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FYN / Tyrosine-protein kinase Fyn · IHC design guide
Design Immunohistochemistry for FYN
Plan FYN IHC-P around cytoplasmic staining in lymphoid organs, including high staining in tonsil and lymph-node non-germinal center cells (HPA tissue IHC). The catalog antibody is shown at 1:25 on paraffin-embedded tonsil with peroxidase and DAB detection (datasheet: IHC image caption).
Evidence assembled Oct 2026 · For research use; verify linked source records and product datasheet before use
FYN 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 staining in lymphoid organs (HPA tissue IHC) | |
| Antigen retrieval | Tris-EDTA pH 9.0 HIER, 95–98 °C, 20 min (rule: nuclear antigen) | |
| Positive control | Fallopian tube+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 | Staining has low consistency with RNA expression (HPA tissue IHC) | |
| Regulation | Isoform 1: brain; isoform 2: T cells (UniProt) | |
| Isoform / epitope | 3 isoforms; antibody epitope coverage is unreported (UniProt) |
Section 1
Recommended FYN IHC & IF Protocols
The catalog antibody’s IHC-P protocol is accompanied by published FYN IHC methods for ovarian, prostate, brain and cervical specimens (PMC11391251; PMC2741693; PMC5358011; PMC9468808).
| Sample | Paraffin-embedded H. tonsil tissue; fixative not specified (datasheet M00684-2) |
| Fixation | Image fixative and duration unreported (datasheet M00684-2); 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 Tris-EDTA buffer, pH 9.0, 20 min at 95–98 °C (standard rule: nuclear 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 | Mouse monoclonal (clone 1302CT390.118.237) anti-FYN, 1:25 (datasheet M00684-2) |
| 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 | FYN-positive staining in ciliated cells (tip of cilia) of fallopian tube (HPA tissue IHC: High). HPA tissue profile: Cytoplasmic expression in several tissues, including lymphoid organs. No signal in the no-primary control. |
💡Decision noteFor paraffin sections, start with Tris-EDTA pH 9.0 at 95–98 °C for 20 min (page retrieval); two published methods also use pH 9.0 retrieval (PMC11391251; PMC9468808).
Section 2
What Is the Expected FYN Staining Pattern?
FYN can localize to the cytoplasm, cell membrane, nucleus and perikaryon; it has no transmembrane segment (UniProt P06241). In tissue IHC, HPA reports cytoplasmic staining across several tissues, including lymphoid organs, with high staining in lymph node and tonsil non-germinal center cells (HPA tissue IHC). HPA rates the tissue staining Approved but reports low consistency with RNA expression; treat these patterns as comparison points, not guarantees (HPA tissue IHC).
| Cytoplasmic staining in lymph node or tonsil non-germinal center cells, with limited surrounding background. | This matches HPA's high staining in those cell populations and its broader cytoplasmic tissue profile (HPA tissue IHC). Judge signal in the named cells rather than treating the whole lymphoid section as uniformly positive; HPA's Approved rating carries a low RNA–staining consistency caveat (HPA tissue IHC). |
| A membrane-associated component accompanies cytoplasmic staining. | This is compatible with FYN's cell membrane and cytoplasmic locations (UniProt P06241) and with plasma membrane as the main supported ICC-IF location, plus cytosol (HPA subcellular). ICC-IF localization helps interpret compartments, but its cell images do not establish the expected intensity in paraffin tissue IHC (HPA subcellular; HPA tissue IHC). |
| Predominantly nuclear or otherwise unexpected staining, without the expected cytoplasmic pattern. | Question the pattern against HPA's cytoplasmic tissue profile and membrane/cytosol ICC-IF result (HPA tissue IHC; HPA subcellular). An exclusively nuclear pattern merits control review; nuclear localization is listed for FYN, so nuclear signal alone cannot prove an artefact (UniProt P06241). |
| Strong staining in a cell population HPA lists as not detected, such as adipocytes or bronchial basal cells. | Check cell identification, the detection controls and antibody specificity before assigning the signal to FYN (HPA tissue IHC; standard IHC practice). Cross-reactivity or endogenous detection activity are possibilities, not diagnoses from location alone (standard IHC practice). HPA's low RNA–staining consistency also limits any single negative comparison (HPA tissue IHC). |
| Diffuse color across tissue and spaces between cells, or no signal in an HPA high-staining population. | Diffuse, poorly localized color is difficult to score as cellular FYN staining (standard IHC practice). Absent signal in lymph node or tonsil non-germinal center cells conflicts with HPA's high-staining examples, but first assess section quality and controls; HPA patterns do not guarantee every specimen will stain (HPA tissue IHC; standard IHC practice). |
💡Expected FYN appearanceA convincing positive is cell-associated cytoplasmic staining, potentially with a membrane component, in lymph node or tonsil non-germinal center cells where HPA reports high staining; broad diffuse color or strong signal in an HPA not-detected cell population calls for control review (HPA tissue IHC; HPA subcellular; standard IHC practice).
| Tissue and cell selection | HPA reports high staining in lymph node and tonsil non-germinal center cells and at fallopian tube cilia tips, medium staining in cerebral cortex neuropil, and no detected staining in adipocytes (HPA tissue IHC). These are cell-specific comparisons, not a single expected intensity for an entire section (HPA tissue IHC). |
| Compartment and trafficking | FYN is listed in cytoplasm, nucleus, cell membrane and perikaryon, with no transmembrane segment (UniProt P06241). UniProt reports lipid-raft activity and a role for palmitoylation in trafficking; those annotations support biological plausibility of membrane-associated signal but do not establish a required IHC pattern (UniProt P06241). |
| Isoform context | UniProt lists three isoforms: isoform 1 is highly expressed in brain, while isoform 2 occurs in hemopoietic lineages, especially T-lymphocytes (UniProt P06241). The supplied HPA tissue staining does not resolve isoforms, so do not infer an isoform from a positive cell or compartment (HPA tissue IHC; UniProt P06241). |
| Evidence and antibody scope | HPA calls tissue IHC Approved despite low consistency with RNA expression; HPA023887, CAB005034 and CAB018387 have Approved IHC status, while HPA063770 has no listed IHC status (HPA tissue IHC; HPA antibodies). These labels do not validate an unspecified catalog antibody or supply a dilution or retrieval setting (HPA antibodies). |
| IF/ICC Q&A: should it look identical to tissue IHC? | No fixed match is established: supported ICC-IF localization is mainly plasma membrane with additional cytosol, whereas HPA summarizes tissue IHC as cytoplasmic (HPA subcellular; HPA tissue IHC). Use the compartment evidence to interpret images, then assess each application with its own controls (standard IHC/IF practice). |
| Situation | Likely cause | Next action |
|---|---|---|
| No stain in lymph node or tonsil non-germinal center cells. | These cells stain high in HPA tissue IHC, so an absent result may reflect specimen or assay performance; HPA's low RNA–staining consistency limits certainty (HPA tissue IHC). | Confirm the intended cells and section quality, then compare a validated positive section and detection control; review the antibody's IHC instructions before adjusting conditions (standard IHC practice). |
| Only diffuse color, with no clear cell boundaries. | Diffuse deposition can come from nonspecific reagent binding or detection background (standard IHC practice); it does not match HPA's described cytoplasmic tissue pattern (HPA tissue IHC). | Compare the primary-omission control and inspect washing, blocking and detection steps; score only localized signal that remains above control background (standard IHC practice). |
| Strong staining in adipocytes or bronchial basal cells. | HPA lists these cell populations as not detected, so the result needs specificity review; cross-reactivity or endogenous detection activity are possible (HPA tissue IHC; standard IHC practice). | Verify cell identity and examine omission and detection controls before interpreting the stain; compare the same run with an HPA high-staining population (HPA tissue IHC; standard IHC practice). |
| Predominantly nuclear staining without cytoplasmic signal. | This differs from HPA's tissue profile and its membrane/cytosol ICC-IF result, although UniProt also lists a nuclear location (HPA tissue IHC; HPA subcellular; UniProt P06241). | Check the control section and antibody specificity, and report the nuclear pattern as unresolved unless supported by additional evidence (standard IHC practice; UniProt P06241). |
| Membrane signal is faint while cytoplasmic signal is visible. | HPA tissue IHC describes cytoplasmic expression, while HPA ICC-IF identifies plasma membrane as the main supported location; application-specific images need not have identical emphasis (HPA tissue IHC; HPA subcellular). | Evaluate the tissue result against tissue controls and its cell-specific pattern; avoid rejecting it solely because the membrane rim is faint (HPA tissue IHC; standard IHC practice). |
| Signal is uneven between tissue regions or runs. | Target-specific fixation effects are not established by the supplied assay evidence. Verify with a matched IHC source before attributing a result to fixation. | Compare section quality and run controls, then review the antibody's IHC instructions before changing retrieval or detection conditions; document any changes alongside the controls (standard IHC practice). |
Experiment evidence
IHC & IF images showing FYN staining
M00684-2 · IHCImmunohistochemical analysis of paraffin-embedded H. tonsil section using FYN. M00684-2 was diluted at 1:25 dilution. A peroxidase-conjugate
M00684-2 · IHCImmunohistochemical analysis of paraffin-embedded M. spleen section using FYN. M00684-2 was diluted at 1:25 dilution. A peroxidase-conjugate
M00684 · IFImmunofluorescent analysis using the Antibody at 1:50 dilution.
HPA · Cerebral cortexHuman Protein Atlas IHC, Cerebral cortex. Source: https://www.proteinatlas.org/ENSG00000010810-FYN/tissue/cerebral+cortex#imid_6099815
HPA · ColonHuman Protein Atlas IHC, Colon. Source: https://www.proteinatlas.org/ENSG00000010810-FYN/tissue/colon#imid_6099749
HPA · LiverHuman Protein Atlas IHC, Liver. Source: https://www.proteinatlas.org/ENSG00000010810-FYN/tissue/liver#imid_6099742
HPA · KidneyHuman Protein Atlas IHC, Kidney. Source: https://www.proteinatlas.org/ENSG00000010810-FYN/tissue/kidney#imid_6099751
HPA · ICC-IF AF22Human Protein Atlas immunofluorescence, AF22, antibody HPA023887; green = FYN, blue = nucleus, red = microtubules.
HPA · ICC-IF AF22Human Protein Atlas immunofluorescence, AF22, antibody HPA023887; green = FYN, blue = nucleus, red = microtubules.
← swipe / scroll for more images →
Real IHC / IF data behind the staining-pattern expectations in this section.
Sample controls for FYN IHC & IF
🧪Run tonsil first and expect staining in non-germinal center cells (HPA: High in tonsil non-germinal center cells). Use adipose tissue adipocytes as the biological negative comparison (HPA: Not detected in adipose tissue adipocytes); within the tonsil slide, unstained cells should show counterstain without specific DAB signal, but should not be assumed FYN-negative solely from their location (HPA: High in non-germinal center cells).
Positive control tissue: Fallopian tube (Ciliated cells (tip of cilia), HPA High)
Negative control tissue: Adipose tissue (HPA Not detected)
ICC-IF cell lines (HPA subcellular resource): HPA ICC-IF images show FYN in AF22, HEK293, U2OS, RPTEC/TERT1, hTERT-RPE1 (serum starved), KOLF2.1J, with annotated localisation: Plasma membrane (supported) (HPA subcellular).
Technical controls: Include a no-primary, secondary-only control and a host-, subclass-, and clonality-matched isotype control; the caption uses anti-mouse secondary antibody, so match the catalog primary’s mouse IgG subclass if applicable (caption: goat anti-mouse IgG). Confirm specificity with FYN-knockout material processed alongside the test sections, or immunizing-peptide competition if the reagent permits (standard IHC practice). Block endogenous peroxidase in tonsil before chromogenic detection (caption: DAB staining; standard IHC practice).
⚠️Feasibility: A target-specific fixation window and antigen-retrieval dependence are unreported; the selected M00684-2 example is a paraffin-embedded tonsil section diluted 1:25, but its fixative is unreported (caption: paraffin-embedded H. tonsil; 1:25; fixative not stated). The supplied evidence does not establish whether frozen sections or IF are easier; ICC-IF images support plasma-membrane and additional cytosolic localization (HPA subcellular: supported). Endogenous peroxidase in tonsil can produce misleading DAB signal unless blocked (caption: DAB staining; standard IHC practice).
HPA tissue IHC evidence for FYN
Comprehensive Human Protein Atlas IHC scoring per tissue (reliability: Approved — Low consistency between antibody staining and RNA expression data.). 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 |
|---|---|---|---|---|
| Fallopian tube | Ciliated cells (tip of cilia) | High | Protein (IHC) | HPA → |
| Lymph node | Non-germinal center cells | High | Protein (IHC) | HPA → |
| Tonsil | Non-germinal center cells | High | Protein (IHC) | HPA → |
| Adrenal gland | Glandular cells | Medium | Protein (IHC) | HPA → |
| Appendix | Lymphoid tissue | Medium | Protein (IHC) | HPA → |
Undetected expression · recommended negative controls
| Tissue | Cell type | Level | Evidence | Source |
|---|---|---|---|---|
| Adipose tissue | Adipocytes | Not detected | Protein (IHC) | HPA → |
| Breast | Adipocytes | Not detected | Protein (IHC) | HPA → |
| Bronchus | Basal cells | Not detected | Protein (IHC) | HPA → |
| Caudate | Glial cells | Not detected | Protein (IHC) | HPA → |
| Cerebellum | Cells in granular layer | Not detected | Protein (IHC) | HPA → |
Section 3
Advanced FYN IHC Tips
Use compartment, cell-type and control patterns together when troubleshooting FYN staining in paraffin sections (UniProt P06241; HPA tissue IHC).
How should I adjust retrieval when FYN staining is weak in paraffin sections?
Begin with Tris-EDTA pH 9.0 heat-induced epitope retrieval at 95–98 °C for 20 min (page retrieval setting). Run a known positive tonsil section alongside the test section; tonsil non-germinal center cells show high staining in the tissue reference (HPA tissue IHC: High in tonsil non-germinal center cells). If signal remains weak, compare a shorter heating time or a citrate pH 6.0 fallback on adjacent sections while holding antibody dilution and detection constant (standard IHC practice). Judge the result by cell-associated staining and preserved morphology, since excessive retrieval can damage sections and make background harder to interpret (standard IHC practice).
Can fixation explain weak or uneven FYN staining?
The selected FYN tissue image reports a paraffin-embedded tonsil section but does not state its fixative, so target-specific fixation sensitivity is unknown (M00684-2 tissue-IHC caption). Record the fixative, fixation duration and processing history for each specimen before comparing staining across blocks (standard IHC practice). For uneven results, stain adjacent sections in the same run and compare preserved central tissue with damaged or detached regions, using the same retrieval and detection conditions (standard IHC practice). Do not attribute a difference to FYN palmitoylation or its membrane association without a controlled fixation comparison; those features describe the protein, not its measured fixation response (UniProt P06241; standard IHC practice).
Which compartments should count as plausible FYN staining?
Assess membrane-associated and cytoplasmic staining as plausible FYN patterns, while recording nuclear staining separately because the protein record also lists the nucleus (UniProt P06241 subcellular location). Supported cell imaging places FYN mainly at the plasma membrane, with additional cytosolic localization (HPA subcellular). FYN has no transmembrane segment, and palmitoylation is important for its trafficking; a membrane rim therefore does not imply a transmembrane epitope (UniProt P06241 topology and trafficking). Compare each compartment in morphologically intact cells with a negative detection control, and avoid calling diffuse staining over empty spaces or damaged edges intracellular signal (standard IHC practice).
Could the antibody epitope alter which FYN-expressing cells stain?
FYN has 3 reported isoforms, with isoform 1 highly expressed in brain and isoform 2 expressed in hematopoietic lineages, especially T lymphocytes (UniProt P06241 isoforms and tissue specificity). Check the catalog antibody’s immunogen or epitope information before treating staining in those settings as an isoform comparison (standard IHC practice). The supplied tissue-IHC caption reports a tonsil result but does not establish which isoforms the antibody recognizes (M00684-2 tissue-IHC caption). If epitope coverage is unspecified, score the result as FYN immunoreactivity and seek an independently characterized isoform-specific reagent before assigning staining to a particular isoform (standard IHC practice).
How can IF help investigate an ambiguous chromogenic FYN pattern?
Use IF as a separate follow-up to localize ambiguous IHC signal, with a marker for the expected cell population in a different channel (standard IF practice). Choose fluorophores after checking tissue autofluorescence and single-channel controls, favoring a well-separated emission channel where background is lowest (standard IF practice). Because FYN can associate with the cell membrane and also occur in cytosol, set permeabilization according to the antibody’s mapped epitope and test a mild condition when intracellular access is required (UniProt P06241 subcellular location; HPA subcellular; standard IF practice). Do not transfer the paraffin-section caption’s staining conditions to IF: it reports chromogenic DAB detection, not an IF protocol (M00684-2 tissue-IHC caption).
What should I check when FYN DAB staining looks diffuse?
Compare the test slide with a primary-antibody omission control to identify background from detection reagents or tissue rather than specific antibody binding (standard IHC practice). Block endogenous peroxidase before the peroxidase-conjugated secondary and DAB steps, and inspect pigment-rich or damaged areas separately from intact cells (standard IHC practice). The selected image used M00684-2 at 1:25, a peroxidase-conjugated goat anti-mouse IgG at 1:400, and DAB; these are image conditions, not a demonstrated optimum for every specimen (M00684-2 tissue-IHC caption). If background persists, titrate the primary and secondary on adjacent sections while retaining a positive tonsil control and identical development time (HPA tissue IHC: High in tonsil non-germinal center cells; standard IHC practice).
How should I score FYN staining across sections? ⚠ ANSWER MARKED FOR VERIFICATION
Define the cell population and compartment before scoring, because FYN may appear at the membrane or in cytoplasm, with nuclear location also reported (UniProt P06241 subcellular location; HPA subcellular). For a cell-based readout, record the percentage of positive intact cells and an H-score from 0–300 using intensity categories 0–3 (standard IHC practice). For spatial patterns, count positive cells per mm² of viable tissue or report stained area relative to the annotated tissue area (standard IHC practice). Normalize comparisons to the same cell population, compartment, section selection and staining run; retain the same threshold and exclude folds, necrosis and section edges consistently (standard IHC practice).
How do I distinguish convincing FYN staining from artefact?
Look for reproducible cell-associated signal in plausible compartments, especially membrane-associated or cytoplasmic staining, rather than isolated DAB deposits (UniProt P06241 subcellular location; HPA subcellular; standard IHC practice). Tonsil non-germinal center cells and lymph-node non-germinal center cells are reported as high-staining reference populations, although the tissue reference notes low consistency between antibody staining and RNA expression (HPA tissue IHC). Treat staining confined to cut edges, folds or necrotic regions as suspect, and compare it with a primary-antibody omission control for endogenous enzyme or detection background (standard IHC practice). Confirm that the apparent positive cells match the annotated population before interpreting a compartment pattern or comparing cases (standard IHC practice).
Boster reagents
Best FYN / Tyrosine-protein kinase Fyn IHC Antibodies
The catalog includes anti-FYN antibodies with IHC data from human tonsil paraffin sections (M00684-2 image caption) and IF data with sample type and species unreported (M00684 image caption).
Real IHC data
Anti-FYN Antibody
Cat # M00684-2
Real IF data
Anti-Fyn Rabbit Monoclonal Antibody
Cat # M00684
M00684-2 is listed for human IHC-P and shows chromogenic staining of a paraffin-embedded human tonsil section at 1:25 (catalog applications and reactivity; M00684-2 image caption). M00684 is listed for human, mouse and rat IF/ICC and has an IF image at 1:50; the image caption does not identify the sample or species (catalog applications and reactivity; M00684 image caption).
Which to pick: Choose mouse monoclonal M00684-2 for human tissue IHC-P: its image documents a paraffin-embedded human tonsil section, but does not report the fixative (catalog host, clone, applications and reactivity; M00684-2 image caption). Choose rabbit monoclonal M00684 for IF/ICC or for its listed human, mouse and rat reactivity; its application list does not include IHC-P, and its IF caption does not identify the sample or species (catalog host, clone, applications and reactivity; M00684 image caption).
Each figure is that product's own IHC / IF validation image from its datasheet.
References
- UniProt Consortium. UniProt entry P06241 (FYN_HUMAN, Tyrosine-protein kinase Fyn).
- Human Protein Atlas. FYN tissue IHC expression (reliability: Approved).
- Human Protein Atlas. FYN subcellular location (ICC-IF): Mainly localized to the plasma membrane. In addition localized to the cytosol..
- Human Protein Atlas. FYN antibody validation summary (4 antibodies).
- Role of Fyn expression in predicting the sensitivity to platinum‑based chemotherapy in patients with ovarian serous carcinoma. Oncology letters 2024 — PMC11391251.
- FYN is overexpressed in human prostate cancer. BJU international 2009 — PMC2741693.
- Regulatory region genetic variation is associated with FYN expression in Alzheimer's disease. Neurobiology of aging 2017 — PMC5358011.
- Fyn expression is associated with the response of patients with locally advanced uterine cervical squamous cell carcinoma to neoadjuvant chemotherapy. Molecular and clinical oncology 2022 — PMC9468808.
- PubMed PMID:3099169 — UniProt-cited evidence.
- PubMed PMID:3526330 — UniProt-cited evidence.
- PubMed PMID:7822789 — UniProt-cited evidence.
Immunohistochemistry protocol sheet for FYN (Tyrosine-protein kinase Fyn). Expected localisation Cytoplasmic tissue staining (HPA tissue IHC). Antigen retrieval: Tris-EDTA pH 9.0 HIER, 95–98 °C, 20 min (rule: nuclear antigen). Validated IHC antibody: M00684-2 at 1:25 (the product's own IHC validation image is shown). Controls (HPA): positive Fallopian tube (Ciliated cells (tip of cilia)); negative Adipose tissue. IHC workflow; specimen preparation unspecified. Protocol steps: 1. Sample: Paraffin-embedded H. tonsil tissue; fixative not specified (datasheet M00684-2); 2. Fixation: Image fixative and duration unreported (datasheet M00684-2); 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 Tris-EDTA buffer, pH 9.0 , 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: Mouse monoclonal (clone 1302CT390.118.237) anti-FYN, 1:25 (datasheet M00684-2); 9. Primary incubation: Overnight at 4 °C (standard). Watch for: Fixation: Keep fixation consistent across sections. (standard IHC practice; not target-specific); Caveat: Staining has low consistency with RNA expression (HPA tissue IHC); Isoform / epitope: 3 isoforms; antibody epitope coverage is unreported (UniProt); Regulation: Isoform 1: brain; isoform 2: T cells (UniProt). Evidence: UniProt P06241, HPA tissue IHC · Approved, HPA ICC-IF · Mainly localized to the plasma membrane. In addition localized to…, Datasheet M00684-2, PMC11391251, PMC2741693. QR code links to https://www.bosterbio.com/bosterbio-gene-info-cards/FYN/immunohistochemistry-ihc-guide.