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THY1 / Thy-1 membrane glycoprotein · IHC design guide
Design Immunohistochemistry for THY1
Plan THY1 chromogenic IHC on paraffin sections around neuronal, neuropil and renal proximal-tubule staining (HPA tissue IHC). Compare the observed cytoplasmic tissue pattern (HPA tissue IHC) with THY1’s GPI-anchored membrane annotation (UniProt).
Evidence assembled Oct 2026 · For research use; verify linked source records and product datasheet before use
THY1 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); cell membrane annotation (UniProt) | |
| Staining pattern | Neuronal/neuropil cytoplasm; renal proximal-tubule microvilli (HPA tissue IHC) | |
| Antigen retrieval | Citrate pH 6.0 HIER, 95–98 °C, 20 min (rule: cytoplasmic / membrane antigen) | |
| Positive control | Caudate+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 | Cytoplasmic IHC differs from the membrane annotation (HPA tissue IHC; UniProt) | |
| Regulation | Staining regulation not established (UniProt; HPA tissue IHC) | |
| Isoform / epitope | 0 isoforms; mature 20–130 chain is surface-facing, with no cytoplasmic tail (UniProt) |
Section 1
Recommended THY1 IHC & IF Protocols
Compare the catalog antibody’s IHC-P protocol (datasheet) with 3 published THY1 IHC methods (PMC5228576; PMC5531053; PMC8770266).
| Sample | Paraffin-embedded human tonsil tissue; fixative not specified (datasheet M01818) |
| Fixation | Image fixative and duration unreported (datasheet M01818); 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 monoclonal (clone CEB-20) anti-THY1, 1:50 (datasheet M01818) |
| 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 | THY1-positive staining in neuronal cells of caudate (HPA tissue IHC: Medium). HPA tissue profile: Cytoplasmic expression most abundant in CNS and peripheral nerves. No signal in the no-primary control. |
💡Decision noteStart with citrate pH 6.0 HIER at 95–98 °C for 20 min (page antigen-retrieval rule). A published alternative uses antigen unmasking buffer (PMC5531053).
Section 2
What Is the Expected THY1 Staining Pattern?
THY1 is a GPI-anchored cell-membrane protein with no transmembrane segment (UniProt P04216 topology). In tissue IHC, expect staining chiefly in central nervous system and peripheral nerves; documented positive sites include neuronal cells, neuropil, and kidney proximal-tubule microvilli (HPA tissue IHC). HPA describes the tissue pattern as predominantly cytoplasmic and rates its reliability Enhanced, with medium agreement between staining and RNA data (HPA tissue IHC).
| Medium staining in caudate or hippocampal neuronal cells, or cerebral-cortex neuropil (HPA tissue IHC). | This matches documented IHC-positive cells and regions (HPA tissue IHC). Interpret the slide by cell type and tissue as well as compartment: HPA describes predominantly cytoplasmic tissue staining, while UniProt places THY1 at the cell membrane (HPA tissue IHC; UniProt P04216 topology). |
| Medium staining at kidney proximal-tubule microvilli (HPA tissue IHC). | This is a second documented positive pattern and can help assess a weak neural-tissue result (HPA tissue IHC). Score the microvillar signal in the named cell type; the supplied HPA record does not establish that every kidney compartment should stain. |
| Only strong nuclear staining in a tissue section, without the documented neuronal, neuropil, or microvillar pattern. | Treat this as discordant with the supplied tissue IHC observations and investigate staining artefact (HPA tissue IHC; general IHC practice). Do not dismiss all nuclear signal as impossible: HPA reports approved nucleoplasmic localization in ICC-IF, a separate application (HPA subcellular ICC-IF). |
| Staining in adipocytes or colon endothelial cells, which HPA lists as not detected (HPA tissue IHC). | This is unexpected for those specified cells and may reflect cross-reactivity or endogenous detection activity (HPA tissue IHC; general IHC practice). The entries are cell-specific; they do not make whole adipose or colon sections universal negative controls. |
| Diffuse deposit across many structures, or no signal in documented positive cells. | Diffuse staining obscures compartment and cell-type assessment and suggests background from the detection workflow (general IHC practice). Absence in a known-positive compartment is inconclusive until antibody, retrieval, detection, and tissue integrity are checked with controls (HPA tissue IHC; general IHC practice). |
💡Expected THY1 appearanceCall positive when caudate or hippocampal neuronal cells, cerebral-cortex neuropil, or kidney proximal-tubule microvilli show the documented Medium IHC signal; diffuse deposit or signal confined to HPA-negative cell types is suspect (HPA tissue IHC; general IHC practice).
| Membrane topology and tissue appearance | THY1 is GPI-anchored and lacks a transmembrane segment (UniProt P04216 topology). HPA nonetheless describes predominantly cytoplasmic tissue IHC; membrane-only scoring would exclude part of its reported pattern (HPA tissue IHC). |
| Cell and tissue selection | HPA reports Medium staining in the listed neuronal cells, neuropil, and proximal-tubule microvilli, but only low staining in cerebellar granular cells and smooth-muscle cells (HPA tissue IHC). Choose and score controls at the specified cell level. |
| Antibody validation | The HPA003733 IHC result is Enhanced; CAB068243 and CAB068244 are Supported (HPA antibodies). Enhanced denotes reproduction by independent antibodies or orthogonal data in the supplied record, but does not establish identical staining under every laboratory workflow (HPA antibodies; general IHC practice). |
| Processing and glycosylation | UniProt lists a signal peptide at residues 1–19, a mature chain at 20–130, a propeptide at 131–161, and four glycosylation sites (UniProt P04216 processing/glycosylation). These features warrant checking which region an antibody recognizes; no epitope or processing-dependent IHC effect is supplied. |
| Antigen retrieval | No THY1-specific retrieval condition or fixation sensitivity is supplied (source scope). For paraffin IHC, assess retrieval with a documented positive tissue and matched negative control; any change in signal is an empirical workflow finding, not an HPA or UniProt prediction (general IHC practice). |
| Chromogenic detection background | Endogenous detection activity can create staining unrelated to antibody binding (general IHC practice). Evaluate it with an appropriate reagent-omission control and blocking matched to the detection system before assigning unexpected staining to THY1. |
| Situation | Likely cause | Next action |
|---|---|---|
| No signal in caudate or hippocampal neuronal cells (HPA tissue IHC). | Possible assay failure, inadequate retrieval, or insufficient detection; the supplied sources identify no THY1-specific fixation mechanism (general IHC practice; source scope). | Run a documented positive tissue alongside the sample, verify each detection step, and compare retrieval conditions empirically (HPA tissue IHC; general IHC practice). |
| Weak staining in cerebellar granular cells or smooth-muscle cells (HPA tissue IHC). | HPA reports low staining in these cells, so weak signal alone does not establish assay failure (HPA tissue IHC). | Judge assay performance in an HPA Medium positive compartment, then score the low-expression cells separately (HPA tissue IHC; general IHC practice). |
| Diffuse chromogen obscures neuronal or microvillar detail. | Nonspecific antibody binding or endogenous detection activity may raise background (general IHC practice). | Check a reagent-omission control; review blocking, antibody concentration, washing, and detection-system controls before interpreting localization (general IHC practice). |
| Predominantly nuclear staining appears in tissue IHC. | It differs from the supplied tissue IHC profile, although nucleoplasmic localization is approved in ICC-IF (HPA tissue IHC; HPA subcellular ICC-IF). | Compare a documented tissue-positive compartment and appropriate negative control; avoid transferring the ICC-IF localization call directly to paraffin-section scoring (HPA tissue IHC; general IHC practice). |
| Adipocytes or colon endothelial cells stain strongly (HPA tissue IHC). | Those specific cells are listed as not detected; cross-reactivity or detection background is possible (HPA tissue IHC; general IHC practice). | Confirm the stained cell identity, inspect omission controls, and compare with a documented positive compartment before calling the signal THY1 (HPA tissue IHC; general IHC practice). |
| Can an ICC-IF nuclear or membrane pattern be used as the IHC acceptance criterion? | HPA approves nucleoplasmic and additional plasma-membrane localization in ICC-IF, while its tissue IHC record describes a different observed profile (HPA subcellular ICC-IF; HPA tissue IHC). | Use the tissue IHC pattern to score paraffin sections; consult the separate IF/ICC guide for that application (HPA tissue IHC; HPA subcellular ICC-IF). |
Experiment evidence
IHC & IF images showing THY1 staining
M01818 · IHCImmunohistochemical analysis of paraffin-embedded human tonsil, using CD90 / Thy1 Antibody.
M01818-1 · IHCImmunohistochemical analysis of paraffin-embedded human kidney, using CD90 Antibody.
M01818-1 · IFImmunofluorescent analysis of U87-MG cells, using CD90 Antibody.
HPA · Cerebral cortexHuman Protein Atlas IHC, Cerebral cortex. Source: https://www.proteinatlas.org/ENSG00000154096-THY1/tissue/cerebral+cortex#imid_19346527
HPA · ColonHuman Protein Atlas IHC, Colon. Source: https://www.proteinatlas.org/ENSG00000154096-THY1/tissue/colon#imid_19346453
HPA · LiverHuman Protein Atlas IHC, Liver. Source: https://www.proteinatlas.org/ENSG00000154096-THY1/tissue/liver#imid_19346462
HPA · KidneyHuman Protein Atlas IHC, Kidney. Source: https://www.proteinatlas.org/ENSG00000154096-THY1/tissue/kidney#imid_19346447
HPA · ICC-IF PC-3Human Protein Atlas immunofluorescence, PC-3, antibody HPA003733; green = THY1, blue = nucleus, red = microtubules.
HPA · ICC-IF PC-3Human Protein Atlas immunofluorescence, PC-3, antibody HPA003733; green = THY1, blue = nucleus, red = microtubules.
← swipe / scroll for more images →
Real IHC / IF data behind the staining-pattern expectations in this section.
Sample controls for THY1 IHC & IF
🧪Run kidney first: proximal-tubule microvilli should stain at the reported Medium level (HPA: kidney, proximal tubules). Use adipose tissue adipocytes as the negative tissue (HPA: adipocytes not detected); cells outside the positive microvilli should show background unless independently shown to express THY1, since the supplied kidney row does not establish an internal-negative cell type.
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 THY1 in PC-3, U-251MG, with annotated localisation: Nucleoplasm (approved) (HPA subcellular).
Technical controls: Include no-primary (secondary-only), a primary host-species and immunoglobulin-isotype matched control, and a THY1 knockout specimen as a biological negative (standard IHC practice). For kidney IHC, quench endogenous peroxidase and block endogenous biotin if using biotin-based detection (standard IHC practice).
⚠️Feasibility: A target-specific fixation window and antigen-retrieval dependency are unreported in the supplied evidence; optimize retrieval empirically (supplied evidence; standard IHC practice). The selected M01818 paraffin-section tonsil caption does not report a fixative (M01818 caption). The evidence does not establish whether frozen sections or IF/ICC are easier; in kidney, endogenous biotin can complicate biotin-based chromogenic detection (standard IHC practice).
HPA tissue IHC evidence for THY1
Comprehensive Human Protein Atlas IHC scoring per tissue (reliability: Enhanced — Medium consistency between antibody staining and RNA expression data. External characterization data supports antibody staining.). 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 → |
| Cerebral cortex | Neuropil | Medium | Protein (IHC) | HPA → |
| Hippocampus | Neuronal cells | Medium | Protein (IHC) | HPA → |
| Kidney | Proximal tubules (microvilli) | 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 THY1 IHC Tips
Troubleshoot THY1 staining in paraffin sections by checking retrieval, compartment, tissue context, and controls before assigning a biological interpretation.
How should I retrieve THY1 in paraffin sections when staining is weak?
Start with citrate buffer at pH 6.0, heated to 95–98 °C for 20 min (page retrieval rule: cytoplasmic / membrane antigen). If staining remains weak, compare an otherwise matched section with a more alkaline retrieval buffer as a fallback, while keeping detection and imaging conditions constant (standard IHC practice). Excessive heating can damage morphology and increase nonspecific staining, so assess tissue integrity alongside signal (standard IHC practice). Judge improvement in the expected cellular context rather than by overall brown intensity: THY1 is annotated at the cell membrane, and tissue staining is reported in neuronal cells, neuropil, and proximal-tubule microvilli (UniProt P04216 localization; HPA tissue IHC).
Can fixation explain variable THY1 staining between paraffin blocks?
Target-specific fixation sensitivity is unknown from the supplied evidence; the catalog image identifies paraffin-embedded human tonsil but does not state its fixative (catalog caption M01818). Record each block’s fixative and fixation history before comparing staining, since routine fixation and processing differences can change antigen accessibility in IHC (standard IHC practice). Run blocks together with the same citrate pH 6.0 retrieval at 95–98 °C for 20 min and the same chromogenic detection conditions (page retrieval rule; standard IHC practice). If staining differs, compare morphology and a consistently processed reference section before attributing that difference to THY1 abundance (standard IHC practice).
Should THY1 staining appear at the membrane or within cells?
Evaluate membrane-associated staining first: THY1 is a GPI-anchored cell-membrane protein without a transmembrane segment (UniProt P04216 topology and keywords). Tissue IHC also reports cytoplasmic expression most abundant in CNS and peripheral nerves, including medium staining in neuronal cells and neuropil (HPA tissue IHC). A separate subcellular dataset lists nucleoplasm as its main approved location and plasma membrane as an additional approved location, so compartment calls require context (HPA subcellular). In paraffin sections, compare staining with cell outlines and a counterstain, then score membrane-associated and intracellular signal separately where resolution permits (standard IHC practice). Do not infer a nuclear THY1 pattern from diffuse brown staining alone (standard IHC practice).
How could THY1 processing and glycosylation affect an IHC epitope?
The annotated mature THY1 chain spans residues 20–130, after removal of the 1–19 signal peptide and 131–161 propeptide (UniProt P04216 processing). Annotated glycosylation sites include residues 42, 79, and 119 within that chain; residue 139 lies in the propeptide (UniProt P04216 glycosylation and processing). The record lists 0 isoforms, so differing IHC patterns should not be assigned to an annotated splice isoform (UniProt P04216 isoforms). Check the catalog antibody’s stated immunogen or epitope, if available, before interpreting absent staining; epitope exposure can change during paraffin processing and citrate pH 6.0 retrieval (standard IHC practice; page retrieval rule).
How can IF help assess an ambiguous chromogenic THY1 pattern?
Use IF as a companion localisation check, while interpreting the result against the paraffin-section IHC pattern (standard IHC / IF practice). Multiplex THY1 with a validated marker for the cell type under study, because tissue IHC reports signal in neuronal cells, neuropil, and proximal-tubule microvilli (HPA tissue IHC; standard IF practice). Select fluorophores after inspecting unstained tissue autofluorescence, and include single-label controls to assess bleed-through (standard IF practice). For a surface-facing epitope on GPI-anchored THY1, compare nonpermeabilised staining first; assess permeabilisation separately if the antibody’s documented epitope requires intracellular access (UniProt P04216 topology; standard IF practice). Keep IF fixation conditions documented rather than borrowing assumptions from the tonsil paraffin caption, whose fixative is unreported (catalog caption M01818).
How do I separate THY1 signal from chromogenic background?
Inspect a matched section without primary antibody to reveal background from the detection system, endogenous peroxidase, or the tissue itself (standard IHC practice). Include a peroxidase block before DAB development and compare counterstained sections processed under the same conditions (standard chromogenic IHC practice). If diffuse staining increases after citrate pH 6.0 retrieval at 95–98 °C for 20 min, review morphology and blocking before increasing primary antibody concentration (page retrieval rule; standard IHC practice). Prioritise reproducible cellular staining over pigment at section edges, folds, or damaged areas (standard IHC practice). THY1’s membrane annotation helps assess whether a brown deposit follows plausible cell boundaries (UniProt P04216 localization).
What should I score when comparing THY1 across paraffin sections? ⚠ ANSWER MARKED FOR VERIFICATION
Define the tissue compartment and eligible cells before scoring, since reported THY1 staining varies by cell type and includes neuronal cells, neuropil, and proximal-tubule microvilli (HPA tissue IHC). For cellular staining, report the percentage of positive cells and, when intensity is reliable, an H-score from 0–300; for neuropil or other diffuse regions, report stained area or signal density per mm² (standard IHC quantification practice). Normalise counts to eligible cells and area measurements to analysed viable tissue area (standard IHC quantification practice). Apply one threshold and imaging setup across sections, and keep membrane-associated and intracellular scores separate when distinguishable (standard IHC practice; UniProt P04216 localization).
When is a THY1-positive IHC result biologically credible?
A credible result is reproducible in intact tissue and fits the scored cell type and compartment: THY1 is annotated at the membrane, while tissue IHC reports neuronal, neuropil, and proximal-tubule microvillar staining (UniProt P04216 localization; HPA tissue IHC). Use reported negative contexts, such as adipocytes and colon endothelial cells, only as context-dependent comparators, since those HPA entries say THY1 was not detected there (HPA tissue IHC). Recheck isolated nuclear or diffuse staining against the separate HPA subcellular observation of approved nucleoplasmic localisation before assigning it biological meaning in paraffin tissue (HPA subcellular; standard IHC practice). Exclude section-edge staining, necrotic areas, and signal persisting without primary antibody; the latter can reflect endogenous enzyme activity or detection background (standard IHC practice).
Boster reagents
Best THY1 / Thy-1 membrane glycoprotein IHC Antibodies
M01818 and M01818-1 have human paraffin-section IHC images (catalog IHC captions). M01818-1 also has a U87-MG cell IF image (catalog IF caption). Listed reactivity spans human and rat (catalog reactivity).
Real IHC data
Anti-CD90 / Thy1 Rabbit Monoclonal Antibody
Cat # M01818
Real IHC data
Anti-THY1/Cd90 Rabbit Monoclonal Antibody
Cat # M01818-1
M01818 is listed for IHC and shows staining of a human tonsil paraffin section; its listed reactivity is human and rat (catalog applications, reactivity and IHC caption). M01818-1 is listed for IHC and IF/ICC, with images of a human kidney paraffin section and U87-MG cells; its listed reactivity is human (catalog applications, reactivity and image captions).
Which to pick: For tissue IHC, choose the rabbit monoclonal M01818 for human tonsil paraffin sections or the rabbit monoclonal M01818-1 for human kidney paraffin sections (catalog host, clone and respective IHC captions); neither caption reports the fixative (catalog IHC captions). For IF/ICC, choose M01818-1, which lists both applications and has a U87-MG IF image (catalog applications and IF caption). For human and rat work, M01818 lists both species and IHC, though its IHC image is human only; A01818-1 lists human, mouse and rat reactivity, but specifies human for paraffin-section IHC (catalog reactivity, applications, IHC caption and dilution_raw).
Each figure is that product's own IHC / IF validation image from its datasheet.
References
- UniProt Consortium. UniProt entry P04216 (THY1_HUMAN, Thy-1 membrane glycoprotein).
- Human Protein Atlas. THY1 tissue IHC expression (reliability: Enhanced).
- Human Protein Atlas. THY1 subcellular location (ICC-IF): Mainly localized to the nucleoplasm. In addition localized to the plasma membrane..
- Human Protein Atlas. THY1 antibody validation summary (3 antibodies).
- Overexpression of Thy1 and ITGA6 is associated with invasion, metastasis and poor prognosis in human gallbladder carcinoma. Oncology letters 2016 — PMC5228576.
- Thy1 (CD90) Expression Is Elevated in Radiation-Induced Periprosthetic Capsular Contracture: Implication for Novel Therapeutics. Plastic and reconstructive surgery 2017 — PMC5531053.
- Detection of pancreatic ductal adenocarcinoma in mice by ultrasound imaging of thymocyte differentiation antigen 1. Gastroenterology 2013 — PMC3783557.
- Identification of Key Pathways and Genes Related to Immunotherapy Resistance of LUAD Based on WGCNA Analysis. Frontiers in oncology 2021 — PMC8770266.
- PubMed PMID:2864690 — UniProt-cited evidence.
- PubMed PMID:10944468 — UniProt-cited evidence.
- PubMed PMID:17974005 — UniProt-cited evidence.
Immunohistochemistry protocol sheet for THY1 (Thy-1 membrane glycoprotein). Expected localisation Cytoplasmic tissue staining (HPA tissue IHC); cell membrane annotation (UniProt). Antigen retrieval: Citrate pH 6.0 HIER, 95–98 °C, 20 min (rule: cytoplasmic / membrane antigen). Validated IHC antibody: M01818 at 1:50 (the product's own IHC validation image is shown). Controls (HPA): positive Caudate (Neuronal cells); negative Adipose tissue. IHC workflow; specimen preparation unspecified. Protocol steps: 1. Sample: Paraffin-embedded human tonsil tissue; fixative not specified (datasheet M01818); 2. Fixation: Image fixative and duration unreported (datasheet M01818); verify before use.; 3. Sectioning: 4–5 µm sections on charged slides (standard); 4. Deparaffinisation: Xylene, graded ethanol series to water (standard); 5. Antigen retrieval: Heat-induced epitope retrieval in citrate buffer, pH 6.0 , 20 min at 95–98 °C…; 6. Peroxidase block: 3% H2O2, 10 min , room temperature (standard); 7. Blocking: 10% normal serum of the secondary host, 30 min , room temperature (standard); 8. Primary antibody: Rabbit monoclonal (clone CEB-20) anti-THY1, 1:50 (datasheet M01818); 9. Primary incubation: Overnight at 4 °C (standard). Watch for: Fixation: Keep fixation consistent across sections (standard IHC practice; not target-specific); Caveat: Cytoplasmic IHC differs from the membrane annotation (HPA tissue IHC; UniProt); Isoform / epitope: 0 isoforms; mature 20–130 chain is surface-facing, with no cytoplasmic tail (UniProt); Regulation: Staining regulation not established (UniProt; HPA tissue IHC). Evidence: UniProt P04216, HPA tissue IHC · Enhanced, HPA ICC-IF · Mainly localized to the nucleoplasm. In addition localized to the…, Datasheet M01818, PMC5228576, PMC5531053. QR code links to https://www.bosterbio.com/bosterbio-gene-info-cards/THY1/immunohistochemistry-ihc-guide.