LY9 / T-lymphocyte surface antigen Ly-9 · IHC design guide

Design Immunohistochemistry for LY9

Plan chromogenic LY9 IHC in paraffin sections with the IHC-validated antibody A05830-1 (datasheet A05830-1). Use lymphoid cell subsets as staining references (HPA tissue IHC), and interpret their observed cytoplasmic signal alongside LY9’s expected cell membrane location (HPA tissue IHC; UniProt).

Evidence assembled Oct 2026 · For research use; verify linked source records and product datasheet before use
Immunohistochemistry protocol sheet for LY9 (IHC for LY9): expected localisation Cell membrane expected (UniProt); lymphoid cytoplasm observed (HPA tissue IHC), antibody A05830-1, validated IHC image, and IHC protocol steps
Printable LY9 IHC protocol sheet — expected localisation Cell membrane expected (UniProt); lymphoid cytoplasm observed (HPA tissue IHC), antibody A05830-1, controls and protocol steps. Open the full LY9 IHC guide →

LY9 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 Cell membrane expected (UniProt); lymphoid cytoplasm observed (HPA tissue IHC)
Staining pattern Cytoplasmic staining in subsets of lymphoid cells (HPA tissue IHC)
Antigen retrieval Citrate pH 6 HIER, heat-mediated (datasheet A05830-1)
Positive control ⓘ Appendix+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 section fixation consistent (standard IHC practice; not target-specific); Matched tissue-IHC evidence does not establish the fixation claim. Validate the specimen-specific method before use. (selected-SKU IHC image A05830-1)
Caveat A secreted variant may alter tissue staining (HPA tissue IHC)
Regulation Surface LY9 increases on SLE T cells (UniProt)
Isoform / epitope Four isoforms; check whether the epitope is extracellular or cytoplasmic (UniProt)
Section 1

Recommended LY9 IHC & IF Protocols

The catalog antibody’s IHC-P protocol (datasheet A05830-1) is accompanied by published LY9 IHC methods for FFPE tissue (PMC10901781) and lung adenocarcinoma tissue (PMC11348898).

Recommended immunohistochemistry (IHC-P) protocol parameters
SampleParaffin-embedded mouse spleen tissues; fixative not specified (datasheet A05830-1)
FixationImage fixative and duration unreported (datasheet A05830-1); verify before use.
Sectioning4–5 µm sections on charged slides (standard)
DeparaffinisationXylene, graded ethanol series to water (standard)
Antigen retrievalHeat retrieval: Citrate pH 6, 20 min (datasheet A05830-1)
Peroxidase block3% H2O2, 10 min, room temperature (standard)
Blocking10% goat serum (datasheet A05830-1)
Primary antibodyRabbit anti-LY9, 0.5-1μg/ml (datasheet A05830-1)
Primary incubationOvernight at 4 °C (datasheet A05830-1)
DetectionStreptavidin-biotin complex (SABC), DAB chromogen (datasheet A05830-1)
CounterstainHematoxylin, blue, dehydrate and mount (standard)
Expected resultLY9-positive staining in lymphoid tissue of appendix (HPA tissue IHC: Medium). HPA tissue profile: Cytoplasmic expression mainly in subsets of lymphoid cells. No signal in the no-primary control.
💡Decision noteStart with citrate pH 6 heat retrieval (datasheet A05830-1); pH 9 retrieval is a published alternative for FFPE tissue (PMC10901781).
Section 2

What Is the Expected LY9 Staining Pattern?

LY9 is a cell membrane protein with an extracellular region and a cytoplasmic tail (UniProt Q9HBG7 topology). In paraffin tissue IHC, HPA reports chiefly cytoplasmic staining in subsets of lymphoid cells, with medium staining in appendix lymphoid tissue, splenic white pulp and tonsil non-germinal center cells (HPA tissue IHC). HPA rates its tissue IHC profile Approved, with medium consistency between staining and RNA data and external verification pending (HPA tissue IHC).

What am I looking at on my slide?
Discrete staining in lymphoid cell subsets, especially in appendix, splenic white pulp or tonsil non-germinal center cells (HPA tissue IHC).This fits the reported IHC distribution; medium is the recorded level for those cell populations, so assess the named cells rather than assigning one intensity to the whole section (HPA tissue IHC).
Predominantly cytoplasmic signal in a subset of lymphoid cells (HPA tissue IHC).This can match the paraffin IHC profile even though LY9 is assigned to the cell membrane by UniProt and mainly to the plasma membrane by HPA ICC-IF (UniProt Q9HBG7 subcellular location; HPA tissue IHC; HPA subcellular ICC-IF). Interpret the two assay readouts separately.
Strong, isolated nuclear staining, without the reported lymphoid cell pattern (HPA tissue IHC).Nuclear localization is absent from the supplied LY9 locations; treat this as suspect staining and compare with an appropriate negative control before scoring it as LY9 (UniProt Q9HBG7 subcellular location; HPA subcellular ICC-IF; standard IHC practice).
Prominent staining of adipocytes or bronchial respiratory epithelial cells (HPA tissue IHC).HPA reports LY9 as not detected in these cell populations; investigate antibody cross-reactivity or endogenous chromogenic activity if they stain, especially when the expected lymphoid distribution is absent (HPA tissue IHC; standard IHC practice).
Diffuse color across cells and surrounding tissue, or no signal in appendix lymphoid tissue (HPA tissue IHC).Diffuse color can obscure cell-specific scoring; absent signal in a reported medium-positive population makes a negative test section difficult to interpret (HPA tissue IHC; standard IHC practice). Check controls and the staining workflow before making a biological call.
💡Expected LY9 appearanceCall a section positive when staining is concentrated in the reported lymphoid cell subsets, often cytoplasmic and reaching the reported medium level in appendix, splenic white pulp or tonsil; broad staining of HPA-undetected adipocytes or bronchial respiratory epithelium is suspect (HPA tissue IHC).
How each factor affects the staining
Compartment and epitope position (UniProt Q9HBG7 topology).LY9 spans residues 455–476, with extracellular residues 48–454 and a cytoplasmic region at 477–655 (UniProt Q9HBG7 topology). The supplied record gives no antibody epitope, so topology alone cannot predict which part this IHC antibody detects.
Protein variants and tissue correlation (UniProt Q9HBG7 isoforms; HPA tissue IHC).UniProt lists four LY9 isoforms; HPA notes that at least one protein variant is secreted and that RNA and protein locations may differ (UniProt Q9HBG7 isoforms; HPA tissue IHC). Do not infer isoform identity from an IHC pattern.
Strength of tissue evidence (HPA tissue IHC; HPA antibodies).The tissue profile is Approved but has medium staining–RNA consistency and awaits external verification; the listed antibody HPA050917 has IHC Approved status (HPA tissue IHC; HPA antibodies). Treat agreement with the reported pattern as support, not proof of antibody specificity.
Reported levels vary by cell population (HPA tissue IHC).HPA reports low staining in lymph node germinal center cells and bone marrow hematopoietic cells, versus medium in appendix lymphoid tissue and splenic white pulp (HPA tissue IHC). A weak result in a low-level population needs a stronger reference population for comparison.
Antigen retrieval and chromogenic detection (standard IHC practice).These are general assay variables to check when controls fail (standard IHC practice). The supplied UniProt and HPA records do not establish an LY9-specific retrieval setting or fixation sensitivity, so do not attribute a tissue result to either without separate evidence.
Why is my staining missing, weak or wrong?
SituationLikely causeNext action
No staining in appendix lymphoid tissue, where HPA reports medium signal (HPA tissue IHC).A run-level failure is possible; absence alone cannot distinguish assay failure from a different sample pattern (standard IHC practice).Check the positive control, reagent omission control, retrieval run, primary antibody step and chromogenic detection before scoring the specimen negative (standard IHC practice).
Broad, low-level color obscures lymphoid cells (HPA tissue IHC).Background from detection reagents, blocking or washing can reduce cell-level contrast (standard IHC practice).Review the reagent omission control and the blocking, washing and detection steps; score only interpretable cells against the reported lymphoid distribution (standard IHC practice; HPA tissue IHC).
Adipocytes or bronchial respiratory epithelial cells stain prominently (HPA tissue IHC).These cell types are reported as not detected; cross-reactivity or endogenous detection activity is plausible (HPA tissue IHC; standard IHC practice).Compare with an omission control and a reported positive lymphoid population, then check endogenous activity controls appropriate to the chromogen (standard IHC practice; HPA tissue IHC).
Only nuclei show a sharp signal (UniProt Q9HBG7 subcellular location).An isolated nuclear pattern lacks support from the supplied membrane and IHC distribution records (UniProt Q9HBG7; HPA tissue IHC).Recheck morphology, counterstain and controls; withhold a positive LY9 call unless cell-associated staining agrees with the reported tissue pattern (standard IHC practice; HPA tissue IHC).
A lymph node germinal center looks weaker than splenic white pulp (HPA tissue IHC).HPA records low staining in lymph node germinal center cells and medium staining in splenic white pulp cells (HPA tissue IHC).Compare like cell populations and their reported levels; do not use equal intensity in these two sites as a pass criterion (HPA tissue IHC).
Q: Should ICC-IF look exactly like paraffin IHC? (HPA tissue IHC; HPA subcellular ICC-IF).HPA reports mainly plasma membrane and additional centriolar satellite localization in ICC-IF, while its tissue IHC profile is chiefly cytoplasmic in lymphoid subsets (HPA subcellular ICC-IF; HPA tissue IHC).A: Interpret ICC-IF on its own guide page using its localization evidence; use the reported tissue IHC pattern to judge paraffin sections (HPA subcellular ICC-IF; HPA tissue IHC).

Sample controls for LY9 IHC & IF

🧪Run spleen first and look for staining in white-pulp cells (HPA: Medium in spleen white pulp). Use adipose tissue as the negative tissue and assess its adipocytes, while using morphologically non-lymphoid cells on the spleen slide as an internal background reference rather than assuming all cells outside white pulp are negative (HPA: Not detected in adipocytes; HPA: Medium in spleen white pulp).
Positive control tissue: Appendix (Lymphoid tissue, HPA Medium)
Negative control tissue: Adipose tissue (HPA Not detected)
ICC-IF cell lines (HPA subcellular resource): HPA ICC-IF images show LY9 in JURKAT, REH, U2OS, with annotated localisation: Plasma membrane (approved) (HPA subcellular).
Technical controls: Include a no-primary, secondary-only control, a concentration-matched rabbit isotype control for the catalog antibody, and LY9-knockout tissue if available (caption: rabbit anti-CD229 antibody; standard IHC practice). Block endogenous peroxidase in spleen and check for endogenous biotin signal when using the caption’s biotin-based detection system (caption: biotinylated secondary and SABC–DAB; standard IHC practice).
⚠️Feasibility: A target-specific fixation window or fixation effect is unreported, and the selected SKU’s paraffin-section caption does not state a fixative (caption: fixative not stated). The demonstrated IHC procedure used heat retrieval in citrate buffer at pH 6 for 20 minutes; whether other retrieval conditions work is unreported (caption: citrate retrieval). No matched evidence establishes that frozen sections or IF are easier; spleen requires attention to endogenous peroxidase and, with biotin-based detection, endogenous biotin background (HPA: spleen white-pulp staining; caption: SABC–DAB; standard IHC practice).

HPA tissue IHC evidence for LY9

Comprehensive Human Protein Atlas IHC scoring per tissue (reliability: Approved — 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. Pending external verification.). Rows are taken directly from the HPA tissue chart — click any row's HPA link to view the source.

Positive expression · recommended positive controls

TissueCell typeLevelEvidenceSource
Appendix Lymphoid tissue Medium Protein (IHC) HPA →
Spleen Cells in white pulp Medium Protein (IHC) HPA →
Testis Spermatogonia cells Medium Protein (IHC) HPA →
Tonsil Non-germinal center cells Medium Protein (IHC) HPA →

Undetected expression · recommended negative controls

TissueCell typeLevelEvidenceSource
Adipose tissue Adipocytes Not detected Protein (IHC) HPA →
Adrenal gland Glandular cells Not detected Protein (IHC) HPA →
Breast Adipocytes Not detected Protein (IHC) HPA →
Bronchus Respiratory epithelial cells Not detected Protein (IHC) HPA →
Caudate Glial cells Not detected Protein (IHC) HPA →
Section 3

Advanced LY9 IHC Tips

Troubleshoot LY9 chromogenic IHC by checking retrieval, staining compartment, cell identity, and controls before interpreting signal (UniProt Q9HBG7; HPA tissue IHC).

Which retrieval conditions should I start with for LY9 in paraffin sections?
Start with heat-mediated antigen retrieval in citrate buffer at pH 6 for 20 minutes (datasheet A05830-1). The selected antibody's paraffin-section image used those conditions, followed by 10% goat serum blocking and 1 μg/mL primary antibody overnight at 4°C (datasheet A05830-1). If staining is weak, compare modest changes in heating time on adjacent sections while holding antibody concentration and detection constant (standard IHC practice). Include a known positive lymphoid section and a no-primary control in that comparison (HPA tissue IHC; standard IHC practice). Excessive retrieval can damage morphology or raise background, so judge signal alongside intact cellular detail (standard IHC practice).
How should I troubleshoot fixation-related loss of LY9 staining?
LY9-specific sensitivity to fixation is unknown: the selected paraffin-section caption does not state its fixative (datasheet A05830-1). Record the fixative and fixation duration for each specimen, then compare specimens processed consistently before attributing a negative result to biology (standard IHC practice). For a controlled comparison, keep citrate retrieval at pH 6 for 20 minutes and the catalog antibody at 1 μg/mL unchanged (datasheet A05830-1). Check morphology and staining in a positive lymphoid section processed alongside the sample (HPA tissue IHC; standard IHC practice). Do not treat differing HPA tissue staining as evidence of a LY9-specific fixation effect (HPA tissue IHC).
Should LY9 staining be membranous or cytoplasmic in tissue sections?
Expect a membrane-associated pattern because LY9 spans residues 455–476, with an extracellular region at 48–454 and a cytoplasmic tail at 477–655 (UniProt Q9HBG7 topology). HPA reports plasma membrane localisation in cell imaging but mainly cytoplasmic staining in subsets of lymphoid cells by tissue IHC (HPA subcellular; HPA tissue IHC). Therefore, score membrane and cytoplasmic signal separately rather than assuming either pattern is definitive in paraffin sections (UniProt Q9HBG7 topology; HPA tissue IHC; standard IHC practice). Compare the pattern with spleen white pulp and tonsil non-germinal-center cells, where HPA reports medium staining (HPA tissue IHC). Diffuse staining across unrelated tissue structures warrants control review (standard IHC practice).
Could isoforms or epitope location explain inconsistent LY9 IHC?
LY9 has 4 listed isoforms, but the supplied antibody caption does not identify its epitope or establish isoform coverage (UniProt Q9HBG7 isoforms; datasheet A05830-1). Map any subsequently documented immunogen to the extracellular 48–454 region or cytoplasmic 477–655 region before interpreting compartment differences (UniProt Q9HBG7 topology; standard IHC practice). The extracellular region contains 8 listed glycosylation sites, so epitope accessibility is a question to test, not an established cause of weak staining (UniProt Q9HBG7 glycosylation; standard IHC practice). Compare adjacent sections under identical retrieval and detection conditions, with positive and no-primary controls (standard IHC practice). Do not assign an isoform from chromogenic staining alone (standard IHC practice).
How can I cross-check a LY9 IHC pattern by multiplex IF?
Use IF as a separate localisation check and multiplex LY9 with a validated marker for the lymphoid cell population under study (HPA tissue IHC; standard IF practice). Choose spectrally separated fluorophores after inspecting tissue autofluorescence, and include single-label and no-primary controls (standard IF practice). If the antibody epitope is extracellular, compare staining without permeabilisation; if it is cytoplasmic, assess controlled permeabilisation, because LY9 spans residues 455–476 (UniProt Q9HBG7 topology; standard IF practice). The supplied caption does not specify this antibody's epitope, so neither condition establishes its performance in IF (datasheet A05830-1). HPA reports approved plasma membrane localisation in cell imaging, which offers a pattern for comparison rather than validation of this catalog antibody (HPA subcellular).
What should I check when LY9 DAB staining is widespread?
First inspect a no-primary section and the tissue edges to separate detection background from cellular staining (standard IHC practice). The selected workflow used biotinylated secondary antibody, a streptavidin–biotin complex, and DAB, so include appropriate detection controls when using that workflow (datasheet A05830-1; standard IHC practice). Apply a peroxidase block and check for endogenous biotin interference where relevant to the detection system (standard IHC practice). Keep the documented 10% goat serum block and 1 μg/mL primary concentration as a starting point while changing one variable at a time (datasheet A05830-1; standard IHC practice). Broad staining in cells expected to be negative deserves closer scrutiny (HPA tissue IHC).
How should I quantify LY9 staining across paraffin sections? ⚠ ANSWER MARKED FOR VERIFICATION
Define the lymphoid region and cell population before scoring, since HPA reports medium staining in spleen white-pulp cells and tonsil non-germinal-center cells (HPA tissue IHC; standard IHC practice). Record the percentage of positive cells and staining intensity separately; an H-score can combine them when intensity categories are prespecified (standard IHC practice). Alternatively, count LY9-positive cells per mm² of viable lymphoid tissue, excluding folds and necrosis (standard IHC practice). Normalise comparisons to the relevant cell population or analysed lymphoid area, and keep section thickness, retrieval at pH 6, and imaging settings consistent (datasheet A05830-1; standard IHC practice). Report membrane and cytoplasmic scores separately because tissue and cell-imaging patterns differ (HPA tissue IHC; HPA subcellular).
How can I distinguish true LY9 positivity from artefact?
Give greatest weight to reproducible staining in identifiable lymphoid cells with a plausible membrane-associated pattern (UniProt Q9HBG7 topology; HPA tissue IHC; standard IHC practice). HPA also describes mainly cytoplasmic tissue staining in lymphoid subsets, so cytoplasmic signal requires comparison with the same controls rather than automatic rejection (HPA tissue IHC; standard IHC practice). Check spleen white-pulp or tonsil non-germinal-center staining against no-primary and detection controls before calling unexpected cells positive (HPA tissue IHC; standard IHC practice). Exclude edge effects, necrosis, and endogenous peroxidase signal from interpretation of DAB sections (standard IHC practice). HPA rates its tissue evidence as Approved with medium RNA–staining consistency and pending external verification, which limits certainty from morphology alone (HPA tissue IHC).
Boster reagents

Best LY9 / T-lymphocyte surface antigen Ly-9 IHC Antibodies

Anti-LY9 antibodies have IHC images from mouse and rat paraffin sections and IF/ICC images from 293 cells; both catalog entries list human, mouse and rat reactivity (catalog images and reactivity).

Real IHC data IHC analysis of CD229 using anti-CD229 antibody (A05830-1). CD229 was detected in paraffin-embedded section of mouse spleen tissues. Heat mediated antigen retrieval was performed in citrate buffer (pH6, epitope retrieval solution) for 20 mins. The tissue section was blocked with 10% goat serum. The tissue section was then incubated with 1μg/ml rabbit anti-CD229 Antibody (A05830-1) overnight at 4°C. Biotinylated goat anti-rabbit IgG was used as secondary antibody and incubated for 30 minutes at 37°C. The tissue section was developed using Strepavidin-Biotin-Complex (SABC)(Catalog # SA1022) with DAB as the chromogen.
Anti-CD229/LY9 Antibody
Cat # A05830-1
Real IF data Immunocytochemistry of SLAMF3 in 293 cells with SLAMF3 antibody at 10 μg/mL.
Anti-SLAMF3 LY9 Antibody
Cat # A05830-2

A05830-1 lists IHC and ICC and shows LY9 staining in mouse and rat paraffin spleen sections (A05830-1 applications and IHC captions). A05830-2 lists IF and ICC and shows staining in 293 cells, with no tissue IHC image supplied (A05830-2 applications and image captions).

Which to pick: Choose A05830-1 for paraffin-section IHC: its captions document heat retrieval in citrate buffer at pH 6 for 20 minutes in mouse and rat spleen, but do not report the fixative (A05830-1 IHC captions). Choose A05830-2 for IF/ICC in cells; its images use 293 cells, and IHC is absent from its application list (A05830-2 applications and IF/ICC captions). For cross-species tissue IHC, A05830-1 has mouse and rat image evidence and listed human reactivity, but no human tissue image; clonality is unreported for both SKUs (catalog reactivity, images and clone fields).

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

References

  1. UniProt Consortium. UniProt entry Q9HBG7 (LY9_HUMAN, T-lymphocyte surface antigen Ly-9).
  2. Human Protein Atlas. LY9 tissue IHC expression (reliability: Approved).
  3. Human Protein Atlas. LY9 subcellular location (ICC-IF): Mainly localized to the plasma membrane. In addition localized to the centriolar satellites..
  4. Human Protein Atlas. LY9 antibody validation summary (1 antibodies).
  5. Molecular and clinical analyses of PHF6 mutant myeloid neoplasia provide their pathogenesis and therapeutic targeting. Nature communications 2024 — PMC10901781.
  6. Study of LY9 as a potential biomarker for prognosis and prediction of immunotherapy efficacy in lung adenocarcinoma. PeerJ 2024 — PMC11348898.
  7. CD229 (Ly9) a Novel Biomarker for B-Cell Malignancies and Multiple Myeloma. Cancers 2022 — PMC9101303.
  8. PubMed PMID:10970093 — UniProt-cited evidence.
  9. PubMed PMID:14702039 — UniProt-cited evidence.
  10. PubMed PMID:16710414 — UniProt-cited evidence.