PTPRR / Receptor-type tyrosine-protein phosphatase R · IHC design guide

Design Immunohistochemistry for PTPRR

Plan chromogenic PTPRR IHC in paraffin sections using caudate neurons and cerebellar granule-layer cells as positive tissue examples (HPA tissue IHC). This guide covers fixation consistency, expected cytoplasmic staining, and scoring in light of uncertain staining reliability and presumed off-target binding (HPA tissue IHC).

Evidence assembled Oct 2026 · For research use; verify linked source records and product datasheet before use

Immunohistochemistry protocol sheet for PTPRR (IHC for PTPRR): expected localisation Cytoplasmic tissue staining (HPA tissue IHC), antibody M06905, validated IHC image, and IHC protocol steps — Printable **PTPRR** IHC protocol sheet — expected localisation Cytoplasmic tissue staining (HPA tissue IHC), antibody M06905, controls and protocol steps. Open the full PTPRR IHC guide →

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PTPRR Immunohistochemistry Experimental Design Guide

Expected localisation, validated protocols, controls and antibodies — the at-a-glance facts below, then the full design guide.

Must know before staining

	Expected localisation	Cytoplasmic tissue staining (HPA tissue IHC)
	Staining pattern	Cytoplasmic in caudate neurons and cerebellar granule cells (HPA tissue IHC)
	Antigen retrieval	EDTA pH 8.0 HIER, heat-mediated (datasheet M06905)
	Positive control ⓘ	Caudate+1 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 matched paraffin sections (standard IHC practice). (selected-SKU IHC image M06905)
	Caveat	Presumed off-target binding can confound staining (HPA tissue IHC)
	Regulation	Expression regulation unreported (UniProt)
	Isoform / epitope	4 isoforms; map the epitope to the extracellular or cytoplasmic region (UniProt)

Section 1

Recommended PTPRR IHC & IF Protocols

The catalog antibody protocol and one published PTPRR IHC method provide starting points for paraffin sections (datasheet M06905; PMC9830783 methods).

Recommended immunohistochemistry (IHC-P) protocol parameters
Sample	Paraffin-embedded human ovarian cancer tissue; fixative not specified (datasheet M06905)
Fixation	Image fixative and duration unreported (datasheet M06905); verify before use.
Sectioning	4–5 µm sections on charged slides (standard)
Deparaffinisation	Xylene, graded ethanol series to water (standard)
Antigen retrieval	Heat retrieval: EDTA pH 8.0 (datasheet M06905); 20 min, 95–100 °C (standard)
Peroxidase block	3% H2O2, 10 min, room temperature (standard)
Blocking	10% goat serum (datasheet M06905)
Primary antibody	Rabbit monoclonal (clone 29P99) anti-PTPRR, 1:50-1:200 recommended; image 2 μg/ml (datasheet M06905)
Primary incubation	Overnight at 4 °C (datasheet M06905)
Detection	HRP-conjugated secondary, DAB chromogen (datasheet M06905)
Counterstain	Hematoxylin, blue, dehydrate and mount (standard)
Expected result	PTPRR-positive staining in neuronal cells of caudate (HPA tissue IHC: Medium). HPA tissue profile: Cytoplasmic expression in several different tissue types. No signal in the no-primary control.

💡Decision noteStart with heat-mediated EDTA pH 8.0 retrieval for the catalog antibody (datasheet M06905); the published method does not specify retrieval (PMC9830783 methods).

Section 2

What Is the Expected PTPRR Staining Pattern?

For IHC-P, expect predominantly cytoplasmic staining in caudate neuronal cells and cerebellar granular-layer cells, both reported at medium intensity (HPA tissue IHC). Membrane-associated or perinuclear signal can also fit PTPRR: it has a transmembrane segment and a reported perinuclear location (UniProt Q15256 topology and subcellular location). Interpret tissue staining cautiously because HPA rates its IHC profile Uncertain and reports presumed off-target binding (HPA tissue IHC reliability).

What am I looking at on my slide?
Moderate cytoplasmic staining marks caudate neuronal cells or cerebellar granular-layer cells.	This matches the reported positive cells and medium staining level (HPA tissue IHC). Record the stained cell type and compartment, then compare them with a negative control (general IHC practice).
Staining appears mainly in nuclei, with little cytoplasmic or membrane signal.	An exclusively nuclear pattern falls outside the reported cytoplasmic tissue profile, perinuclear location, and membrane topology (HPA tissue IHC; UniProt Q15256). Check the counterstain and detection controls before calling it PTPRR (general IHC practice).
Strong staining appears in cells reported as undetected, such as adipocytes in adipose tissue.	That conflicts with the reported cell-specific result (HPA tissue IHC). Consider cross-reactivity or endogenous chromogen-generating activity; HPA reports presumed off-target binding in its IHC assessment (HPA tissue IHC reliability; general IHC practice).
Brown signal spreads across tissue and spaces between cells without clear cell boundaries.	This is difficult to score as cell-specific PTPRR because HPA describes a cytoplasmic tissue pattern (HPA tissue IHC). Examine the no-primary control and assess blocking, washing, and detection background (general IHC practice).
Caudate neuronal cells and cerebellar granular-layer cells show no signal.	Both are reported at medium intensity, so a negative result warrants a run-level check (HPA tissue IHC). Inspect tissue integrity, the positive control, antibody application, retrieval conditions, and detection reagents (general IHC practice).

💡Expected PTPRR appearanceCall a result compatible when caudate neuronal cells or cerebellar granular-layer cells show medium, mainly cytoplasmic staining (HPA tissue IHC); isolated nuclear or widespread cell-independent color is suspect (HPA tissue IHC; general IHC practice).

How each factor affects the staining
Membrane topology and compartment	PTPRR has an extracellular region, one transmembrane segment, and a cytoplasmic region (UniProt Q15256 topology). Membrane or perinuclear staining is biologically plausible (UniProt Q15256 subcellular location); the supplied record does not identify the IHC antibody epitope.
Isoforms and tissue distribution	UniProt lists four isoforms with differing reported tissue expression, including brain-restricted alpha (UniProt Q15256 tissue specificity). Antibody coverage of those isoforms is unspecified, so an IHC result cannot identify an isoform from location alone.
Secreted variants and tissue interpretation	UniProt lists secreted and membrane-associated locations (UniProt Q15256 subcellular location). HPA warns that a secreted protein variant can complicate RNA–protein tissue comparisons and notes splice or transcript discrepancies (HPA tissue IHC reliability).
IHC antibody evidence	HPA rates the tissue profile Uncertain and lists HPA011851 and CAB011461 as IHC Uncertain (HPA tissue IHC; HPA antibodies). Treat a matching pattern as supportive rather than definitive, and assess controls alongside the slide (general IHC practice).
Retrieval and detection	The supplied UniProt and HPA records give no PTPRR-specific fixation or retrieval response. Evaluate retrieval, blocking, and chromogenic detection with run controls as general IHC practice; do not infer a PTPRR-specific effect from topology or tissue intensity.

Why is my staining missing, weak or wrong?
Situation	Likely cause	Next action
Expected brain cells are blank.	The run may have weak detection or an unsuitable retrieval condition (general IHC practice); the named cells are reported as medium positive (HPA tissue IHC).	Check a positive-control section, tissue integrity, antibody application, retrieval, and detection steps (general IHC practice). The supplied sources give no PTPRR-specific retrieval setting.
Every cell appears brown, including cells reported as undetected.	Broad staining may reflect detection background or cross-reactivity (general IHC practice); HPA reports presumed off-target binding (HPA tissue IHC reliability).	Compare a no-primary control and inspect blocking and washing (general IHC practice). Reassess staining in the reported positive cell types (HPA tissue IHC).
The no-primary control develops color.	Endogenous detection activity or reagent background can produce chromogenic signal without primary antibody (general IHC practice).	Address the detection system’s background, then repeat the no-primary control before assigning color to PTPRR (general IHC practice).
Only nuclei stain in an otherwise well-preserved section.	Exclusive nuclear staining does not match the reported cytoplasmic tissue profile or UniProt membrane and perinuclear locations (HPA tissue IHC; UniProt Q15256).	Review the counterstain and controls, and score nuclear-only signal separately from the expected pattern (general IHC practice).
Kidney glomeruli are negative despite reported kidney expression.	HPA reports glomerular cells as undetected, while UniProt reports kidney expression for isoform delta (HPA tissue IHC; UniProt Q15256 tissue specificity).	Keep the cell-specific IHC result distinct from isoform-level tissue expression; use the reported brain-positive cells to assess the stain (HPA tissue IHC; general IHC practice).
Does ICC-IF need to reproduce the IHC-P tissue pattern?	The assays report different contexts: HPA tissue IHC is Uncertain, while its ICC-IF locations are supported (HPA tissue IHC; HPA subcellular; HPA antibodies).	Interpret ICC-IF membrane, junctional, and cytosolic localization within its own guide; use the tissue IHC profile for IHC-P interpretation (HPA subcellular; HPA tissue IHC).

Source: UniProt Q15256 Human Protein Atlas tissue Human Protein Atlas subcellular

Experiment evidence

IHC & IF images showing PTPRR staining

IHC analysis of PTPRR using anti-PTPRR antibody (M06905) . PTPRR was detected in a paraffin-embedded section of human ovarian cancer 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-PTPRR Antibody (M06905) 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.

M06905 · IHCIHC analysis of PTPRR using anti-PTPRR antibody (M06905) . PTPRR was detected in a paraffin-embedded section of human ovarian cancer tissue.

HPA · Cerebral cortexHuman Protein Atlas IHC, Cerebral cortex. Source: https://www.proteinatlas.org/ENSG00000153233-PTPRR/tissue/cerebral+cortex#imid_3330900

HPA · ColonHuman Protein Atlas IHC, Colon. Source: https://www.proteinatlas.org/ENSG00000153233-PTPRR/tissue/colon#imid_3330842

HPA · LiverHuman Protein Atlas IHC, Liver. Source: https://www.proteinatlas.org/ENSG00000153233-PTPRR/tissue/liver#imid_3330835

HPA · KidneyHuman Protein Atlas IHC, Kidney. Source: https://www.proteinatlas.org/ENSG00000153233-PTPRR/tissue/kidney#imid_3330836

HPA · ICC-IF RT-4Human Protein Atlas immunofluorescence, RT-4, antibody HPA071067; green = PTPRR, blue = nucleus, red = microtubules.

← swipe / scroll for more images →

Real IHC / IF data behind the staining-pattern expectations in this section.

Sample controls for PTPRR IHC & IF

🧪Run caudate first: neuronal cells should stain at a medium level (HPA: caudate neuronal cells, Medium). Use adipose tissue as the negative tissue because adipocytes are not detected there (HPA: adipose adipocytes, Not detected); on the caudate slide, use neighboring cells without DAB signal above background as an internal negative comparison, without assuming a particular cell type is negative.

Positive control tissue: Caudate (Neuronal cells, HPA Medium)

Negative control tissue: Adipose tissue (HPA Not detected)

ICC-IF cell lines (HPA subcellular resource): HPA ICC-IF images show PTPRR in RT-4, Rh30, U2OS, with annotated localisation: Plasma membrane (supported), Cell Junctions (supported), Cytosol (supported) (HPA subcellular).

Technical controls: Include a no-primary, secondary-only control; a matched nonimmune rabbit IgG control for the rabbit catalog antibody; and a PTPRR knockout specimen, if available, as a biological negative (caption: rabbit anti-PTPRR; standard IHC controls). Quench endogenous peroxidase before DAB detection in caudate, and check for tissue autofluorescence if evaluating IF (caption: peroxidase/DAB detection; standard IHC/IF practice).

⚠️Feasibility: No target-specific fixation window or fixation effect is reported in the supplied evidence, and the selected M06905 paraffin-section caption does not state a fixative (M06905 caption: fixative unreported). Heat retrieval in EDTA at pH 8.0 is a documented IHC starting condition, but retrieval dependence has not been established (M06905 caption: heat-mediated EDTA retrieval). The supplied evidence does not show that frozen sections or IF are easier than paraffin IHC; for IF in neuronal tissue, assess lipofuscin autofluorescence before interpreting signal (M06905 caption: paraffin-section IHC; standard IF practice).

HPA tissue IHC evidence for PTPRR

Comprehensive Human Protein Atlas IHC scoring per tissue (reliability: Uncertain — At least one protein variant secreted, tissue location of RNA and protein might differ and correlation is complex. Presumed off target binding observed and disregarded. Caution, Splice and/or transcript discrepancy exists.). 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
Caudate	Neuronal cells	Medium	Protein (IHC)	HPA →
Cerebellum	Cells in granular layer	Medium	Protein (IHC)	HPA →

Undetected expression · recommended negative controls

Tissue	Cell type	Level	Evidence	Source
Adipose tissue	Adipocytes	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 →
Esophagus	Squamous epithelial cells	Not detected	Protein (IHC)	HPA →

Section 3

Advanced PTPRR IHC Tips

Troubleshoot PTPRR staining in paraffin sections using the catalog antibody’s IHC evidence, expected localisation, and appropriate controls.

What retrieval should I use if PTPRR staining is weak in paraffin sections?

Start with heat-mediated retrieval in EDTA at pH 8.0 (datasheet M06905). The selected paraffin-section image used this retrieval before incubation with 2 μg/ml antibody overnight at 4°C (datasheet M06905). If staining remains weak, keep the buffer and pH fixed while comparing heating cycles on adjacent sections, and include a no-primary control to check whether stronger retrieval raises background (standard IHC practice). Compare the intensity and distribution in viable cells across sections processed together; the image demonstrates staining under its stated conditions but does not establish an optimal heating time or fixation method (datasheet M06905).

How can I assess whether fixation is masking PTPRR?

Target-specific fixation sensitivity is unknown: the selected PTPRR image identifies a paraffin section but does not state its fixative or fixation duration (datasheet M06905). Record those details for each specimen, then compare similarly processed sections using the documented EDTA pH 8.0 retrieval and 2 μg/ml primary concentration (datasheet M06905). If material fixed for different durations is available, process it in the same staining run and compare signal in viable tissue alongside morphology and no-primary controls (standard IHC practice). Treat a fixation-associated difference as an observation of that comparison, rather than inferring target-specific masking from tissue patterns or predicted protein structure.

Which compartments should contain credible PTPRR staining?

Assess membrane-associated, cytoplasmic, and perinuclear staining: PTPRR has a transmembrane segment at residues 228–248 and a cytoplasmic region at 249–657 (UniProt Q15256 topology; UniProt Q15256 subcellular location). Supported subcellular observations also place it at the plasma membrane, cell junctions, and cytosol (HPA subcellular). In chromogenic sections, score these patterns separately from diffuse DAB deposits or isolated nuclear staining, using the counterstain to identify intact cells (standard IHC practice). Tissue IHC reports cytoplasmic expression across several tissue types, but its reliability is uncertain; use that pattern as context rather than proof of antibody specificity (HPA tissue IHC).

Could isoform choice or epitope position explain different staining patterns?

Yes: PTPRR has 4 listed isoforms, and their reported tissue distributions differ (UniProt Q15256 isoforms; UniProt Q15256 tissue specificity). Isoform alpha has been observed only in brain, while delta is reported in brain and several other tissues (UniProt Q15256 tissue specificity). The record places the extracellular region at residues 22–227 and the cytoplasmic region at 249–657, but the selected antibody’s epitope is not supplied here (UniProt Q15256 topology; datasheet M06905). Request its epitope information before assigning membrane or cytoplasmic staining to a particular isoform, and interpret discordant sections alongside matched controls because HPA flags splice or transcript discrepancies (HPA tissue IHC).

How should IF help resolve ambiguous PTPRR localisation?

Use IF/ICC as a separate localisation check, pairing PTPRR with a neuronal-cell marker where the selected HPA tissue observations show neuronal staining in caudate (HPA tissue IHC). Choose a spectrally separated, preferably far-red fluorophore after checking unstained tissue autofluorescence, and inspect each channel for bleed-through (standard IF practice). The expected epitope side matters: intracellular access would require permeabilisation for an epitope in the cytoplasmic residues 249–657, whereas an accessible extracellular epitope at 22–227 may not (UniProt Q15256 topology; standard IF practice). Because the antibody epitope is unspecified, establish its location before interpreting differences between permeabilised and nonpermeabilised samples (datasheet M06905).

How do I separate PTPRR signal from chromogenic background?

Run a no-primary section and inspect it beside the stained section for endogenous enzyme activity or nonspecific deposits before attributing brown signal to PTPRR (standard IHC practice). The selected image used a peroxidase-conjugated secondary and DAB, with primary antibody at 2 μg/ml overnight at 4°C (datasheet M06905). Apply a peroxidase block and compare blocking and washing conditions consistently across adjacent sections when background obscures cells (standard IHC practice). HPA reports presumed off-target binding and uncertain tissue-IHC reliability, so require a coherent cellular pattern and appropriate controls before calling weak diffuse staining positive (HPA tissue IHC).

What is a defensible way to quantify PTPRR IHC? ⚠ ANSWER MARKED FOR VERIFICATION

Define the compartment and cell population before scoring, then record the percentage of viable cells at intensity scores 0–3 (standard IHC practice). An H-score sums each intensity multiplied by its percentage of cells, yielding 0–300; alternatively report positive-cell percentage or positive-cell density per mm² of viable tissue (standard IHC practice). Normalise counts to the corresponding viable-cell denominator or measured viable area, and apply the same threshold and section-processing conditions across samples (standard IHC practice). Report membrane-associated and cytoplasmic results separately because both are plausible PTPRR locations, and flag HPA tissue-IHC reliability as uncertain when using its patterns for comparison (UniProt Q15256 subcellular location; HPA tissue IHC).

What makes a PTPRR-positive IHC result convincing?

Look for reproducible staining in intact cells with a plausible membrane, cytoplasmic, or perinuclear distribution, rather than relying on DAB colour alone (UniProt Q15256 subcellular location; standard IHC practice). HPA reports medium neuronal-cell staining in caudate and medium granular-layer-cell staining in cerebellum, but classifies its tissue-IHC reliability as uncertain (HPA tissue IHC). Treat isolated nuclear-only deposits, tissue-edge accentuation, and staining concentrated in necrotic areas as possible artefacts requiring review of adjacent morphology and controls (standard IHC practice). Check no-primary sections for endogenous peroxidase signal, and avoid declaring an unexpected cell population positive solely from weak staining because presumed off-target binding was observed (standard IHC practice; HPA tissue IHC).

Boster reagents

Best PTPRR / Receptor-type tyrosine-protein phosphatase R IHC Antibodies

The catalog antibody M06905 has IHC data from a human ovarian cancer paraffin section (M06905 image caption) and listed Human, Mouse, and Rat reactivity (M06905 catalog); no IF data are provided (M06905 catalog).

Real IHC data

Anti-PTPRR Rabbit Monoclonal Antibody

Cat # M06905

View product →

M06905 will render with an IHC image from a human ovarian cancer paraffin section (M06905 image caption). Its listed applications are IHC and WB, and its listed reactivity is Human, Mouse, and Rat (M06905 catalog).

Which to pick: Choose the rabbit monoclonal M06905 for paraffin-section IHC, supported by its own human ovarian cancer image caption and 1:50–1:200 IHC dilution range (M06905 catalog; M06905 image caption). The caption does not report the fixative (M06905 image caption). M06905 lists Human, Mouse, and Rat reactivity, but the supplied image documents human tissue only; no IF/ICC application or figure is provided, so there is no evidenced IF/ICC pick (M06905 catalog; M06905 image caption).

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

References

UniProt Consortium. UniProt entry Q15256 (PTPRR_HUMAN, Receptor-type tyrosine-protein phosphatase R).
Human Protein Atlas. PTPRR tissue IHC expression (reliability: Uncertain).
Human Protein Atlas. PTPRR subcellular location (ICC-IF): Localized to the plasma membrane, cell junctions and cytosol..
Human Protein Atlas. PTPRR antibody validation summary (3 antibodies).
Parvimonas micra activates the Ras/ERK/c-Fos pathway by upregulating miR-218-5p to promote colorectal cancer progression. Journal of experimental & clinical cancer research : CR 2023 — PMC9830783.
Downregulation of Protein Tyrosine Phosphatase Receptor Type R Accounts for the Progression of Hirschsprung Disease. Frontiers in molecular neuroscience 2019 — PMC6468927.
PubMed PMID:7557444 — UniProt-cited evidence.
PubMed PMID:10705342 — UniProt-cited evidence.
PubMed PMID:11147789 — UniProt-cited evidence.