RUNX1 / Runt-related transcription factor 1 · IHC design guide

Design Immunohistochemistry for RUNX1

Plan chromogenic RUNX1 IHC in paraffin sections around the expected nuclear signal (HPA tissue IHC). Use HPA-positive basal or eccrine gland cells as reference material, and check antibody specificity before scoring (HPA tissue IHC; datasheet M00086).

Evidence assembled Oct 2026 · For research use; verify linked source records and product datasheet before use
Immunohistochemistry protocol sheet for RUNX1 (IHC for RUNX1): expected localisation Nuclear staining in several tissues (HPA tissue IHC), antibody PB9157, validated IHC image, and IHC protocol steps
Printable RUNX1 IHC protocol sheet — expected localisation Nuclear staining in several tissues (HPA tissue IHC), antibody PB9157, controls and protocol steps. Open the full RUNX1 IHC guide →

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 signal in basal and eccrine gland cells (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 paraffin sections (standard IHC practice; not target-specific)
Caveat M00086 recognizes RUNX1/2/3; verify specificity (datasheet M00086)
Regulation Highest in thymus, marrow and blood (UniProt)
Isoform / epitope 11 isoforms; verify epitope coverage (UniProt)
Section 1

Recommended RUNX1 IHC & IF Protocols

The catalog antibody protocol uses citrate pH 6 heat retrieval (datasheet: PB9157). The published IHC protocols below provide sample-specific staining conditions (PMC4481134; PMC4420729; PMC13040063; PMC5725115).

Recommended immunohistochemistry (IHC-P) protocol parameters
SampleParaffin-embedded rat thymus tissue; fixative not specified (datasheet PB9157)
FixationImage fixative and duration unreported (datasheet PB9157); verify before use.
Sectioning4–5 µm sections on charged slides (standard)
DeparaffinisationXylene, graded ethanol series to water (standard)
Antigen retrievalHeat retrieval: Citrate pH 6, 20 min (datasheet PB9157)
Peroxidase block3% H2O2, 10 min, room temperature (standard)
Blocking10% goat serum (datasheet PB9157)
Primary antibodyRabbit anti-RUNX1, 0.5-1μg/ml (datasheet PB9157)
Primary incubationOvernight at 4 °C (datasheet PB9157)
DetectionStreptavidin-biotin complex (SABC), DAB chromogen (datasheet PB9157)
CounterstainHematoxylin, blue, dehydrate and mount (standard)
Expected resultRUNX1-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 citrate pH 6 heat retrieval for the catalog antibody (datasheet: PB9157); the published EDTA pH 8.0 condition used a different antibody (PMC13040063).
Section 2

What Is the Expected RUNX1 Staining Pattern?

RUNX1 should appear mainly in nuclei in paraffin-section IHC (UniProt Q01196: nucleus; HPA: nuclear expression in several tissues). Look for staining in nasopharyngeal basal cells, skin eccrine glands and bone-marrow hematopoietic cells (HPA: High, High and Medium, respectively). RUNX1 has no transmembrane segment (UniProt Q01196: topology). HPA rates the tissue IHC profile Enhanced, with medium consistency between antibody staining and RNA expression (HPA: tissue IHC).

What am I looking at on my slide?
Distinct nuclear staining in nasopharyngeal basal cells or skin eccrine glands.This matches two reported High cell populations and the expected compartment (HPA: tissue IHC; UniProt Q01196: nucleus). Judge the named cells, since staining across an entire tissue is not the reported pattern (HPA: cell-specific tissue IHC).
Strong cytoplasmic staining with little or no nuclear staining in an expected-positive cell population.Treat this as an IHC localisation problem and review specificity and detection controls (UniProt Q01196: nucleus; general IHC practice). HPA also reports vesicles in ICC-IF, but that additional IF location does not establish a predominantly cytoplasmic chromogenic IHC pattern (HPA: subcellular ICC-IF).
Signal in adipocytes or skeletal-muscle myocytes while the expected-positive cells are unstained.HPA reports both cell types as Not detected (HPA: tissue IHC). Suspect cross-reactivity or endogenous detection activity and compare control sections (general IHC practice); the unexpected signal alone does not identify its cause.
Broad, diffuse colour obscures nuclei and tissue boundaries.The slide cannot be scored reliably for the reported nuclear pattern (HPA: tissue IHC; general IHC practice). Nonspecific binding, excess detection signal or endogenous enzyme activity are possible workflow causes; inspect controls before calling cells positive (general IHC practice).
No nuclear signal in nasopharyngeal basal cells, skin eccrine glands or bone-marrow hematopoietic cells.These are reported High, High and Medium populations, respectively (HPA: tissue IHC). Check that the chosen population is present and that the IHC detection run worked (general IHC practice). An absent signal on one slide does not by itself establish absent RUNX1.
💡Expected RUNX1 appearanceCall a result positive when discernible nuclear signal occurs in the named cells, especially High nasopharyngeal basal cells or skin eccrine glands (HPA: tissue IHC); isolated diffuse background or staining confined to HPA Not detected cell types is suspect (HPA: tissue IHC; general IHC practice).
How each factor affects the staining
Cell population selected for scoringHPA reports High nasopharyngeal basal cells and skin eccrine glands, but Medium bone-marrow hematopoietic cells and Not detected adipocytes (HPA: tissue IHC). Select and score the named cells; these labels do not promise uniform staining within a whole section.
Tissue expression versus slide intensityUniProt reports highest expression in thymus, bone marrow and peripheral blood (UniProt Q01196: tissue specificity). HPA assigns bone-marrow hematopoietic cells Medium by IHC (HPA: tissue IHC). Do not convert the UniProt expression ranking into an expected chromogenic intensity.
Antibody validationHPA004176 is IHC Enhanced, a status supported by independent antibody agreement or orthogonal data (HPA: antibody validation). HPA037912 has an ICC Enhanced entry but no IHC rating in the supplied record (HPA: antibody validation); its IF result is not IHC validation.
Isoform and epitope coverageUniProt lists 11 RUNX1 isoforms and the Runt domain at residues 50–178 (UniProt Q01196: isoforms and domain). The supplied record gives no antibody epitope, so isoform recognition cannot be inferred; consult the IHC-validated antibody's documentation before interpreting a missing population.
Processing and staining compartmentUniProt reports no signal peptide, propeptide or transmembrane segment and lists one RUNX1 chain spanning residues 1–453 (UniProt Q01196: processing and topology). These facts support a nuclear expectation, but do not establish fixation sensitivity or predict how a particular epitope survives processing.
IF/ICC Q&A: what location should IF show?Mainly nucleoplasmic staining, with an additional vesicular location reported by HPA ICC-IF (HPA: subcellular ICC-IF). Interpret that observation within the separate IF/ICC guide; this section offers no IF protocol option.
Why is my staining missing, weak or wrong?
SituationLikely causeNext action
Expected-positive cells show no nuclear colour.The cells may be absent from the section, or the IHC run may have failed (general IHC practice). HPA reports High nasopharyngeal basal and skin eccrine cells and Medium bone-marrow hematopoietic cells (HPA: tissue IHC).Confirm the named cells on the section; review the IHC-validated antibody's documented conditions and a run control (general IHC practice). Do not assign a RUNX1-specific retrieval or fixation failure from these sources.
Signal is mostly cytoplasmic rather than nuclear.Possible nonspecific staining or detection artefact (general IHC practice); a mostly cytoplasmic IHC result conflicts with the reported nuclear pattern (UniProt Q01196: nucleus; HPA: tissue IHC).Compare the same cell population with a control section and inspect nuclear counterstain and signal distribution (general IHC practice). HPA's additional vesicular ICC-IF location does not validate diffuse cytoplasmic IHC (HPA: subcellular ICC-IF).
Negative-reference cells stain strongly.Adipocytes and skeletal-muscle myocytes are Not detected in the supplied HPA tissue IHC record (HPA: tissue IHC). Cross-reactivity or endogenous detection activity is possible, but the appearance alone cannot distinguish them (general IHC practice).Compare reagent controls and expected-positive cells on the run; investigate endogenous detection activity and nonspecific binding using standard IHC controls (general IHC practice).
Colour is diffuse across tissue or obscures cell boundaries.Background or excessive detection signal can prevent compartment-level scoring (general IHC practice). HPA describes nuclear expression, so diffuse colour is not sufficient evidence of a RUNX1-positive cell (HPA: tissue IHC).Inspect control sections and review blocking, antibody dilution and detection conditions against the IHC-validated antibody's documentation (general IHC practice). Score only cells with separable nuclear signal.
Bone marrow looks weaker than nasopharynx or skin.HPA calls bone-marrow hematopoietic cells Medium, versus High nasopharyngeal basal cells and skin eccrine glands (HPA: tissue IHC). UniProt's high bone-marrow expression is a different type of evidence (UniProt Q01196: tissue specificity).Score the identified hematopoietic cells against local background and the run control (general IHC practice). Avoid requiring identical intensity across the three HPA populations.
An IF image shows puncta in addition to nuclear signal.HPA reports nucleoplasm as the main ICC-IF location and vesicles as an additional location (HPA: subcellular ICC-IF). The IF observation alone does not establish the expected chromogenic IHC appearance.Use the separate IF/ICC guide to evaluate the image (HPA: subcellular ICC-IF). For this IHC section, base the positive call on discernible nuclear staining in the HPA-reported cell populations (HPA: tissue IHC).

Sample controls for RUNX1 IHC & IF

🧪Run nasopharynx first: basal cells should show nuclear RUNX1 staining (HPA: High in nasopharyngeal basal cells; UniProt Q01196: nucleus). Use adipose tissue as the negative tissue, focusing on adipocytes (HPA: Not detected in adipocytes); on the positive slide, adjacent non-basal cells should show only control-level nuclear staining, but their absence of RUNX1 is not established by the supplied HPA row.
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 no-primary (secondary-only), concentration-matched rabbit IgG isotype, and RUNX1-knockout biological controls (PB9157 caption: rabbit anti-RUNX1 antibody). For chromogenic staining, block endogenous peroxidase and check for endogenous biotin background because the selected caption uses a biotin-based detection system with DAB (PB9157 tissue-IHC caption).
⚠️Feasibility: A target-specific fixation window or fixation effect is unreported, and the fixative in the selected paraffin-section caption is unreported (PB9157 tissue-IHC caption). That caption reports heat-mediated citrate retrieval at pH 6 for 20 minutes, but does not establish that retrieval is essential (PB9157 tissue-IHC caption). The supplied evidence does not establish frozen sections or IF/ICC as easier; for the nasopharynx slide, check epithelial edges and folds for DAB background that could obscure basal-cell nuclear staining (HPA: High in nasopharyngeal basal cells; PB9157 tissue-IHC caption: DAB detection).

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

TissueCell typeLevelEvidenceSource
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

TissueCell typeLevelEvidenceSource
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 nuclear localisation, cell identity and matched controls before comparing staining intensity.

How should I optimize retrieval when RUNX1 nuclear staining is weak?
Start with heat mediated citrate retrieval at pH 6 for 20 minutes (datasheet PB9157). That condition produced RUNX1 staining in a paraffin section of rat thymus, although the caption does not state its fixative (datasheet PB9157). Compare a retrieved section with a section processed without retrieval, keeping antibody concentration, detection and development constant (standard IHC practice). If nuclear staining remains weak, test a longer heating period or an alternative retrieval buffer on adjacent sections while monitoring tissue damage (standard IHC practice). Score signal in intact nuclei rather than treating diffuse staining as successful recovery (UniProt Q01196: nucleus; standard IHC practice).
Could fixation explain absent RUNX1 staining in my paraffin sections?
RUNX1 specific sensitivity to fixation is unknown from the supplied evidence; the selected paraffin tissue caption does not state a fixative (datasheet PB9157). Record the actual fixative and fixation duration for each specimen before comparing staining across cases (standard IHC practice). Process adjacent sections together and compare nuclear signal in a known positive compartment, such as hematopoietic cells in bone marrow (HPA: medium in bone marrow hematopoietic cells). If fixation histories differ, interpret a weak result cautiously and optimize retrieval and antibody conditions using matched material (standard IHC practice). Neither tissue staining patterns nor RUNX1 modifications establish a preferred fixation condition (HPA tissue IHC; UniProt Q01196: modified residues).
Where should I expect RUNX1 signal, and how should I handle cytoplasmic staining?
Expect predominantly nuclear staining in paraffin IHC because RUNX1 is annotated as nuclear and tissue IHC shows nuclear expression (UniProt Q01196: nucleus; HPA tissue IHC: nuclear expression). Assess signal against a nuclear counterstain and document the proportion of positive nuclei within each cell population (standard IHC practice). Nucleoplasmic localisation and additional vesicular localisation have been reported by ICC/IF, but those observations do not establish a cytoplasmic IHC scoring pattern (HPA subcellular: nucleoplasm and vesicles). Investigate diffuse cytoplasmic only staining with a no primary control and a reviewed positive section (standard IHC practice). RUNX1 has no transmembrane segment, so membrane outlining would warrant scrutiny (UniProt Q01196: topology).
Can isoforms or epitope changes explain discordant RUNX1 staining?
RUNX1 has 11 listed isoforms, so an antibody's epitope may determine which forms it detects (UniProt Q01196: isoforms; standard IHC practice). The supplied PB9157 caption gives an IHC staining procedure but does not identify its epitope or establish isoform coverage (datasheet PB9157). Check the antibody's immunogen or epitope documentation before attributing a negative section to absent RUNX1 (standard IHC practice). The Runt domain spans residues 50–178, and RUNX1 has documented modified residues; either feature makes epitope location relevant to interpretation without proving an effect on this antibody (UniProt Q01196: domains and modified residues). Compare staining with a second, independently characterized epitope when isoform discrimination matters (standard IHC practice).
How can IF help resolve ambiguous RUNX1 staining?
Use IF as a separate validation experiment, pairing RUNX1 with a marker for the expected cell population, such as a leukocyte marker when assessing marrow hematopoietic cells (HPA tissue IHC: bone marrow hematopoietic cells; standard IF practice). Select a red or far red fluorophore after checking the specimen's autofluorescence in each channel (standard IF practice). RUNX1 is nuclear and lacks a transmembrane segment, so permeabilization must allow antibody access to the nuclear compartment; optimize its strength against nuclear morphology (UniProt Q01196: localisation and topology; standard IF practice). Include single stain controls to check channel bleed through and a no primary control for background (standard IF practice). Score nuclear colocalisation before comparing IF with chromogenic IHC (standard IF practice).
What should I check when RUNX1 IHC has widespread brown background?
First compare a no primary section with the stained section to identify signal arising from detection reagents or tissue (standard IHC practice). The PB9157 tissue example used 10% goat serum blocking, 1 μg/mL primary antibody overnight at 4°C, and biotin based DAB detection (datasheet PB9157). With that detection scheme, check endogenous peroxidase and endogenous biotin controls, then adjust blocking and washing as needed (datasheet PB9157: detection scheme; standard IHC practice). Keep DAB development matched across sections so background does not become a false intensity difference (standard IHC practice). Favor distinct nuclear signal over uniform haze when evaluating RUNX1 (UniProt Q01196: nucleus; standard IHC practice).
How should I quantify RUNX1 across sections with different cell mixtures? ⚠ ANSWER MARKED FOR VERIFICATION
Define the cell population and region before scoring, because RUNX1 staining varies by tissue and cell type (HPA tissue IHC: positive and undetected populations). For nuclear chromogenic staining, report the percentage of positive nuclei and an H-score from 0–300 using intensity grades 0–3 (standard IHC practice). If spatial abundance matters, also report positive nuclei per mm² of viable tissue (standard IHC practice). Normalize positive counts to the total nuclei of the same identified cell population, and exclude necrotic or damaged regions consistently (standard IHC practice). Apply one threshold and imaging procedure across the comparison set, with blinded review when practical (standard IHC practice).
How do I distinguish true RUNX1 positivity from IHC artefact?
Call a result convincing when staining is nuclear in intact cells and matches an expected cell population, such as marrow hematopoietic cells (UniProt Q01196: nucleus; HPA tissue IHC: bone marrow hematopoietic cells). Compare the same compartment in a positive control and the test section under matched detection conditions (standard IHC practice). Be cautious with staining limited to cut edges, necrotic areas or broadly colored tissue, and inspect a no primary control (standard IHC practice). Diffuse cytoplasmic only or membrane outlined staining needs independent confirmation before being scored as RUNX1 (UniProt Q01196: nucleus and no transmembrane segment; standard IHC practice). Check endogenous peroxidase when brown signal persists without primary antibody (standard IHC practice).
Boster reagents

Best RUNX1 / Runt-related transcription factor 1 IHC Antibodies

Real IHC figures show RUNX1 staining in rat thymus paraffin sections and RUNX-family staining in mouse lung paraffin sections (PB9157 and M00086 image captions); M00086 also lists IF/ICC (catalog applications).

Real IHC data IHC analysis of RUNX1 using anti-RUNX1 antibody (PB9157). RUNX1 was detected in paraffin-embedded section of rat thymus tissue. Heat mediated antigen retrieval was performed in citrate buffer (pH6, epitope retrieval solution) for 20 mins. The tissue section was blocked with 10% goat serum. The tissue section was then incubated with 1μg/ml rabbit anti-RUNX1 Antibody (PB9157) overnight at 4°C. Biotinylated goat anti-rabbit IgG was used as secondary antibody and incubated for 30 minutes at 37°C. The tissue section was developed using Strepavidin-Biotin-Complex (SABC)(Catalog # SA1022) with DAB as the chromogen.
Anti-RUNX1/AML1 Antibody ®
Cat # PB9157
Real IHC data Immunohistochemical analysis of paraffin-embedded mouse lung, using RUNX1/RUNX2/RUNX3 Antibody.
Anti-RUNX1/RUNX2/RUNX3 Rabbit Monoclonal Antibody
Cat # M00086

PB9157 will render with a RUNX1 IHC figure from rat thymus paraffin sections; its listed IHC reactivity is human, mouse and rat (PB9157 image caption; catalog reactivity). M00086 will render with a RUNX1/RUNX2/RUNX3 IHC figure from mouse lung paraffin sections; it lists IHC and IF/ICC for human, mouse and rat, but supplies no IF figure (M00086 image caption; catalog applications and reactivity; IF image alts).

Which to pick: For RUNX1 tissue IHC, start with PB9157 at 0.5–1 μg/ml: its own figure shows rat thymus paraffin sections with citrate retrieval, and the fixative is unreported (PB9157 catalog dilution; PB9157 image caption). For IF/ICC, consider rabbit monoclonal M00086 at 1:50; IF/ICC is listed, while its own figure documents only paraffin-section IHC of mouse lung and reports no fixative (M00086 title; catalog applications and dilution; M00086 image caption). Both list human, mouse and rat reactivity for cross-species work; M00086 targets RUNX1/RUNX2/RUNX3, so choose PB9157 when RUNX1 specificity is the priority (catalog titles and reactivity).

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

References

  1. UniProt Consortium. UniProt entry Q01196 (RUNX1_HUMAN, Runt-related transcription factor 1).
  2. Human Protein Atlas. RUNX1 tissue IHC expression (reliability: Enhanced).
  3. Human Protein Atlas. RUNX1 subcellular location (ICC-IF): Mainly localized to the nucleoplasm. In addition localized to vesicles..
  4. Human Protein Atlas. RUNX1 antibody validation summary (2 antibodies).
  5. 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.
  6. Runx1 Activities in Superficial Zone Chondrocytes, Osteoarthritic Chondrocyte Clones and Response to Mechanical Loading. Journal of cellular physiology 2015 — PMC4420729.
  7. RUNX1 restrains STAT1-GITRL signaling to shape an immunosuppressive CRC microenvironment. Cell death discovery 2026 — PMC13040063.
  8. RUNX1 promote invasiveness in pancreatic ductal adenocarcinoma through regulating miR-93. Oncotarget 2017 — PMC5725115.
  9. PubMed PMID:1720541 — UniProt-cited evidence.
  10. PubMed PMID:7533526 — UniProt-cited evidence.
  11. PubMed PMID:8490181 — UniProt-cited evidence.