CD79B / B-cell antigen receptor complex-associated protein beta chain · IHC design guide

Design Immunohistochemistry for CD79B

Plan chromogenic CD79B IHC in paraffin sections using lymphoid tissue controls and the observed cytoplasmic pattern in lymphoid cells (HPA tissue IHC). Compare staining with CD79B's membrane topology (UniProt) and consider the HPA antibody specificity caution (HPA tissue IHC).

Evidence assembled Oct 2026 · For research use; verify linked source records and product datasheet before use
Immunohistochemistry protocol sheet for CD79B (IHC for CD79B): expected localisation Lymphoid-cell cytoplasm (HPA tissue IHC); cell membrane (UniProt), antibody M01399-1, validated IHC image, and IHC protocol steps
Printable CD79B IHC protocol sheet — expected localisation Lymphoid-cell cytoplasm (HPA tissue IHC); cell membrane (UniProt), antibody M01399-1, controls and protocol steps. Open the full CD79B IHC guide →

CD79B 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 Lymphoid-cell cytoplasm (HPA tissue IHC); cell membrane (UniProt)
Staining pattern Strong, selective cytoplasmic staining in lymphoid cells (HPA tissue IHC)
Antigen retrieval EDTA pH 8.0 HIER, heat-mediated (datasheet M01399-1)
Positive control ⓘ Appendix+3 more · see all
Negative control ⓘ Adipose tissue+4 more · see all
Important caveats
Reasons your staining may differ from the expected pattern.
Fixation Keep paraffin-section fixation consistent (standard IHC practice; not target-specific)
Caveat HPA antibody may detect proteins from multiple genes (HPA tissue IHC)
Regulation B-cell-specific expression (UniProt)
Isoform / epitope 3 isoforms; map epitopes to extracellular or cytoplasmic regions (UniProt)
Section 1

Recommended CD79B IHC & IF Protocols

The catalog antibody protocol is paired with one published CD79B IHC method (PMC7032881).

Recommended immunohistochemistry (IHC-P) protocol parameters
SampleParaffin-embedded human tonsil tissue; fixative not specified (datasheet M01399-1)
FixationImage fixative and duration unreported (datasheet M01399-1); 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 M01399-1); 20 min, 95–100 °C (standard)
Peroxidase block3% H2O2, 10 min, room temperature (standard)
Blocking10% goat serum (datasheet M01399-1)
Primary antibodyMouse monoclonal (clone 6H11) anti-CD79B, 1μg/ml (datasheet M01399-1)
Primary incubationOvernight at 4 °C (datasheet M01399-1)
DetectionStreptavidin-biotin complex (SABC), DAB chromogen (datasheet M01399-1)
CounterstainHematoxylin, blue, dehydrate and mount (standard)
Expected resultCD79B-positive staining in non-germinal center cells of appendix (HPA tissue IHC: High). HPA tissue profile: High and selective cytoplasmic expression in lymphoid cells. No signal in the no-primary control.
💡Decision noteStart with heat-mediated EDTA retrieval at pH 8.0 for the catalog antibody (datasheet M01399-1). The published method does not specify retrieval (PMC7032881).
Section 2

What Is the Expected CD79B Staining Pattern?

CD79B is a B-cell membrane protein with an extracellular region, one transmembrane segment and a cytoplasmic tail (UniProt P40259 topology; UniProt P40259 tissue specificity). In paraffin-section IHC, expect selective staining of lymphoid cells; HPA describes a high, mainly cytoplasmic tissue pattern (HPA: tissue IHC). Interpret that pattern with caution: HPA rates tissue reliability Enhanced but reports only medium consistency with RNA and warns that the antibodies may target proteins from multiple genes (HPA: tissue IHC reliability).

What am I looking at on my slide?
Strong, selective staining in lymphoid areas of appendix, lymph node, spleen or tonsil.This agrees with HPA's High staining in appendix non-germinal center cells, lymph-node germinal center cells, splenic white-pulp cells and tonsil non-germinal center cells (HPA: tissue IHC). Compare the stained cell population with the relevant tissue, since the listed positive populations differ by organ (HPA: tissue IHC).
Membrane-associated staining, with apparent cytoplasmic color in lymphoid cells.A membrane component fits CD79B topology (UniProt P40259 topology). Apparent cytoplasmic staining is also compatible with HPA's reported high, selective cytoplasmic IHC pattern in lymphoid cells (HPA: tissue IHC). A crisp membrane rim is therefore not required to call the paraffin-section result plausible.
Predominantly nuclear staining, with little signal in the expected lymphoid population.Treat this as an uncertain IHC result: UniProt places CD79B at the cell membrane, while HPA's tissue IHC profile is cytoplasmic in lymphoid cells (UniProt P40259 subcellular location; HPA: tissue IHC). HPA calls nucleoplasmic localization uncertain in ICC-IF, so nuclear color alone does not establish a specific IHC signal (HPA: subcellular ICC-IF).
Strong color in adipocytes, glandular cells or respiratory epithelial cells.Those cell types are Not detected in the listed adipose, adrenal or bronchus IHC observations (HPA: tissue IHC). Check whether the color persists in a no-primary control; cross-reactivity or endogenous chromogenic activity are possible general IHC explanations. HPA's multiple-gene antibody caution makes cell identity especially important (HPA: tissue IHC reliability).
Diffuse color across the section, or no staining in a listed positive lymphoid tissue.Diffuse color is difficult to score as selective lymphoid staining against the HPA pattern (HPA: tissue IHC). A blank positive tissue calls for checking the IHC run before interpreting the sample as negative: the listed lymphoid populations have High staining in HPA, but that evidence does not establish CD79B's sensitivity to fixation or retrieval (HPA: tissue IHC).
💡Expected CD79B appearanceCall a positive paraffin-section IHC result when lymphoid cells show strong, selective cytoplasmic or membrane-associated color, consistent with HPA's High tissue staining and UniProt membrane localization; widespread color in unrelated cells is suspect (HPA: tissue IHC; UniProt P40259 subcellular location).
How each factor affects the staining
Tissue and cell populationUse a listed positive population when assessing the stain: appendix and tonsil non-germinal center cells, lymph-node germinal center cells, or splenic white-pulp cells are High in HPA (HPA: tissue IHC). Bone-marrow hematopoietic cells are Not detected in the supplied HPA record, so do not assume every hematopoietic compartment is a positive control (HPA: tissue IHC).
Epitope position and processingCD79B has a signal peptide at residues 1–28, an extracellular region at 29–159, a transmembrane segment at 160–180, and a cytoplasmic tail at 181–229 (UniProt P40259 topology and processing). Antibody epitope location is unspecified here; these coordinates cannot predict that antibody's retrieval requirement or staining intensity.
Molecular variants and modificationsUniProt lists 3 isoforms, glycosylation sites at residues 73, 101, 127 and 128, and phosphorylated tyrosines at 196 and 207 (UniProt P40259 isoforms and modifications). The supplied records do not show whether these features alter recognition by the IHC antibody, so do not infer an isoform-specific or modification-specific slide pattern.
Antibody evidenceHPA marks HPA044107 IHC Enhanced and HPA009178 and CAB009751 IHC Supported (HPA: antibody validation). The tissue profile's Enhanced reliability comes with medium RNA–staining consistency and a multiple-gene targeting caution; agreement with a tissue pattern supports interpretation but cannot alone prove antibody specificity (HPA: tissue IHC reliability).
IF/ICC: where should signal appear?Mainly at the plasma membrane (supported); HPA also reports nucleoplasm and cytosol as uncertain additional locations (HPA: subcellular ICC-IF). This IF/ICC observation provides context for localization; it does not replace the separate IF/ICC guide or define a paraffin-section protocol.
Why is my staining missing, weak or wrong?
SituationLikely causeNext action
No color in a listed positive lymphoid tissue.The run may have failed, or staining may be below detection; HPA reports High staining in specified lymphoid populations (HPA: tissue IHC).Confirm that the chosen section contains the relevant cells, then review the general IHC steps: retrieval, primary-antibody application, detection reagents and chromogen. Use the catalog antibody's IHC-P instructions for its specified conditions; no target-specific retrieval or fixation effect is established here.
Diffuse brown color obscures cell boundaries.Excess background from the staining workflow can hide HPA's selective lymphoid pattern (general IHC practice; HPA: tissue IHC).Inspect a no-primary control and review general IHC blocking, washes, antibody concentration and chromogen development. Score CD79B only where stained cells remain identifiable against neighboring tissue (general IHC practice; HPA: tissue IHC).
Color appears in a listed negative cell population.Adipocytes, adrenal glandular cells and bronchial respiratory epithelial cells are Not detected in the supplied HPA observations (HPA: tissue IHC).Check cell identity and a no-primary control, then review endogenous detection activity and primary-antibody specificity (general IHC practice). The HPA multiple-gene targeting caution means this discrepancy needs verification before a CD79B call (HPA: tissue IHC reliability).
Only nuclei appear strongly positive.This does not match the principal membrane localization or selective cytoplasmic tissue IHC description; HPA labels nucleoplasmic ICC-IF localization uncertain (UniProt P40259 subcellular location; HPA: tissue IHC; HPA: subcellular ICC-IF).Recheck counterstain versus chromogen and compare with no-primary and known-positive sections (general IHC practice). Do not score isolated nuclear color as confirmed CD79B on the basis of the uncertain ICC-IF observation.
A membrane rim is weak but lymphoid-cell cytoplasmic color is clear.HPA describes the tissue IHC profile as cytoplasmic, despite UniProt membrane localization (HPA: tissue IHC; UniProt P40259 subcellular location).Assess whether staining is selective for the expected lymphoid cells and agrees with the positive control (HPA: tissue IHC). Do not reject an otherwise matching paraffin-section result solely because a sharp membrane outline is absent.
Positive and negative controls both show substantial color.The contrast needed to recognize selective HPA lymphoid staining is lost; background or detection activity is possible (HPA: tissue IHC; general IHC practice).Review no-primary staining, blocking, washing and chromogen development, then repeat the comparison with an HPA-listed positive population and an appropriate listed negative cell population (general IHC practice; HPA: tissue IHC).

Sample controls for CD79B IHC & IF

🧪Run tonsil first: its non-germinal center cells should stain strongly (HPA: High in tonsil non-germinal center cells). Use adrenal gland glandular cells as the negative comparison (HPA: Not detected in adrenal gland glandular cells); on the tonsil slide, epithelial and stromal cells should lack specific staining (UniProt P40259: B-cell tissue specificity).
Positive control tissue: Appendix (Non-germinal center cells, HPA High)
Negative control tissue: Adipose tissue (HPA Not detected)
ICC-IF cell lines (HPA subcellular resource): HPA ICC-IF images show CD79B in A-431, REH, U2OS, with annotated localisation: Plasma membrane (supported) (HPA subcellular).
Technical controls: Include a no-primary, secondary-only control, a mouse IgG isotype control matched to the catalog primary antibody, and CD79B knockout material as a biological negative (selected-SKU caption: mouse anti-CD79b antibody; standard IHC controls). For tonsil chromogenic IHC, block endogenous peroxidase and check for endogenous biotin signal when using the caption’s streptavidin–biotin detection system (selected-SKU caption: SABC with DAB; standard IHC practice).
⚠️Feasibility: A target-specific fixation window and fixation effect are unreported, and the selected-SKU tonsil caption does not state its fixative (selected-SKU caption: fixative unreported). The demonstrated paraffin-section workflow uses heat retrieval in EDTA at pH 8.0; whether retrieval is strictly required is unreported (selected-SKU caption: EDTA heat retrieval). The supplied evidence does not establish frozen sections or IF/ICC as easier; tonsil’s mixed cell populations make cell-level scoring important (HPA: High in tonsil non-germinal center cells; UniProt P40259: B-cell tissue specificity).

HPA tissue IHC evidence for CD79B

Comprehensive Human Protein Atlas IHC scoring per tissue (reliability: Enhanced — Medium consistency between antibody staining and RNA expression data. Caution, targets protein from more than one gene.). 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
Appendix Non-germinal center cells High Protein (IHC) HPA →
Lymph node Germinal center cells High Protein (IHC) HPA →
Spleen Cells in white pulp High Protein (IHC) HPA →
Tonsil Non-germinal center cells High Protein (IHC) HPA →

Undetected expression · recommended negative controls

TissueCell typeLevelEvidenceSource
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 CD79B IHC Tips

Troubleshoot CD79B staining in paraffin sections by checking retrieval, cellular context and controls before interpreting signal intensity.

What should I change if CD79B staining is weak after retrieval?
Start with heat-mediated retrieval in EDTA at pH 8.0 (datasheet M01399-1). The documented paraffin-section workflow detected CD79B in human tonsil after this retrieval, followed by 1 μg/mL primary antibody overnight at 4°C (datasheet M01399-1). If staining is weak, first compare a known positive tonsil section across runs and confirm that heating, cooling and section adhesion were consistent (datasheet M01399-1; standard IHC practice). Then adjust retrieval duration in small steps while keeping EDTA and pH constant, because excessive heating can damage tissue morphology (standard IHC practice). Judge any gain against background in the same run (standard IHC practice).
Could fixation explain variable CD79B staining between paraffin blocks?
The selected CD79B paraffin-section caption does not report a fixative, so target-specific fixation sensitivity is unknown (datasheet M01399-1). Record each block’s fixative, fixation duration and processing history before comparing staining across specimens (standard IHC practice). Run a positive tonsil section alongside the affected blocks using EDTA at pH 8.0 and the same detection conditions (datasheet M01399-1; standard IHC practice). If staining varies, review tissue preservation and retrieval consistency, but do not assign the difference to a particular fixation effect without a controlled comparison (standard IHC practice). Score only intact, interpretable cells and document compromised areas (standard IHC practice).
Should CD79B appear on the membrane or in the cytoplasm?
Expect a membrane-associated pattern because CD79B has an extracellular region at residues 29–159, a transmembrane segment at 160–180 and a cytoplasmic tail at 181–229 (UniProt P40259 topology). The HPA subcellular assessment supports plasma-membrane localisation, while its cytosol and nucleoplasm assignments are uncertain and based on antibodies targeting proteins from multiple genes (HPA subcellular). In paraffin-section IHC, examine whether staining follows the borders of morphologically appropriate lymphoid cells before accepting diffuse colour as CD79B (UniProt P40259 tissue specificity; standard IHC practice). HPA also reports high, selective cytoplasmic staining in lymphoid cells, so record membrane and cytoplasmic patterns separately (HPA tissue IHC). Treat isolated nuclear staining cautiously (HPA subcellular).
How can an unknown epitope affect my CD79B IHC result?
CD79B has 3 reported isoforms, but the selected antibody’s recognised epitope and isoform coverage are not specified here (UniProt P40259 isoforms; datasheet M01399-1). Its extracellular region spans residues 29–159, and its cytoplasmic tail spans 181–229 (UniProt P40259 topology). Four glycosylation sites occur in the extracellular region, while phosphorylation is reported at cytoplasmic residues 196 and 207 (UniProt P40259 glycosylation and modified residues). These features identify possible sources of epitope dependence, but they do not establish this antibody’s binding site (UniProt P40259; datasheet M01399-1). If discordance persists, compare an independently characterised epitope antibody on matched sections (standard IHC practice).
How should I check CD79B by multiplex IF alongside this IHC assay?
Use the chromogenic IHC pattern as a tissue reference: CD79B is associated with B cells, and the selected paraffin-section example uses human tonsil (UniProt P40259 tissue specificity; datasheet M01399-1). For a separate IF assay, pair CD79B with a validated B-cell marker and include single-colour and no-primary controls to assess overlap and bleed-through (standard IF practice). Choose fluorophores after checking tissue autofluorescence in each channel, and favour a brighter, spectrally separated channel for a weak CD79B signal (standard IF practice). Match permeabilisation to the recognised epitope: an extracellular epitope may be accessible without it, whereas a cytoplasmic-tail epitope may require it (UniProt P40259 topology; standard IF practice). The epitope is unspecified here (datasheet M01399-1).
What should I check when DAB obscures CD79B staining?
Start with a no-primary section and inspect whether colour appears in tissue regions lacking plausible B cells (UniProt P40259 tissue specificity; standard IHC practice). The documented assay uses a biotinylated secondary antibody, a streptavidin–biotin complex and DAB, so check secondary-only background and reagent-dependent staining in that detection chain (datasheet M01399-1; standard IHC practice). Apply a peroxidase block and control DAB development as routine chromogenic steps, then compare sections processed together (standard IHC practice). The example used 10% goat serum blocking and 1 μg/mL primary antibody overnight at 4°C (datasheet M01399-1). Preserve those settings initially while tracing the background source (standard IHC practice).
How should I score CD79B staining across tissue sections? ⚠ ANSWER MARKED FOR VERIFICATION
Define the cell population and region of interest before scoring, because CD79B is associated with B cells and HPA reports selective staining in lymphoid cells (UniProt P40259 tissue specificity; HPA tissue IHC). For each region, report the percentage of positive eligible cells and an intensity-weighted H-score, using the same threshold across sections (standard IHC practice). Where cell abundance differs, also report CD79B-positive cell density per mm² of viable tissue and normalise staining to the number of eligible lymphoid cells (standard IHC practice). Record membrane and cytoplasmic staining separately because their interpretation differs (UniProt P40259 subcellular location; HPA tissue IHC). Exclude damaged tissue and document the exclusions (standard IHC practice).
How can I distinguish genuine CD79B staining from artefact?
Prioritise staining in morphologically intact lymphoid cells: CD79B is B-cell associated, and HPA reports high staining in selected lymphoid compartments (UniProt P40259 tissue specificity; HPA tissue IHC). A membrane-associated component supports the expected location, although HPA tissue IHC also describes cytoplasmic expression (UniProt P40259 subcellular location; HPA tissue IHC). Treat colour restricted to section edges, necrotic areas or implausible cell types as suspect and compare it with a no-primary control (standard IHC practice). Check endogenous peroxidase activity when DAB colour persists without primary antibody (standard IHC practice). Interpret weak or unusual patterns cautiously because the HPA tissue assessment notes medium RNA–staining consistency and antibody recognition of proteins from multiple genes (HPA tissue IHC).
Boster reagents

Best CD79B / B-cell antigen receptor complex-associated protein beta chain IHC Antibodies

IHC images show CD79B staining in human tonsil, human spleen and rat spleen (M01399-1 and PB9169 IHC captions); an IF image shows human spleen (PB9169 IF caption).

Real IHC data IHC analysis of CD79b using anti-CD79b antibody (M01399-1). CD79b was detected in paraffin-embedded section of human tonsil tissue. Heat mediated antigen retrieval was performed in EDTA buffer (pH8.0, epitope retrieval solution). The tissue section was blocked with 10% goat serum. The tissue section was then incubated with 1μg/ml mouse anti-CD79b Antibody (M01399-1) overnight at 4°C. Biotinylated goat anti-mouse IgG was used as secondary antibody and incubated for 30 minutes at 37°C. The tissue section was developed using Strepavidin-Biotin-Complex (SABC) (Catalog # SA1021) with DAB as the chromogen.
Anti-CD79b Antibody ®(monoclonal, 6H11)
Cat # M01399-1
Real IHC data IHC analysis of CD79b using anti-CD79b antibody (PB9169). CD79b was detected in a paraffin-embedded section of human spleen 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-CD79b Antibody (PB9169) 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-CD79b Antibody ®
Cat # PB9169

M01399-1 has paraffin-section IHC images from human tonsil and rat spleen (M01399-1 IHC captions). PB9169 has paraffin-section IHC and IF images from human spleen (PB9169 IHC and IF captions).

Which to pick: For paraffin-section IHC, choose mouse monoclonal M01399-1 for human tonsil or rat spleen, or rabbit PB9169 for human spleen (catalog hosts; M01399-1 and PB9169 IHC captions). For IF, PB9169 has a human spleen image; for ICC, rabbit monoclonals M01399 and M01399-3 list that application (PB9169 IF caption; catalog hosts and applications). For cross-species tissue IHC, M01399-1 has human and rat images; the fixative is unreported in its captions (M01399-1 IHC captions).

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

References

  1. UniProt Consortium. UniProt entry P40259 (CD79B_HUMAN, B-cell antigen receptor complex-associated protein beta chain).
  2. Human Protein Atlas. CD79B tissue IHC expression (reliability: Enhanced).
  3. Human Protein Atlas. CD79B subcellular location (ICC-IF): Mainly localized to the plasma membrane. In addition localized to the nucleoplasm and cytosol. Caution: Based on antibodies targeting proteins from multiple genes..
  4. Human Protein Atlas. CD79B antibody validation summary (3 antibodies).
  5. Polatuzumab Vedotin in Relapsed or Refractory Diffuse Large B-Cell Lymphoma. Journal of clinical oncology : official journal of the American Society of Clinical Oncology 2020 — PMC7032881.
  6. Gene Expression Profiling Provides an Improved Characterization of CD79B-Mutated Diffuse Large B-Cell Lymphomas. Journal of personalized medicine 2025 — PMC12653173.
  7. Exploring CD79b, LC3, and TERT expression in NON-GCB DLBCL: markers associated with Rituximab-Cyclophosphamide-Doxorubicin-Vincristin-Prednisone treatment response. Blood research 2026 — PMC13168377.
  8. Primary refractory plasmablastic lymphoma: A precision oncology approach. Frontiers in oncology 2023 — PMC10008852.
  9. PubMed PMID:1534761 — UniProt-cited evidence.
  10. PubMed PMID:8486355 — UniProt-cited evidence.
  11. PubMed PMID:8419481 — UniProt-cited evidence.