LRRTM1 / Leucine-rich repeat transmembrane neuronal protein 1 · IHC design guide

Design Immunohistochemistry for LRRTM1

This LRRTM1 IHC guide covers cytoplasmic brain staining, including neuronal staining in caudate, cerebral cortex and hippocampus, and Purkinje cell staining in cerebellum (HPA tissue IHC). The catalog antibody is validated for human IHC-P at a starting concentration of 5 μg/mL (datasheet: A08006).

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

Immunohistochemistry protocol sheet for LRRTM1 (IHC for LRRTM1): expected localisation Brain cytoplasm (HPA tissue IHC); postsynaptic membrane (UniProt), antibody A08006, validated IHC image, and IHC protocol steps — Printable **LRRTM1** IHC protocol sheet — expected localisation Brain cytoplasm (HPA tissue IHC); postsynaptic membrane (UniProt), antibody A08006, controls and protocol steps. Open the full LRRTM1 IHC guide →

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LRRTM1 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	Brain cytoplasm (HPA tissue IHC); postsynaptic membrane (UniProt)
	Staining pattern	Cytoplasmic staining in brain neuronal cells (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	Keep fixation consistent across sections. (standard IHC practice; not target-specific)
	Caveat	Presumed off-target staining has been observed (HPA tissue IHC)
	Regulation	Regulation not reported (UniProt)
	Isoform / epitope	No isoforms annotated; extracellular vs cytoplasmic epitope matters (UniProt)

Section 1

Recommended LRRTM1 IHC & IF Protocols

The catalog antibody protocol is paired with one published LRRTM1 IHC protocol using paraffin sections of human teeth (PMC3620385).

Recommended immunohistochemistry (IHC-P) protocol parameters
Sample	Tissue sections; selected-image fixative not specified (standard IHC workflow)
Fixation	Image fixative and duration unreported (datasheet A08006); 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-LRRTM1, 5 μg/mL (datasheet A08006)
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	LRRTM1-positive staining in elongated or late spermatids of testis (HPA tissue IHC: High). HPA tissue profile: Cytoplasmic expression in brain. No signal in the no-primary control.

💡Decision noteStart with citrate pH 6.0 retrieval at 95–98 °C for 20 min (page retrieval rule: membrane antigen); the published protocol does not state a retrieval method (PMC3620385).

Section 2

What Is the Expected LRRTM1 Staining Pattern?

LRRTM1 is a cell membrane protein with a postsynaptic location and an extracellular region spanning residues 35–427 (UniProt Q86UE6 topology). In tissue IHC, expect cytoplasmic staining in brain, including neuronal cells in the cerebral cortex and caudate (HPA tissue IHC). HPA rates its tissue staining “Approved,” with medium agreement between staining and RNA data and presumed off-target binding disregarded (HPA tissue IHC).

What am I looking at on my slide?
Medium staining in cerebral cortex or caudate neuronal cells, with a cytoplasmic pattern.	This matches the reported brain tissue pattern (HPA tissue IHC: Medium in neuronal cells; cytoplasmic expression in brain). Interpret the visible compartment as tissue IHC staining; UniProt’s postsynaptic membrane annotation describes protein location, not a requirement that chromogenic sections resolve synapses (UniProt Q86UE6 subcellular location; standard IHC practice).
Strong nuclear-only staining in brain cells, with little staining in the expected neuronal cytoplasm.	Nuclear-only staining is outside the reported brain pattern (HPA tissue IHC: cytoplasmic expression in brain). Review the no-primary control and tissue morphology for detection artefact (standard IHC practice). A compartment mismatch alone does not identify the offending reagent or establish that LRRTM1 is absent.
Prominent staining in cells reported as not detected, such as adipocytes in adipose tissue or glandular cells in adrenal gland.	These cells are negative comparators in the HPA tissue survey (HPA tissue IHC: Not detected in adipocytes and adrenal glandular cells). Consider antibody cross-reactivity or endogenous chromogenic activity, then compare controls and localisation (standard IHC practice). Staining outside the survey pattern warrants investigation, not automatic exclusion.
A uniform haze across tissue and blank areas, obscuring differences between cells.	A haze without anatomical structure is difficult to score as LRRTM1 staining (standard IHC practice). Check the no-primary slide for detection background and review blocking, washes and chromogen exposure (standard IHC practice). HPA’s reported neuronal and spermatid staining is cell-specific, so a uniform haze lacks that supporting distribution (HPA tissue IHC).
No visible signal in cerebral cortex neuronal cells on an otherwise intact section.	This conflicts with the reported medium cortical neuronal staining (HPA tissue IHC: Cerebral cortex, Medium). First verify that the positive control and detection system worked; then review antibody use and the section’s neuronal content (standard IHC practice). A single negative section cannot overturn the HPA pattern or establish target absence.

💡Expected LRRTM1 appearanceCall a positive IHC result when neuronal cells show medium cytoplasmic staining in cerebral cortex or caudate (HPA tissue IHC); strong nuclear-only staining or uniform haze is an unsupported pattern to investigate (HPA tissue IHC; standard IHC practice).

How each factor affects the staining
Compartment and topology	UniProt places LRRTM1 at the cell and postsynaptic membranes, with one transmembrane span at 428–448 and a cytoplasmic region at 449–522 (UniProt Q86UE6 topology). HPA nevertheless describes tissue IHC as cytoplasmic in brain (HPA tissue IHC). Score the observed IHC pattern against that tissue evidence; do not demand a resolved synaptic outline in routine chromogenic sections (standard IHC practice).
Choice of tissue and cell population	The strongest listed staining is in elongated or late spermatids in testis; listed brain neuronal populations are medium, including cortex, caudate and hippocampus (HPA tissue IHC). Select and score the specified cell population, because a tissue-wide intensity label would obscure these differences (standard IHC practice).
Strength of tissue evidence	The tissue profile is “Approved,” with medium staining–RNA consistency and presumed off-target binding disregarded (HPA tissue IHC). The listed patterns guide expectations, but an isolated positive cell population needs morphological and control review (standard IHC practice). HPA062660 has IHC “Approved”; HPA046607 has ICC “Approved,” with no IHC status listed (HPA antibody validation).
IF/ICC Q&A: Should its localisation match IHC?	HPA reports an approved Golgi apparatus location in ICC-IF images from SH-SY5Y and U2OS, while its tissue IHC summary reports cytoplasmic expression in brain (HPA subcellular; HPA tissue IHC). These are different assay contexts; use the tissue IHC profile to judge paraffin sections (standard IHC practice).

Why is my staining missing, weak or wrong?
Situation	Likely cause	Next action
Cortical neurons are unstained.	The result differs from the reported medium cortical neuronal signal (HPA tissue IHC); a failed stain or poorly represented target cells is possible (standard IHC practice).	Check section morphology and neuronal content, then compare a known-positive section and detection controls processed in the same run (standard IHC practice). Review the antibody’s IHC validation before interpreting a negative sample (HPA antibody validation).
Brain staining is predominantly nuclear.	The compartment differs from HPA’s cytoplasmic brain profile and UniProt’s membrane annotation (HPA tissue IHC; UniProt Q86UE6 subcellular location). The cause remains unresolved from localisation alone.	Inspect morphology, compare the no-primary control and repeat the stain with appropriate controls if needed (standard IHC practice). Do not score nuclear-only signal as the expected LRRTM1 pattern (HPA tissue IHC).
Adipose adipocytes stain strongly.	HPA reports these cells as not detected (HPA tissue IHC). Cross-reactivity or chromogenic background is possible (standard IHC practice).	Compare matched no-primary and negative-tissue controls; check whether colour follows cells or appears broadly across the section (standard IHC practice). Record the mismatch with the HPA tissue profile before assigning target specificity (HPA tissue IHC).
Colour appears throughout tissue and on the no-primary control.	Detection background, including endogenous activity, is plausible when signal persists without primary antibody (standard IHC practice).	Review blocking and detection controls, washing and chromogen development using the assay’s instructions (standard IHC practice). Reassess cell-specific staining only after the background is controlled (standard IHC practice).
Testis stains strongly but brain appears weaker.	That ranking matches the listed High signal in elongated or late spermatids and Medium signal in several neuronal populations (HPA tissue IHC).	Compare the specified cell types rather than whole-section darkness (standard IHC practice). Accept a weaker neuronal signal when its distribution and controls fit the reported brain pattern (HPA tissue IHC; standard IHC practice).
ICC-IF shows Golgi signal, but the paraffin IHC slide looks cytoplasmic.	HPA reports approved Golgi localisation for ICC-IF and cytoplasmic expression for brain tissue IHC (HPA subcellular; HPA tissue IHC).	Judge the paraffin slide against tissue IHC evidence and its controls (standard IHC practice). Treat the ICC-IF image as assay-specific localisation evidence, not a requirement for Golgi-shaped chromogenic staining (HPA subcellular; standard IHC practice).

Source: UniProt Q86UE6 Human Protein Atlas tissue Human Protein Atlas subcellular

Experiment evidence

IHC & IF images showing LRRTM1 staining

A08006 · IHCImmunohistochemistry of LRRTM1 in human brain tissue with LRRTM1 antibody at 5 μg/mL.

A08006 · IFImmunofluorescence of LRRTM1 in human brain tissue with LRRTM1 antibody at 20 μg/mL.

HPA · Cerebral cortexHuman Protein Atlas IHC, Cerebral cortex. Source: https://www.proteinatlas.org/ENSG00000162951-LRRTM1/tissue/cerebral+cortex#imid_17788875

HPA · CerebellumHuman Protein Atlas IHC, Cerebellum. Source: https://www.proteinatlas.org/ENSG00000162951-LRRTM1/tissue/cerebellum#imid_17788862

HPA · ColonHuman Protein Atlas IHC, Colon. Source: https://www.proteinatlas.org/ENSG00000162951-LRRTM1/tissue/colon#imid_17788793

HPA · LiverHuman Protein Atlas IHC, Liver. Source: https://www.proteinatlas.org/ENSG00000162951-LRRTM1/tissue/liver#imid_17788802

HPA · ICC-IF SH-SY5YHuman Protein Atlas immunofluorescence, SH-SY5Y, antibody HPA046607; green = LRRTM1, blue = nucleus, red = microtubules.

← swipe / scroll for more images →

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

Sample controls for LRRTM1 IHC & IF

🧪Run testis first and expect staining in elongated or late spermatids (HPA: High in testis elongated or late spermatids). Use adipose tissue as a negative tissue, focusing on adipocytes (HPA: Not detected in adipose adipocytes); on the testis slide, assess other cells for background staining rather than assuming they are negative.

Positive control tissue: Testis (Elongated or late spermatids, HPA High)

Negative control tissue: Adipose tissue (HPA Not detected)

ICC-IF cell lines (HPA subcellular resource): HPA ICC-IF images show LRRTM1 in SH-SY5Y, U2OS, with annotated localisation: Golgi apparatus (approved) (HPA subcellular).

Technical controls: Include a no-primary, secondary-only control and an isotype control matched to the primary antibody’s host species and clonality; confirm specificity with knockout tissue or a peptide block if an appropriate blocking peptide is available (standard IHC practice). For chromogenic detection in testis, block endogenous peroxidase and check whether any staining persists in the no-primary control (standard IHC practice).

⚠️Feasibility: A target-specific fixation window and retrieval dependency are unreported in the supplied evidence; the selected A08006 brain IHC caption also does not report its fixative (caption: fixative not stated). The evidence does not establish whether frozen sections or IF/ICC are easier for LRRTM1 (HPA: ICC-IF images in SH-SY5Y and U2OS). In testis, assess background carefully around the strongly positive spermatids (HPA: High in elongated or late spermatids).

HPA tissue IHC evidence for LRRTM1

Comprehensive Human Protein Atlas IHC scoring per tissue (reliability: Approved — Medium consistency between antibody staining and RNA expression data. Presumed off target binding observed and disregarded.). 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	Elongated or late spermatids	High	Protein (IHC)	HPA →
Caudate	Neuronal cells	Medium	Protein (IHC)	HPA →
Cerebellum	Purkinje cells	Medium	Protein (IHC)	HPA →
Cerebral cortex	Neuronal cells	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 LRRTM1 IHC Tips

Troubleshoot LRRTM1 chromogenic IHC in paraffin sections using the product image, protein topology, and tissue staining evidence as reference points.

How should I optimize antigen retrieval when LRRTM1 staining is weak?

Start with citrate buffer at pH 6.0, heated to 95–98 °C for 20 min (page retrieval setting). If staining is weak, compare a longer citrate incubation or an alkaline retrieval buffer on matched sections, changing one condition at a time (standard IHC practice). Keep the catalog antibody concentration constant during that comparison; its human brain IHC image used 5 µg/mL, although the caption does not report retrieval conditions (A08006 caption). Check neuronal staining alongside tissue damage and diffuse background, since stronger retrieval can also increase nonspecific signal (standard IHC practice; HPA tissue IHC: medium neuronal staining in cerebral cortex).

Could fixation explain faint or patchy LRRTM1 staining?

LRRTM1-specific fixation sensitivity is unknown because the supplied human brain IHC caption does not state a fixative (A08006 caption). Record fixative, fixation duration, tissue thickness, and processing history for each paraffin section before comparing staining runs (standard IHC practice). If archived sections stain inconsistently, compare sections with matched processing and run the same retrieval, antibody concentration, and detection conditions side by side (standard IHC practice). Include a human brain reference section when available; the catalog image establishes staining at 5 µg/mL, but does not establish which fixation conditions preserve the epitope (A08006 caption).

Where should convincing LRRTM1 staining appear in brain sections?

Assess neuronal staining in context: LRRTM1 is annotated at the cell membrane and postsynaptic membrane, with an extracellular region at residues 35–427 and a cytoplasmic tail at 449–522 (UniProt Q86UE6). Tissue IHC also reports cytoplasmic brain expression and medium staining in cerebral cortex and hippocampal neuronal cells (HPA tissue IHC). Distinguish cell body, neuropil, and membrane-associated chromogen where section resolution permits; a diffuse brown field alone is insufficient for assigning synaptic localisation (standard IHC interpretation). An approved cell imaging record places LRRTM1 at the Golgi apparatus, so assess compartment patterns without forcing every positive cell into a single pattern (HPA subcellular).

How can epitope position change the LRRTM1 staining pattern?

Map the antibody immunogen before interpreting compartment differences; no isoforms or antibody epitope coordinates are supplied here (UniProt Q86UE6; supplied A08006 caption). LRRTM1 has a signal peptide at residues 1–34, an extracellular region at 35–427, one transmembrane segment at 428–448, and a cytoplasmic region at 449–522 (UniProt Q86UE6). Four annotated glycosylation sites lie in the extracellular region, at 56, 63, 130, and 380, but the payload does not establish their effect on this antibody's staining (UniProt Q86UE6). Compare retrieval conditions and appropriate controls before attributing a different pattern to an isoform or altered epitope access (standard IHC practice).

How would I check an LRRTM1 IHC pattern with multiplex IF?

Treat IF as a separate validation experiment: the supplied catalog image documents human brain IHC at 5 µg/mL, without an IF condition (A08006 caption). Multiplex LRRTM1 with a validated neuronal marker, and include single-stain and secondary-only controls to assess colocalisation and bleed-through (HPA tissue IHC: neuronal staining; standard IF practice). Choose fluorophores after measuring brain-section autofluorescence, favoring channels with clear signal above the unstained section (standard IF practice). If the immunogen maps to residues 449–522, test permeabilisation for the cytoplasmic tail; an extracellular epitope at 35–427 calls for a separate access check (UniProt Q86UE6 topology; standard IF practice).

What should I adjust if brown background obscures neuronal staining?

Run no-primary and detection-only controls to identify chromogen or detection background, and inspect tissue edges before adjusting antibody concentration (standard IHC practice). Block endogenous peroxidase for a peroxidase and DAB workflow, then optimize protein blocking, washes, and chromogen development on matched sections (standard IHC practice). The catalog human brain image used 5 µg/mL; treat that as an IHC reference concentration, not proof that it minimizes background under your conditions (A08006 caption). Compare suspect staining with neuronal patterns and negative tissue controls, while allowing for presumed off-target binding in the tissue atlas record (HPA tissue IHC: approved, medium consistency; standard IHC practice).

How should I score LRRTM1 staining across brain sections? ⚠ ANSWER MARKED FOR VERIFICATION

Define the neuronal population and anatomical region before scoring; the tissue atlas reports medium staining in cerebral cortex, hippocampus, caudate, and cerebellar Purkinje cells (HPA tissue IHC). Score the percentage of positive neurons with an intensity scale to calculate an H-score, or count positive cells per mm² within a consistent region of interest (standard IHC quantification). Normalize counts to total evaluable neurons or tissue area, and apply identical staining thresholds, counterstain, imaging, and exclusion rules across sections (standard IHC practice). Report cell body and neuropil measurements separately when both are measured, since a single pooled score can obscure their distribution (standard IHC quantification).

How can I distinguish true LRRTM1 signal from an artefact?

Prioritize reproducible neuronal staining in brain regions supported by the tissue atlas, while checking whether membrane-associated or cytoplasmic signal fits the reported localisation evidence (HPA tissue IHC; UniProt Q86UE6; HPA subcellular). Mark staining in unexpected cells or compartments for review, especially because the atlas reports presumed off-target binding and only medium agreement with RNA data (HPA tissue IHC). Exclude tissue-edge deposits, necrotic areas, and signal reproduced by no-primary or detection-only controls; check a peroxidase control when endogenous enzyme activity is suspected (standard IHC practice). Confirm the remaining pattern across matched sections before calling a focal deposit LRRTM1-positive (standard IHC interpretation).

Boster reagents

Best LRRTM1 / Leucine-rich repeat transmembrane neuronal protein 1 IHC Antibodies

The catalog antibody has IHC and IF images in human brain tissue (IHC/IF image captions) and lists Human, Mouse and Rat reactivity (catalog reactivity).

Real IHC data Immunohistochemistry of LRRTM1 in human brain tissue with LRRTM1 antibody at 5 μg/mL.

Anti-LRRTM1 Antibody

Cat # A08006

View product →

A08006 has an IHC image in human brain tissue at 5 μg/mL (IHC image caption). A08006 also has an IF image in human brain tissue at 20 μg/mL (IF image caption).

Which to pick: For paraffin-section IHC, choose A08006: IHC-P is listed (catalog applications), and its own IHC image shows human brain tissue at 5 μg/mL; the fixative is unreported (IHC image caption). For IF, A08006 has a human brain tissue image at 20 μg/mL (IF image caption); ICC validation is unreported (catalog applications). For cross-species work, A08006 lists Human, Mouse and Rat reactivity (catalog reactivity), but the supplied IHC and IF images show human brain tissue only (IHC/IF image captions); it is rabbit-hosted, with clonality unreported (catalog host/clone).

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

References

UniProt Consortium. UniProt entry Q86UE6 (LRRT1_HUMAN, Leucine-rich repeat transmembrane neuronal protein 1).
Human Protein Atlas. LRRTM1 tissue IHC expression (reliability: Approved).
Human Protein Atlas. LRRTM1 subcellular location (ICC-IF): Localized to the Golgi apparatus..
Human Protein Atlas. LRRTM1 antibody validation summary (2 antibodies).
LRRTM1 underlies synaptic convergence in visual thalamus. eLife 2018 — PMC5826289.
Comparative gene expression analysis of the human periodontal ligament in deciduous and permanent teeth. PloS one 2013 — PMC3620385.
Impaired cognitive function and altered hippocampal synapse morphology in mice lacking Lrrtm1, a gene associated with schizophrenia. PloS one 2011 — PMC3144940.
PubMed PMID:12676565 — UniProt-cited evidence.
PubMed PMID:14702039 — UniProt-cited evidence.
PubMed PMID:12975309 — UniProt-cited evidence.