). Both IHC examples use EDTA retrieval at pH 8.0, and neither caption reports the fixative (M03126 and A03126-2 IHC captions).

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

References

  1. UniProt Consortium. UniProt entry Q96AE4 (FUBP1_HUMAN, Far upstream element-binding protein 1).
  2. Human Protein Atlas. FUBP1 tissue IHC expression (reliability: Supported).
  3. Human Protein Atlas. FUBP1 subcellular location (ICC-IF): Localized to the nucleoplasm..
  4. Human Protein Atlas. FUBP1 antibody validation summary (1 antibodies).
  5. Delayed Mesoderm and Erythroid Differentiation of Murine Embryonic Stem Cells in the Absence of the Transcriptional Regulator FUBP1. Stem cells international 2017 — PMC5447289.
  6. MiR-16 mediates trastuzumab and lapatinib response in ErbB-2-positive breast and gastric cancer via its novel targets CCNJ and FUBP1. Oncogene 2016 — PMC5832962.
  7. Circulating autoantibodies to alpha-enolase (ENO1) and far upstream element-binding protein 1 (FUBP1) are negative prognostic factors for pancreatic cancer patient survival. Clinical and experimental medicine 2023 — PMC10725354.
  8. Pan-Cancer Transcriptome and Immune Infiltration Analyses Reveal the Oncogenic Role of Far Upstream Element-Binding Protein 1 (FUBP1). Frontiers in molecular biosciences 2022 — PMC8902172.
  9. PubMed PMID:8125259 — UniProt-cited evidence.
  10. PubMed PMID:16710414 — UniProt-cited evidence.
  11. PubMed PMID:15489334 — UniProt-cited evidence.