This website uses cookies to ensure you get the best experience on our website.
- Table of Contents
PTPRZ1 / Receptor-type tyrosine-protein phosphatase zeta · IHC design guide
Design Immunohistochemistry for PTPRZ1
Plan PTPRZ1 chromogenic IHC in paraffin sections using brain staining reported in glial and neuronal subsets as a reference (HPA tissue IHC). Consider the membrane-bound and shed forms when interpreting staining, and check which region the antibody recognizes (UniProt).
Evidence assembled Oct 2026 · For research use; verify linked source records and product datasheet before use
PTPRZ1 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 | Cerebellar molecular layer cells: cytoplasm/membrane (HPA tissue IHC) | |
| Staining pattern | Subsets of glia and neurons; cerebellar cytoplasm/membrane (HPA tissue IHC) | |
| Antigen retrieval | Tris-EDTA pH 9.0 HIER, heat-mediated (datasheet A03510) | |
| Positive control | Cerebral cortex+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 fixation consistent across sections. (standard IHC practice; not target-specific) | |
| Caveat | A shed extracellular form may shift the staining pattern (UniProt) | |
| Regulation | Developmentally regulated in brain (UniProt) | |
| Isoform / epitope | 3 isoforms; check extracellular vs cytoplasmic epitope (UniProt) |
Section 1
Recommended PTPRZ1 IHC & IF Protocols
The catalog antibody protocol specifies heat-mediated Tris-EDTA pH 9.0 retrieval (datasheet A03510). Published IHC methods add conditions for tumor sections and glioma tissue microarrays (PMC12667478; PMC13523290).
| Sample | Paraffin-embedded human tonsil tissue; fixative not specified (datasheet A03510) |
| Fixation | Image fixative and duration unreported (datasheet A03510); 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 A03510); 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-PTPRZ1, 1:50 recommended; image 1:200 (datasheet A03510) |
| 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 | PTPRZ1-positive staining in glial cells of cerebral cortex (HPA tissue IHC: Medium). HPA tissue profile: Distinct expression in brain, both in subsets of neurons and a subset of glial cells. No signal in the no-primary control. |
💡Decision noteStart with heat-mediated Tris-EDTA pH 9.0 retrieval (datasheet A03510); the published IHC excerpts do not specify retrieval conditions (PMC12667478; PMC13523290).
Section 2
What Is the Expected PTPRZ1 Staining Pattern?
PTPRZ1 is a cell-membrane protein with a secreted form generated by extracellular-domain shedding (UniProt P23471). In paraffin-section IHC, expect staining chiefly in subsets of brain neurons and glial cells (HPA tissue IHC: Enhanced); HPA reports medium staining in the listed positive cells and medium consistency between antibody staining and RNA expression. Cerebellar molecular-layer cells show cytoplasmic/membranous staining (HPA tissue IHC).
| Medium staining in cerebral-cortex or caudate glial cells, or hippocampal neurons (HPA tissue IHC). | These are documented positive cell populations (HPA tissue IHC). Score staining by cell type and region; an unstained neighboring cell does not negate a subset-specific pattern (HPA tissue IHC: subsets of neurons and glia). |
| Medium cytoplasmic/membranous staining in cerebellar molecular-layer cells (HPA tissue IHC). | This matches the reported cerebellar appearance (HPA tissue IHC) and is compatible with membrane-associated PTPRZ1 (UniProt P23471 topology). Cytoplasmic appearance alone is not grounds for rejection: HPA also reports cytosol and vesicles in ICC-IF (HPA subcellular). |
| Predominantly nuclear staining, without the documented brain-cell pattern. | A nuclear location is not reported in the supplied UniProt or HPA localization records (UniProt P23471; HPA tissue IHC; HPA subcellular). Treat the result as suspect and review controls and staining conditions before assigning it to PTPRZ1. |
| Strong staining in cells reported as not detected, such as adipocytes or colon endothelial cells (HPA tissue IHC). | The cell-type mismatch raises concern for nonspecific binding, cross-reactivity, or endogenous chromogenic activity; it does not independently identify the cause. Compare with a no-primary control and a documented brain-positive section before interpreting it as target staining. |
| Diffuse staining across the section, or no signal in documented positive brain cells (HPA tissue IHC). | Diffuse signal obscures the reported cell-restricted pattern; absent signal prevents its assessment. Check the no-primary and positive-tissue controls, detection reagents, background blocking, and primary-antibody conditions before drawing a biological conclusion. |
💡Expected PTPRZ1 appearanceCall an IHC result positive when medium staining identifies the documented brain neuronal or glial subsets, including cerebellar cytoplasmic/membranous staining (HPA tissue IHC); isolated nuclear or widespread unrelated-cell staining is suspect against that reference pattern.
| Membrane topology and shedding | PTPRZ1 has an extracellular region at residues 25–1636, one transmembrane segment at 1637–1662, and a cytoplasmic region at 1663–2315 (UniProt P23471 topology). Extracellular-domain shedding can produce a secreted form (UniProt P23471); do not require every signal to trace a cell boundary. |
| Antibody epitope and isoforms | UniProt lists 3 isoforms and a shed extracellular form (UniProt P23471). The supplied record does not locate this antibody’s epitope, so it cannot establish which forms the stain detects. Interpret compartment differences with that limit in mind. |
| Evidence strength | The tissue profile is rated Enhanced, but its description reports medium consistency between staining and RNA data and notes that secretion complicates their correspondence (HPA tissue IHC). HPA015103 is IHC Enhanced and ICC Uncertain (HPA antibodies); these labels should not be interchanged. |
| IF/ICC: what pattern is reported? | HPA reports mainly cytosolic signal with additional vesicular signal in ICC-IF (HPA subcellular: approved locations). That observation belongs to a different application; the listed antibody has ICC Uncertain status (HPA antibodies), so do not turn it into an IHC compartment requirement. |
| Situation | Likely cause | Next action |
|---|---|---|
| No staining in a cerebral-cortex or caudate glial-cell area reported as positive (HPA tissue IHC). | The section may lack an evaluable positive population, or the IHC workflow may have failed; the supplied sources do not establish PTPRZ1-specific fixation sensitivity. | Confirm the relevant cell type is present, then review the positive control, primary-antibody conditions, antigen-retrieval step, and detection reagents as general IHC checks. |
| Diffuse chromogen obscures individual cells. | Background from antibody or detection reagents can hide the subset-specific brain pattern (HPA tissue IHC: neuronal and glial subsets). | Compare a no-primary control; review blocking, washes, primary concentration, and chromogen development. Reassess whether staining resolves into the documented positive cells (HPA tissue IHC). |
| Adipocytes or colon endothelial cells stain strongly despite being reported as not detected (HPA tissue IHC). | Nonspecific binding, cross-reactivity, or endogenous detection activity are possible explanations; the slide alone cannot distinguish them. | Run a no-primary control and a documented brain-positive section; review endogenous-activity blocking where applicable to the chromogenic system, then compare cell-specific signal. |
| Signal appears nuclear while documented cerebellar cytoplasmic/membranous staining is absent (HPA tissue IHC). | The observed compartment does not match the supplied IHC reference pattern or UniProt membrane topology (HPA tissue IHC; UniProt P23471). | Check counterstain interpretation and no-primary background, then reassess antibody and detection conditions using a documented positive brain section. |
| Cerebellar staining looks cytoplasmic rather than sharply membrane-bound. | Cytoplasmic/membranous staining is itself reported in molecular-layer cells (HPA tissue IHC); secreted protein may also complicate a simple membrane-only expectation (UniProt P23471). | Score the documented cell population and distribution first. Avoid rejecting the section solely because cell borders are indistinct; compare with controls if the staining is diffuse. |
| An ICC-IF image appears cytosolic or vesicular while the IHC interpretation emphasizes brain-cell distribution. | HPA reports cytosol and vesicles for ICC-IF, while its tissue IHC profile describes neuronal and glial subsets (HPA subcellular; HPA tissue IHC). | Interpret each application against its own HPA record. For this paraffin-section IHC result, prioritize the documented tissue, cell type, and cerebellar cytoplasmic/membranous appearance (HPA tissue IHC). |
Experiment evidence
IHC & IF images showing PTPRZ1 staining
A03510 · IHCImmunohistochemical analysis of paraffin-embedded human tonsil. 1, Antibody was diluted at 1:200 (4° overnight). 2, Tris-EDTA, pH9.0 was use
HPA · Cerebral cortexHuman Protein Atlas IHC, Cerebral cortex. Source: https://www.proteinatlas.org/ENSG00000106278-PTPRZ1/tissue/cerebral+cortex#imid_1479
HPA · Cerebral cortexHuman Protein Atlas IHC, Cerebral cortex. Source: https://www.proteinatlas.org/ENSG00000106278-PTPRZ1/tissue/cerebral+cortex#imid_20815780
HPA · ColonHuman Protein Atlas IHC, Colon. Source: https://www.proteinatlas.org/ENSG00000106278-PTPRZ1/tissue/colon#imid_20815698
HPA · LiverHuman Protein Atlas IHC, Liver. Source: https://www.proteinatlas.org/ENSG00000106278-PTPRZ1/tissue/liver#imid_20815691
HPA · ICC-IF AF22Human Protein Atlas immunofluorescence, AF22, antibody HPA015103; green = PTPRZ1, blue = nucleus, red = microtubules.
HPA · ICC-IF AF22Human Protein Atlas immunofluorescence, AF22, antibody HPA015103; green = PTPRZ1, blue = nucleus, red = microtubules.
← swipe / scroll for more images →
Real IHC / IF data behind the staining-pattern expectations in this section.
Sample controls for PTPRZ1 IHC & IF
🧪Run cerebral cortex first and look for staining in glial cells (HPA: Medium in cerebral cortex glial cells). Use adipose tissue as the negative tissue (HPA: Not detected in adipocytes); on the cortex slide, assess neighboring cells without specific staining as internal negatives without assuming a particular cell type is negative.
Positive control tissue: Cerebral cortex (Glial cells, HPA Medium)
Negative control tissue: Adipose tissue (HPA Not detected)
ICC-IF cell lines (HPA subcellular resource): HPA ICC-IF images show PTPRZ1 in AF22, U-251MG, U2OS, with annotated localisation: Cytosol (approved) (HPA subcellular).
Technical controls: Include no-primary (secondary-only) and host- and clonality-matched isotype controls, plus a PTPRZ1 knockout specimen or validated peptide-block control (standard IHC practice). Block endogenous peroxidase for chromogenic detection in cortex (standard IHC practice).
⚠️Feasibility: A target-specific fixation window or fixation effect is unreported in the supplied evidence, and the selected A03510 paraffin-section caption does not report a fixative (A03510 tissue-IHC caption). The caption uses Tris-EDTA at pH 9.0 for retrieval in tonsil, so retrieval conditions for cortex need optimization (A03510 tissue-IHC caption: tonsil); the supplied evidence does not establish that frozen sections or IF are easier. For brain IF, assess autofluorescence before interpreting signal (standard IF practice).
HPA tissue IHC evidence for PTPRZ1
Comprehensive Human Protein Atlas IHC scoring per tissue (reliability: Enhanced — Medium consistency between antibody staining and RNA expression data. At least one protein variant secreted, tissue location of RNA and protein might differ and correlation is complex.). 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 |
|---|---|---|---|---|
| Cerebral cortex | Glial cells | Medium | Protein (IHC) | HPA → |
| Caudate | Glial cells | Medium | Protein (IHC) | HPA → |
| Cerebellum | Molecular layer cells - cytoplasm/membrane | Medium | Protein (IHC) | HPA → |
| Hippocampus | Neuronal 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 → |
| Breast | Adipocytes | Not detected | Protein (IHC) | HPA → |
Section 3
Advanced PTPRZ1 IHC Tips
Troubleshoot PTPRZ1 chromogenic IHC in paraffin sections using the catalog image conditions, tissue distribution, and known membrane and secreted forms (datasheet A03510; HPA tissue IHC; UniProt P23471).
What should I change when PTPRZ1 staining is weak after antigen retrieval?
Start with heat-mediated Tris-EDTA at pH 9.0 for paraffin-section PTPRZ1 IHC (datasheet A03510). Compare controlled retrieval times while keeping section preparation and detection conditions constant, and check tissue retention after heating (standard IHC practice). Apply the catalog antibody at 1:200, incubated at 4°C overnight, to match the reported image conditions (datasheet A03510). If signal remains weak, test citrate at pH 6.0 as a fallback on adjacent sections, with the original retrieval alongside it (standard IHC practice). Assess changes in neuronal and glial regions of brain tissue, where expression is documented, as well as nonspecific staining (HPA tissue IHC; standard IHC practice).
How can I assess fixation when PTPRZ1 IHC varies between specimens?
The selected image identifies paraffin-embedded human tonsil but gives no fixative, so target-specific fixation sensitivity is unknown (datasheet A03510). Record fixative identity, time before fixation, and fixation duration for each specimen; compare similarly processed sections before attributing differences to PTPRZ1 abundance (standard IHC practice). Keep retrieval at Tris-EDTA pH 9.0 and the primary antibody at 1:200 while investigating that variation (datasheet A03510; standard IHC practice). Include a consistently processed reference section in each staining run to reveal changes caused by processing or detection (standard IHC practice). Do not infer fixation tolerance from the tissue expression pattern or protein topology (HPA tissue IHC; UniProt P23471 topology).
Which staining compartments are plausible for PTPRZ1 in tissue sections?
Inspect cell boundaries and nearby extracellular material because PTPRZ1 has a membrane-spanning segment at residues 1637–1662 and an extracellular domain that can be shed (UniProt P23471 topology and subcellular location). Cerebellar molecular-layer cells show cytoplasmic or membrane staining, while neuronal and glial subsets stain elsewhere in brain (HPA tissue IHC). Cytosolic and vesicular signals have also been reported by cell-based IF, so a diffuse intracellular pattern alone cannot establish which protein form is detected in paraffin IHC (HPA subcellular; UniProt P23471). Compare each compartment with cell morphology, neighboring sections, and background controls before assigning it to PTPRZ1 (standard IHC practice). Document membrane, cytoplasmic, and extracellular staining separately rather than combining them into one score (standard IHC practice).
Could isoforms or epitope placement explain discordant PTPRZ1 staining?
PTPRZ1 has 3 reported isoforms, but the selected image does not map the catalog antibody’s epitope or establish isoform recognition (UniProt P23471; datasheet A03510). The extracellular region spans residues 25–1636, whereas residues 1663–2315 are cytoplasmic (UniProt P23471 topology). An extracellular-domain epitope could detect shed material as well as the receptor; a cytoplasmic-domain epitope would require a different interpretation (UniProt P23471 subcellular location and topology). Check the antibody’s documented immunogen against isoform sequences before claiming form-specific staining, and compare independently mapped antibodies if available (standard IHC practice). The extracellular region also contains multiple listed glycosylation sites, so record epitope location before interpreting retrieval-dependent differences (UniProt P23471 glycosylation; standard IHC practice).
How should I investigate PTPRZ1 localisation with multiplex IF?
Use IF as a separate localisation check while retaining chromogenic paraffin IHC as this page’s primary assay (datasheet A03510; standard IHC practice). Pair PTPRZ1 with a neuronal marker such as NeuN or an astrocyte marker such as GFAP according to the cell population being tested; brain staining includes neuronal and glial subsets (HPA tissue IHC; standard IF practice). Choose spectrally separated fluorophores, favoring a far-red channel when green tissue autofluorescence obscures signal, and include single-stain controls (standard IF practice). For a cytoplasmic epitope, compare controlled permeabilisation conditions; for an extracellular epitope, limit permeabilisation when testing surface staining (UniProt P23471 topology; standard IF practice). Confirm the antibody’s epitope side before treating a surface or intracellular IF pattern as evidence for a specific PTPRZ1 form (UniProt P23471 topology; standard IF practice).
What should I check when PTPRZ1 chromogenic staining looks widespread?
Run no-primary and detection-only controls to identify secondary-reagent or chromogen background before changing the PTPRZ1 interpretation (standard IHC practice). Block endogenous peroxidase before DAB development and inspect whether pigment, damaged tissue, or section edges explain the apparent signal (standard IHC practice). Titrate around the caption’s 1:200 primary dilution while holding Tris-EDTA retrieval at pH 9.0 constant (datasheet A03510; standard IHC practice). Compare staining with documented neuronal and glial subsets in brain and with tissue compartments reported as undetected, using matched processing where possible (HPA tissue IHC; standard IHC practice). Extracellular staining needs separate scrutiny because the receptor’s extracellular domain can be shed (UniProt P23471 subcellular location).
How should I score PTPRZ1 IHC across brain sections? ⚠ ANSWER MARKED FOR VERIFICATION
Define the anatomical region and cell population before scoring because documented brain staining occurs in subsets of neurons and glial cells (HPA tissue IHC). Report either an H-score from staining intensity and the percentage of positive cells, or positive-cell density per mm², using the same rule across sections (standard IHC practice). Normalize cell-based results to the number of eligible cells and area-based results to viable, analyzable tissue area (standard IHC practice). Score membrane, cytoplasmic, and extracellular signal separately when distinguishable, since a shed extracellular form is reported (UniProt P23471 subcellular location; standard IHC practice). Keep retrieval at pH 9.0 and document any departure from the caption’s 1:200 antibody dilution across compared runs (datasheet A03510; standard IHC practice).
How can I distinguish convincing PTPRZ1 staining from an artefact?
Give greatest weight to reproducible staining in anatomically appropriate neuronal or glial populations, which are documented in brain sections (HPA tissue IHC; standard IHC practice). Membrane-adjacent, cytoplasmic, or extracellular staining can each merit investigation because the receptor spans the membrane and its extracellular domain can be shed (UniProt P23471 topology and subcellular location). Scrutinize staining restricted to section edges, necrotic regions, or compartments dominated by the no-primary control, and check the endogenous-peroxidase block when DAB is used (standard IHC practice). An unexpected cell type or compartment needs independent confirmation before being called a new expression pattern (HPA tissue IHC; standard IHC practice). The catalog’s 1:200 tonsil image documents staining conditions, but its caption does not establish a fixative or prove cell-specific PTPRZ1 expression there (datasheet A03510).
Boster reagents
Best PTPRZ1 / Receptor-type tyrosine-protein phosphatase zeta IHC Antibodies
The catalog lists one anti-PTPRZ1 antibody for IHC in human, mouse and rat; its image shows paraffin-embedded human tonsil, with no IF image provided (catalog applications/reactivity; IHC image caption).
Real IHC data
Anti-PTP zeta PTPRZ1 Antibody
Cat # A03510
A03510 is listed for IHC and shows staining of paraffin-embedded human tonsil (catalog applications; IHC image caption). Human, mouse and rat reactivity is listed, but the supplied image documents only human tissue (catalog reactivity; IHC image caption).
Which to pick: Choose A03510 for tissue IHC: its own caption documents paraffin-embedded human tonsil, while the fixative is unreported (IHC image caption). For cross-species work, A03510 lists human, mouse and rat reactivity, but the supplied IHC image shows only human tissue (catalog reactivity; IHC image caption). No IF/ICC application or image is supplied for A03510, so this payload does not support an IF/ICC recommendation (catalog applications; IF image list).
Each figure is that product's own IHC / IF validation image from its datasheet.
References
- UniProt Consortium. UniProt entry P23471 (PTPRZ_HUMAN, Receptor-type tyrosine-protein phosphatase zeta).
- Human Protein Atlas. PTPRZ1 tissue IHC expression (reliability: Enhanced).
- Human Protein Atlas. PTPRZ1 subcellular location (ICC-IF): Mainly localized to the cytosol. In addition localized to vesicles..
- Human Protein Atlas. PTPRZ1 antibody validation summary (1 antibodies).
- PTPRZ1 regulates calmodulin phosphorylation and tumor progression in small-cell lung carcinoma. BMC cancer 2012 — PMC3577502.
- Expression of the pleiotrophin-midkine axis in a sheep tooth socket model of bone healing. Journal of periodontal research 2023 — PMC10099163.
- Enhancer Reprogramming Reveals the Tumorigenic Role of PTPRZ1 in Lung Squamous Cell Carcinoma. Advanced science (Weinheim, Baden-Wurttemberg, Germany) 2025 — PMC12667478.
- Spatial enrichment of PTPRZ1 in the peritumoral niche drives glioblastoma migration via the OPA1/ROS/CDH2 axis. Journal of translational medicine 2026 — PMC13523290.
- PubMed PMID:1323835 — UniProt-cited evidence.
- PubMed PMID:8387522 — UniProt-cited evidence.
- PubMed PMID:12853948 — UniProt-cited evidence.
Immunohistochemistry protocol sheet for PTPRZ1 (Receptor-type tyrosine-protein phosphatase zeta). Expected localisation Cerebellar molecular layer cells: cytoplasm/membrane (HPA tissue IHC). Antigen retrieval: Tris-EDTA pH 9.0 HIER, heat-mediated (datasheet A03510). Validated IHC antibody: A03510 at 1:50 recommended; image 1:200 (the product's own IHC validation image is shown). Controls (HPA): positive Cerebral cortex (Glial cells); negative Adipose tissue. IHC workflow; specimen preparation unspecified. Protocol steps: 1. Sample: Paraffin-embedded human tonsil tissue; fixative not specified (datasheet A03510); 2. Fixation: Image fixative and duration unreported (datasheet A03510); 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 A03510); 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-PTPRZ1, 1:50 recommended; image 1:200 (datasheet A03510); 9. Primary incubation: Overnight at 4 °C (standard). Watch for: Fixation: Keep fixation consistent across sections. (standard IHC practice; not target-specific); Caveat: A shed extracellular form may shift the staining pattern (UniProt); Isoform / epitope: 3 isoforms; check extracellular vs cytoplasmic epitope (UniProt); Regulation: Developmentally regulated in brain (UniProt). Evidence: UniProt P23471, HPA tissue IHC · Enhanced, HPA ICC-IF · Mainly localized to the cytosol. In addition localized to vesicles., Datasheet A03510, PMC12667478, PMC13523290. QR code links to https://www.bosterbio.com/bosterbio-gene-info-cards/PTPRZ1/immunohistochemistry-ihc-guide.