TNR / Tenascin-R · IHC design guide

Design Immunohistochemistry for TNR

Plan chromogenic TNR IHC in paraffin sections using the catalog antibody’s documented workflow (datasheet PA1695). Assess neuropil staining in the context of TNR’s extracellular location and the observed tissue pattern (UniProt; HPA tissue IHC).

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

Immunohistochemistry protocol sheet for TNR (IHC for TNR): expected localisation Extracellular matrix (UniProt); CNS processes (HPA tissue IHC), antibody PA1695, validated IHC image, and IHC protocol steps — Printable **TNR** IHC protocol sheet — expected localisation Extracellular matrix (UniProt); CNS processes (HPA tissue IHC), antibody PA1695, controls and protocol steps. Open the full TNR IHC guide →

Navigate to: Protocols Staining pattern Controls Antibodies

TNR 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	Extracellular matrix (UniProt); CNS processes (HPA tissue IHC)
	Staining pattern	Cerebellar molecular-layer and cortical neuropil staining (HPA tissue IHC)
	Antigen retrieval	EDTA pH 8.0 HIER, heat-mediated (datasheet PA1695)
	Positive control ⓘ	Cerebellum+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 paraffin sections (standard IHC practice; not target-specific)
	Caveat	Secreted TNR may stain away from RNA-positive cells (HPA tissue IHC)
	Regulation	Brain- and retina-enriched RNA (HPA tissue RNA)
	Isoform / epitope	2 isoforms; no cytoplasmic region (UniProt)

Section 1

Recommended TNR IHC & IF Protocols

The catalog antibody protocol is paired with two published paraffin-section IHC methods for TNR (PMC10527205; PMC5595121).

Recommended immunohistochemistry (IHC-P) protocol parameters
Sample	Paraffin-embedded human glioma tissue; fixative not specified (datasheet PA1695)
Fixation	Image fixative and duration unreported (datasheet PA1695); 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 PA1695); 20 min, 95–100 °C (standard)
Peroxidase block	3% H2O2, 10 min, room temperature (standard)
Blocking	10% goat serum (datasheet PA1695)
Primary antibody	Rabbit anti-TNR, 2-5μg/ml (datasheet PA1695)
Primary incubation	Overnight at 4 °C (datasheet PA1695)
Detection	HRP-conjugated secondary, DAB chromogen (datasheet PA1695)
Counterstain	Hematoxylin, blue, dehydrate and mount (standard)
Expected result	TNR-positive staining in molecular layer - neuropil of cerebellum (HPA tissue IHC: Medium). HPA tissue profile: Distinct expression in processes in CNS. No signal in the no-primary control.

💡Decision noteStart with EDTA pH 8.0 heat retrieval for the catalog antibody (datasheet PA1695). Both published methods use heat retrieval but do not specify a buffer (PMC10527205; PMC5595121).

Section 2

What Is the Expected TNR Staining Pattern?

TNR is secreted into the extracellular matrix and has no transmembrane segment (UniProt Q92752 topology). In paraffin-section IHC, expect staining in CNS processes and neuropil, including cerebellar molecular-layer neuropil and cerebral cortical neuropil (HPA: distinct expression in CNS processes; Medium staining in both sites). HPA rates the tissue IHC pattern Enhanced, while noting only medium consistency with RNA expression because secreted protein and its source cells may occupy different locations (HPA: reliability description).

What am I looking at on my slide?
Cerebellar molecular-layer neuropil or cerebral cortical neuropil stains at medium intensity.	This matches the reported CNS process pattern (HPA: Medium in both neuropil sites). Interpret the signal as extracellular or process-associated staining, consistent with secreted matrix TNR; the stain alone does not identify which cell produced it (UniProt Q92752 subcellular location; HPA: reliability description).
A sharply nuclear or predominantly intracellular signal replaces the neuropil pattern.	That compartment conflicts with the expected extracellular location and lacks a supporting HPA tissue pattern (UniProt Q92752 subcellular location; HPA: CNS processes). Treat it as suspect and compare it with the matched control and tissue morphology before scoring it as TNR (standard IHC practice).
Unexpected strong staining appears in a cell population outside the reported pattern.	Possible explanations include cross-reactivity or endogenous detection activity (standard IHC practice). Do not label every non-CNS cell positive by default: HPA also reports Medium staining in placental cytotrophoblasts and testicular preleptotene spermatocytes (HPA: tissue IHC).
Colour is spread broadly across tissue or the slide without a discernible neuropil pattern.	A distribution that obscures structures is less persuasive than the reported CNS process pattern (HPA: tissue IHC). Diffuse chromogen may reflect nonspecific binding or detection background; assess it against the no-primary control and section edges (standard IHC practice).
Cerebellar molecular-layer neuropil and cerebral cortical neuropil show no detectable signal.	Both are reported Medium-positive sites, so a blank result in a known-positive section warrants a technical check before a biological conclusion (HPA: tissue IHC; standard IHC practice). HPA's Enhanced rating supports the reported pattern but does not guarantee every specimen or assay will stain (HPA: reliability).

💡Expected TNR appearanceCall positive when Medium chromogenic staining follows cerebellar molecular-layer or cortical neuropil and CNS processes (HPA: tissue IHC); isolated nuclear staining or uniform colour without that architecture is suspect (UniProt Q92752 subcellular location; standard IHC practice).

How each factor affects the staining
Secreted extracellular location	TNR is an extracellular matrix protein without a transmembrane segment (UniProt Q92752 topology and subcellular location). The deposit can be spatially separate from the cell that synthesized it, so avoid assigning cell of origin from chromogen position alone (HPA: reliability description).
Tissue and validation context	HPA reports Medium staining in cerebellar and cortical neuropil and rates tissue IHC Enhanced (HPA: tissue IHC). Its reliability note reports medium consistency with RNA expression; RNA location alone is an imperfect check for this secreted protein (HPA: reliability description).
Other reported positive cells	HPA also lists placental cytotrophoblasts and testicular preleptotene spermatocytes at Medium intensity (HPA: tissue IHC). These observations should be read alongside UniProt's brain-specific tissue annotation, without treating either source as proof that every specimen has the same pattern (UniProt Q92752 tissue specificity).
Processing and molecular forms	The signal peptide spans residues 1–31, with the annotated mature chain at 32–1358; UniProt lists two isoforms and 17 glycosylation sites (UniProt Q92752 processing, isoforms, glycosylation). The supplied record gives no antibody epitope, so it cannot establish whether these features change this assay's staining.
Negative tissue interpretation	HPA reports adipocytes in adipose tissue and glandular cells in adrenal gland as Not detected (HPA: tissue IHC). That is a cell-level observation, not proof that every compartment in either tissue is negative; evaluate the named cell population when using such a comparison (standard IHC practice).
IF/ICC applicability	Q: Should this IHC-P appearance be assumed for IF/ICC? A: No ICC-IF images or main subcellular location are available in HPA's subcellular record (HPA: subcellular). Use this section's neuropil observations as IHC tissue evidence only; interpret IF/ICC on its own guide page.

Why is my staining missing, weak or wrong?
Situation	Likely cause	Next action
Known-positive CNS neuropil is blank.	The run may have failed, or the selected antibody and detection settings may be unsuitable for the section (standard IHC practice); HPA reports Medium staining at these sites (HPA: tissue IHC).	Confirm tissue identity and neuropil preservation; inspect the positive control, antibody dilution, antigen-retrieval setting and detection reagents against the assay's validated IHC-P instructions (standard IHC practice). Do not infer target-specific retrieval sensitivity from this record.
Nuclei dominate the staining.	A nuclear-dominant pattern is inconsistent with secreted extracellular TNR (UniProt Q92752 subcellular location). Detection background or off-target binding is possible (standard IHC practice).	Check a no-primary control and compare morphology with an HPA-reported CNS neuropil site; score the nuclear signal separately until its specificity is resolved (standard IHC practice; HPA: tissue IHC).
Stain is diffuse across the section.	Broad colour without tissue structure can arise from nonspecific binding or excess detection signal (standard IHC practice), whereas HPA describes distinct CNS processes (HPA: tissue IHC).	Review no-primary staining, blocking, wash steps, antibody dilution and chromogen development using the validated assay settings (standard IHC practice); reassess whether neuropil structure emerges.
An unexpected cell type stains strongly.	Cross-reactivity or endogenous detection activity is possible (standard IHC practice). Placental cytotrophoblasts and testicular preleptotene spermatocytes are reported exceptions to a CNS-only reading (HPA: tissue IHC).	Check the exact tissue and cell identity against HPA, then compare a no-primary control and an independently validated antibody where available (HPA: tissue IHC and antibody validation; standard IHC practice).
A reported Not detected cell population stains.	The observation differs from HPA's cell-level call; background or assay-specific staining may account for it (HPA: tissue IHC; standard IHC practice).	Confirm the named population, such as adipocytes in adipose tissue, and compare it with controls before calling a biological difference (HPA: Not detected in adipocytes; standard IHC practice).
IF/ICC looks unlike the IHC neuropil pattern.	HPA supplies no ICC-IF images or main location for TNR, so direct modality agreement is unestablished (HPA: subcellular).	Assess IF/ICC with its own controls and guide; retain the HPA neuropil calls as paraffin-section IHC observations (HPA: tissue IHC; standard IF practice).

Source: UniProt Q92752 Human Protein Atlas tissue Human Protein Atlas subcellular

Experiment evidence

IHC & IF images showing TNR staining

IHC analysis of TNR using anti-TNR antibody (PA1695). TNR was detected in a paraffin-embedded section of human glioma 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-TNR Antibody (PA1695) 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.

PA1695 · IHCIHC analysis of TNR using anti-TNR antibody (PA1695). TNR was detected in a paraffin-embedded section of human glioma tissue. Heat mediated

IHC analysis of TNR using anti-TNR antibody (PA1695). TNR was detected in a paraffin-embedded section of mouse brain 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-TNR Antibody (PA1695) 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.

PA1695 · IHCIHC analysis of TNR using anti-TNR antibody (PA1695). TNR was detected in a paraffin-embedded section of mouse brain tissue. Heat mediated a

HPA · Cerebral cortexHuman Protein Atlas IHC, Cerebral cortex. Source: https://www.proteinatlas.org/ENSG00000116147-TNR/tissue/cerebral+cortex#imid_5747020

HPA · ColonHuman Protein Atlas IHC, Colon. Source: https://www.proteinatlas.org/ENSG00000116147-TNR/tissue/colon#imid_5746938

HPA · LiverHuman Protein Atlas IHC, Liver. Source: https://www.proteinatlas.org/ENSG00000116147-TNR/tissue/liver#imid_5746939

HPA · KidneyHuman Protein Atlas IHC, Kidney. Source: https://www.proteinatlas.org/ENSG00000116147-TNR/tissue/kidney#imid_5746932

← swipe / scroll for more images →

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

Sample controls for TNR IHC & IF

🧪Run cerebellum first and look for TNR staining in the molecular-layer neuropil (HPA: Medium). Use adipose tissue as the negative tissue, focusing on adipocytes (HPA: Not detected); nuclei on the cerebellar slide should lack specific TNR staining (UniProt Q92752: extracellular matrix localisation).

Positive control tissue: Cerebellum (Molecular layer - neuropil, HPA Medium)

Negative control tissue: Adipose tissue (HPA Not detected)

ICC-IF cell lines (HPA subcellular resource): HPA carries no ICC-IF cell line for TNR; derive a cell-line control from the positive tissue's cell type (Molecular layer - neuropil) and confirm it by RNA or western blot first.

Technical controls: Include a no-primary, secondary-only control; a rabbit control immunoglobulin matched to the primary antibody’s clonality once confirmed (caption: rabbit anti-TNR; clonality unreported); and TNR-knockout tissue or a validated peptide-block control. Quench endogenous peroxidase and inspect vascular blood cells for background when using HRP/DAB (caption: HRP/DAB detection; standard IHC practice).

⚠️Feasibility: A target-specific fixation window or fixation effect is unreported, and the selected PA1695 caption does not state the fixative. That caption reports heat retrieval in EDTA at pH 8.0 for a paraffin section, but does not establish that retrieval is required (PA1695 tissue-IHC caption). The supplied evidence does not establish that frozen sections or IF are easier; assess diffuse neuropil background against the expected extracellular staining pattern (HPA: cerebellar molecular-layer neuropil, Medium; UniProt Q92752: extracellular matrix localisation).

HPA tissue IHC evidence for TNR

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
Cerebellum	Molecular layer - neuropil	Medium	Protein (IHC)	HPA →
Cerebral cortex	Neuropil	Medium	Protein (IHC)	HPA →
Placenta	Cytotrophoblasts	Medium	Protein (IHC)	HPA →
Testis	Preleptotene spermatocytes	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	Endocrine 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 TNR IHC Tips

Troubleshoot TNR staining by checking retrieval, tissue handling, extracellular localisation and controls before interpreting chromogenic signal.

What retrieval should I start with for TNR in paraffin sections?

Start with heat-mediated retrieval in EDTA at pH 8.0 for paraffin sections (datasheet PA1695). The selected image documents TNR staining in human glioma tissue after this retrieval, followed by 2 μg/ml primary antibody overnight at 4°C (caption PA1695). Keep the antibody concentration and detection method consistent while adjusting retrieval time according to the tissue and retrieval equipment (standard IHC practice). If staining remains weak, compare a limited retrieval-time series with a known positive section; record any tissue damage alongside signal, because stronger staining alone does not establish specificity (HPA: CNS-process staining; standard IHC practice).

How should I assess fixation when TNR staining is weak or patchy?

Treat target-specific fixation sensitivity as unknown: the selected paraffin-section caption does not state a fixative, and no TNR fixation comparison is supplied (caption PA1695). Record the fixative, time to fixation and fixation duration for each specimen, then compare sections processed under matched conditions (standard IHC practice). Use the documented EDTA pH 8.0 retrieval and 2 μg/ml primary concentration as starting conditions when evaluating a change in processing (datasheet PA1695; caption PA1695). Check tissue preservation and section adhesion alongside staining, and avoid attributing a difference between specimens to TNR biology until processing differences have been assessed (standard IHC practice).

Where should convincing TNR staining appear in a brain section?

Expect an extracellular pattern around neural structures, since TNR is secreted into the extracellular matrix and has no transmembrane segment (UniProt Q92752: subcellular location and topology). In tissue IHC, reported positive patterns include cerebellar molecular-layer neuropil and cerebral-cortex neuropil, both at medium staining levels (HPA: tissue IHC). Compare the distribution with tissue architecture and a counterstain; a sharply nuclear pattern would need independent validation before assignment to TNR (UniProt Q92752: subcellular location; standard IHC practice). Do not require staining in every cell body: extracellular protein can be detected away from the cells that produced it (UniProt Q92752: secreted; HPA: reliability description).

Could TNR isoforms or glycosylation change the staining pattern?

TNR has 2 listed isoforms and 17 annotated glycosylation sites, so an antibody's epitope and its accessibility matter when comparing stains (UniProt Q92752: isoforms and glycosylation). The supplied caption does not map the PA1695 epitope or establish which isoform it recognizes (caption PA1695). Review the antibody's documented immunogen or epitope before making an isoform-specific claim, and compare sections under the same EDTA pH 8.0 retrieval conditions (datasheet PA1695; standard IHC practice). If patterns disagree across antibodies, test them on matched sections with appropriate controls; a difference alone cannot identify an isoform or a glycosylation effect (standard IHC practice).

How can I investigate a TNR pattern by multiplex immunofluorescence?

Use IF as a follow-up to the chromogenic tissue pattern, pairing TNR with a neuronal-process marker to place signal relative to the neuropil reported by tissue IHC (HPA: cerebellar and cortical neuropil; standard IF practice). Choose spectrally separated fluorophores and inspect an unstained section in each channel to identify tissue autofluorescence before assigning faint extracellular signal (standard IF practice). TNR is secreted and lacks a transmembrane segment, but the antibody's exact epitope is not supplied; begin without detergent permeabilisation for accessible extracellular staining, then add mild permeabilisation only if the companion marker requires it (UniProt Q92752: topology and location; standard IF practice). Keep IF observations distinct from validation of the catalog antibody's chromogenic paraffin-section result (caption PA1695).

How do I reduce diffuse or misleading DAB background?

First compare a no-primary control with the stained section, and inspect whether brown signal follows the extracellular distribution expected for TNR (UniProt Q92752: subcellular location; standard IHC practice). The selected procedure used 10% goat serum, 2 μg/ml primary antibody overnight at 4°C, and a peroxidase-linked secondary for 30 minutes at 37°C (caption PA1695). For excess background, check wash adequacy, antibody concentration and blocking on matched sections before changing several variables together (standard IHC practice). Include a peroxidase block and inspect the no-primary control for endogenous enzyme activity; these are general chromogenic IHC safeguards, not TNR-specific findings (standard IHC practice).

What should I measure when TNR staining is mostly extracellular? ⚠ ANSWER MARKED FOR VERIFICATION

Define a tissue region before scoring, then measure DAB-positive extracellular area or optical density per mm² of intact region, using identical acquisition and threshold settings (UniProt Q92752: extracellular matrix; standard IHC practice). Normalise to the analysed tissue area and report the sampled compartment, such as neuropil, because HPA describes TNR staining in CNS processes (HPA: tissue IHC; standard IHC practice). A cell-based H-score or percentage of positive cells can be reported only when cell boundaries and the scoring rule are explicit; extracellular signal may otherwise be assigned to the wrong cell (UniProt Q92752: secreted; standard IHC practice). Exclude folds, edges and necrotic regions by a rule set before comparing specimens (standard IHC practice).

How can I distinguish true TNR staining from artefact?

A convincing result should show a reproducible extracellular pattern consistent with TNR's secreted matrix location and the reported CNS neuropil staining (UniProt Q92752: subcellular location; HPA: tissue IHC). Compare the same region with its counterstain, a no-primary control and a known positive section processed in the same run (standard IHC practice). Treat isolated nuclear or cell-body staining, edge-only signal, necrotic deposits and staining present in the no-primary control as reasons to investigate section damage, nonspecific binding or endogenous peroxidase before calling positivity (UniProt Q92752: subcellular location; standard IHC practice). Interpret peripheral-tissue signals cautiously because HPA reports medium consistency between staining and RNA expression for this secreted protein (HPA: reliability description).

Boster reagents

Best TNR / Tenascin-R IHC Antibodies

The IHC-validated anti-TNR antibody has paraffin-section images from human glioma and brain, plus mouse and rat brain; no IF image is provided (PA1695 IHC image captions; PA1695 IF image alts).

Real IHC data

Anti-Tenascin-R TNR Antibody ®

Cat # PA1695

View product →

PA1695 is listed for IHC and has paraffin-section images from human glioma, human brain, mouse brain, and rat brain (PA1695 catalog applications; PA1695 IHC image captions). It is listed as reactive with Human, Mouse, and Rat; IF/ICC is absent from its applications and image data (PA1695 catalog reactivity/applications; PA1695 IF image alts).

Which to pick: Choose PA1695 for paraffin-section IHC: its own captions show EDTA retrieval at pH 8.0 and 2 μg/ml primary antibody, but do not report the fixative (PA1695 IHC image captions). No listed SKU is validated for IF/ICC, so there is no supported IF/ICC pick (PA1695 catalog applications; PA1695 IF image alts). For cross-species paraffin IHC, PA1695 is the available choice: it is rabbit-hosted, lists Human, Mouse, and Rat reactivity, and has corresponding tissue images; its clone is unreported (PA1695 catalog host/reactivity/clone; PA1695 IHC image captions).

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

References

UniProt Consortium. UniProt entry Q92752 (TENR_HUMAN, Tenascin-R).
Human Protein Atlas. TNR tissue IHC expression (reliability: Enhanced).
Human Protein Atlas. TNR subcellular location (ICC-IF): Secreted.
Human Protein Atlas. TNR antibody validation summary (4 antibodies).
Tenascin-R Autoimmunity: Isolated Tremor Reversed with Immunotherapy. Annals of neurology 2023 — PMC10527205.
The Extracellular Matrix Proteins Tenascin-C and Tenascin-R Retard Oligodendrocyte Precursor Maturation and Myelin Regeneration in a Cuprizone-Induced Long-Term Demyelination Animal Model. Cells 2022 — PMC9179356.
Neural extracellular matrix regulates visual sensory motor integration. iScience 2024 — PMC10839651.
Quantitative Visualization of Dynamic Tracer Transportation in the Extracellular Space of Deep Brain Regions Using Tracer-Based Magnetic Resonance Imaging. Medical science monitor : international medical journal of experimental and clinical research 2017 — PMC5595121.
PubMed PMID:8626505 — UniProt-cited evidence.
PubMed PMID:16710414 — UniProt-cited evidence.
PubMed PMID:19838169 — UniProt-cited evidence.