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RUNX1 / Runt-related transcription factor 1 · IHC design guide
Design Immunohistochemistry for RUNX1
Plan paraffin-section RUNX1 IHC around the nuclear tissue pattern (HPA tissue IHC) and the catalog antibody’s 0.5–1 μg/mL range (datasheet PB9157). Nasopharyngeal basal cells show high staining, while adipocytes have no detected staining (HPA tissue IHC).
Evidence assembled Oct 2026 · For research use; verify linked source records and product datasheet before use
RUNX1 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 several tissues (HPA tissue IHC) | |
| Staining pattern | Nuclear staining in several tissue cell types (HPA tissue IHC) | |
| Antigen retrieval | Citrate pH 6 HIER, heat-mediated (datasheet PB9157) | |
| Positive control | Nasopharynx+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 | PB9157 image captions also name RUNX2 and RUNX3 (datasheet PB9157) | |
| Regulation | Highest in thymus, marrow and blood (UniProt) | |
| Isoform / epitope | 11 isoforms; epitope coverage needs checking (UniProt) |
Section 1
Recommended RUNX1 IHC & IF Protocols
The catalog antibody’s IHC-P protocol is paired with four published RUNX1 IHC protocols (PMC4481134; PMC4420729; PMC13040063; PMC5725115).
| Sample | Paraffin-embedded rat thymus tissue; fixative not specified (datasheet PB9157) |
| Fixation | Image fixative and duration unreported (datasheet PB9157); verify before use. |
| Sectioning | 4–5 µm sections on charged slides (standard) |
| Deparaffinisation | Xylene, graded ethanol series to water (standard) |
| Antigen retrieval | Heat retrieval: Citrate pH 6, 20 min (datasheet PB9157) |
| Peroxidase block | 3% H2O2, 10 min, room temperature (standard) |
| Blocking | 10% goat serum (datasheet PB9157) |
| Primary antibody | Rabbit anti-RUNX1, 0.5-1μg/ml (datasheet PB9157) |
| Primary incubation | Overnight at 4 °C (datasheet PB9157) |
| Detection | Streptavidin-biotin complex (SABC), DAB chromogen (datasheet PB9157) |
| Counterstain | Hematoxylin, blue, dehydrate and mount (standard) |
| Expected result | RUNX1-positive staining in basal cells of nasopharynx (HPA tissue IHC: High). HPA tissue profile: Nuclear expression in several tissues. No signal in the no-primary control. |
💡Decision noteStart with heat-mediated citrate retrieval at pH 6 (datasheet: PB9157); optimize against the published conditions for your sample (PMC4481134; PMC4420729; PMC13040063).
Section 2
What Is the Expected RUNX1 Staining Pattern?
RUNX1 is a nuclear transcription factor with no transmembrane segment (UniProt Q01196). In paraffin sections, expect nuclear staining in selected cells, including nasopharyngeal basal cells, skin eccrine glands, and bone marrow hematopoietic cells (HPA tissue IHC). HPA describes nuclear expression in several tissues, with Enhanced IHC reliability and medium consistency between antibody staining and RNA expression (HPA tissue IHC).
| Distinct nuclear stain in nasopharyngeal basal cells or skin eccrine glands, with limited background (HPA tissue IHC). | This matches the reported High staining in those cell populations and RUNX1's nuclear location (HPA tissue IHC; UniProt Q01196). Score the named cells and their nuclei; neighboring cells need not share the same intensity (standard IHC practice). |
| Predominantly cytoplasmic or membranous chromogen in cells expected to be positive (HPA tissue IHC). | That conflicts with RUNX1's nuclear location (UniProt Q01196). Treat it as a possible artefact and check morphology, detection controls, and staining conditions before calling the section positive (standard IHC practice). |
| Strong stain in adipocytes, skeletal myocytes, or smooth muscle cells (HPA tissue IHC). | HPA reports RUNX1 as Not detected in these cell types (HPA tissue IHC). Investigate nonspecific antibody binding or endogenous detection activity with appropriate controls; staining alone cannot distinguish those causes (standard IHC practice). |
| Diffuse chromogen across nuclei, cytoplasm, and tissue spaces without a clear cell pattern (standard IHC practice). | This does not provide a convincing RUNX1 readout against the reported nuclear pattern (HPA tissue IHC; UniProt Q01196). Compare a no-primary control and review blocking, washing, and detection settings (standard IHC practice). |
| No nuclear signal in an adequately preserved nasopharyngeal basal-cell or skin eccrine-gland sample (HPA tissue IHC). | Those are High-staining examples, so a blank result warrants a technical check (HPA tissue IHC). Confirm that the expected cells are present, then review the antibody's IHC validation and the run's positive control (standard IHC practice). |
💡Expected RUNX1 appearanceCall a result positive when identifiable nasopharyngeal basal cells or skin eccrine glands show clear nuclear chromogen at the reported High level; diffuse cytoplasmic or background staining alone is unconvincing (HPA tissue IHC; UniProt Q01196).
| Cell and tissue selection (HPA tissue IHC) | HPA reports High staining in nasopharyngeal basal cells and skin eccrine glands, Medium in bone marrow hematopoietic cells, and Not detected in adipocytes or skeletal myocytes (HPA tissue IHC). Compare the specified cell types rather than whole-section darkness (standard IHC practice). |
| Antibody evidence (HPA antibodies; HPA tissue IHC) | HPA004176 has Enhanced IHC validation; HPA037912 has Enhanced ICC validation but no listed IHC status (HPA antibodies). The tissue profile has medium antibody–RNA consistency, so its intensity categories are reference observations, not guaranteed results for every section (HPA tissue IHC). |
| Isoforms and epitope coverage (UniProt Q01196) | UniProt lists 11 RUNX1 isoforms and a Runt domain at residues 50–178 (UniProt Q01196). The supplied evidence gives no antibody epitope, so it cannot establish which isoforms an antibody recognizes or explain a missing signal by isoform choice. |
| Processing and topology (UniProt Q01196) | RUNX1 is listed as one chain spanning residues 1–453, without a signal peptide, propeptide, or transmembrane segment (UniProt Q01196). These features support interpreting a nuclear pattern; they do not establish fixation sensitivity or an antigen retrieval setting. |
| IF/ICC? (HPA subcellular; HPA antibodies) | Q: What should IF/ICC show? A: Mainly nucleoplasmic RUNX1, with additional vesicular localization reported in HPA's ICC-IF images (HPA subcellular). That additional IF observation does not make vesicular chromogen an expected paraffin IHC result; HPA004176 and HPA037912 have Enhanced ICC validation (HPA antibodies). |
| Situation | Likely cause | Next action |
|---|---|---|
| The positive tissue appears blank (HPA tissue IHC). | The expected cell population may be absent from the section, or the staining run may have failed (standard IHC practice). | Locate the relevant basal or eccrine cells and compare the run's positive control; then check the chosen antibody's IHC validation and its documented staining conditions (HPA tissue IHC; standard IHC practice). |
| Nuclear stain is weak in bone marrow hematopoietic cells (HPA tissue IHC). | HPA reports Medium staining there, versus High in nasopharyngeal basal cells and skin eccrine glands (HPA tissue IHC). | Assess recognizable hematopoietic nuclei and compare a High-staining reference tissue before calling the run insensitive (HPA tissue IHC; standard IHC practice). |
| Cytoplasmic stain dominates in an expected positive cell type (HPA tissue IHC). | The pattern conflicts with nuclear RUNX1 localization and may reflect nonspecific staining or detection background (UniProt Q01196; standard IHC practice). | Compare a no-primary control, inspect nuclear morphology, and review blocking and detection steps before scoring a positive (standard IHC practice). |
| Cells reported as Not detected stain strongly (HPA tissue IHC). | For adipocytes or skeletal myocytes, this disagrees with the HPA observations; nonspecific binding or endogenous detection activity is possible (HPA tissue IHC; standard IHC practice). | Verify cell identity and compare no-primary and detection controls. Do not reclassify the HPA negative category from one unexplained stain (HPA tissue IHC; standard IHC practice). |
| The slide has widespread diffuse chromogen (standard IHC practice). | Background from the detection workflow can obscure a cell-specific nuclear pattern (standard IHC practice; UniProt Q01196). | Inspect a no-primary control and review blocking, washes, chromogen development, and counterstain; reassess only nuclei whose cell type remains identifiable (standard IHC practice). |
| Brain shows occasional weak nuclear staining (HPA tissue IHC). | HPA lists Low staining in several brain cell populations, while UniProt's tissue summary says expression was absent from brain among the tissues examined (HPA tissue IHC; UniProt Q01196). | Record the sampled region and cell type, and use appropriate controls. Treat weak brain staining cautiously because the supplied sources do not resolve this difference (HPA tissue IHC; UniProt Q01196). |
Experiment evidence
IHC & IF images showing RUNX1 staining
PB9157 · IHCIHC analysis of RUNX1 using anti-RUNX1 antibody (PB9157). RUNX1 was detected in paraffin-embedded section of rat thymus tissue. Heat mediate
PB9157 · IHCIHC analysis of RUNX2 using anti-RUNX2 antibody (PB9157). RUNX2 was detected in paraffin-embedded section of human mammary cancer tissue. He
M00086 · IHCImmunohistochemical analysis of paraffin-embedded mouse lung, using RUNX1/RUNX2/RUNX3 Antibody.
HPA · Cerebral cortexHuman Protein Atlas IHC, Cerebral cortex. Source: https://www.proteinatlas.org/ENSG00000159216-RUNX1/tissue/cerebral+cortex#imid_1451652
HPA · ColonHuman Protein Atlas IHC, Colon. Source: https://www.proteinatlas.org/ENSG00000159216-RUNX1/tissue/colon#imid_1457394
HPA · LiverHuman Protein Atlas IHC, Liver. Source: https://www.proteinatlas.org/ENSG00000159216-RUNX1/tissue/liver#imid_1457403
HPA · KidneyHuman Protein Atlas IHC, Kidney. Source: https://www.proteinatlas.org/ENSG00000159216-RUNX1/tissue/kidney#imid_1457388
HPA · ICC-IF A-431Human Protein Atlas immunofluorescence, A-431, antibody HPA037912; green = RUNX1, blue = nucleus, red = microtubules.
HPA · ICC-IF A-431Human Protein Atlas immunofluorescence, A-431, antibody HPA037912; green = RUNX1, blue = nucleus, red = microtubules.
← swipe / scroll for more images →
Real IHC / IF data behind the staining-pattern expectations in this section.
Sample controls for RUNX1 IHC & IF
🧪Run nasopharynx first and expect staining in basal cells (HPA: High in nasopharynx basal cells). Use adipose tissue as the negative tissue, focusing on adipocytes (HPA: Not detected in adipocytes); on the positive slide, compare basal-cell staining with unstained neighboring cells as a background reference, without assuming those cells are RUNX1-negative.
Positive control tissue: Nasopharynx (Basal cells, HPA High)
Negative control tissue: Adipose tissue (HPA Not detected)
ICC-IF cell lines (HPA subcellular resource): HPA ICC-IF images show RUNX1 in A-431, U2OS, U-251MG, NIH 3T3, with annotated localisation: Nucleoplasm (enhanced) (HPA subcellular).
Technical controls: Include a no-primary (secondary-only) slide, a concentration-matched rabbit IgG isotype control, and RUNX1-knockout material as a biological negative (caption: rabbit primary antibody; standard IHC practice). For chromogenic detection, quench endogenous peroxidase and assess endogenous biotin background because the reported method uses a biotinylated secondary, streptavidin-biotin complex, and DAB (caption: biotinylated secondary and SABC/DAB).
⚠️Feasibility: The selected paraffin-section caption reports citrate retrieval at pH 6 for 20 minutes, but gives no retrieval comparison or fixative; a target-specific fixation window and fixation effect are unreported (caption: citrate retrieval; fixative not stated). The supplied evidence does not establish whether frozen sections or IF are easier than paraffin IHC (caption: paraffin-section IHC; HPA: ICC-IF images). In nasopharynx, interpret staining by cell type because the HPA positive reference is the basal-cell compartment; use the chromogenic background controls to check for peroxidase or biotin artefact (HPA: High in nasopharynx basal cells; caption: SABC/DAB).
HPA tissue IHC evidence for RUNX1
Comprehensive Human Protein Atlas IHC scoring per tissue (reliability: Enhanced — 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 |
|---|---|---|---|---|
| Nasopharynx | Basal cells | High | Protein (IHC) | HPA → |
| Skin | Eccrine glands | High | Protein (IHC) | HPA → |
| Appendix | Lymphoid tissue | Medium | Protein (IHC) | HPA → |
| Bone marrow | Hematopoietic cells | Medium | Protein (IHC) | HPA → |
| Breast | Glandular cells | Medium | Protein (IHC) | HPA → |
Undetected expression · recommended negative controls
| Tissue | Cell type | Level | Evidence | Source |
|---|---|---|---|---|
| Adipose tissue | Adipocytes | Not detected | Protein (IHC) | HPA → |
| Esophagus | Squamous epithelial cells | Not detected | Protein (IHC) | HPA → |
| Liver | Cholangiocytes | Not detected | Protein (IHC) | HPA → |
| Oral mucosa | Squamous epithelial cells | Not detected | Protein (IHC) | HPA → |
| Parathyroid gland | Glandular cells | Not detected | Protein (IHC) | HPA → |
Section 3
Advanced RUNX1 IHC Tips
Troubleshoot RUNX1 staining in paraffin sections by checking retrieval, nuclear localisation, controls and cell-specific scoring before interpreting chromogenic signal.
Which retrieval conditions should I try when RUNX1 nuclear staining is weak?
Start with heat-mediated retrieval in citrate buffer at pH 6 for 20 minutes (PB9157 tissue-IHC caption). Run a known positive section alongside the test section and keep heating, cooling and subsequent staining conditions consistent so retrieval is the variable being assessed (standard IHC practice). The documented paraffin-section example used 1 µg/mL primary antibody overnight at 4°C, providing a starting point for PB9157 (PB9157 tissue-IHC caption). If nuclear staining remains weak, evaluate an alternative retrieval buffer on parallel sections while checking for tissue damage and increased background; that alternative has no supplied RUNX1-specific validation (standard IHC practice).
Could fixation explain loss of RUNX1 signal in my paraffin sections?
Target-specific sensitivity of RUNX1 staining to fixation is unknown from the supplied evidence; the PB9157 paraffin-section caption does not state its fixative (PB9157 tissue-IHC caption). Record the specimen's fixative, fixation duration and processing history, then compare sections processed consistently before attributing a weak result to fixation (standard IHC practice). Use the documented citrate pH 6, 20-minute retrieval as a controlled starting condition for PB9157 (PB9157 tissue-IHC caption). If staining varies between specimens, include a concurrently stained positive tissue control and examine preservation of nuclear morphology; neither HPA expression patterns nor RUNX1 modifications establish a fixation effect (standard IHC practice; HPA tissue IHC; UniProt Q01196).
How should I evaluate RUNX1 staining outside nuclei?
Prioritise staining within intact nuclei because RUNX1 is annotated as nuclear and HPA reports nuclear expression across several tissues (UniProt Q01196; HPA tissue IHC). Compare chromogen placement with a nuclear counterstain at high magnification, particularly where crowded cells make adjacent cytoplasm appear positive (standard IHC practice). HPA also reports nucleoplasmic localisation with an additional vesicular signal in cellular imaging, so a nonnuclear pattern alone should not establish tissue-section specificity (HPA subcellular). If cytoplasmic or diffuse staining dominates, review retrieval, antibody concentration, secondary-only controls and endogenous detection background before assigning a RUNX1-positive cell (standard IHC practice).
Can this stain distinguish RUNX1 isoforms or modified epitopes?
Do not assign an isoform from chromogenic staining unless the antibody epitope and isoform coverage have been established independently; RUNX1 has 11 listed isoforms (UniProt Q01196). Its Runt domain spans residues 50–178, while listed modified residues include phosphorylation and acetylation sites, so epitope placement can matter when comparing reagents (UniProt Q01196). The supplied PB9157 caption documents tissue staining conditions but does not map its epitope or demonstrate isoform discrimination (PB9157 tissue-IHC caption). If staining differs across specimens, check antibody epitope documentation and use an independently validated isoform-specific assay before treating intensity differences as evidence of alternative splicing (standard IHC interpretation).
How can I check RUNX1 localisation by IF alongside paraffin-section IHC?
For the separate IF/ICC assay, multiplex RUNX1 with a validated marker of the expected cell population and a nuclear dye, then compare cell identity and nuclear localisation with the chromogenic sections (standard IF practice; UniProt Q01196). HPA reports RUNX1 mainly in the nucleoplasm, with an additional vesicular location in cellular imaging (HPA subcellular). Choose fluorophores whose emission can be separated from specimen autofluorescence and include single-stain controls when assessing overlap (standard IF practice). RUNX1 has no transmembrane segment, so use controlled permeabilisation to reach its intracellular nuclear epitope; optimise that step for the IF antibody because no IF fixation or permeabilisation conditions are supplied here (UniProt Q01196; standard IF practice).
What should I check when RUNX1 DAB staining is diffuse?
First inspect a section without primary antibody to identify signal from secondary reagents, endogenous enzymes or the detection system (standard IHC practice). The PB9157 example used 10% goat serum blocking, a biotinylated secondary antibody, a streptavidin–biotin complex and DAB (PB9157 tissue-IHC caption). Because that workflow uses biotin-based detection, evaluate a biotin-related control if background persists, and apply an endogenous peroxidase block as a general chromogenic IHC step (standard IHC practice). Titrate primary antibody around the documented 1 µg/mL condition on matched sections and judge improvement by nuclear contrast rather than overall brown intensity (PB9157 tissue-IHC caption; standard IHC practice).
How should I score RUNX1 across mixed-cell tissue sections? ⚠ ANSWER MARKED FOR VERIFICATION
Define the cell population and a nuclear positivity threshold using concurrently stained controls before counting RUNX1-positive cells (standard IHC practice; UniProt Q01196). Report the percentage of positive nuclei and, when intensity is reproducible, an H-score calculated from the proportions at each intensity level (standard IHC practice). For heterogeneous tissue, record positive-cell density per mm² within a specified compartment and normalise percentages to all evaluable nuclei of the same cell population, not to every cell on the slide (standard IHC practice). Keep retrieval, detection, counterstaining and image analysis settings consistent, and exclude folds, damaged edges and necrotic regions from scoring (standard IHC practice).
How do I distinguish genuine RUNX1-positive cells from staining artefact?
A credible positive call places chromogen over intact nuclei in an anatomically identified cell population, consistent with RUNX1's nuclear annotation and HPA's tissue staining profile (UniProt Q01196; HPA tissue IHC). HPA reports medium RUNX1 staining in bone-marrow hematopoietic cells and no detection in adipocytes, offering tissue-specific comparisons rather than universal positive and negative standards (HPA tissue IHC). Treat edge-restricted staining, necrotic deposits and signal in a secondary-only control as possible technical artefacts, including endogenous enzyme activity (standard IHC practice). Interpret unexpected cytoplasmic staining cautiously, and remember that HPA rates its tissue-IHC evidence Enhanced while describing only medium consistency with RNA expression (HPA tissue IHC).
Boster reagents
Best RUNX1 / Runt-related transcription factor 1 IHC Antibodies
Explore IHC antibodies with images of rat thymus and mouse lung paraffin sections (PB9157 and M00086 image captions); both list human, mouse and rat reactivity (catalog reactivity).
Real IHC data
Anti-RUNX1/AML1 Antibody ®
Cat # PB9157
Real IHC data
Anti-RUNX1/RUNX2/RUNX3 Rabbit Monoclonal Antibody
Cat # M00086
PB9157 has a RUNX1 IHC image from a rat thymus paraffin section and lists human, mouse and rat IHC reactivity (PB9157 image caption; catalog applications/reactivity). M00086 has an IHC image from a mouse lung paraffin section, lists human, mouse and rat reactivity, and includes IF/ICC among its applications (M00086 image caption; catalog applications/reactivity).
Which to pick: For tissue IHC focused on RUNX1, choose PB9157: its rat thymus paraffin image documents citrate retrieval and a primary concentration of 1 μg/ml (PB9157 image caption). For IF/ICC, choose M00086 because IF and ICC are listed applications, while its antibody title covers RUNX1, RUNX2 and RUNX3; no IF image is supplied (M00086 catalog title/applications/image alts). Both list human, mouse and rat reactivity, but their IHC images document rat and mouse tissue respectively; the fixative is unreported in both captions (catalog reactivity; PB9157 and M00086 image captions).
Each figure is that product's own IHC / IF validation image from its datasheet.
References
- UniProt Consortium. UniProt entry Q01196 (RUNX1_HUMAN, Runt-related transcription factor 1).
- Human Protein Atlas. RUNX1 tissue IHC expression (reliability: Enhanced).
- Human Protein Atlas. RUNX1 subcellular location (ICC-IF): Mainly localized to the nucleoplasm. In addition localized to vesicles..
- Human Protein Atlas. RUNX1 antibody validation summary (2 antibodies).
- Runx1 is associated with breast cancer progression in MMTV-PyMT transgenic mice and its depletion in vitro inhibits migration and invasion. Journal of cellular physiology 2015 — PMC4481134.
- Runx1 Activities in Superficial Zone Chondrocytes, Osteoarthritic Chondrocyte Clones and Response to Mechanical Loading. Journal of cellular physiology 2015 — PMC4420729.
- RUNX1 restrains STAT1-GITRL signaling to shape an immunosuppressive CRC microenvironment. Cell death discovery 2026 — PMC13040063.
- RUNX1 promote invasiveness in pancreatic ductal adenocarcinoma through regulating miR-93. Oncotarget 2017 — PMC5725115.
- PubMed PMID:1720541 — UniProt-cited evidence.
- PubMed PMID:7533526 — UniProt-cited evidence.
- PubMed PMID:8490181 — UniProt-cited evidence.
Immunohistochemistry protocol sheet for RUNX1 (Runt-related transcription factor 1). Expected localisation Nuclear staining in several tissues (HPA tissue IHC). Antigen retrieval: Citrate pH 6 HIER, heat-mediated (datasheet PB9157). Validated IHC antibody: PB9157 at 0.5-1μg/ml (the product's own IHC validation image is shown). Controls (HPA): positive Nasopharynx (Basal cells); negative Adipose tissue. IHC-P workflow on paraffin sections; fixative unspecified. Protocol steps: 1. Sample: Paraffin-embedded rat thymus tissue; fixative not specified (datasheet PB9157); 2. Fixation: Image fixative and duration unreported (datasheet PB9157); 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: Citrate pH 6 , 20 min (datasheet PB9157); 6. Peroxidase block: 3% H2O2, 10 min , room temperature (standard); 7. Blocking: 10% goat serum (datasheet PB9157); 8. Primary antibody: Rabbit anti-RUNX1, 0.5-1μg/ml (datasheet PB9157); 9. Primary incubation: Overnight at 4 °C (datasheet PB9157). Watch for: Fixation: Keep fixation consistent across sections. (standard IHC practice; not target-specific); Caveat: PB9157 image captions also name RUNX2 and RUNX3 (datasheet PB9157); Isoform / epitope: 11 isoforms; epitope coverage needs checking (UniProt); Regulation: Highest in thymus, marrow and blood (UniProt). Evidence: UniProt Q01196, HPA tissue IHC · Enhanced, HPA ICC-IF · Mainly localized to the nucleoplasm. In addition localized to…, Datasheet PB9157, PMC4481134, PMC4420729. QR code links to https://www.bosterbio.com/bosterbio-gene-info-cards/RUNX1/immunohistochemistry-ihc-guide.