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BAIAP2L2 / BAR/IMD domain-containing adapter protein 2-like 2 · IHC design guide
Design Immunohistochemistry for BAIAP2L2
Plan chromogenic IHC for BAIAP2L2 in paraffin sections using a primary antibody dilution of 1:100–1:300 (datasheet A09681-1). Assess cytoplasmic staining in gastrointestinal glandular cells while accounting for presumed off-target binding and low RNA–IHC consistency (HPA tissue IHC).
Evidence assembled Oct 2026 · For research use; verify linked source records and product datasheet before use
BAIAP2L2 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 | Cytoplasmic staining (HPA tissue IHC); junction and vesicle membrane location annotated (UniProt) | |
| Staining pattern | Gastrointestinal glandular cells show high cytoplasmic staining (HPA tissue IHC) | |
| Antigen retrieval | Tris-EDTA pH 9.0 HIER, heat-mediated (datasheet A09681-1) | |
| Positive control | Colon+4 more · see all | |
| Negative control | Bone marrow+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 | Presumed off-target staining and low RNA–IHC consistency (HPA tissue IHC) | |
| Regulation | Intestine/kidney group-enriched RNA (HPA RNA) | |
| Isoform / epitope | 2 isoforms; no transmembrane segment; epitope effects unknown (UniProt) |
Section 1
Recommended BAIAP2L2 IHC & IF Protocols
The catalog antibody's IHC-P protocol (datasheet A09681-1) is accompanied by one published osteosarcoma tissue protocol (PMC8577457).
| Sample | Paraffin-embedded human tonsil tissue; fixative not specified (datasheet A09681-1) |
| Fixation | Image fixative and duration unreported (datasheet A09681-1); 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 9.0 (datasheet A09681-1); 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-BAIAP2L2, 1:100-1:300 (datasheet A09681-1) |
| 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 | BAIAP2L2-positive staining in glandular cells of colon (HPA tissue IHC: High). HPA tissue profile: Cytoplasmic expression in several different tissue types, most abundant in gastrointestinal tract. No signal in the no-primary control. |
💡Decision noteStart with heat-mediated Tris-EDTA retrieval at pH 9.0 (datasheet A09681-1); the osteosarcoma paper does not specify its retrieval conditions (PMC8577457).
Section 2
What Is the Expected BAIAP2L2 Staining Pattern?
BAIAP2L2 is observed as cytoplasmic staining, strongest in gastrointestinal glandular cells (HPA: tissue IHC). UniProt places the protein at cell membranes, cell junctions, and cytoplasmic vesicle membranes, including RAB13-positive vesicles and intercellular contacts; it has no transmembrane segment (UniProt Q6UXY1). Interpret the pattern cautiously: HPA rates the IHC evidence Approved but reports low agreement with RNA data and disregarded presumed off-target staining (HPA: reliability description).
| Strong cytoplasmic stain in colon, duodenal, small-intestinal, stomach, or gallbladder glandular cells. | This matches the reported High glandular-cell staining in those tissues (HPA: tissue IHC). Membrane-adjacent detail at cell contacts is plausible from UniProt localisation, but HPA describes the tissue pattern chiefly as cytoplasmic (UniProt Q6UXY1; HPA: tissue IHC). |
| Predominantly nuclear stain, with little cytoplasmic signal in gastrointestinal glandular cells. | A nuclear-dominant result conflicts with the reported cytoplasmic IHC pattern and membrane, junction, and vesicle localisation (HPA: tissue IHC; UniProt Q6UXY1). Treat it as an unconfirmed pattern; review controls and antibody specificity before scoring it as BAIAP2L2 (general IHC practice). |
| Strong stain in cells HPA lists as undetected, such as bone-marrow hematopoietic cells. | That result conflicts with HPA's cell-specific observation (HPA: bone marrow, hematopoietic cells, Not detected). Consider cross-reactivity or endogenous detection activity, then compare a reagent control and an independent antibody before assigning target expression (general IHC practice; HPA: reliability description). |
| Diffuse stain covers glandular cells and surrounding tissue without a clear cellular boundary. | A broad haze cannot establish the reported glandular-cell pattern (HPA: tissue IHC). Nonspecific antibody binding or chromogen background may obscure localisation; examine a control lacking primary antibody and compare staining with tissue morphology (general IHC practice). |
| No stain in a gastrointestinal glandular-cell positive reference section. | Absence of signal conflicts with HPA's High observations in the listed gastrointestinal glandular cells (HPA: tissue IHC). Check section integrity, detection reagents, and the antibody's validated IHC conditions before interpreting other sections as negative (general IHC practice). |
💡Expected BAIAP2L2 appearanceCall a result supportive when gastrointestinal glandular cells show clear High cytoplasmic staining, with possible membrane-adjacent detail at contacts; isolated nuclear or cell-inappropriate staining is suspect (HPA: tissue IHC; UniProt Q6UXY1).
| Observed tissue and cell distribution | Colon, duodenum, gallbladder, small intestine, and stomach glandular cells are High; appendix glandular cells are Medium (HPA: tissue IHC). Choose the exact cell population when comparing slides, since whole-tissue positivity does not describe every cell (general IHC practice). |
| Compartment and topology | HPA reports cytoplasmic staining, while UniProt locates BAIAP2L2 at the cell membrane, junctions, and cytoplasmic vesicle membranes; there is no transmembrane segment (HPA: tissue IHC; UniProt Q6UXY1). Do not require an exclusively surface-membrane outline to call a glandular-cell result concordant. |
| IHC evidence and specificity | HPA calls the tissue IHC result Approved, while noting low consistency with RNA expression and presumed off-target binding that was disregarded (HPA: reliability description). HPA lists HPA003043 as IHC Approved, not Enhanced (HPA: antibodies). Use tissue and cell context when interpreting unexpected staining. |
| RNA versus protein readout | HPA reports RNA group enrichment in intestine and kidney, but the supplied IHC observations identify gastrointestinal glandular-cell staining and give no kidney IHC level (HPA: RNA specificity; HPA: tissue IHC). RNA enrichment alone cannot assign a kidney protein-staining intensity. |
| Situation | Likely cause | Next action |
|---|---|---|
| Positive reference section is blank. | A detection or staining-step failure is possible when a cell population reported as High is unstained (HPA: tissue IHC; general IHC practice). | Confirm that the reference section contains the relevant glandular cells, then check primary antibody, detection reagent, and counterstain performance against the catalog antibody's IHC-P instructions (general IHC practice). |
| All tissue regions stain evenly. | Diffuse background can arise from nonspecific binding or the detection system and prevents assessment of HPA's cell-specific pattern (general IHC practice; HPA: tissue IHC). | Inspect a section processed without primary antibody; review blocking, washes, and detection development under the assay's established conditions (general IHC practice). |
| Unexpectedly strong nuclear signal appears. | Nuclear dominance is unsupported by the supplied tissue pattern or UniProt localisation (HPA: tissue IHC; UniProt Q6UXY1). | Check cell boundaries and counterstain, compare a positive reference and reagent control, and seek independent antibody agreement before assigning nuclear localisation (general IHC practice). |
| Strong staining appears in an HPA-undetected cell population. | Cross-reactivity or endogenous detection activity is possible; HPA also reports presumed off-target staining in its reliability assessment (general IHC practice; HPA: reliability description). | Compare the same cell population with a no-primary control and, where available, an independently validated antibody; record the discrepancy instead of calling it confirmed expression (general IHC practice). |
| A kidney section is expected to be strongly positive from RNA data. | The payload reports kidney RNA enrichment but supplies no kidney tissue-IHC staining level (HPA: RNA specificity; HPA: tissue IHC). | Use a listed gastrointestinal glandular-cell positive section to assess IHC performance; treat any kidney result as a separate observation requiring validation (HPA: tissue IHC; general IHC practice). |
| Can IF/ICC images establish the expected subcellular pattern? | The supplied HPA subcellular record has no main location or ICC-IF image-bearing cell lines, although UniProt annotates membrane, junction, and vesicle localisation (HPA: subcellular; UniProt Q6UXY1). | Do not infer an observed IF/ICC pattern from the IHC slide. Interpret IF/ICC with its own controls and guide; use the UniProt locations as hypotheses, not an image-validated result (HPA: subcellular; general IF practice). |
Experiment evidence
IHC & IF images showing BAIAP2L2 staining
A09681-1 · IHCImmunohistochemical analysis of paraffin-embedded human tonsil. 1, Antibody was diluted at 1:200 (4° overnight). 2, Tris-EDTA, pH9.0 was use
A30580 · IHCImmunohistochemical analysis of paraffin-embedded human tonsil. 1, Antibody was diluted at 1:200(4° overnight). 2, Tris-EDTA,pH9.0 was used
HPA · Cerebral cortexHuman Protein Atlas IHC, Cerebral cortex. Source: https://www.proteinatlas.org/ENSG00000128298-BAIAP2L2/tissue/cerebral+cortex#imid_1090880
HPA · Small intestineHuman Protein Atlas IHC, Small intestine. Source: https://www.proteinatlas.org/ENSG00000128298-BAIAP2L2/tissue/small+intestine#imid_1090773
HPA · ColonHuman Protein Atlas IHC, Colon. Source: https://www.proteinatlas.org/ENSG00000128298-BAIAP2L2/tissue/colon#imid_1090798
HPA · LiverHuman Protein Atlas IHC, Liver. Source: https://www.proteinatlas.org/ENSG00000128298-BAIAP2L2/tissue/liver#imid_1090807
← swipe / scroll for more images →
Real IHC / IF data behind the staining-pattern expectations in this section.
Sample controls for BAIAP2L2 IHC & IF
🧪Run colon first: glandular cells should stain for BAIAP2L2 (HPA: High in colon glandular cells). Use bone marrow hematopoietic cells as the negative tissue (HPA: Not detected); on the colon slide, compare non-glandular cells with the glandular signal, but do not assume they are antigen-negative because their staining level is not supplied.
Positive control tissue: Colon (Glandular cells, HPA High)
Negative control tissue: Bone marrow (HPA Not detected)
ICC-IF cell lines (HPA subcellular resource): HPA carries no ICC-IF cell line for BAIAP2L2; derive a cell-line control from the positive tissue's cell type (Glandular cells) and confirm it by RNA or western blot first.
Technical controls: Include a no-primary (secondary-only) control, an irrelevant immunoglobulin control matched to the primary antibody’s host species and isotype or clonality, and BAIAP2L2-knockout tissue as a biological negative where available; a validated immunizing-peptide block is another specificity check. Quench endogenous peroxidase for chromogenic IHC and check colon sections for nonspecific signal in luminal mucus and at tissue edges.
⚠️Feasibility: No target-specific fixation window or fixation effect is reported, and the selected SKU A09681-1 paraffin-section caption does not state its fixative (caption: fixative unreported). That caption uses Tris-EDTA retrieval at pH 9.0 in tonsil, but it does not establish a retrieval requirement for colon (caption: Tris-EDTA, pH 9.0). Whether frozen sections or IF are easier is unreported; HPA supplies no ICC-IF images for this gene, so assess any fluorescence against colon autofluorescence controls (HPA: no cell lines with ICC-IF images).
HPA tissue IHC evidence for BAIAP2L2
Comprehensive Human Protein Atlas IHC scoring per tissue (reliability: Approved — Low consistency between antibody staining and RNA expression data. Presumed off target binding observed and disregarded.). 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 |
|---|---|---|---|---|
| Colon | Glandular cells | High | Protein (IHC) | HPA → |
| Duodenum | Glandular cells | High | Protein (IHC) | HPA → |
| Gallbladder | Glandular cells | High | Protein (IHC) | HPA → |
| Small intestine | Glandular cells | High | Protein (IHC) | HPA → |
| Stomach | Glandular cells | High | Protein (IHC) | HPA → |
Undetected expression · recommended negative controls
| Tissue | Cell type | Level | Evidence | Source |
|---|---|---|---|---|
| Bone marrow | Hematopoietic cells | Not detected | Protein (IHC) | HPA → |
| Breast | Adipocytes | Not detected | Protein (IHC) | HPA → |
| Cervix | Glandular cells | Not detected | Protein (IHC) | HPA → |
| Epididymis | Glandular cells | Not detected | Protein (IHC) | HPA → |
| Fallopian tube | Glandular cells | Not detected | Protein (IHC) | HPA → |
Section 3
Advanced BAIAP2L2 IHC Tips
Troubleshoot BAIAP2L2 staining in paraffin sections by checking retrieval, tissue pattern, compartment, and controls before interpreting chromogenic signal.
Which retrieval conditions should I try first for weak BAIAP2L2 staining?
Use heat-mediated Tris-EDTA at pH 9.0 for antigen retrieval of paraffin sections (datasheet A09681-1). The selected tissue image used this buffer with primary antibody at 1:200 overnight at 4°C, so reproduce those documented conditions before changing several variables (caption A09681-1). Compare a small retrieval time series, such as 10–20 minutes, while watching for tissue lifting or loss of morphology (standard IHC practice). If staining remains weak, test citrate at pH 6.0 as a fallback on matched sections, keeping detection and exposure conditions constant (standard IHC practice).
Could fixation explain weak or uneven BAIAP2L2 IHC?
Target-specific sensitivity to fixation is unknown because the selected paraffin-section caption does not state a fixative (caption A09681-1). Record the actual fixative and fixation interval for each specimen, then compare sections processed under matched conditions before attributing differences to BAIAP2L2 abundance (standard IHC practice). Excessive or uneven fixation can affect antigen accessibility in IHC generally, so inspect morphology and compare retrieval under the documented Tris-EDTA pH 9.0 condition (standard IHC practice; datasheet A09681-1). Do not infer a BAIAP2L2-specific fixation effect from its membrane association, phosphorylation sites, or tissue staining pattern (UniProt Q6UXY1; HPA tissue IHC).
What staining pattern is plausible for BAIAP2L2 in tissue sections?
Assess cytoplasmic staining in glandular epithelium first, especially in gastrointestinal tissue, where tissue IHC reports prominent expression (HPA tissue IHC). Enrichment near cell contacts or in punctate cytoplasmic structures is biologically plausible because BAIAP2L2 localizes to the plasma membrane at intercellular contacts and to RAB13-positive vesicles (UniProt Q6UXY1). It has no annotated transmembrane segment, so a continuous outline of every cell should not automatically be scored as specific staining (UniProt Q6UXY1). Compare the pattern with adjacent morphology and a negative control on the same run, using identical 1:200 primary dilution where reproducing the selected image (standard IHC practice; caption A09681-1).
How could isoforms or epitope accessibility change the IHC result?
BAIAP2L2 has 2 annotated isoforms, and its IMD and SH3 domains span residues 1–239 and 324–387, respectively (UniProt Q6UXY1). The supplied caption does not identify the antibody epitope or establish equal recognition of both isoforms, so avoid interpreting a negative section as loss of all BAIAP2L2 forms (caption A09681-1; UniProt Q6UXY1). Several phosphoserines are annotated, including residues 231 and 478, but their effect on this antibody's staining is unknown (UniProt Q6UXY1). If isoform selectivity matters, obtain the immunogen sequence and compare it with isoform sequences, then validate the resulting interpretation with an independent antibody or orthogonal assay (standard IHC practice).
How should I adapt the tissue finding for multiplex IF?
For multiplex IF, pair BAIAP2L2 with an epithelial marker such as cytokeratin and assess signal within glandular cells, where tissue IHC reports high staining in several gastrointestinal sites (HPA tissue IHC; standard IF practice). Select a far-red fluorophore if the specimen shows strong short-wavelength autofluorescence, and check single-stain controls before assigning overlap (standard IF practice). Because BAIAP2L2 lacks a transmembrane segment and associates with junctions and vesicles, test gentle permeabilisation when the antibody recognizes an intracellular-facing epitope; the supplied evidence does not locate that epitope (UniProt Q6UXY1; caption A09681-1). Optimize IF fixation and permeabilisation directly, since no IF/ICC fixation result is supplied here (standard IF practice).
What should I check when chromogenic BAIAP2L2 staining looks diffuse?
Start with a no-primary control and inspect whether pigment persists after the detection steps; persistent color indicates a detection or tissue background problem (standard IHC practice). Include a peroxidase block before DAB development and compare matched development times, because endogenous enzyme activity and overdevelopment can mimic weak diffuse staining (standard IHC practice). Titrate the primary around the caption's 1:200 condition while keeping retrieval at Tris-EDTA pH 9.0, and check whether signal retains cellular structure (caption A09681-1; standard IHC practice). Treat widespread staining cautiously: the tissue atlas reports presumed off-target binding and low consistency with RNA expression despite its approved IHC classification (HPA tissue IHC).
How should I score BAIAP2L2 across paraffin sections? ⚠ ANSWER MARKED FOR VERIFICATION
Define a viable glandular-cell region before scoring, because high tissue IHC staining is reported in glandular cells of colon, duodenum, gallbladder, small intestine, and stomach (HPA tissue IHC). Report the percentage of positive glandular cells and intensity categories 0–3, or calculate an H-score from 0–300 using those categories (standard IHC practice). Normalize counts to viable glandular cells, or report positive-cell density per mm² of the same annotated compartment when tissue architecture varies (standard IHC practice). Apply one threshold across matched runs and exclude necrosis, folds, and section edges before comparing groups (standard IHC practice).
How can I distinguish true BAIAP2L2 staining from artefact?
A credible result should track viable glandular epithelium and show a reproducible cytoplasmic pattern, with possible enrichment at cell contacts or vesicular structures (HPA tissue IHC; UniProt Q6UXY1). Signal restricted to necrosis, torn edges, or every cell regardless of type warrants investigation with no-primary and detection controls (standard IHC practice). Check whether color disappears after a peroxidase block and controlled DAB development before calling it BAIAP2L2 expression (standard IHC practice). Use an independently validated antibody or orthogonal expression evidence for consequential claims, because the tissue atlas notes presumed off-target binding and low staining–RNA consistency (HPA tissue IHC).
Boster reagents
Best BAIAP2L2 / BAR/IMD domain-containing adapter protein 2-like 2 IHC Antibodies
Both antibodies have human tonsil paraffin-section IHC images and list IF and human/mouse reactivity (catalog applications, reactivity and IHC captions); no IF image is supplied (catalog image records).
Real IHC data
Anti-BAIAP2L2 Antibody
Cat # A09681-1
Real IHC data
Anti-BAIAP2L2 Antibody
Cat # A30580
A09681-1 lists IHC and IF for human and mouse; its IHC image shows paraffin-embedded human tonsil (catalog applications and reactivity; A09681-1 IHC caption). A30580 lists IHC, IF and ICC for human and mouse; its IHC image also shows paraffin-embedded human tonsil (catalog applications and reactivity; A30580 IHC caption).
Which to pick: For tissue IHC, either SKU has its own paraffin-section example; each caption reports 1:200 primary antibody overnight at 4°C with Tris-EDTA retrieval at pH 9.0 (A09681-1 IHC caption; A30580 IHC caption). For IF, either lists the application; choose A30580 if ICC is needed, since only its application list includes ICC (catalog applications). Both are rabbit polyclonal antibodies listing human and mouse reactivity, but their pictured IHC samples are human tonsil and neither caption reports the fixative (catalog host, dilution records and reactivity; A09681-1 IHC caption; A30580 IHC caption).
Each figure is that product's own IHC / IF validation image from its datasheet.
References
- UniProt Consortium. UniProt entry Q6UXY1 (BI2L2_HUMAN, BAR/IMD domain-containing adapter protein 2-like 2).
- Human Protein Atlas. BAIAP2L2 tissue IHC expression (reliability: Approved).
- Human Protein Atlas. BAIAP2L2 subcellular location (ICC-IF): Highest expression in SK-MEL-30: 83.8 nTPM.
- Human Protein Atlas. BAIAP2L2 antibody validation summary (1 antibodies).
- Comprehensive analysis of malignant subtypes of lung adenocarcinoma based on multi-omics landscape and functional validation of prognostic biomarker BAIAP2L2. Scientific reports 2025 — PMC12830839.
- BAIAP2L2 promotes the proliferation, migration and invasion of osteosarcoma associated with the Wnt/β-catenin pathway. Journal of bone oncology 2021 — PMC8577457.
- Identification of prognostic hub genes and functional role of BAIAP2L2 in prostate cancer progression: a transcriptomic and experimental study. Frontiers in immunology 2025 — PMC12066489.
- BAIAP2L2 is a novel prognostic biomarker related to migration and invasion of HCC and associated with cuprotosis. Scientific reports 2023 — PMC10227027.
- PubMed PMID:12975309 — UniProt-cited evidence.
- PubMed PMID:10591208 — UniProt-cited evidence.
- PubMed PMID:15489334 — UniProt-cited evidence.
Immunohistochemistry protocol sheet for BAIAP2L2 (BAR/IMD domain-containing adapter protein 2-like 2). Expected localisation Cytoplasmic staining (HPA tissue IHC); junction and vesicle membrane location annotated (UniProt). Antigen retrieval: Tris-EDTA pH 9.0 HIER, heat-mediated (datasheet A09681-1). Validated IHC antibody: A09681-1 at 1:100-1:300 (the product's own IHC validation image is shown). Controls (HPA): positive Colon (Glandular cells); negative Bone marrow. IHC workflow; specimen preparation unspecified. Protocol steps: 1. Sample: Paraffin-embedded human tonsil tissue; fixative not specified (datasheet A09681-1); 2. Fixation: Image fixative and duration unreported (datasheet A09681-1); verify before use.; 3. Sectioning: 4–5 µm sections on charged slides (standard); 4. Deparaffinisation: Xylene, graded ethanol series to water (standard); 5. Antigen retrieval: Heat retrieval: Tris-EDTA pH 9.0 (datasheet A09681-1); 20 min, 95–100 °C (standard); 6. Peroxidase block: 3% H2O2, 10 min , room temperature (standard); 7. Blocking: 10% normal serum of the secondary host, 30 min , room temperature (standard); 8. Primary antibody: Rabbit anti-BAIAP2L2, 1:100-1:300 (datasheet A09681-1); 9. Primary incubation: Overnight at 4 °C (standard). Watch for: Fixation: Keep fixation consistent across paraffin sections. (standard IHC practice; not target-specific); Caveat: Presumed off-target staining and low RNA–IHC consistency (HPA tissue IHC); Isoform / epitope: 2 isoforms; no transmembrane segment; epitope effects unknown (UniProt); Regulation: Intestine/kidney group-enriched RNA (HPA RNA). Evidence: UniProt Q6UXY1, HPA tissue IHC · Approved, HPA cell-line RNA · Highest expression in SK-MEL-30: 83.8 nTPM, Datasheet A09681-1, PMC8577457. QR code links to https://www.bosterbio.com/bosterbio-gene-info-cards/BAIAP2L2/immunohistochemistry-ihc-guide.