BATF / Basic leucine zipper transcriptional factor ATF-like · IHC design guide

Design Immunohistochemistry for BATF

Plan chromogenic BATF IHC on paraffin sections with the catalog antibody at 1:100–1:300 (datasheet A04089-1). Assess cytoplasmic staining in peripheral leukocytes (HPA tissue IHC) and consider activation-linked nuclear localization (UniProt).

Evidence assembled Oct 2026 · For research use; verify linked source records and product datasheet before use

Immunohistochemistry protocol sheet for BATF (IHC for BATF): expected localisation Leukocyte cytoplasm (HPA tissue IHC); nucleus after T-cell activation (UniProt), antibody A04089-1, validated IHC image, and IHC protocol steps — Printable **BATF** IHC protocol sheet — expected localisation Leukocyte cytoplasm (HPA tissue IHC); nucleus after T-cell activation (UniProt), antibody A04089-1, controls and protocol steps. Open the full BATF IHC guide →

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BATF 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	Leukocyte cytoplasm (HPA tissue IHC); nucleus after T-cell activation (UniProt)
	Staining pattern	Cytoplasmic staining in peripheral leukocytes (HPA tissue IHC)
	Antigen retrieval	Tris-EDTA pH 8.0 HIER, heat-mediated (datasheet A04089-1)
	Positive control ⓘ	Testis
	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); Matched tissue-IHC evidence does not establish the fixation claim. Validate the specimen-specific method before use. (selected-SKU IHC image A04089-1)
	Caveat	Tissue staining and RNA show low consistency (HPA tissue IHC)
	Regulation	T-cell activation increases nuclear BATF (UniProt)
	Isoform / epitope	No reported isoforms or cleavage; one 1–125 chain (UniProt)

Section 1

Recommended BATF IHC & IF Protocols

The catalog antibody’s IHC-P protocol is supplemented by published BATF staining protocols for colorectal cancer and hepatocellular carcinoma tissue (PMC11165778; PMC12047759).

Recommended immunohistochemistry (IHC-P) protocol parameters
Sample	Paraffin-embedded Human breast cancer tissue; fixative not specified (datasheet A04089-1)
Fixation	Image fixative and duration unreported (datasheet A04089-1); verify before use.
Sectioning	4–5 µm sections on charged slides (standard)
Deparaffinisation	Xylene, graded ethanol series to water (standard)
Antigen retrieval	Heat retrieval: Tris-EDTA pH 8.0 (datasheet A04089-1); 20 min, 95–100 °C (standard)
Peroxidase block	3% H2O2, 10 min, room temperature (standard)
Blocking	10% normal serum of the secondary host, 30 min, room temperature (standard)
Primary antibody	Rabbit anti-BATF, 1:100-1:300 (datasheet A04089-1)
Primary incubation	Overnight at 4 °C (standard)
Detection	HRP-polymer secondary, DAB chromogen 5–10 min (standard)
Counterstain	Hematoxylin, blue, dehydrate and mount (standard)
Expected result	BATF-positive staining in sertoli cells of testis (HPA tissue IHC: High). HPA tissue profile: Cytoplasmic expression in peripheral leukocytes. No signal in the no-primary control.

💡Decision noteStart with the catalog antibody’s heat-mediated Tris-EDTA retrieval at pH 8.0 (datasheet A04089-1). The HCC paper reports two alternative buffers without assigning either specifically to BATF (PMC12047759).

Section 2

What Is the Expected BATF Staining Pattern?

BATF is a nonmembrane protein found in the nucleus and cytoplasm, with increased nuclear translocation after T-cell activation (UniProt Q16520 topology and subcellular location). In tissue IHC, expect cytoplasmic staining in peripheral leukocytes; Sertoli cells show high staining in the HPA images (HPA tissue IHC). Treat these as context-specific observations: HPA rates the tissue profile Approved but reports low consistency between antibody staining and RNA expression (HPA tissue IHC).

What am I looking at on my slide?
Peripheral leukocytes show cytoplasmic chromogenic staining, while adjacent cells have little signal.	This matches the reported tissue IHC profile (HPA tissue IHC: cytoplasmic expression in peripheral leukocytes). Assess the stained cells and compartment together; BATF can also enter the nucleus after T-cell activation, so nuclear signal in an appropriate context is biologically plausible (UniProt Q16520 subcellular location).
Signal is confined to an unexpected compartment, such as a cell-surface rim, with no credible intracellular pattern.	A surface-only pattern conflicts with BATF’s nuclear and cytoplasmic locations and lack of a transmembrane segment (UniProt Q16520). Consider nonspecific staining or a detection artifact (standard IHC practice); morphology and controls are needed before assigning either cause.
Cells expected to be unstained show strong signal, especially adipocytes or bone-marrow hematopoietic cells.	HPA reports no detection in those cell types in its tissue images (HPA tissue IHC). Cross-reactivity or endogenous detection activity is possible (standard IHC practice). Do not treat one discordant field as proof of either: the HPA tissue profile has low staining–RNA consistency (HPA tissue IHC).
Color spreads across the section and obscures cell boundaries or compartment assignment.	Diffuse background prevents a defensible BATF call (standard IHC practice). Review blocking, washes, detection controls and counterstain before interpreting intensity (standard IHC practice). A broad chromogenic haze is not the defined peripheral-leukocyte cytoplasmic pattern (HPA tissue IHC).
No signal appears in a section chosen as an expected positive control.	First check whether its expected cells are present: HPA shows high Sertoli-cell staining in testis, while UniProt reports strong expression in mature B- and T-lymphocytes (HPA tissue IHC; UniProt Q16520 tissue specificity). A negative slide alone cannot distinguish absent target from a failed IHC run (standard IHC practice).

💡Expected BATF appearanceCall a tissue IHC result positive when stain resolves to the relevant cells and compartment—cytoplasmic peripheral leukocytes or high-staining Sertoli cells in the HPA examples; uniform signal in HPA-negative cell types or a cell-surface-only rim is suspect (HPA tissue IHC; UniProt Q16520 topology).

How each factor affects the staining
Cell state and compartment	BATF occurs in nucleus and cytoplasm, with increased nuclear translocation after T-cell activation (UniProt Q16520). Record nuclear and cytoplasmic staining separately; a single fixed compartment rule would miss this stated change (UniProt Q16520 subcellular location).
Tissue choice and evidence limits	HPA shows high Sertoli-cell staining, cytoplasmic peripheral-leukocyte staining, and no detection in the listed adipocytes or bone-marrow hematopoietic cells (HPA tissue IHC). Its Approved tissue profile has low staining–RNA consistency, so use those examples as observed patterns rather than universal controls (HPA tissue IHC).
Antibody validation	HPA064962 has Approved IHC status; HPA059588 has no listed IHC status (HPA antibodies). The Enhanced designation for their ICC results does not establish an IHC result for HPA059588 (HPA antibodies). Keep validation specific to the antibody and application used.
BATF molecular features	BATF has one listed 1–125 chain, no signal peptide, no propeptide, no transmembrane segment and no listed isoforms (UniProt Q16520). Those annotations do not support a predicted secreted or membrane-rim IHC pattern (UniProt Q16520 topology and processing).
IF/ICC comparison	What should IF/ICC show? HPA reports enhanced nucleoplasmic localization in its ICC-IF images, while UniProt also records cytoplasmic BATF and activation-related nuclear translocation (HPA subcellular; UniProt Q16520). Compare localization across applications cautiously; the HPA ICC-IF observation is not an IHC protocol or a tissue-wide staining rule.

Why is my staining missing, weak or wrong?
Situation	Likely cause	Next action
Expected cells are present, but the IHC slide has no BATF signal.	The run may have failed, or the selected tissue may lack detectable protein in those cells (standard IHC practice). HPA’s tissue profile also has low staining–RNA consistency (HPA tissue IHC).	Check an appropriate positive section, antibody application status and the chromogenic detection controls before concluding biological absence (standard IHC practice; HPA antibodies: HPA064962 IHC Approved).
Only a cell-surface outline stains.	A rim does not fit BATF’s reported nuclear and cytoplasmic locations or its lack of a transmembrane segment (UniProt Q16520). Nonspecific signal is possible (standard IHC practice).	Review cell morphology and a detection-only control, then reassess whether any intracellular staining remains (standard IHC practice).
Adipocytes or bone-marrow hematopoietic cells stain strongly.	Both are reported as not detected in the HPA tissue examples (HPA tissue IHC). Cross-reactivity or endogenous detection activity may explain discordant color (standard IHC practice).	Inspect controls and cell identification, and compare with the reported HPA pattern; do not infer BATF solely from stain intensity (standard IHC practice; HPA tissue IHC).
The whole section has diffuse chromogenic color.	Background can arise from blocking, washes or the detection system (standard IHC practice); it makes BATF’s cellular pattern hard to resolve.	Review the blocking and wash steps and a detection-only control, then judge signal against an appropriate counterstained section (standard IHC practice).
Nuclear stain appears where cytoplasmic leukocyte staining was expected.	UniProt reports BATF in both compartments and increased nuclear translocation after T-cell activation (UniProt Q16520); HPA’s tissue IHC summary describes cytoplasmic peripheral leukocytes (HPA tissue IHC).	Score the cell type and each compartment separately, and compare matched controls before calling the nuclear signal artifactual (standard IHC practice; UniProt Q16520).
An ICC-IF image and a chromogenic tissue section suggest different compartments.	HPA describes enhanced nucleoplasmic ICC-IF localization but cytoplasmic peripheral-leukocyte tissue IHC staining; UniProt permits both locations (HPA subcellular; HPA tissue IHC; UniProt Q16520).	Interpret each result in its own cell and application context. Confirm the tissue call with an IHC-validated antibody and appropriate controls (HPA antibodies; standard IHC practice).

Source: UniProt Q16520 Human Protein Atlas tissue Human Protein Atlas subcellular

Experiment evidence

IHC & IF images showing BATF staining

Immunohistochemical analysis of paraffin-embedded Human breast cancer. Antibody was diluted at 1:100 (4° overnight). High-pressure and temperature Tris-EDTA, pH8.0 was used for antigen retrieval. Negetive contrl (right) obtaned from antibody was pre-absorbed by immunogen peptide.

A04089-1 · IHCImmunohistochemical analysis of paraffin-embedded Human breast cancer. Antibody was diluted at 1:100 (4° overnight). High-pressure and tempe

Immunohistochemistry analysis of paraffin-embedded human breast carcinoma tissue, using BATF Antibody. The picture on the right is blocked with the synthesized peptide.

A04089-1 · IHCImmunohistochemistry analysis of paraffin-embedded human breast carcinoma tissue, using BATF Antibody. The picture on the right is blocked w

A04089 · IFImmunofluorescence of BATF in human spleen tissue with BATF antibody at 20 μg/mL.

HPA · Cerebral cortexHuman Protein Atlas IHC, Cerebral cortex. Source: https://www.proteinatlas.org/ENSG00000156127-BATF/tissue/cerebral+cortex#imid_18829091

HPA · ColonHuman Protein Atlas IHC, Colon. Source: https://www.proteinatlas.org/ENSG00000156127-BATF/tissue/colon#imid_18829025

HPA · LiverHuman Protein Atlas IHC, Liver. Source: https://www.proteinatlas.org/ENSG00000156127-BATF/tissue/liver#imid_18829026

HPA · KidneyHuman Protein Atlas IHC, Kidney. Source: https://www.proteinatlas.org/ENSG00000156127-BATF/tissue/kidney#imid_18829019

HPA · ICC-IF MCF-7Human Protein Atlas immunofluorescence, MCF-7, antibody HPA059588; green = BATF, blue = nucleus, red = microtubules.

← swipe / scroll for more images →

Real IHC / IF data behind the staining-pattern expectations in this section.

Sample controls for BATF IHC & IF

🧪Run testis first: Sertoli cells should stain (HPA: High in Sertoli cells). Use adipose tissue as the negative tissue, with adipocytes expected to lack detectable staining (HPA: Not detected in adipocytes); on the testis slide, assess background in neighboring cells without assuming any named cell type is BATF-negative (HPA: only Sertoli cells are listed as High).

Positive control tissue: Testis (Sertoli cells, HPA High)

Negative control tissue: Adipose tissue (HPA Not detected)

ICC-IF cell lines (HPA subcellular resource): HPA ICC-IF images show BATF in MCF-7, RT-4, U2OS, with annotated localisation: Nucleoplasm (enhanced) (HPA subcellular).

Technical controls: Include no-primary (secondary-only) and host- and isotype-matched controls, plus a BATF knockout specimen or immunogen-peptide block (standard IHC practice; selected-SKU caption: peptide-preabsorbed negative control). Quench endogenous peroxidase for chromogenic IHC and block endogenous biotin if using biotin-based detection (standard IHC practice).

⚠️Feasibility: A target-specific fixation window or fixation effect is unreported, and the selected-SKU paraffin-section caption does not state a fixative (selected-SKU caption). The caption reports high-pressure, high-temperature Tris-EDTA retrieval at pH 8.0 and antibody dilution 1:100 overnight at 4°C; this describes one staining condition, not a demonstrated retrieval requirement (selected-SKU caption). The supplied evidence does not establish that frozen sections or IF/ICC are easier, and reports no testis-specific artefact; for IF/ICC, HPA reports enhanced nucleoplasmic localization (HPA: subcellular summary).

HPA tissue IHC evidence for BATF

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

Tissue	Cell type	Level	Evidence	Source
Testis	Sertoli cells	High	Protein (IHC)	HPA →

Undetected expression · recommended negative controls

Tissue	Cell type	Level	Evidence	Source
Adipose tissue	Adipocytes	Not detected	Protein (IHC)	HPA →
Adrenal gland	Glandular cells	Not detected	Protein (IHC)	HPA →
Bone marrow	Hematopoietic cells	Not detected	Protein (IHC)	HPA →
Breast	Adipocytes	Not detected	Protein (IHC)	HPA →
Bronchus	Respiratory epithelial cells	Not detected	Protein (IHC)	HPA →

Section 3

Advanced BATF IHC Tips

Use the catalog antibody’s paraffin-section IHC evidence as the starting point, then check compartment, cell identity, and controls before scoring BATF staining.

Which retrieval conditions should I try first for BATF in paraffin sections?

Start with heat-mediated Tris-EDTA retrieval at pH 8.0 (datasheet A04089-1). The selected paraffin-section image used high pressure and temperature for retrieval, followed by antibody at 1:100 overnight at 4°C (caption A04089-1). Keep section thickness, heating, and cooling consistent across comparison slides so retrieval differences do not masquerade as biological differences (standard IHC practice). If staining is weak, optimize heating within that buffer before testing an alternative buffer as a fallback, with a matched positive control on each run (standard IHC practice). Score nuclear and cytoplasmic staining separately because BATF can occupy both compartments (UniProt Q16520 subcellular location).

Could fixation explain weak or uneven BATF staining?

Target-specific sensitivity to fixation is unknown from the supplied evidence; the selected tissue caption says paraffin-embedded breast cancer but does not report a fixative (caption A04089-1). Record the fixative and processing history for every block, and compare suspect sections with a consistently processed control before changing antibody conditions (standard IHC practice). In the selected image, retrieval was Tris-EDTA at pH 8.0, with antibody at 1:100 overnight at 4°C (caption A04089-1). If staining varies across blocks, review fixation and processing records alongside retrieval and detection controls (standard IHC practice). Do not infer a BATF-specific fixation effect from its intracellular location or phosphorylation sites (UniProt Q16520 topology and modified residues).

Should BATF staining be nuclear, cytoplasmic, or both?

Assess nuclear and cytoplasmic signals separately: BATF is reported in both compartments, with increased nuclear translocation after T-cell activation (UniProt Q16520 subcellular location). Tissue IHC reports cytoplasmic staining in peripheral leukocytes, while cell imaging places BATF in the nucleoplasm (HPA tissue IHC profile; HPA subcellular summary). These observations make compartment alone an insufficient positive-call rule, particularly because HPA reports low agreement between antibody staining and RNA expression (HPA tissue IHC reliability description). Use a consistent counterstain and score cells with clearly visible nuclei, excluding folded or damaged regions (standard IHC practice). For comparisons, report the percentage of nuclear-positive cells alongside cytoplasmic staining rather than combining them into one score (standard IHC practice).

How should an unknown epitope affect interpretation of BATF staining?

The supplied record lists 0 isoforms and does not define the catalog antibody’s epitope, so an isoform-specific staining claim is unsupported (UniProt Q16520 isoforms; caption A04089-1). BATF has a bZIP domain at residues 26–89 and reported phosphorylation at residues 43 and 48 (UniProt Q16520 domains and modified residues). Without an epitope map, those features cannot establish whether retrieval or modification changes antibody binding (UniProt Q16520 domains and modified residues; caption A04089-1). The selected image includes an immunogen-peptide-preabsorbed negative control, which supports signal competition in that preparation but does not locate the epitope (caption A04089-1). Compare staining with an independent antibody or orthogonal expression measure before assigning a disputed pattern to BATF (standard IHC practice).

How can IF help assess BATF localisation seen by IHC?

Use IF as a separate localisation check, since BATF is reported in the nucleoplasm by cell imaging and in both nucleus and cytoplasm in the protein record (HPA subcellular summary; UniProt Q16520 subcellular location). Multiplex BATF with a validated marker for the cell population being assessed, plus a nuclear counterstain, to assign signal to individual cells (standard IF practice). Choose fluorophores and detection channels after checking unstained tissue for autofluorescence, and include single-stain controls for channel overlap (standard IF practice). BATF has no transmembrane segment, so intracellular epitope access generally calls for permeabilisation; tune it to the fixation and antibody used because the catalog epitope is unspecified (UniProt Q16520 topology; standard IF practice). Keep IF findings distinct from chromogenic IHC scores when comparing compartments (standard image-analysis practice).

What should I check when BATF IHC shows widespread brown staining?

First inspect a no-primary control for detection-system background and an unstained or substrate-control section for pigment that resembles chromogen (standard IHC practice). In chromogenic IHC, block endogenous peroxidase before DAB development and check whether residual signal follows red blood cells or damaged tissue (standard IHC practice). The selected paraffin-section image used antibody at 1:100 overnight at 4°C and included an immunogen-peptide-preabsorbed negative control (caption A04089-1). Compare that control with intact areas of the stained section, but do not treat loss of signal after peptide absorption as proof of cell-type specificity (standard IHC interpretation). HPA reports low agreement between BATF staining and RNA expression, so broad unexpected staining merits independent confirmation (HPA tissue IHC reliability description).

How should I quantify BATF-positive cells across IHC sections? ⚠ ANSWER MARKED FOR VERIFICATION

Define the cell population and tissue area before scoring, then report nuclear and cytoplasmic staining as separate measurements (standard IHC scoring practice; UniProt Q16520 subcellular location). For nuclear signal, record the percentage of positive cells and, if intensity is reproducible, an H-score based on intensity-weighted percentages (standard IHC scoring practice). For sparse immune cells, report positive-cell density per mm² of viable tissue or per mm² of the defined compartment (standard image-analysis practice). Normalize counts to eligible cells or viable area, and use identical thresholds and counterstain rules across sections (standard image-analysis practice). Record activation context because BATF can show increased nuclear translocation after T-cell activation (UniProt Q16520 subcellular location).

How can I distinguish convincing BATF staining from artefact?

A convincing call links signal to intact cells, a plausible compartment, and an appropriate control; BATF can be nuclear or cytoplasmic, and nuclear enrichment can follow T-cell activation (UniProt Q16520 subcellular location). Check whether apparent positive cells match the population under study, since BATF is strongly expressed in mature B- and T-lymphocytes (UniProt Q16520 tissue specificity). Exclude section edges, folds, necrosis, and pigment before scoring, and investigate diffuse DAB signal with a no-primary and peroxidase-control section (standard IHC practice). The selected image’s peptide-preabsorbed control supports antibody-dependent staining in that preparation, but it cannot establish every stained cell’s identity (caption A04089-1). Treat isolated unexpected patterns cautiously because HPA reports low consistency between tissue staining and RNA expression (HPA tissue IHC reliability description).

Boster reagents

Best BATF / Basic leucine zipper transcriptional factor ATF-like IHC Antibodies

Anti-BATF antibodies have IHC data from paraffin-embedded human breast cancer (A04089-1 image caption) and IF data from human spleen tissue (A04089 image caption).

Real IHC data Immunohistochemical analysis of paraffin-embedded Human breast cancer. Antibody was diluted at 1:100 (4° overnight). High-pressure and temperature Tris-EDTA, pH8.0 was used for antigen retrieval. Negetive contrl (right) obtaned from antibody was pre-absorbed by immunogen peptide.

Anti-B-ATF Antibody

Cat # A04089-1

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Real IF data Immunofluorescence of BATF in human spleen tissue with BATF antibody at 20 μg/mL.

Anti-BATF Antibody

Cat # A04089

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A04089-1 will render with an IHC image of paraffin-embedded human breast cancer (A04089-1 image caption). A04089 will render with an IF image of human spleen tissue (A04089 image caption).

Which to pick: Choose A04089-1 for chromogenic IHC on paraffin sections: its IHC image used 1:100 antibody and Tris-EDTA retrieval at pH 8.0 (A04089-1 image caption); the fixative is unreported (A04089-1 image caption). Choose A04089 for IF: its human spleen image used 20 μg/mL (A04089 image caption); ICC is not listed as a tested application (A04089 applications). For rat samples, A04089 lists rat reactivity (A04089 catalog reactivity), but its IF image documents human tissue only (A04089 image caption); neither catalog record specifies clonality (catalog clone fields).

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

References

UniProt Consortium. UniProt entry Q16520 (BATF_HUMAN, Basic leucine zipper transcriptional factor ATF-like).
Human Protein Atlas. BATF tissue IHC expression (reliability: Approved).
Human Protein Atlas. BATF subcellular location (ICC-IF): Localized to the nucleoplasm..
Human Protein Atlas. BATF antibody validation summary (2 antibodies).
Increased expression of the Th17-IL-6R/pSTAT3/BATF/RorγT-axis in the tumoural region of adenocarcinoma as compared to squamous cell carcinoma of the lung. Scientific reports 2014 — PMC4261178.
BATF promotes tumor progression and association with FDG PET-derived parameters in colorectal cancer. Journal of translational medicine 2024 — PMC11165778.
Integration of single-cell and bulk RNA sequencing identifies and validates T cell-related prognostic model in hepatocellular carcinoma. PloS one 2025 — PMC12047759.
Development and validation of a prognostic prediction model for endometrial cancer based on CD8+ T cell infiltration-related genes. Medicine 2024 — PMC11630932.
PubMed PMID:8570175 — UniProt-cited evidence.
PubMed PMID:8630063 — UniProt-cited evidence.
PubMed PMID:9745044 — UniProt-cited evidence.