RUNX1T1 / Protein CBFA2T1 · IHC design guide

Design Immunohistochemistry for RUNX1T1

Plan RUNX1T1 staining in paraffin sections using the catalog antibody at 0.5–1 μg/mL (datasheet A01792-1). Use the reported tissue patterns to choose controls, and interpret staining in light of the low consistency with RNA data (HPA tissue IHC).

Evidence assembled Oct 2026 · For research use; verify linked source records and product datasheet before use
Immunohistochemistry protocol sheet for RUNX1T1 (IHC for RUNX1T1): expected localisation Low nucleolar tissue staining (HPA tissue IHC); nuclear protein (UniProt), antibody A01792-1, validated IHC image, and IHC protocol steps
Printable RUNX1T1 IHC protocol sheet — expected localisation Low nucleolar tissue staining (HPA tissue IHC); nuclear protein (UniProt), antibody A01792-1, controls and protocol steps. Open the full RUNX1T1 IHC guide →

RUNX1T1 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 Low nucleolar tissue staining (HPA tissue IHC); nuclear protein (UniProt)
Staining pattern Most tissues show low nucleolar staining (HPA tissue IHC)
Antigen retrieval Citrate pH 6 HIER, heat-mediated (datasheet A01792-1)
Positive control ⓘ Bronchus+3 more · see all
Negative control ⓘ Adrenal gland+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 Antibody staining has low consistency with RNA data (HPA tissue IHC)
Regulation Expression is enriched in brain (UniProt)
Isoform / epitope Six isoforms; check antibody epitope coverage (UniProt)
Section 1

Recommended RUNX1T1 IHC & IF Protocols

The catalog antibody’s IHC-P protocol is accompanied by three published RUNX1T1 IHC protocols covering pancreatic endocrine neoplasm, gastric, and neuroblastoma sections (PMC4732279; PMC5143359; PMC11239676).

Recommended immunohistochemistry (IHC-P) protocol parameters
SampleParaffin-embedded human mammary cancer tissue; fixative not specified (datasheet A01792-1)
FixationImage fixative and duration unreported (datasheet A01792-1); 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 A01792-1)
Peroxidase block3% H2O2, 10 min, room temperature (standard)
Blocking10% goat serum (datasheet A01792-1)
Primary antibodyRabbit anti-RUNX1T1, 0.5-1μg/ml (datasheet A01792-1)
Primary incubationOvernight at 4 °C (datasheet A01792-1)
DetectionStreptavidin-biotin complex (SABC), DAB chromogen (datasheet A01792-1)
CounterstainHematoxylin, blue, dehydrate and mount (standard)
Expected resultRUNX1T1-positive staining in ciliated cells (ciliary rootlets) of bronchus (HPA tissue IHC: Medium). HPA tissue profile: Low nucleolar expression in most tissues. No signal in the no-primary control.
💡Decision noteStart with heat-mediated citrate pH 6 retrieval for the catalog antibody (datasheet A01792-1); published protocols also report protease retrieval and citrate treatment (PMC4732279; PMC5143359).
Section 2

What Is the Expected RUNX1T1 Staining Pattern?

RUNX1T1 is a nuclear protein without a transmembrane segment (UniProt Q06455: subcellular location and topology). In paraffin-section IHC, expect low nucleolar staining in most tissues, with medium staining reported in ciliary rootlets of bronchus, fallopian tube and nasopharynx, and in testis Leydig cells (HPA: tissue IHC). Treat these as reference patterns: HPA rates the tissue IHC evidence Approved but reports low consistency between antibody staining and RNA expression (HPA: reliability).

What am I looking at on my slide?
Low staining within nucleoli across a tissue section, with cell-to-cell variation.This matches the broad tissue IHC profile (HPA: low nucleolar expression in most tissues). Score the stained compartment and cell type alongside intensity; a weak, restricted signal can fit this reference better than uniformly strong staining. The HPA Approved rating carries a low RNA–staining consistency caveat (HPA: reliability).
Medium staining concentrated at ciliary rootlets in respiratory or fallopian-tube epithelium.This matches the reported ciliated-cell pattern in bronchus, nasopharynx and fallopian tube (HPA: Medium in ciliary rootlets). Record the rootlet location explicitly. It differs from the broad low nucleolar profile (HPA: tissue IHC), so evaluate each compartment against its corresponding reference rather than imposing one pattern on every cell.
Strong, widespread cytoplasmic or membrane-like chromogen that obscures nuclei and cell boundaries.That distribution warrants review against the nuclear UniProt annotation and low nucleolar tissue profile (UniProt Q06455: nucleus; HPA: tissue IHC). HPA also lists cytosol as an additional ICC-IF location, so cytoplasmic signal alone is not proof of artefact (HPA: subcellular). Check tissue morphology and controls before assigning RUNX1T1 specificity (standard IHC practice).
Intense staining in a cell population reported as not detected, such as bone-marrow hematopoietic cells.This conflicts with that cell-specific tissue IHC observation (HPA: bone marrow hematopoietic cells, Not detected). Consider cross-reactivity or endogenous detection activity as possibilities, then inspect the negative control and a known-positive reference on the same run (standard IHC practice). One discrepant section does not establish which cause is responsible.
No staining in an otherwise well-preserved testis section's Leydig cells.Leydig cells are a reported medium-staining reference (HPA: testis Leydig cells, Medium). A blank result can reflect a failed staining run, unsuitable assay conditions or sample variation (standard IHC practice). Check a positive control and the detection workflow before interpreting this section as biological absence; the HPA pattern is a reference, not a guarantee for every specimen.
💡Expected RUNX1T1 appearanceCall a result compatible when low nucleolar staining is resolved in tissue cells or medium signal appears in the reported ciliary rootlets or Leydig cells (HPA: tissue IHC); broad, intense staining in an HPA Not detected cell population is a specificity warning, not an expected positive (HPA: tissue IHC).
How each factor affects the staining
Which reference cell population is being scored?HPA reports Medium signal in ciliated-cell rootlets in bronchus, fallopian tube and nasopharynx and in testis Leydig cells; it reports Not detected in bone-marrow hematopoietic cells (HPA: tissue IHC). State the cell population when scoring, because a whole-section positive or negative label loses this distinction.
How much weight should RNA expression carry?UniProt describes strongest tissue expression in brain, and HPA calls brain RNA tissue enhanced (UniProt Q06455: tissue specificity; HPA: RNA specificity). HPA nevertheless reports low staining in cerebral-cortex endothelial cells and cerebellar Purkinje cells, and none in hippocampal glial cells (HPA: tissue IHC). Do not infer uniform brain-cell IHC positivity from tissue-level RNA.
What does antibody validation establish?The IHC antibody HPA070951 is Approved, while HPA049852 has Supported ICC validation and no listed IHC status (HPA: antibodies). HPA describes low consistency between antibody staining and RNA expression (HPA: reliability). Use the tissue images as pattern references, with controls for the specific assay; these labels do not establish equivalent IHC performance for the two antibodies.
Does IF/ICC show the same pattern?IF/ICC has its own guide page. Its supported main location is nucleoplasm, with cytosol listed as an additional location; images are listed for HEK293, U2OS and NIH 3T3 (HPA: subcellular ICC-IF). UniProt also notes discrete nuclear dots with ATN1 (UniProt Q06455: subcellular location). These annotations inform localisation, without defining an IF/ICC protocol or overriding the tissue IHC patterns.
Why is my staining missing, weak or wrong?
SituationLikely causeNext action
The positive-reference Leydig cells appear blank.The result differs from the reported Medium Leydig-cell signal (HPA: testis tissue IHC); the cause is unresolved.Check section morphology, primary-antibody application, chromogenic detection and a run-level positive control (standard IHC practice). If the run works, document the specimen-level discrepancy rather than assuming RUNX1T1 is absent.
Chromogen covers nearly every cell or fills empty tissue spaces.Diffuse background can arise from nonspecific binding, incomplete washing or detection chemistry (standard IHC practice).Compare with a no-primary control, inspect blocking and washes, and reassess dilution under the assay's established conditions (standard IHC practice). Re-evaluate against the low nucleolar and cell-restricted reference patterns (HPA: tissue IHC).
Hematopoietic cells show strong staining in bone marrow.That conflicts with the reported Not detected result (HPA: bone marrow hematopoietic cells); cross-reactivity or endogenous detection activity is possible (standard IHC practice).Compare a no-primary control and a positive reference, then review the chromogenic detection controls before calling the signal RUNX1T1 (standard IHC practice).
Brain sections show less staining than expected from RNA data.Brain is tissue enhanced by RNA, but the listed brain-cell IHC observations are low or not detected (HPA: RNA specificity and tissue IHC).Score the specified cells and compartment: cerebral-cortex endothelial cells and cerebellar Purkinje cells are Low; hippocampal glial cells are Not detected (HPA: tissue IHC). Avoid using bulk brain RNA as a cell-level IHC threshold.
The signal seems cytoplasmic rather than nuclear or nucleolar.Tissue IHC is broadly low nucleolar, while ICC-IF lists cytosol as an additional location (HPA: tissue IHC; HPA: subcellular). The discrepancy alone cannot identify the cause.Inspect focus, counterstain and compartment boundaries, then compare an appropriate positive tissue and no-primary control (standard IHC practice). Record the actual distribution rather than relabeling it nuclear.
Different antibodies give different tissue patterns.HPA lists Approved IHC for HPA070951 and Supported ICC for HPA049852, with no IHC status listed for the latter (HPA: antibodies). Equivalent paraffin-section performance is unestablished.Check each antibody's stated application and validation before comparing results (HPA: antibodies). For IHC interpretation, use an IHC-validated antibody with matched positive and negative controls (standard IHC practice).

Sample controls for RUNX1T1 IHC & IF

🧪Run bronchus first and score the ciliated cells’ ciliary rootlets, where staining is reported at Medium level (HPA: Bronchus, ciliated cells). Run adrenal gland as the negative tissue, where glandular cells are Not detected (HPA: Adrenal gland, glandular cells). On the bronchus slide, use neighboring cells without ciliary rootlets to assess background; do not assume they lack RUNX1T1.
Positive control tissue: Bronchus (Ciliated cells (ciliary rootlets), HPA Medium)
Negative control tissue: Adrenal gland (HPA Not detected)
ICC-IF cell lines (HPA subcellular resource): HPA ICC-IF images show RUNX1T1 in HEK293, U2OS, NIH 3T3, with annotated localisation: Nucleoplasm (supported) (HPA subcellular).
Technical controls: Include a no-primary (secondary-only) control, a concentration-matched nonimmune rabbit IgG isotype control, and RUNX1T1 knockout material as a biological negative (selected caption: rabbit primary antibody). For DAB detection, block endogenous peroxidase and check endogenous biotin because the selected method uses a streptavidin–biotin complex (selected IHC caption: SABC with DAB).
⚠️Feasibility: A target-specific fixation window or fixation effect is unreported, and the selected paraffin-section caption does not state the fixative (selected IHC caption: fixative unreported). The demonstrated IHC procedure uses heat retrieval in citrate buffer at pH 6 for 20 minutes; a retrieval requirement across specimens is unreported (selected IHC caption: citrate retrieval). Neither frozen sections nor IF is established as easier by the supplied evidence; in bronchus, distinguish ciliary-rootlet staining from background along the ciliated surface (HPA: Bronchus, ciliated cells at ciliary rootlets).

HPA tissue IHC evidence for RUNX1T1

Comprehensive Human Protein Atlas IHC scoring per tissue (reliability: Approved — Low 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
Bronchus Ciliated cells (ciliary rootlets) Medium Protein (IHC) HPA →
Fallopian tube Ciliated cells (ciliary rootlets) Medium Protein (IHC) HPA →
Nasopharynx Ciliated cells (ciliary rootlets) Medium Protein (IHC) HPA →
Testis Leydig cells Medium Protein (IHC) HPA →

Undetected expression · recommended negative controls

TissueCell typeLevelEvidenceSource
Adrenal gland Glandular cells Not detected Protein (IHC) HPA →
Bone marrow Hematopoietic cells Not detected Protein (IHC) HPA →
Epididymis Glandular cells Not detected Protein (IHC) HPA →
Heart muscle Cardiomyocytes Not detected Protein (IHC) HPA →
Hippocampus Glial cells Not detected Protein (IHC) HPA →
Section 3

Advanced RUNX1T1 IHC Tips

Troubleshoot RUNX1T1 staining by checking retrieval, nuclear localisation, antibody specificity and the cell types being scored (UniProt Q06455; HPA tissue IHC).

What retrieval conditions should I try first for paraffin-section RUNX1T1 IHC?
Start with heat-mediated citrate retrieval at pH 6 for 20 minutes on paraffin sections (datasheet A01792-1). Allow sections to cool consistently, then compare staining with a section processed without retrieval to distinguish epitope exposure from retrieval-associated background (standard IHC practice). The published product image used 1 μg/mL primary antibody overnight at 4°C, so keep those conditions fixed while assessing retrieval (datasheet A01792-1). Score nuclear signal alongside tissue morphology; RUNX1T1 is nuclear, whereas HPA reports only low nucleolar staining in most tissues (UniProt Q06455; HPA tissue IHC). If signal remains weak, optimise heating and cooling before testing another retrieval condition (standard IHC practice).
How should I assess whether fixation is masking RUNX1T1?
The A01792-1 tissue image identifies a paraffin section but does not state its fixative, so target-specific fixation sensitivity is unknown (datasheet A01792-1). Record the fixative and fixation duration for each specimen, and compare sections with similar processing histories before attributing differences to RUNX1T1 abundance (standard IHC practice). Run citrate retrieval at pH 6 for 20 minutes consistently across that comparison (datasheet A01792-1). Examine nuclear detail and tissue preservation when adjusting fixation or retrieval, because damaged morphology can make chromogenic scoring unreliable (standard IHC practice). Neither RUNX1T1 topology nor its reported phosphorylation establishes a preferred fixative (UniProt Q06455).
Where should convincing RUNX1T1 staining appear in IHC sections?
Prioritise staining within intact nuclei: RUNX1T1 is nuclear and can colocalise with ATN1 in discrete nuclear dots (UniProt Q06455). HPA also reports supported nucleoplasmic localisation in ICC/IF, while its tissue IHC profile describes low nucleolar expression in most tissues (HPA subcellular; HPA tissue IHC). Compare DAB with the nuclear counterstain at high magnification, and record diffuse nuclear, punctate and nucleolar patterns separately rather than pooling them (standard IHC practice). Strong staining confined to cytoplasm, section edges or damaged cells warrants a control review before assignment to RUNX1T1; HPA lists cytosol only as an additional ICC/IF location (HPA subcellular; standard IHC practice).
Can this stain distinguish RUNX1T1 isoforms or an AML1–ETO fusion?
Do not assign an isoform from this IHC stain without an antibody epitope map and isoform-specific validation; the record lists 6 RUNX1T1 isoforms (UniProt Q06455; standard IHC interpretation). RUNX1T1 also contributes to the AML1–MTG8/ETO fusion protein, so staining alone cannot establish which molecular form produced the signal (UniProt Q06455; standard IHC interpretation). Check whether the antibody epitope is retained in the isoform or fusion being investigated, then use an independent assay suited to that distinction (standard IHC practice). Keep retrieval at citrate pH 6 and evaluate nuclear staining with the same scoring rules while comparing specimens; the product image establishes that retrieval condition, not isoform specificity (datasheet A01792-1; standard IHC practice).
How can IF help resolve an ambiguous RUNX1T1 IHC pattern?
Use IF as a localisation cross-check by pairing RUNX1T1 with a marker of the expected cell type, such as a ciliated-cell marker in bronchus, where HPA reports medium staining at ciliary rootlets (HPA tissue IHC; standard IF practice). Choose a fluorophore away from the specimen’s strongest autofluorescence and inspect single-label controls before interpreting overlap (standard IF practice). RUNX1T1 has no transmembrane segment and its principal location is nuclear, so permeabilise sufficiently to admit antibody to nuclear epitopes while preserving nuclear structure (UniProt Q06455; standard IF practice). Compare nuclear and ciliary-rootlet signals explicitly; HPA supports nucleoplasmic localisation in ICC/IF, and its tissue IHC reliability is marked Approved despite low RNA–staining consistency (HPA subcellular; HPA tissue IHC).
What should I check when RUNX1T1 DAB staining looks diffuse?
First compare a no-primary control with the test section to identify signal generated by detection reagents or endogenous tissue activity (standard IHC practice). For chromogenic detection, include a peroxidase block when the detection system requires it, and evaluate DAB development time across sections processed together (standard IHC practice). The product image used 10% goat serum block, 1 μg/mL primary antibody overnight at 4°C, and a biotinylated secondary for 30 minutes at 37°C (datasheet A01792-1). If diffuse colour persists, shorten chromogen development or titrate primary antibody while checking that intact nuclear signal remains; RUNX1T1 is principally nuclear (standard IHC practice; UniProt Q06455).
How should I quantify RUNX1T1 staining across tissue sections? ⚠ ANSWER MARKED FOR VERIFICATION
Define the cell population and nuclear scoring rule before reviewing experimental groups, then report the percentage of positive nuclei and an intensity-weighted H-score (standard IHC practice). Normalise positive counts to the number of evaluable cells in the same compartment, or report positive-cell density per mm² of viable annotated tissue when cell counts are impractical (standard IHC practice). Exclude folds, necrosis and tissue edges using identical criteria across sections, and keep retrieval at citrate pH 6 for 20 minutes if following the product condition (standard IHC practice; datasheet A01792-1). Report nucleolar, diffuse nuclear and nonnuclear staining separately because the reported tissue and subcellular patterns differ (HPA tissue IHC; HPA subcellular).
How do I distinguish true RUNX1T1 staining from artefact?
Look for reproducible signal in intact nuclei and assess any discrete nuclear dots against RUNX1T1’s reported nuclear localisation and ATN1 colocalisation (UniProt Q06455; standard IHC practice). Check cell identity rather than assuming every positive field is expected: HPA reports medium staining in bronchial ciliated-cell rootlets and testicular Leydig cells, but no detectable staining in several other listed cell populations (HPA tissue IHC). Discount signal restricted to cut edges, necrotic regions or the no-primary control, and investigate possible endogenous enzyme colour before calling a section positive (standard IHC practice). Interpret isolated positive cells cautiously because HPA marks its tissue staining Approved while reporting low consistency with RNA expression (HPA tissue IHC).
Boster reagents

Best RUNX1T1 / Protein CBFA2T1 IHC Antibodies

A01792-1 has IHC images from human mammary cancer and mouse brain paraffin sections (catalog IHC captions), plus IF data from U20S cells (catalog IF caption).

Real IHC data IHC analysis of RUNX1T1/ETO using anti-RUNX1T1/ETO antibody (A01792-1). RUNX1T1/ETO was detected in paraffin-embedded section of human mammary cancer 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-RUNX1T1/ETO Antibody (A01792-1) 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-RUNX1T1/ETO Antibody ®
Cat # A01792-1

A01792-1 has documented paraffin-section IHC in human mammary cancer and mouse brain (catalog IHC captions). The same SKU has documented IF in U20S cells and lists human, mouse, and rat reactivity (catalog IF caption; catalog reactivity).

Which to pick: For tissue IHC, choose A01792-1: its paraffin-section captions document 1 μg/ml antibody after citrate retrieval at pH 6 (catalog IHC captions). For IF/ICC, A01792-1 lists both applications and shows IF in U20S cells at 2 μg/ml (catalog applications; catalog IF caption). For cross-species planning, A01792-1 lists human, mouse, and rat reactivity, while its IHC images document human and mouse tissue only; clone and tissue fixative are unreported (catalog reactivity; catalog IHC captions; catalog clone field).

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

References

  1. UniProt Consortium. UniProt entry Q06455 (MTG8_HUMAN, Protein CBFA2T1).
  2. Human Protein Atlas. RUNX1T1 tissue IHC expression (reliability: Approved).
  3. Human Protein Atlas. RUNX1T1 subcellular location (ICC-IF): Localized to the nucleoplasm..
  4. Human Protein Atlas. RUNX1T1 antibody validation summary (2 antibodies).
  5. RUNX1T1: a novel predictor of liver metastasis in primary pancreatic endocrine neoplasms. Pancreas 2011 — PMC4732279.
  6. C/EBPβ regulates homeostatic and oncogenic gastric cell proliferation. Journal of molecular medicine (Berlin, Germany) 2016 — PMC5143359.
  7. The transcriptional co-repressor Runx1t1 is essential for MYCN-driven neuroblastoma tumorigenesis. Nature communications 2024 — PMC11239676.
  8. High-resolution melting curve analysis, a rapid and affordable method for mutation analysis in childhood acute myeloid leukemia. Frontiers in pediatrics 2014 — PMC4158872.
  9. PubMed PMID:8334990 — UniProt-cited evidence.
  10. PubMed PMID:9661669 — UniProt-cited evidence.
  11. PubMed PMID:14702039 — UniProt-cited evidence.