BCLAF1 / Bcl-2-associated transcription factor 1 · IHC design guide

Design Immunohistochemistry for BCLAF1

Plan BCLAF1 chromogenic IHC in paraffin sections using its predominantly nuclear tissue pattern and high staining in bone marrow hematopoietic cells (HPA tissue IHC). This guide covers fixation consistency, antibody selection and interpretation of staining.

Evidence assembled Oct 2026 · For research use; verify linked source records and product datasheet before use
Immunohistochemistry protocol sheet for BCLAF1 (IHC for BCLAF1): expected localisation Nuclear in tissue; cytoplasmic location also annotated (HPA tissue IHC; UniProt), antibody A04100-3, validated IHC image, and IHC protocol steps
Printable BCLAF1 IHC protocol sheet — expected localisation Nuclear in tissue; cytoplasmic location also annotated (HPA tissue IHC; UniProt), antibody A04100-3, controls and protocol steps. Open the full BCLAF1 IHC guide →

BCLAF1 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 in tissue; cytoplasmic location also annotated (HPA tissue IHC; UniProt)
Staining pattern Widespread nuclear staining; high in marrow cells (HPA tissue IHC)
Antigen retrieval EDTA pH 8.0 HIER, heat-mediated (datasheet A04100-3)
Positive control ⓘ Adrenal gland+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 paraffin sections (standard IHC practice; not target-specific)
Caveat Marrow peroxidase may mimic DAB staining (HPA tissue IHC; standard IHC practice)
Regulation Bone marrow has enhanced RNA expression (HPA tissue RNA)
Isoform / epitope 4 isoforms; no extracellular domain; epitope coverage unknown (UniProt)
Section 1

Recommended BCLAF1 IHC & IF Protocols

Compare the catalog antibody’s IHC protocol (datasheet A04100-3) with published methods for osteoarthritic cartilage (PMC11844276), mouse tumors (PMC11496133), and human ESCC (PMC8486183).

Recommended immunohistochemistry (IHC-P) protocol parameters
SampleParaffin-embedded mouse brain tissue; fixative not specified (datasheet A04100-3)
FixationImage fixative and duration unreported (datasheet A04100-3); 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 A04100-3); 20 min, 95–100 °C (standard)
Peroxidase block3% H2O2, 10 min, room temperature (standard)
Blocking10% goat serum (datasheet A04100-3)
Primary antibodyRabbit anti-BCLAF1, 2-5 μg/ml (datasheet A04100-3)
Primary incubationOvernight at 4 °C (datasheet A04100-3)
DetectionHRP-conjugated secondary, DAB chromogen (datasheet A04100-3)
CounterstainHematoxylin, blue, dehydrate and mount (standard)
Expected resultBCLAF1-positive staining in glandular cells of adrenal gland (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 A04100-3); the human ESCC protocol used the same buffer and pH (PMC8486183).
Section 2

What Is the Expected BCLAF1 Staining Pattern?

BCLAF1 should appear predominantly in nuclei across many cell types (HPA: ubiquitous nuclear expression; UniProt Q9NYF8: nucleus and nucleoplasm). High staining is reported in bone marrow hematopoietic cells, bronchial respiratory epithelium, and several glandular cell populations (HPA: tissue IHC). HPA rates the tissue pattern Enhanced because antibody staining is consistent with RNA expression (HPA: reliability description). BCLAF1 has no transmembrane segment (UniProt Q9NYF8: topology).

What am I looking at on my slide?
Distinct nuclear chromogen in bone marrow hematopoietic cells or bronchial respiratory epithelial cells.This matches reported high staining in those cells and the broadly nuclear tissue pattern (HPA: tissue IHC). Compare signal with a nuclear counterstain so cytoplasmic pigment is not scored as nuclear staining (general IHC practice).
Strong cytoplasmic or membrane staining with little or no nuclear signal.An exclusively extranuclear IHC pattern conflicts with the reported nuclear tissue pattern (HPA: tissue IHC). Cytoplasmic localization is listed by UniProt, so limited cytoplasmic signal alone is not proof of artefact (UniProt Q9NYF8: subcellular location). Review controls and staining distribution before assigning specificity (general IHC practice).
Signal is concentrated in unexpected cells while the expected cells in the same section remain unstained.For example, absent hematopoietic-cell staining in bone marrow conflicts with its reported high level (HPA: bone marrow). Consider antibody cross-reactivity or endogenous chromogen-generating activity (general IHC practice). BCLAF1 is broadly expressed, so staining in another cell type alone does not establish a false positive (HPA: ubiquitous nuclear expression).
Diffuse color covers nuclei, cytoplasm, and extracellular spaces without clear cell boundaries.This is poor localization rather than a convincing nuclear result (HPA: ubiquitous nuclear expression). Nonspecific antibody binding, inadequate washing, or detection background can produce diffuse chromogen (general IHC practice); assess the negative reagent control before scoring (general IHC practice).
No nuclear signal in a known-positive tissue, including bone marrow hematopoietic cells.A blank result is inconsistent with the reported high staining in that cell population (HPA: bone marrow). Check the assay controls and detection steps before concluding that the specimen lacks BCLAF1 (general IHC practice). HPA tissue data do not identify a BCLAF1-specific fixation sensitivity (HPA: tissue IHC scope).
💡Expected BCLAF1 appearanceCall a result positive when chromogen is clearly nuclear in the sampled cells, with readily visible signal in reported high-staining populations such as bone marrow hematopoietic cells (HPA: tissue IHC); diffuse extracellular color or strong membrane-only staining is suspicious background, not a matching nuclear pattern (HPA: ubiquitous nuclear expression; general IHC practice).
How each factor affects the staining
Tissue and cell population (HPA: tissue IHC)HPA reports ubiquitous nuclear expression and high staining in listed glandular, hematopoietic, respiratory epithelial, and selected neural cell populations. Use the relevant cell population within the section as the comparison, rather than treating every nucleus as equally intense (HPA: tissue IHC).
Subcellular resolution (HPA: subcellular ICC-IF; UniProt Q9NYF8: location)ICC-IF places BCLAF1 in nuclear speckles, while tissue IHC reports a nuclear pattern (HPA: subcellular ICC-IF; HPA: tissue IHC). Chromogenic IHC need not resolve speckles to support a nuclear call (general IHC practice). UniProt also lists nucleoplasm and cytoplasm (UniProt Q9NYF8: location).
Antibody validation (HPA: antibodies; HPA: tissue reliability)HPA lists Enhanced IHC validation for HPA006669 and HPA027770, while HPA006484 has Enhanced ICC validation without an IHC designation (HPA: antibodies). Those ratings support the stated assays; they do not validate every catalog antibody or transfer ICC image detail directly to paraffin IHC (HPA: antibodies).
Protein forms and topology (UniProt Q9NYF8: isoforms and processing)Four isoforms are listed, but the supplied record does not assign separate tissue staining patterns to them (UniProt Q9NYF8: isoforms; HPA: tissue IHC). No signal peptide, propeptide, or transmembrane segment is annotated, so these data give no basis to predict a membrane or secreted staining pattern (UniProt Q9NYF8: topology and processing).
Why is my staining missing, weak or wrong?
SituationLikely causeNext action
A positive-control bone marrow section shows no nuclear stain (HPA: bone marrow).The expected hematopoietic-cell signal is missing; assay failure is one possibility (HPA: bone marrow; general IHC practice).Verify that the control section, primary antibody, detection reagents, and chromogen worked, then review the validated IHC procedure used for that antibody (general IHC practice).
Only cytoplasm or cell borders stain in a tissue expected to show nuclear BCLAF1 (HPA: tissue IHC).The compartment disagrees with the reported tissue pattern; nonspecific binding or detection background is possible (HPA: tissue IHC; general IHC practice).Compare the signal with the nuclear counterstain and a negative reagent control, and reassess antibody and detection conditions (general IHC practice).
Staining appears in unexpected cells, but reported high-staining cells are blank (HPA: tissue IHC).Cross-reactivity or endogenous detection activity may explain the distribution; cell identity alone cannot prove either cause (general IHC practice).Check cell identity on the section, compare a negative reagent control, and use an independently validated antibody if available (general IHC practice; HPA: antibody validation).
Brown color is spread across the section and obscures nuclear boundaries (general IHC practice).Diffuse nonspecific binding or detection background can prevent localization-based interpretation (general IHC practice).Inspect negative controls, washing, blocking, and chromogen development; score only cells whose nuclear signal can be distinguished from background (general IHC practice).
An IF image shows speckles, but the chromogenic section shows broader nuclear staining (HPA: subcellular ICC-IF; HPA: tissue IHC).The assays present nuclear localization at different visual resolution (general IHC practice); HPA reports speckles for ICC-IF and a nuclear tissue pattern for IHC (HPA: subcellular ICC-IF; HPA: tissue IHC).Evaluate this section against the nuclear tissue pattern; use the separate IF/ICC guide when punctate subnuclear localization is the experimental question (HPA: tissue IHC; HPA: subcellular ICC-IF).
The investigator attributes weak staining to a BCLAF1-specific fixation effect.The supplied UniProt and HPA records do not establish target-specific fixation sensitivity (UniProt Q9NYF8: supplied record; HPA: tissue IHC scope).Check section and assay controls first; record fixation and retrieval conditions as general IHC workflow variables without assigning a BCLAF1-specific cause (general IHC practice).

Sample controls for BCLAF1 IHC & IF

🧪Run bone marrow first: hematopoietic cells should show strong staining (HPA: High in hematopoietic cells). HPA detects BCLAF1 in all 45 scored tissues, so there is no validated negative tissue; use no-primary and isotype controls, and expect cells without specific staining on the positive slide to show counterstain only, without treating any cell population as a validated internal negative (HPA: no negative tissue rows; UniProt Q9NYF8: nuclear localization).
Positive control tissue: Adrenal gland (Glandular cells, HPA High)
Negative control tissue: None in HPA: BCLAF1 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 BCLAF1 in A-431, U-251MG, U2OS, Rh30, SiHa, with annotated localisation: Nuclear speckles (enhanced) (HPA subcellular).
Technical controls: Include a no-primary, secondary-only slide and a concentration-matched rabbit isotype control for the rabbit catalog antibody; use BCLAF1 knockout material, if available, as a biological negative (selected-SKU IHC caption: rabbit primary). Quench endogenous peroxidase in bone marrow before HRP/DAB detection because hematopoietic cells can produce peroxidase background (HPA: bone marrow hematopoietic cells; selected-SKU IHC caption: HRP/DAB).
⚠️Feasibility: No target-specific fixation window or fixation effect is reported, and the selected-SKU paraffin-section caption does not state a fixative (selected-SKU tissue-IHC caption: fixative unreported). That caption uses heat-mediated EDTA retrieval at pH 8.0, but does not establish that retrieval is required (selected-SKU tissue-IHC caption: EDTA pH 8.0). No matched evidence establishes whether frozen sections or IF are easier; IF can help assess the reported nuclear-speckle localization, while endogenous peroxidase is a particular background concern for bone marrow HRP/DAB staining (HPA: nuclear speckles; HPA: bone marrow hematopoietic cells; selected-SKU tissue-IHC caption: HRP/DAB).

HPA tissue IHC evidence for BCLAF1

Comprehensive Human Protein Atlas IHC scoring per tissue (reliability: Enhanced — High 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
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 →
Bronchus Respiratory epithelial cells High Protein (IHC) HPA →

Undetected expression · recommended negative controls

TissueCell typeLevelEvidenceSource
None in HPA: BCLAF1 is detected in all 45 scored tissues. Use a no-primary (secondary-only) and an isotype control instead.
Section 3

Advanced BCLAF1 IHC Tips

Troubleshoot BCLAF1 staining in paraffin sections by checking retrieval, nuclear localisation, assay background and cell-specific scoring.

What retrieval conditions should I start with for BCLAF1 paraffin-section IHC?
Start with heat-mediated retrieval in EDTA, pH 8.0, the condition used for the selected antibody in a paraffin-embedded mouse brain section (datasheet A04100-3). Keep heating, cooling and section thickness consistent across comparison slides, then assess nuclear staining before changing conditions (standard IHC practice; HPA tissue IHC: ubiquitous nuclear expression). The caption reports 2 μg/ml primary antibody overnight at 4°C, providing a documented starting condition for this antibody (datasheet A04100-3). If staining remains weak, optimise retrieval intensity on adjacent sections while monitoring tissue damage and nonspecific colour (standard IHC practice). Record any changed condition separately from the documented method (datasheet A04100-3).
How should I investigate weak staining when fixation history varies?
The selected paraffin-section caption does not state a fixative, so BCLAF1-specific sensitivity to fixation is unknown (datasheet A04100-3). Record the available fixation and processing history for each specimen, and compare sections processed together before attributing intensity differences to biology (standard IHC practice). Run the documented EDTA, pH 8.0 retrieval and 2 μg/ml primary condition consistently across those sections (datasheet A04100-3). If nuclear signal varies with processing history, assess morphology and background alongside staining, then test retrieval changes on adjacent sections (standard IHC practice; HPA tissue IHC: ubiquitous nuclear expression). Report unresolved fixation differences as a limit on quantitative comparisons (standard IHC practice).
Which staining compartment should count as a convincing BCLAF1 signal?
Score nuclear staining first: tissue IHC describes ubiquitous nuclear expression, while subcellular imaging places BCLAF1 in nuclear speckles (HPA tissue IHC: ubiquitous nuclear expression; HPA subcellular: nuclear speckles). UniProt also lists nucleoplasm and cytoplasm, so cytoplasmic colour alone should prompt a specificity check rather than automatic rejection (UniProt Q9NYF8: subcellular location). Compare the chromogenic signal with a nuclear counterstain and score intact cells within a defined compartment (standard IHC practice). A diffuse nuclear DAB signal may not resolve speckles at routine tissue-IHC resolution; avoid requiring visible puncta for positivity (HPA subcellular: nuclear speckles; standard IHC practice). Document nuclear and cytoplasmic staining separately when both appear (UniProt Q9NYF8: subcellular location).
Could isoforms or epitope masking explain discordant BCLAF1 staining?
BCLAF1 has 4 annotated isoforms, so establish which sequence the antibody immunogen represents before interpreting discordant staining as isoform biology (UniProt Q9NYF8: isoforms 1–4). The supplied caption documents tissue staining but does not identify an epitope or establish recognition of each isoform (datasheet A04100-3). UniProt lists modified residues, including phosphoserines at 102 and 104 and acetyllysine at 152; these annotations alone do not show that a modification affects this antibody (UniProt Q9NYF8: modified residues). Compare retrieval and primary-antibody conditions across adjacent sections, then seek epitope mapping or independent validation before assigning a staining difference to splicing or modification (standard IHC practice; UniProt Q9NYF8: isoforms and modified residues).
How should I adapt BCLAF1 localisation checks to multiplex IF?
Treat multiplex IF as a separate assay: the selected antibody caption documents chromogenic staining in a paraffin-embedded section, while HPA subcellular imaging reports nuclear speckles (datasheet A04100-3; HPA subcellular: nuclear speckles). Pair BCLAF1 with a glial marker when examining cerebral cortex, where HPA reports high staining in glial cells (HPA tissue IHC: cerebral cortex glial cells, High). Choose a fluorophore channel with low tissue autofluorescence and include single-colour controls to assess bleed-through (standard IF practice). Because BCLAF1 is nuclear and has no transmembrane segment, optimise permeabilisation for access to the nucleus without assuming a membrane-facing epitope (UniProt Q9NYF8: subcellular location and topology; standard IF practice). Compare puncta with the nuclear counterstain and IF controls (HPA subcellular: nuclear speckles; standard IF practice).
What should I check when DAB colour obscures nuclear BCLAF1 staining?
First compare the test slide with a no-primary control to identify colour arising from detection reagents or tissue rather than primary-antibody binding (standard IHC practice). Include an endogenous peroxidase block and inspect whether DAB deposits follow tissue structures instead of nuclei; these are general chromogenic controls (standard IHC practice; HPA tissue IHC: ubiquitous nuclear expression). The documented section used 10% goat serum blocking, 2 μg/ml primary antibody overnight at 4°C, and DAB detection (datasheet A04100-3). If background persists, optimise blocking, washing and primary concentration while keeping exposure and development comparable between slides (standard IHC practice). Score only interpretable cells with intact morphology and a visible nuclear counterstain (standard IHC practice).
How should I quantify BCLAF1 across paraffin sections? ⚠ ANSWER MARKED FOR VERIFICATION
Define the scored cell population and nuclear compartment before examining outcome groups, since HPA describes ubiquitous nuclear expression and high staining in several distinct cell populations (HPA tissue IHC: expression profile and positive tissues). For intensity, use a nuclear H-score from 0–300, or report the percentage of positive nuclei at a prespecified threshold (standard IHC practice). If the question concerns cell abundance, report positive nuclei per mm² and normalise to the sampled viable tissue area (standard IHC practice). Keep retrieval, antibody incubation and DAB development comparable, using the documented EDTA, pH 8.0 condition as the starting method (datasheet A04100-3; standard IHC practice). Record cell-type composition separately so it does not masquerade as a change in nuclear signal (standard IHC practice).
How can I distinguish genuine BCLAF1 staining from section artefacts?
Prioritise reproducible staining in intact nuclei, consistent with the tissue-IHC profile, and compare the pattern with the expected cell population on the same section (HPA tissue IHC: ubiquitous nuclear expression and cell-specific positives). Cytoplasmic staining requires review because UniProt also lists a cytoplasmic location, but isolated cytoplasmic DAB cannot establish specificity (UniProt Q9NYF8: subcellular location; standard IHC practice). Exclude section edges, necrotic regions and pigment-like deposits from scoring when morphology or control slides indicate artefact (standard IHC practice). A no-primary slide and endogenous peroxidase block help assess enzyme-derived colour, while a nuclear counterstain helps locate the signal (standard IHC practice). Interpret differences only after checking processing and cell-type composition across sections (standard IHC practice).
Boster reagents

Best BCLAF1 / Bcl-2-associated transcription factor 1 IHC Antibodies

Anti-BCLAF1 antibodies have IHC images from mouse and rat brain paraffin sections and an IF image from HeLa cells (catalog image captions).

Real IHC data IHC analysis of BCLAF1 using anti-BCLAF1 antibody (A04100-3). BCLAF1 was detected in a paraffin-embedded section of mouse brain 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-BCLAF1 Antibody (A04100-3) 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-BCLAF1 Antibody ®
Cat # A04100-3
Real IHC data Immunohistochemistry of BCLAF1 in mouse brain tissue with BCLAF1 antibody at 5 μg/mL.
Anti-BCLAF1 Antibody
Cat # A04100-1

A04100-3 has IHC images from mouse and rat brain paraffin sections and an IF/ICC image from HeLa cells (catalog image captions). A04100-1 has an IHC image from mouse brain tissue and lists IHC-P among its applications (catalog image caption; catalog applications).

Which to pick: For tissue IHC, choose A04100-3 when a documented paraffin-section workflow or images from both mouse and rat brain matter; A04100-1 has a mouse brain IHC image (each SKU’s IHC image caption). For IF/ICC, choose A04100-3 because IF and ICC are listed applications with a HeLa cell image; A04100-1 lists neither application, and neither rendered SKU reports a clone (catalog applications; catalog IF image caption; catalog clone fields). Both list human, mouse and rat reactivity, but A04100-3 has IHC images from two species; the fixative is unreported in both SKUs’ IHC captions (catalog reactivity; each SKU’s IHC image caption).

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

References

  1. UniProt Consortium. UniProt entry Q9NYF8 (BCLF1_HUMAN, Bcl-2-associated transcription factor 1).
  2. Human Protein Atlas. BCLAF1 tissue IHC expression (reliability: Enhanced).
  3. Human Protein Atlas. BCLAF1 subcellular location (ICC-IF): Localized to the nuclear speckles..
  4. Human Protein Atlas. BCLAF1 antibody validation summary (3 antibodies).
  5. BCLAF1 Regulates Osteoarthritic Cartilage Degradation Through Interaction with LAMTOR2. International journal of biological sciences 2025 — PMC11844276.
  6. Sorbaria sorbifolia flavonoid derivative induces mitochondrial apoptosis in human hepatoma cells through Bclaf1. Frontiers in pharmacology 2024 — PMC11496133.
  7. BCLAF1-induced HIF-1α accumulation under normoxia enhances PD-L1 treatment resistances via BCLAF1-CUL3 complex. Cancer immunology, immunotherapy : CII 2023 — PMC10700218.
  8. Role of BCLAF-1 in PD-L1 stabilization in response to ionizing irradiation. Cancer science 2021 — PMC8486183.
  9. PubMed PMID:10330179 — UniProt-cited evidence.
  10. PubMed PMID:8724849 — UniProt-cited evidence.
  11. PubMed PMID:14574404 — UniProt-cited evidence.