This website uses cookies to ensure you get the best experience on our website.
- Table of Contents
BAIAP2L1 / BAR/IMD domain-containing adapter protein 2-like 1 · IHC design guide
Design Immunohistochemistry for BAIAP2L1
Plan BAIAP2L1 chromogenic IHC in paraffin sections using cytoplasmic staining and gastrointestinal glandular cells as reference patterns (HPA tissue IHC). This guide covers fixation consistency, the catalog antibody’s 1:100–1:300 IHC dilution range (datasheet A30579), and interpretation of staining with medium consistency against RNA expression (HPA tissue IHC).
Evidence assembled Oct 2026 · For research use; verify linked source records and product datasheet before use
BAIAP2L1 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 | Cytoplasm (HPA tissue IHC) | |
| Staining pattern | Widespread cytoplasmic staining, highest in the GI tract (HPA tissue IHC) | |
| Antigen retrieval | Tris-EDTA pH 9.0 HIER, heat-mediated (datasheet A30579) | |
| Positive control | Appendix+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 sections (standard IHC practice; not target-specific) | |
| Caveat | Staining and RNA expression have medium consistency (HPA tissue IHC) | |
| Regulation | No expression regulator annotated (UniProt) | |
| Isoform / epitope | No annotated isoforms or cleavage to alter the epitope map (UniProt) |
Section 1
Recommended BAIAP2L1 IHC & IF Protocols
The catalog antibody’s IHC-P protocol (datasheet: A30579) is accompanied by a published protocol for ovarian cancer and normal ovary sections (PMC4519316 methods).
| Sample | Paraffin-embedded human Colon cancer tissue; fixative not specified (datasheet A30579) |
| Fixation | Image fixative and duration unreported (datasheet A30579); 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 A30579); 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-BAIAP2L1, 1:100 - 1:300 (datasheet A30579) |
| 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 | BAIAP2L1-positive staining in glandular cells of appendix (HPA tissue IHC: High). HPA tissue profile: Ubiquitous cytoplasmic expression. Highest expression in the gastrointestinal tract. No signal in the no-primary control. |
💡Decision noteStart with heat-mediated Tris-EDTA retrieval at pH 9.0 (datasheet: A30579); the published ovarian protocol does not specify retrieval (PMC4519316 methods).
Section 2
What Is the Expected BAIAP2L1 Staining Pattern?
In paraffin-section IHC, expect predominantly cytoplasmic BAIAP2L1 staining, with strong signal in gastrointestinal glandular cells and other listed high-staining cell types (HPA: ubiquitous cytoplasmic expression; high in appendix, colon and duodenum glandular cells). Interpret membrane-associated staining in context: BAIAP2L1 has no transmembrane segment and is linked to the cytoskeleton (UniProt Q9UHR4 topology and subcellular location). HPA rates the tissue profile Enhanced, with medium staining–RNA consistency (HPA: tissue IHC reliability).
| Clear cytoplasmic staining in colon or duodenum glandular cells. | This matches a strong expected IHC result (HPA: High in colon and duodenum glandular cells). Compare staining within the same section before assigning intensity; HPA's tissue profile is broad rather than restricted to these glands (HPA: ubiquitous cytoplasmic expression). |
| Staining is predominantly nuclear, with little cytoplasmic signal. | An isolated nuclear pattern does not match the reported locations (UniProt Q9UHR4: cytoplasm and cytoskeleton; HPA: cytoplasmic tissue IHC). Treat it as a suspected artefact and review morphology, detection background and a known-positive section before interpreting it as BAIAP2L1. |
| Strong staining occurs chiefly in cells expected to stain weakly. | For example, strong signal confined to cerebral-cortex endothelial cells conflicts with their Low HPA rating (HPA: cerebral-cortex endothelial cells, Low). Consider cross-reactivity or endogenous detection activity; staining elsewhere is not automatically suspect because the overall tissue profile is ubiquitous (HPA: tissue IHC profile). |
| Colour is diffuse across cells and tissue spaces, obscuring cell borders. | This cannot establish the expected cell-specific cytoplasmic pattern (HPA: tissue IHC profile). In general IHC practice, excess detection signal or inadequate background control can make staining uninterpretable; assess a control section before scoring the specimen. |
| A colon glandular-cell section has no detectable signal. | That conflicts with a reported High-staining cell type (HPA: colon glandular cells, High), but one blank section does not establish biological absence. Check tissue preservation, retrieval and detection with appropriate controls (general IHC practice); no BAIAP2L1-specific fixation sensitivity is reported in the supplied sources. |
💡Expected BAIAP2L1 appearanceCall a result positive when glandular cells show clear, predominantly cytoplasmic chromogenic staining of high intensity in an HPA high-staining tissue (HPA: colon and duodenum glandular cells, High); isolated nuclear colour or diffuse noncellular colour is suspect against the reported localization (UniProt Q9UHR4; HPA: cytoplasmic tissue IHC).
| Tissue and cell selection | Colon, duodenum and appendix glandular cells offer reported High IHC signal (HPA: tissue IHC); cerebral-cortex endothelial cells are rated Low, so they provide a contrast rather than an assumed absolute negative (HPA: tissue IHC). |
| Localization across methods; IF/ICC Q&A | What should IF/ICC show? Mainly plasma membrane with additional cytosol (HPA: subcellular ICC-IF, enhanced); tissue IHC is described as cytoplasmic (HPA: tissue IHC). Read each pattern in its own assay context. |
| Protein topology and processing | BAIAP2L1 has no transmembrane segment, signal peptide or annotated propeptide; its chain spans residues 1–511 (UniProt Q9UHR4 topology and processing). These annotations do not establish shedding or an IHC retrieval requirement. |
| Independent staining support | Four listed rabbit polyclonal antibodies have Enhanced IHC validation (HPA: HPA019484, HPA021257, HPA023874, HPA029503). This supports the reported pattern but does not prove that every antibody or specimen will give identical staining. |
| Target-specific fixation evidence | The supplied HPA and UniProt records report no BAIAP2L1-specific fixation effect. Treat retrieval adjustments as general IHC optimization; do not infer epitope masking or sensitivity from HPA staining levels or UniProt topology. |
| Situation | Likely cause | Next action |
|---|---|---|
| Known-positive gastrointestinal glands stain weakly or remain blank. | The result disagrees with reported High staining (HPA: colon and duodenum glandular cells); a failed staining run is possible (general IHC practice). | Confirm gland identity and section quality, then check the IHC-validated antibody, retrieval and detection controls (general IHC practice). Do not assign a target-specific retrieval condition from these sources. |
| The entire section has a brown haze. | Diffuse colour prevents assessment of the cytoplasmic cell pattern (HPA: tissue IHC profile); nonspecific detection background is possible (general IHC practice). | Review a detection-only control, blocking, washing and chromogen development (general IHC practice). Score BAIAP2L1 only where individual cells and compartments remain distinguishable. |
| Signal appears mainly in nuclei. | This disagrees with cytoplasmic and cytoskeletal annotations (UniProt Q9UHR4) and the cytoplasmic tissue profile (HPA: tissue IHC). | Check the counterstain and detection controls, then compare with a known-positive tissue (general IHC practice). Do not score an isolated nuclear pattern as the expected BAIAP2L1 result. |
| A purported negative-control tissue shows some staining. | HPA lists no negative tissue and describes expression as ubiquitous (HPA: tissue IHC); a low-staining cell population is not an absolute negative. | Use the named HPA cell types to compare intensity, and include an appropriate reagent control to assess background (HPA: tissue IHC; general IHC practice). |
| Staining is strongest in an HPA Low cell population. | The distribution conflicts with that cell's reported level (HPA: cerebral-cortex endothelial cells, Low); cross-reactivity or endogenous activity is possible (general IHC practice). | Verify cell identity and compare a High-staining cell population in the same run; inspect detection controls before assigning target-specific staining (HPA: tissue IHC; general IHC practice). |
| Membrane-associated colour is seen alongside cytoplasmic IHC signal. | ICC-IF reports mainly plasma membrane and additional cytosol, while tissue IHC reports cytoplasmic staining (HPA: subcellular ICC-IF; HPA: tissue IHC). | Assess whether the cytoplasmic cell pattern and expected tissue distribution are present; do not reject the section solely for membrane-associated colour (HPA: tissue IHC and subcellular ICC-IF). |
Experiment evidence
IHC & IF images showing BAIAP2L1 staining
A30579 · IHCImmunohistochemical analysis of paraffin-embedded human Colon cancer. 1, Antibody was diluted at 1:200(4° overnight). 2, Tris-EDTA,pH9.0 was
HPA · Cerebral cortexHuman Protein Atlas IHC, Cerebral cortex. Source: https://www.proteinatlas.org/ENSG00000006453-BAIAP2L1/tissue/cerebral+cortex#imid_7337712
HPA · StomachHuman Protein Atlas IHC, Stomach. Source: https://www.proteinatlas.org/ENSG00000006453-BAIAP2L1/tissue/stomach+1#imid_7336548
HPA · ColonHuman Protein Atlas IHC, Colon. Source: https://www.proteinatlas.org/ENSG00000006453-BAIAP2L1/tissue/colon#imid_7336566
HPA · LiverHuman Protein Atlas IHC, Liver. Source: https://www.proteinatlas.org/ENSG00000006453-BAIAP2L1/tissue/liver#imid_7336559
HPA · ICC-IF A-431Human Protein Atlas immunofluorescence, A-431, antibody HPA019484; green = BAIAP2L1, blue = nucleus, red = microtubules.
HPA · ICC-IF A-431Human Protein Atlas immunofluorescence, A-431, antibody HPA019484; green = BAIAP2L1, blue = nucleus, red = microtubules.
← swipe / scroll for more images →
Real IHC / IF data behind the staining-pattern expectations in this section.
Sample controls for BAIAP2L1 IHC & IF
🧪Start with colon: its glandular cells should stain (HPA: High in colon glandular cells). HPA detects BAIAP2L1 in all 45 scored tissues, so there is no validated negative tissue; use no-primary and isotype controls, and treat any unstained non-glandular cells on the positive slide as an internal background reference only (HPA: no negative tissues; standard IHC practice).
Positive control tissue: Appendix (Glandular cells, HPA High)
Negative control tissue: None in HPA: BAIAP2L1 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 BAIAP2L1 in A-431, U-251MG, U2OS, with annotated localisation: Plasma membrane (enhanced) (HPA subcellular).
Technical controls: Run a secondary-only slide with the primary omitted, an isotype control matched to the primary antibody’s host species and clonality, and BAIAP2L1 knockout material if available to test specificity (standard IHC practice). For chromogenic detection in colon, block endogenous peroxidase; block endogenous biotin if using a biotin-based detection system (standard IHC practice).
⚠️Feasibility: No BAIAP2L1-specific fixation window or fixation effect is reported in the supplied evidence, and the selected A30579 paraffin-section caption does not state the fixative (A30579 caption). That caption reports Tris-EDTA retrieval at pH 9.0 and primary antibody dilution of 1:200, but does not establish whether retrieval is essential (A30579 caption). The evidence does not establish that frozen sections or IF/ICC are easier; in colon sections, inspect glandular lumens and debris for nonspecific chromogen before scoring (A30579 caption; HPA: colon glandular cells High; standard IHC practice).
HPA tissue IHC evidence for BAIAP2L1
Comprehensive Human Protein Atlas IHC scoring per tissue (reliability: Enhanced — Medium consistency between antibody staining and RNA expression data.). Rows are taken directly from the HPA tissue chart — click any row's HPA link to view the source.
Positive expression · recommended positive controls
| Tissue | Cell type | Level | Evidence | Source |
|---|---|---|---|---|
| Appendix | Glandular cells | High | Protein (IHC) | HPA → |
| Colon | Glandular cells | High | Protein (IHC) | HPA → |
| Duodenum | Glandular cells | High | Protein (IHC) | HPA → |
| Fallopian tube | Ciliated cells (cell body) | High | Protein (IHC) | HPA → |
| Gallbladder | Glandular cells | High | Protein (IHC) | HPA → |
Undetected expression · recommended negative controls
| Tissue | Cell type | Level | Evidence | Source |
|---|---|---|---|---|
| None in HPA: BAIAP2L1 is detected in all 45 scored tissues. Use a no-primary (secondary-only) and an isotype control instead. | ||||
Section 3
Advanced BAIAP2L1 IHC Tips
Troubleshoot BAIAP2L1 staining in paraffin sections by checking retrieval, compartment, controls, and cell-specific scoring before interpreting chromogenic signal.
Which retrieval conditions should I try first for BAIAP2L1 paraffin-section IHC?
Start with heat-mediated retrieval in Tris-EDTA at pH 9.0 (datasheet A30579). The selected paraffin-section image used that retrieval with primary antibody at 1:200 overnight at 4 °C, so keep those reported conditions together for the first comparison (caption A30579). Record heating time and cooling conditions because variation in either can change staining across a run (standard IHC practice). If signal is weak, compare a cautiously adjusted heating time on serial sections while holding antibody dilution and detection constant (standard IHC practice). Evaluate epithelial signal alongside a no-primary control before calling a retrieval change beneficial (HPA: high in colon glandular cells; standard IHC practice).
How should I investigate fixation-related loss of BAIAP2L1 staining?
Target-specific fixation sensitivity is unknown: the selected paraffin-section caption does not state a fixative (caption A30579). Record each specimen’s fixative, fixation duration, processing history, and section age before comparing staining intensity (standard IHC practice). Run sections from differently processed specimens in the same staining batch using Tris-EDTA at pH 9.0 and the reported 1:200 primary dilution (datasheet A30579; standard IHC practice). Include a gastrointestinal glandular reference section to distinguish a specimen-specific failure from a run-wide failure (HPA: high in colon glandular cells; standard IHC practice). Do not infer fixation tolerance from staining patterns or protein topology (HPA: tissue IHC profile; UniProt Q9UHR4 topology).
Should BAIAP2L1 appear at the cell membrane or in the cytoplasm?
Assess cytoplasmic staining and staining along cell boundaries: tissue IHC reports ubiquitous cytoplasmic expression, while subcellular IF reports a main plasma-membrane location with additional cytosolic signal (HPA: tissue IHC profile; HPA: enhanced subcellular localisation). BAIAP2L1 has no transmembrane segment and interacts with F-actin, so a sharp boundary signal alone does not establish that it spans the membrane (UniProt Q9UHR4 topology and interactions). Compare glandular cells within intact epithelium, especially where HPA reports high expression, using the same counterstain and exposure to chromogen (HPA: colon and appendix glandular cells; standard IHC practice). Treat exclusively nuclear staining as discordant with the supplied localisation evidence and investigate controls (UniProt Q9UHR4 subcellular location; HPA: subcellular localisation; standard IHC practice).
Could epitope location explain discordant BAIAP2L1 IHC results?
Check the antibody’s disclosed immunogen before assigning a domain-specific cause to discordant staining; the supplied caption gives no epitope sequence (caption A30579). The annotated protein has an IMD region at residues 1–249 and an SH3 domain at 339–402, with no annotated isoforms in the supplied record (UniProt Q9UHR4 domains and isoforms). Several phosphorylation sites are annotated, including residues 248, 257, and 261, but their effect on this antibody’s IHC signal is unknown (UniProt Q9UHR4 modified residues; caption A30579). Compare serial sections under identical retrieval and detection conditions, then use an independent epitope or orthogonal assay if available to assess specificity (standard IHC practice).
How can IF help assess a puzzling chromogenic BAIAP2L1 pattern?
Use IF on a separate section to compare BAIAP2L1 with a validated marker for the cell type being scored; gastrointestinal glandular cells provide a relevant reference (HPA: high in colon and appendix glandular cells; standard IF practice). Choose spectrally separated fluorophores and consider a far-red channel where tissue autofluorescence obscures shorter-wavelength signal (standard IF practice). If the antibody epitope is intracellular, test controlled permeabilisation; an external epitope would require a different access strategy, and the supplied caption does not specify epitope location (standard IF practice; caption A30579). Include single-stain and no-primary controls, and compare membrane-adjacent with cytosolic signal rather than treating either as automatically nonspecific (HPA: enhanced subcellular localisation; standard IF practice).
What should I change when BAIAP2L1 IHC has diffuse brown background?
First inspect a no-primary control and a secondary-only control to locate signal arising from detection reagents (standard IHC practice). For peroxidase-based chromogenic detection, verify the peroxidase block and assess whether DAB development is excessive; these are general workflow checks, not BAIAP2L1-specific findings (standard IHC practice). The selected image reports primary antibody at 1:200 overnight at 4 °C and secondary antibody at 1:200 for 45 minutes at room temperature (caption A30579). If background persists, adjust blocking, washes, and detection development one variable at a time while checking whether glandular-cell contrast is retained (HPA: high in colon glandular cells; standard IHC practice).
How should I score BAIAP2L1 staining across paraffin sections? ⚠ ANSWER MARKED FOR VERIFICATION
Define the compartment and cell population before scoring because HPA reports cytoplasmic tissue staining, while subcellular IF also places BAIAP2L1 at the plasma membrane (HPA: tissue IHC profile; HPA: enhanced subcellular localisation). For epithelial samples, report the percentage of positive glandular cells and an intensity-based H-score from 0–300, keeping boundary and cytoplasmic scores separate if both are reproducible (HPA: colon glandular cells high; standard IHC scoring practice). Normalize counts to evaluable cells or glandular area, and use stained area per mm² only with a defined tissue mask (standard IHC quantification practice). Apply one threshold and exclude folds, necrosis, and section edges consistently across specimens (standard IHC practice).
How do I distinguish credible BAIAP2L1 staining from artefact?
A credible pattern should recur in intact cells and fit cytoplasmic or membrane-adjacent localisation, with glandular cells in gastrointestinal tissue offering a useful reference (UniProt Q9UHR4 subcellular location; HPA: enhanced subcellular localisation; HPA: gastrointestinal tissue profile). Strong signal confined to section edges, folds, or necrotic regions is suspect and should be excluded from interpretation (standard IHC practice). Exclusively nuclear staining, or brown deposits that persist without primary antibody, warrants investigation before a positive call (UniProt Q9UHR4 subcellular location; standard IHC practice). Check the no-primary and peroxidase-block controls for endogenous enzyme contribution, then confirm uncertain cell identity against morphology or a cell-type marker (standard IHC practice).
Boster reagents
Best BAIAP2L1 / BAR/IMD domain-containing adapter protein 2-like 1 IHC Antibodies
Two anti-BAIAP2L1 antibodies list IHC and IF for human, mouse and rat samples (catalog: applications and reactivity); a paraffin-section IHC image is available for A30579 (A30579 IHC caption).
Real IHC data
Anti-BAIAP2L1 Antibody
Cat # A30579
A06770-1 lists IHC and IF for human, mouse and rat, with no IHC or IF image supplied (A06770-1 catalog). A30579 lists IHC, IF and ICC for those species; its IHC image shows human colon cancer in a paraffin section (A30579 catalog; A30579 IHC caption).
Which to pick: For tissue IHC, choose A30579 if a documented paraffin-section example is useful: its caption specifies 1:200 primary antibody overnight at 4°C and Tris-EDTA retrieval at pH 9.0; the fixative is unreported (A30579 IHC caption). For IF/ICC, A30579 lists both applications, while A06770-1 lists IF without ICC; neither has an IF image in the payload (A30579 catalog; A06770-1 catalog). Both are rabbit polyclonal antibodies listed as reactive with human, mouse and rat, but the supplied tissue image documents only human tissue (catalog: host and reactivity; A30579 IHC caption).
Each figure is that product's own IHC / IF validation image from its datasheet.
References
- UniProt Consortium. UniProt entry Q9UHR4 (BI2L1_HUMAN, BAR/IMD domain-containing adapter protein 2-like 1).
- Human Protein Atlas. BAIAP2L1 tissue IHC expression (reliability: Enhanced).
- Human Protein Atlas. BAIAP2L1 subcellular location (ICC-IF): Mainly localized to the plasma membrane. In addition localized to the cytosol..
- Human Protein Atlas. BAIAP2L1 antibody validation summary (4 antibodies).
- BAIAP2L1 accelerates breast cancer progression and chemoresistance by activating AKT signaling through binding with ribosomal protein L3. Cancer science 2023 — PMC9986062.
- BAI1-Associated Protein 2-Like 1 (BAIAP2L1) Is a Potential Biomarker in Ovarian Cancer. PloS one 2015 — PMC4519316.
- Immunoglobulin M regulates airway hyperresponsiveness independent of T helper 2 allergic inflammation. eLife 2025 — PMC12707823.
- PubMed PMID:10931946 — UniProt-cited evidence.
- PubMed PMID:12853948 — UniProt-cited evidence.
- PubMed PMID:12690205 — UniProt-cited evidence.
Immunohistochemistry protocol sheet for BAIAP2L1 (BAR/IMD domain-containing adapter protein 2-like 1). Expected localisation Cytoplasm (HPA tissue IHC). Antigen retrieval: Tris-EDTA pH 9.0 HIER, heat-mediated (datasheet A30579). Validated IHC antibody: A30579 at 1:100 - 1:300 (the product's own IHC validation image is shown). Controls (HPA): positive Appendix (Glandular cells); negative None in HPA (detected in all 45 tissues); use no-primary + isotype controls. IHC workflow; specimen preparation unspecified. Protocol steps: 1. Sample: Paraffin-embedded human Colon cancer tissue; fixative not specified (datasheet A30579); 2. Fixation: Image fixative and duration unreported (datasheet A30579); 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 A30579); 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-BAIAP2L1, 1:100 - 1:300 (datasheet A30579); 9. Primary incubation: Overnight at 4 °C (standard). Watch for: Fixation: Keep fixation consistent across sections (standard IHC practice; not target-specific); Caveat: Staining and RNA expression have medium consistency (HPA tissue IHC); Isoform / epitope: No annotated isoforms or cleavage to alter the epitope map (UniProt); Regulation: No expression regulator annotated (UniProt). Evidence: UniProt Q9UHR4, HPA tissue IHC · Enhanced, HPA ICC-IF · Mainly localized to the plasma membrane. In addition localized to…, Datasheet A30579, PMC4519316. QR code links to https://www.bosterbio.com/bosterbio-gene-info-cards/BAIAP2L1/immunohistochemistry-ihc-guide.