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PDGFRB / Platelet-derived growth factor receptor beta · IHC design guide
Design Immunohistochemistry for PDGFRB
Plan chromogenic FFPE IHC for PDGFRB using testis peritubular cells as a positive control and adipocytes as a cell-level negative reference (HPA tissue IHC). Interpret staining alongside the receptor’s membrane location and ligand-dependent internalization (UniProt).
Evidence assembled Oct 2026 · For research use; verify linked source records and product datasheet before use
PDGFRB 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 | Cell membrane; cytoplasmic vesicles and lysosome lumen (UniProt) | |
| Staining pattern | Endothelial, decidual and fibroblast staining; compartment unspecified (HPA tissue IHC) | |
| Antigen retrieval | Citrate pH 6.0 HIER, 95–98 °C, 20 min (rule: cytoplasmic / membrane antigen) | |
| Positive control | Testis+4 more · see all | |
| Negative control | Adipose tissue+4 more · see all |
Important caveats
Reasons your staining may differ from the expected pattern.
| Fixation | Matched tissue-IHC evidence does not establish the fixation claim. Validate the specimen-specific method before use. (selected-SKU IHC image M00096-6) | |
| Caveat | Ligand binding can shift receptor signal from membrane to vesicles (UniProt) | |
| Regulation | Ligand binding promotes degradation (UniProt) | |
| Isoform / epitope | 2 isoforms; epitope differences are unspecified—map extracellular versus cytoplasmic domains (UniProt) |
Section 1
Recommended PDGFRB IHC & IF Protocols
The catalog antibody’s IHC-P protocol is accompanied by 4 published PDGFRB IHC protocols covering glomus tumors, colorectal lesions, human FFPE sections, and mouse tissues (PMC7554116; PMC9497196; PMC3244048; PMC2848338).
| Sample | Tissue sections; selected-image fixative not specified (standard IHC workflow) |
| Fixation | Image fixative and duration unreported (datasheet M00096-6); verify before use. |
| Sectioning | 4–5 µm sections on charged slides (standard) |
| Deparaffinisation | Xylene, graded ethanol series to water (standard) |
| Antigen retrieval | Heat-induced epitope retrieval in citrate buffer, pH 6.0, 20 min at 95–98 °C (standard rule: cytoplasmic / membrane antigen) |
| 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-PDGFRB, 1:200-1:1000 (datasheet M00096-6) |
| 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 | PDGFRB-positive staining in peritubular cells of testis (HPA tissue IHC: High). HPA tissue profile: High expression in endothelial cells, decidual cells and fibroblasts with distinct positivity in connective tissue. No signal in the no-primary control. |
💡Decision noteStart with citrate pH 6.0 HIER at 95–98 °C for 20 min (page antigen retrieval); EDTA pH 9 is published for human FFPE sections (PMC9497196).
Section 2
What Is the Expected PDGFRB Staining Pattern?
PDGFRB is a single-pass receptor with an extracellular region and a cytoplasmic kinase region; UniProt places it at the cell membrane and in cytoplasmic vesicles (UniProt P09619 topology; subcellular location). In tissue IHC, assess staining in the relevant cells, including fibroblasts, endothelial cells and decidual cells (HPA tissue IHC). HPA rates the tissue pattern “Enhanced,” while reporting medium consistency between staining and RNA data (HPA tissue IHC).
| Cell-associated staining in connective tissue, including fibroblasts or endothelial cells; strong staining of testis peritubular cells. | This fits the reported tissue distribution: HPA describes distinct connective-tissue positivity and high expression in fibroblasts and endothelial cells, while grading testis peritubular cells High (HPA tissue IHC). Judge the stained cell population as well as intensity; a positive-looking region alone does not identify which cells carry the signal. |
| Membrane-associated staining, with possible cytoplasmic puncta, in an expected cell population. | A membrane component agrees with the receptor’s single transmembrane segment; puncta can agree with its reported cytoplasmic vesicle location and internalization after ligand binding (UniProt P09619 topology; subcellular location). Chromogenic IHC may not resolve small vesicles individually (general IHC practice), so interpret puncta alongside cell identity and the overall pattern. |
| A dominant nuclear-only pattern, without convincing cell-surface or vesicular staining. | Treat this as a localization mismatch rather than a characteristic PDGFRB result: the supplied locations are membrane, cytoplasmic vesicles and lysosome lumen, with no nuclear location listed (UniProt P09619 subcellular location). Review morphology, counterstain and controls before assigning the chromogen to the nucleus (general IHC practice). |
| Strong staining mainly in adipocytes or glandular cells expected to be unstained in the chosen reference tissue. | HPA reports adipocytes as Not detected in adipose tissue and glandular cells as Not detected in several listed tissues (HPA tissue IHC). Check the exact tissue and cell type before calling cross-reactivity: other cells in the same section may legitimately stain, and HPA’s tissue assessment has medium staining–RNA consistency (HPA tissue IHC). |
| Diffuse chromogen across cells and spaces, or no signal in testis peritubular cells. | Neither is an interpretable positive pattern. Diffuse signal can reflect nonspecific background or endogenous detection activity (general IHC practice). Complete absence in a well-preserved reference area conflicts with HPA’s High peritubular-cell result, but does not alone distinguish a failed stain from sample variation (HPA tissue IHC; general IHC practice). |
💡Expected PDGFRB appearanceCall a result positive when cell-associated membrane staining, with possible vesicular cytoplasmic signal, occurs in the relevant connective-tissue or vascular-associated cells (UniProt P09619 subcellular location; HPA tissue IHC); expect High testis peritubular-cell staining in the HPA reference, while dominant nuclear-only signal or uniform haze warrants investigation (HPA tissue IHC; UniProt P09619 subcellular location; general IHC practice).
| Topology and unknown antibody epitope | The receptor spans residues 533–553, with extracellular residues 33–532 and cytoplasmic residues 554–1106 (UniProt P09619 topology). The supplied record does not identify the IHC antibody’s epitope, so topology cannot predict which region that antibody recognizes. |
| Ligand-dependent trafficking | After ligand binding, autophosphorylated PDGFRB is ubiquitinated and internalized, then degraded (UniProt P09619 subcellular location). Membrane and intracellular patterns can therefore both fit its biology; a vesicular pattern alone does not establish ligand exposure or activation state in a fixed section. |
| Reference-pattern confidence | HPA labels tissue IHC reliability “Enhanced” and lists two IHC antibodies with Enhanced validation, CAB003842 and CAB018144 (HPA tissue IHC; HPA antibodies). HPA also reports only medium consistency with RNA expression, so use its cell-specific observations as references rather than absolute pass–fail thresholds. |
| IF/ICC: what localization should I expect? | HPA reports mainly vesicles, with additional Golgi localization, in ICC-IF; its ICC-supported antibody is HPA028499 (HPA subcellular; HPA antibodies). This answers the localization question for the separate IF/ICC guide. It does not establish a staining protocol or transfer an ICC validation claim to IHC. |
| Situation | Likely cause | Next action |
|---|---|---|
| No staining in testis peritubular cells | HPA grades these cells High, so absence may indicate an assay or section problem; the observation alone cannot identify which one (HPA tissue IHC; general IHC practice). | Confirm the peritubular cells are present and preserved, then review antibody identity, controls, retrieval conditions and detection steps against the validated IHC procedure (general IHC practice). |
| Uniform brown haze obscures cell boundaries | Nonspecific reagent binding, incomplete blocking or endogenous detection activity can produce diffuse chromogenic background (general IHC practice). | Inspect appropriate negative controls and reagent-only areas; review blocking, washes and endogenous-enzyme quenching for the detection system used (general IHC practice). |
| Apparent signal is confined to nuclei | That compartment conflicts with the membrane and vesicle locations supplied for PDGFRB (UniProt P09619 subcellular location). | Compare the chromogen with the counterstain and cell borders, then check control sections before scoring nuclear signal as PDGFRB (general IHC practice). |
| Adipocytes appear strongly positive | HPA reports adipocytes as Not detected in adipose tissue; signal may instead arise from adjacent connective-tissue cells or background (HPA tissue IHC; general IHC practice). | Identify the stained cell boundaries and compare with a negative control; score adipocytes separately from nearby stromal cells (general IHC practice). |
| A glandular region stains despite an expected negative reference | HPA lists glandular cells as Not detected in several specified tissues, but its observations must be matched to the actual tissue and cell type (HPA tissue IHC). | Verify that the reference tissue matches an HPA-listed negative, then inspect morphology and detection controls before treating the signal as cross-reactivity (HPA tissue IHC; general IHC practice). |
| Membrane staining is faint while cytoplasmic puncta remain | PDGFRB can occupy cytoplasmic vesicles and undergo internalization after ligand binding; intensity alone cannot establish why a particular section looks this way (UniProt P09619 subcellular location). | Assess whether the puncta are cell-associated in an HPA-supported cell population, and compare positive and negative controls before changing the interpretation (HPA tissue IHC; general IHC practice). |
Experiment evidence
IHC & IF images showing PDGFRB staining
M00096-6 · IHCMouse spleen was stained with anti-PDGFR-β rabbit antibody
M00096-6 · IHCRat spleen was stained with anti-PDGFR-β rabbit antibody
M00096-1 · IHCImmunohistochemical analysis of paraffin-embedded human uterus, using PDGF Receptor beta Antibody.
M00096-1 · IFImmunofluorescent analysis of 3T3 cells, using PDGF Receptor beta Antibody.
HPA · Cerebral cortexHuman Protein Atlas IHC, Cerebral cortex. Source: https://www.proteinatlas.org/ENSG00000113721-PDGFRB/tissue/cerebral+cortex#imid_1221472
HPA · ColonHuman Protein Atlas IHC, Colon. Source: https://www.proteinatlas.org/ENSG00000113721-PDGFRB/tissue/colon#imid_1221390
HPA · LiverHuman Protein Atlas IHC, Liver. Source: https://www.proteinatlas.org/ENSG00000113721-PDGFRB/tissue/liver#imid_1221399
HPA · KidneyHuman Protein Atlas IHC, Kidney. Source: https://www.proteinatlas.org/ENSG00000113721-PDGFRB/tissue/kidney#imid_1221392
HPA · ICC-IF ASC52teloHuman Protein Atlas immunofluorescence, ASC52telo, antibody HPA028499; green = PDGFRB, blue = nucleus, red = microtubules.
HPA · ICC-IF ASC52teloHuman Protein Atlas immunofluorescence, ASC52telo, antibody HPA028499; green = PDGFRB, blue = nucleus, red = microtubules.
← swipe / scroll for more images →
Real IHC / IF data behind the staining-pattern expectations in this section.
Sample controls for PDGFRB IHC & IF
🧪Run testis first and look for staining in peritubular cells (HPA: High in testis peritubular cells). Use adipose tissue as the negative comparison, assessing adipocytes (HPA: Not detected in adipocytes); on the testis slide, cells outside the peritubular compartment should retain counterstain without specific chromogen, but they are background references rather than validated PDGFRB-negative cells (HPA: testis peritubular-cell staining only).
Positive control tissue: Testis (Peritubular cells, HPA High)
Negative control tissue: Adipose tissue (HPA Not detected)
ICC-IF cell lines (HPA subcellular resource): HPA ICC-IF images show PDGFRB in ASC52telo, U-251MG, U2OS, hTERT-RPE1 (serum starved), with annotated localisation: Vesicles (supported) (HPA subcellular).
Technical controls: Include a no-primary, secondary-only control; a host-species-, isotype-, and clonality-matched irrelevant-primary control; and PDGFRB-knockout material as a biological negative (standard IHC practice). Quench endogenous peroxidase and check the no-primary testis section for residual chromogen background (standard IHC practice).
⚠️Feasibility: No target-specific fixation window or fixation effect is reported in the supplied evidence, and the M00096-6 mouse-spleen IHC caption does not state a fixative (selected-SKU caption: fixative unreported). Retrieval dependence is unreported, so optimize antigen retrieval empirically for paraffin sections (standard IHC practice). The supplied evidence does not establish whether frozen sections or IF are easier; blood-associated endogenous peroxidase may complicate chromogenic interpretation in testis (standard IHC practice).
HPA tissue IHC evidence for PDGFRB
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 |
|---|---|---|---|---|
| Testis | Peritubular cells | High | Protein (IHC) | HPA → |
| Breast | Myoepithelial cells | Medium | Protein (IHC) | HPA → |
| Endometrium | Cells in endometrial stroma | Medium | Protein (IHC) | HPA → |
| Kidney | Cells in glomeruli | Medium | Protein (IHC) | HPA → |
| Ovary | Ovarian stroma cells | Medium | 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 → |
| Appendix | Glandular cells | Not detected | Protein (IHC) | HPA → |
| Bone marrow | Hematopoietic cells | Not detected | Protein (IHC) | HPA → |
| Bronchus | Respiratory epithelial cells | Not detected | Protein (IHC) | HPA → |
Section 3
Advanced PDGFRB IHC Tips
Troubleshoot PDGFRB staining by checking retrieval, cellular location, controls, and scoring against the expected vascular and stromal pattern.
How should I retrieve PDGFRB in paraffin sections when staining is weak?
Start with citrate buffer at pH 6.0, heated to 95–98 °C for 20 min (page IHC retrieval rule). If signal remains weak, compare a second retrieval condition on serial sections while keeping the antibody dilution, detection chemistry, and tissue controls constant (standard IHC practice). Score membrane and vesicular staining in the same expected cell populations across conditions, since PDGFRB occupies the cell membrane and intracellular vesicles (UniProt P09619 localisation; HPA subcellular). Excessive retrieval can damage morphology or increase diffuse staining, so select the mildest condition that preserves identifiable cells and a clear separation between positive and negative controls (standard IHC practice).
Could fixation explain weak or uneven PDGFRB IHC staining?
Target-specific sensitivity of PDGFRB to fixation is unknown from the supplied evidence; the catalog antibody’s mouse spleen caption does not state a fixative (catalog antibody M00096-6 tissue-IHC caption). Record the fixative, fixation duration, tissue thickness, and processing history before comparing sections, because these variables can change antigen accessibility and morphology in paraffin IHC (standard IHC practice). Compare matched sections processed together with the same citrate pH 6.0 retrieval at 95–98 °C for 20 min (page IHC retrieval rule). Interpret differences only after checking section integrity and internal positive cells, rather than assigning a PDGFRB-specific fixation effect to an untested processing condition (standard IHC practice).
Should PDGFRB staining be membranous or cytoplasmic in IHC?
Evaluate both membrane-associated and punctate cytoplasmic staining: PDGFRB is a cell-membrane receptor that can enter cytoplasmic vesicles and the lysosome lumen after ligand-dependent internalisation (UniProt P09619 localisation). Vesicles are the supported main subcellular location in the supplied imaging record, with additional Golgi localisation reported (HPA subcellular). In paraffin sections, assess whether staining follows cell boundaries or forms discrete intracellular puncta in morphologically identifiable cells, using a matched negative control to judge diffuse colour (standard IHC practice). A purely nuclear pattern should prompt review of antibody specificity, detection background, and tissue morphology before being scored as PDGFRB positive (UniProt P09619 localisation; standard IHC practice).
How do epitope location and isoforms affect PDGFRB IHC interpretation?
Confirm the catalog antibody’s immunogen and epitope documentation before interpreting an absent signal, because the supplied record identifies 2 isoforms but does not map this antibody’s epitope (UniProt P09619 isoforms; supplied antibody evidence). The annotated extracellular region spans residues 33–532, the transmembrane segment 533–553, and the cytoplasmic region 554–1106 (UniProt P09619 topology). Extracellular-region interpretation may be complicated by annotated glycosylation sites, while cytoplasmic-region interpretation must account for documented phosphotyrosines; neither annotation establishes this antibody’s sensitivity to those modifications (UniProt P09619 modifications). Compare staining across independently validated reagents or controls before attributing a pattern to a particular isoform or modified epitope (standard IHC practice).
How can I investigate PDGFRB localisation with multiplex IF?
For a separate IF experiment, pair PDGFRB with a validated marker of the expected pericyte or smooth muscle population and check whether the signals occupy compatible cells (UniProt P09619 function; standard IF practice). Choose spectrally separated fluorophores and compare unstained tissue autofluorescence before assigning the weaker signal, especially when evaluating puncta (standard IF practice). If the antibody recognises a cytoplasmic epitope, permeabilise fixed cells sufficiently for intracellular access; an extracellular epitope may be assessed without permeabilisation, subject to antibody validation (UniProt P09619 topology; standard IF practice). Include single-stain and secondary-only controls, then distinguish surface signal from vesicular or Golgi-associated signal without transferring conclusions from IF directly to chromogenic IHC (HPA subcellular; standard IF practice).
What should I check when PDGFRB IHC shows diffuse brown background?
First compare the stained section with a primary-antibody omission control and inspect whether colour follows tissue edges, folds, or damaged areas rather than intact cell contours (standard IHC practice). Check the peroxidase block and DAB development as general chromogenic workflow steps, and shorten development if both positive and negative regions accumulate colour (standard IHC practice). Reassess blocking, washes, and antibody concentration by titration without assuming that every brown deposit represents receptor signal (standard IHC practice). Genuine staining is more credible when it is cell-associated in expected stromal or vascular populations and resembles membrane or vesicular localisation (HPA tissue IHC; UniProt P09619 localisation).
How should I score PDGFRB staining across paraffin sections? ⚠ ANSWER MARKED FOR VERIFICATION
Define the scored compartment and cell population before analysis, separating membrane-associated from punctate cytoplasmic signal where morphology permits (UniProt P09619 localisation; standard IHC practice). For a defined cell population, report the percentage of positive cells or an H-score based on intensity and percentage; for spatial analyses, report positive-cell density per mm² of viable tissue (standard IHC practice). Normalise to the number of eligible cells or viable tissue area, and apply the same threshold, sampled regions, and detection settings across sections (standard IHC practice). Report stromal and vascular regions separately when relevant, because the tissue atlas describes endothelial, fibroblast, connective-tissue, and decidual staining patterns (HPA tissue IHC).
How can I distinguish true PDGFRB staining from artefact?
A credible positive pattern follows identifiable cells in plausible vascular or stromal locations and may appear at the membrane or in intracellular vesicles (HPA tissue IHC; UniProt P09619 localisation). Treat isolated nuclear colour as suspicious because the supplied localisation record places PDGFRB at the membrane, in vesicles, and in the lysosome lumen (UniProt P09619 localisation). Exclude edge effects, folds, necrotic regions, and deposits that also appear in a primary-antibody omission control; check peroxidase blocking when unexplained DAB colour persists (standard IHC practice). Use matched positive and negative tissue regions to assess specificity, while recognising that the atlas reports only medium consistency between staining and RNA expression (HPA tissue IHC).
Boster reagents
Best PDGFRB / Platelet-derived growth factor receptor beta IHC Antibodies
Two anti-PDGFRB antibodies support IHC in human, mouse, and rat samples (catalog: applications and reactivity); the catalog also provides an IF image from 3T3 cells (M00096-1: IF image caption).
Real IHC data
Anti-PDGFR-β Rabbit Monoclonal Antibody
Cat # M00096-6
Real IHC data
Anti-PDGF Receptor beta PDGFRB Rabbit Monoclonal Antibody
Cat # M00096-1
M00096-6 has IHC images from mouse spleen, rat spleen, and human kidney, and lists IF among its applications (M00096-6: IHC image captions; catalog: applications). M00096-1 has an IHC image from paraffin-embedded human uterus and an IF image from 3T3 cells; its listed reactivity is human, mouse, and rat (M00096-1: image captions; catalog: reactivity).
Which to pick: For paraffin-section IHC, choose M00096-1 when the human uterus example is relevant; its caption reports paraffin embedding but does not report the fixative (M00096-1: IHC image caption). For IF/ICC, choose M00096-1 because ICC and IF are listed applications and it has a 3T3 IF image (M00096-1: applications; IF image caption). For IHC across species, consider M00096-6 because its own IHC images show mouse spleen, rat spleen, and human kidney; both SKUs are rabbit monoclonals with human, mouse, and rat listed as reactive species (M00096-6: IHC image captions; catalog: antibody titles and reactivity).
Each figure is that product's own IHC / IF validation image from its datasheet.
References
- UniProt Consortium. UniProt entry P09619 (PGFRB_HUMAN, Platelet-derived growth factor receptor beta).
- Human Protein Atlas. PDGFRB tissue IHC expression (reliability: Enhanced).
- Human Protein Atlas. PDGFRB subcellular location (ICC-IF): Mainly localized to vesicles. In addition localized to the Golgi apparatus..
- Human Protein Atlas. PDGFRB antibody validation summary (3 antibodies).
- A Molecular Reappraisal of Glomus Tumors and Related Pericytic Neoplasms With Emphasis on NOTCH-gene Fusions. The American journal of surgical pathology 2020 — PMC7554116.
- Detection of Experimental Colorectal Peritoneal Metastases by a Novel PDGFRβ-Targeting Nanobody. Cancers 2022 — PMC9497196.
- Characterization of Pdgfrb-Cre transgenic mice reveals reduction of ROSA26 reporter activity in remodeling arteries. Genesis (New York, N.Y. : 2000) 2011 — PMC3244048.
- Identification of key genes for carcinogenic pathways associated with colorectal adenoma-to-carcinoma progression. Tumour biology : the journal of the International Society for Oncodevelopmental Biology and Medicine 2010 — PMC2848338.
- PubMed PMID:2835772 — UniProt-cited evidence.
- PubMed PMID:2850496 — UniProt-cited evidence.
- PubMed PMID:18593464 — UniProt-cited evidence.
Immunohistochemistry protocol sheet for PDGFRB (Platelet-derived growth factor receptor beta). Expected localisation Cell membrane; cytoplasmic vesicles and lysosome lumen (UniProt). Antigen retrieval: Citrate pH 6.0 HIER, 95–98 °C, 20 min (rule: cytoplasmic / membrane antigen). Validated IHC antibody: M00096-6 at 1:200-1:1000 (the product's own IHC validation image is shown). Controls (HPA): positive Testis (Peritubular cells); negative Adipose tissue. IHC workflow; specimen preparation unspecified. Protocol steps: 1. Sample: Tissue sections; selected-image fixative not specified (standard IHC workflow); 2. Fixation: Image fixative and duration unreported (datasheet M00096-6); 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-induced epitope retrieval in citrate buffer, pH 6.0 , 20 min at 95–98 °C…; 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-PDGFRB, 1:200-1:1000 (datasheet M00096-6); 9. Primary incubation: Overnight at 4 °C (standard). Watch for: Fixation: Matched tissue-IHC evidence does not establish the fixation claim. Validate the specimen-specific method before use. (selected-SKU IHC image M00096-6); Caveat: Ligand binding can shift receptor signal from membrane to vesicles (UniProt); Isoform / epitope: 2 isoforms; epitope differences are unspecified—map extracellular versus cytoplasmic domains (UniProt); Regulation: Ligand binding promotes degradation (UniProt). Evidence: UniProt P09619, HPA tissue IHC · Enhanced, HPA ICC-IF · Mainly localized to vesicles. In addition localized to the Golgi…, Datasheet M00096-6, PMC7554116, PMC9497196. QR code links to https://www.bosterbio.com/bosterbio-gene-info-cards/PDGFRB/immunohistochemistry-ihc-guide.