EME1 / Structure-specific endonuclease subunit EME1 · IHC design guide

Design Immunohistochemistry for EME1

Plan EME1 staining in paraffin sections using the catalog antibody’s chromogenic IHC protocol (datasheet PB9804). Expect widespread nuclear staining (HPA tissue IHC), and interpret intensity cautiously because antibody staining and RNA show low consistency (HPA tissue IHC).

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

Immunohistochemistry protocol sheet for EME1 (IHC for EME1): expected localisation Nuclear staining (HPA tissue IHC), antibody PB9804, validated IHC image, and IHC protocol steps — Printable **EME1** IHC protocol sheet — expected localisation Nuclear staining (HPA tissue IHC), antibody PB9804, controls and protocol steps. Open the full EME1 IHC guide →

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EME1 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	Nuclear staining (HPA tissue IHC)
	Staining pattern	Widespread nuclear staining across tissues (HPA tissue IHC)
	Antigen retrieval	Citrate pH 6 HIER, heat-mediated (datasheet PB9804)
	Positive control ⓘ	Adipose tissue+4 more · see all
	Negative control ⓘ	None in HPA (detected in all 45 tissues); use no-primary + isotype controls

Important caveats

Reasons your staining may differ from the expected pattern.

	Fixation	Keep fixation consistent across paraffin specimens (standard IHC practice). (selected-SKU IHC image PB9804)
	Caveat	Antibody staining and RNA show low consistency (HPA tissue IHC)
	Regulation	No expression regulator annotated (UniProt)
	Isoform / epitope	Two isoforms; epitope coverage is unspecified (UniProt)

Section 1

Recommended EME1 IHC & IF Protocols

The catalog antibody has a citrate pH 6 IHC-P protocol (datasheet: PB9804). Two published EME1 IHC protocols provide additional conditions (PMC5217507; PMC8810030).

Recommended immunohistochemistry (IHC-P) protocol parameters
Sample	Paraffin-embedded Human Lung Cancer tissue; fixative not specified (datasheet PB9804)
Fixation	Image fixative and duration unreported (datasheet PB9804); verify before use.
Sectioning	4–5 µm sections on charged slides (standard)
Deparaffinisation	Xylene, graded ethanol series to water (standard)
Antigen retrieval	Heat retrieval: Citrate pH 6, 20 min (datasheet PB9804)
Peroxidase block	3% H2O2, 10 min, room temperature (standard)
Blocking	10% goat serum (datasheet PB9804)
Primary antibody	Rabbit anti-EME1, 0.5-1μg/ml (datasheet PB9804)
Primary incubation	Overnight at 4 °C (datasheet PB9804)
Detection	Streptavidin-biotin complex (SABC), DAB chromogen (datasheet PB9804)
Counterstain	Hematoxylin, blue, dehydrate and mount (standard)
Expected result	EME1-positive staining in adipocytes of adipose tissue (HPA tissue IHC: High). HPA tissue profile: Ubiquitous nuclear expression. No signal in the no-primary control.

💡Decision noteStart with heat-mediated citrate pH 6 for the catalog antibody (datasheet: PB9804). An EAC study used low-pH retrieval for 20 minutes (PMC5217507).

Section 2

What Is the Expected EME1 Staining Pattern?

EME1 should appear mainly in nuclei: HPA describes ubiquitous nuclear tissue staining and approved nucleoplasmic ICC-IF localization; UniProt also lists the nucleus and nucleolus and records no transmembrane segment (HPA tissue IHC; HPA subcellular; UniProt Q96AY2). High staining is reported in adipocytes and bone marrow hematopoietic cells, among other listed cells (HPA tissue IHC). Interpret tissue results cautiously: HPA rates the IHC evidence Supported but reports low consistency with RNA expression (HPA tissue IHC).

What am I looking at on my slide?
Nuclear staining in adipocytes or bone marrow hematopoietic cells.	This fits the reported High staining in those cells and HPA’s ubiquitous nuclear profile (HPA tissue IHC). Judge the nuclear pattern before comparing intensity across sections, since preparation and detection can affect apparent strength (general IHC practice).
Predominantly cytoplasmic or membranous staining, with little nuclear signal.	That compartment conflicts with HPA’s nuclear tissue profile and approved nucleoplasmic ICC-IF localization; UniProt records no transmembrane segment (HPA tissue IHC; HPA subcellular; UniProt Q96AY2). Review controls and detection background before assigning it to EME1 (general IHC practice).
Strong staining confined to a cell population outside the HPA examples.	HPA describes ubiquitous nuclear expression and supplies no negative cell population here, so cell identity alone cannot establish cross-reactivity (HPA tissue IHC). A nonnuclear pattern, staining in a negative reagent control, or poor antibody agreement would strengthen concern for nonspecific signal (general IHC practice).
Diffuse color over nuclei, cytoplasm, and surrounding tissue.	Diffuse staining obscures the expected nuclear pattern (HPA tissue IHC). Possible causes include inadequate blocking, excess detection signal, or endogenous enzyme activity; compare a primary-omission control and adjust the relevant step (general chromogenic IHC practice).
No nuclear signal in a section containing a listed high-staining cell population.	Adipocytes and bone marrow hematopoietic cells are reported High by HPA, so their absence of signal warrants a run-level check (HPA tissue IHC). Check tissue preservation, primary and detection controls, and the documented IHC conditions; HPA does not establish an EME1-specific fixation effect (general IHC practice; HPA tissue IHC scope).

💡Expected EME1 appearanceCall a result positive when staining is predominantly nuclear in identifiable cells, with clear High signal possible in HPA-listed adipocytes or bone marrow hematopoietic cells; dominant cytoplasmic or membranous color is suspect (HPA tissue IHC; HPA subcellular; UniProt Q96AY2).

How each factor affects the staining
Compartment and cell context	HPA reports ubiquitous nuclear tissue staining, while UniProt lists nucleus and nucleolus; the approved ICC-IF location is nucleoplasm (HPA tissue IHC; UniProt Q96AY2; HPA subcellular). These sources support a nuclear call, without requiring every nucleus to stain equally.
Strength of tissue evidence	HPA labels the IHC evidence Supported while noting low consistency between antibody staining and RNA expression and pending external verification (HPA tissue IHC). Treat listed High cells as useful comparisons, not proof that every positive mark is specific.
Antibody and application validation	The listed mouse monoclonal CAB016127 has Supported IHC status; ICC status is not supplied for it (HPA antibodies). HPA023854 has Approved ICC status but no listed IHC status, so its ICC result does not validate an IHC pattern (HPA antibodies).
Isoforms and modifications	UniProt lists 2 isoforms and modified residues, including phosphoserines, but the payload gives no antibody epitope or isoform coverage (UniProt Q96AY2). Neither a staining difference nor an epitope-specific explanation can be assigned from those annotations alone.
Detection chemistry	In chromogenic IHC, endogenous enzyme activity and nonspecific detection binding can create color independent of primary-antibody binding (general IHC practice). Use appropriate blocking and a primary-omission control when background makes nuclear scoring uncertain (general IHC practice).

Why is my staining missing, weak or wrong?
Situation	Likely cause	Next action
Expected nuclei are unstained across the section.	Target-specific fixation effects are not established by the supplied assay evidence. Verify with a matched IHC source before attributing a result to fixation.	Check a section containing HPA-listed High cells, primary and detection steps, and the antibody’s documented IHC conditions before interpreting a negative result (HPA tissue IHC; general IHC practice).
Signal appears mainly outside nuclei.	This differs from the nuclear tissue profile and approved nucleoplasmic ICC-IF location (HPA tissue IHC; HPA subcellular). Nonspecific binding or background is possible (general IHC practice).	Compare primary-omission and tissue controls, then score only a reproducible nuclear pattern supported by the control results (general IHC practice).
Brown precipitate or diffuse color masks cell boundaries.	Excess detection signal or endogenous enzyme activity can obscure localization in chromogenic IHC (general IHC practice).	Inspect a primary-omission control; optimize detection exposure and the relevant endogenous-activity block, then reassess nuclear staining (general IHC practice).
A listed high-staining population looks weak.	Apparent intensity can vary with section quality and staining conditions; HPA’s High label does not establish a fixed signal threshold for this run (general IHC practice; HPA tissue IHC).	Compare matched sections and run controls under the same conditions. Record whether nuclei remain distinguishable before changing the staining conditions (general IHC practice).
Two antibodies give different IHC patterns.	HPA supplies Supported IHC status for CAB016127, while the other listed antibodies have no IHC status in this payload (HPA antibodies). Their application evidence is therefore unequal.	Check each antibody’s IHC validation and controls separately; do not treat Approved ICC status as IHC confirmation (HPA antibodies; general IHC practice).
An IF image seems to conflict with the chromogenic IHC result.	HPA’s approved ICC-IF localization is nucleoplasm, but application and antibody validation differ: HPA023854 is Approved for ICC and CAB016127 is Supported for IHC (HPA subcellular; HPA antibodies).	Use the IF result as a compartment comparison, then resolve the IHC result with its own antibody validation and controls; keep IF setup decisions in the separate IF/ICC guide (HPA antibodies; general IHC practice).

Source: UniProt Q96AY2 Human Protein Atlas tissue Human Protein Atlas subcellular

Experiment evidence

IHC & IF images showing EME1 staining

IHC analysis of EME1 using anti-EME1 antibody (PB9804). EME1 was detected in paraffin-embedded section of Human Lung Cancer Tissue. 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-EME1 Antibody (PB9804) 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.

PB9804 · IHCIHC analysis of EME1 using anti-EME1 antibody (PB9804). EME1 was detected in paraffin-embedded section of Human Lung Cancer Tissue. Heat med

IHC analysis of EME1 using anti-EME1 antibody (PB9804). EME1 was detected in paraffin-embedded section of Rat Intestine Tissue. 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-EME1 Antibody (PB9804) 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.

PB9804 · IHCIHC analysis of EME1 using anti-EME1 antibody (PB9804). EME1 was detected in paraffin-embedded section of Rat Intestine Tissue. Heat mediate

HPA · Cerebral cortexHuman Protein Atlas IHC, Cerebral cortex. Source: https://www.proteinatlas.org/ENSG00000154920-EME1/tissue/cerebral+cortex#imid_4099000

HPA · ColonHuman Protein Atlas IHC, Colon. Source: https://www.proteinatlas.org/ENSG00000154920-EME1/tissue/colon#imid_4098926

HPA · LiverHuman Protein Atlas IHC, Liver. Source: https://www.proteinatlas.org/ENSG00000154920-EME1/tissue/liver#imid_4098911

HPA · KidneyHuman Protein Atlas IHC, Kidney. Source: https://www.proteinatlas.org/ENSG00000154920-EME1/tissue/kidney#imid_4098920

HPA · ICC-IF HAP1Human Protein Atlas immunofluorescence, HAP1, antibody HPA021202; green = EME1, blue = nucleus, red = microtubules.

← swipe / scroll for more images →

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

Sample controls for EME1 IHC & IF

🧪Run bone marrow first and score nuclear staining in hematopoietic cells (High; HPA: bone marrow). HPA detects EME1 in all 45 scored tissues, so there is no validated negative tissue; no-primary and isotype controls carry the negative comparison, while cells without nuclear staining on the positive slide should remain at background and cannot be designated true internal negatives from these data (HPA: no negative rows; HPA: EME1 detected in all 45 scored tissues).

Positive control tissue: Adipose tissue (Adipocytes, HPA High)

Negative control tissue: None in HPA: EME1 is detected in all 45 scored tissues. Use a no-primary (secondary-only) and an isotype control instead.

ICC-IF cell lines (HPA subcellular resource): HPA ICC-IF images show EME1 in HAP1, Rh30, U2OS, with annotated localisation: Nucleoplasm (approved) (HPA subcellular).

Technical controls: Include a no-primary, secondary-only slide, a species- and format-matched rabbit IgG control, and EME1-knockout material as a biological negative (PB9804 tissue-IHC caption: rabbit primary; standard IHC control practice). Quench endogenous peroxidase in bone marrow, and check for endogenous biotin background if using the caption’s streptavidin–biotin detection (HPA: bone marrow hematopoietic cells; PB9804 tissue-IHC caption: SABC with DAB).

⚠️Feasibility: A target-specific fixation window or fixation effect is unreported, and the selected PB9804 paraffin-section caption does not state the fixative (PB9804 tissue-IHC caption: fixative unreported). That caption uses heat retrieval in citrate buffer at pH 6 for 20 minutes; it supports starting with retrieval but does not establish that EME1 staining depends on it (PB9804 tissue-IHC caption). HPA reports nucleoplasmic ICC-IF images in HAP1, Rh30 and U2OS, but the supplied evidence does not show that IF or frozen sections are easier than paraffin IHC; in bone marrow, endogenous peroxidase in myeloid cells can mimic DAB signal (HPA: subcellular ICC-IF; HPA: bone marrow hematopoietic cells; standard IHC practice).

HPA tissue IHC evidence for EME1

Comprehensive Human Protein Atlas IHC scoring per tissue (reliability: Supported — Low consistency between antibody staining and RNA expression data. 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

Tissue	Cell type	Level	Evidence	Source
Adipose tissue	Adipocytes	High	Protein (IHC)	HPA →
Adrenal gland	Glandular cells	High	Protein (IHC)	HPA →
Appendix	Lymphoid tissue	High	Protein (IHC)	HPA →
Bone marrow	Hematopoietic cells	High	Protein (IHC)	HPA →
Breast	Glandular cells	High	Protein (IHC)	HPA →

Undetected expression · recommended negative controls

Tissue	Cell type	Level	Evidence	Source
None in HPA: EME1 is detected in all 45 scored tissues. Use a no-primary (secondary-only) and an isotype control instead.

Section 3

Advanced EME1 IHC Tips

Troubleshoot EME1 staining in paraffin sections by checking retrieval, nuclear localisation, processing controls and the reliability of tissue-level evidence.

What retrieval conditions should I try when EME1 staining is weak in paraffin sections?

Start with heat-mediated citrate retrieval at pH 6 (datasheet PB9804). The selected paraffin-section image used 20 minutes of this retrieval before detecting EME1 in human lung cancer tissue (caption PB9804). If nuclear staining is weak, compare retrieval duration on adjacent sections while keeping antibody concentration, detection and imaging conditions fixed (standard IHC practice). Include a matched section with the primary antibody omitted to check whether stronger retrieval also raises background (standard IHC practice). Record nuclear signal and tissue damage together, since apparent signal gains are unhelpful if morphology becomes difficult to score (standard IHC practice).

Could fixation explain weak EME1 staining in my paraffin sections?

Target-specific fixation sensitivity is unknown: the selected paraffin-section caption does not state its fixative, and the supplied evidence does not establish an EME1 fixation requirement (caption PB9804). Compare sections with documented fixation and processing histories before changing the antibody concentration or detection system (standard IHC practice). Keep section thickness, citrate pH 6 retrieval and staining batches matched when assessing a suspected fixation effect (datasheet PB9804; standard IHC practice). Evaluate nuclear signal alongside morphology and a primary-omission control (UniProt Q96AY2 localisation; standard IHC practice). Do not attribute a difference to fixation unless the comparison isolates that variable (standard IHC practice).

Where should convincing EME1 staining appear, and how should I assess cytoplasmic colour?

Expect predominantly nuclear staining: EME1 is annotated in the nucleus and nucleolus, and the subcellular profile identifies the nucleoplasm as its main location (UniProt Q96AY2 localisation; HPA subcellular). EME1 can be recruited to DNA-damage regions in S-phase cells, so nuclear intensity need not be uniform across cells (UniProt Q96AY2 localisation). Assess cytoplasmic colour against a primary-omission section and the local background before treating it as EME1 signal (standard IHC practice). Because EME1 has no annotated transmembrane segment, a crisp membrane-only pattern warrants a specificity check (UniProt Q96AY2 topology). Score nuclei separately from cytoplasm and document the compartment used (standard IHC practice).

Could isoforms or phosphorylation explain different EME1 staining patterns between samples?

EME1 has 2 annotated isoforms, but the supplied antibody evidence does not identify the recognised epitope or establish isoform-specific detection (UniProt Q96AY2 isoforms; caption PB9804). Several modified residues are annotated, including phosphoserines at positions 12, 15 and 84 (UniProt Q96AY2 modified residues). Do not assign a staining difference to an isoform or phosphorylation without epitope information and a suitable independent comparison (standard IHC practice). First check whether the same retrieval, primary concentration, detection exposure and scoring threshold were used across sections (standard IHC practice). Report unresolved differences as staining differences rather than molecular identities (standard IHC practice).

How can I check an EME1 pattern by IF without treating it as an IHC protocol?

Use IF as a separate validation experiment and compare its nuclear pattern with the chromogenic section result (UniProt Q96AY2 localisation; standard IF practice). Multiplex EME1 with a marker that identifies the cell population being assessed, and include single-label controls for spectral bleed-through (standard IF practice). Select fluorophores after checking tissue autofluorescence in the intended channels, especially where endogenous fluorescence could obscure a weak nuclear signal (standard IF practice). Optimise permeabilisation for access to EME1 on the nuclear side of cellular membranes, since EME1 has no annotated transmembrane segment (UniProt Q96AY2 topology; standard IF practice). Keep IF fixation and staining conditions distinct from the paraffin-section caption, which reports no fixative (caption PB9804).

How do I reduce diffuse DAB or nuclear background without losing EME1 signal?

Check a primary-omission section to separate antibody-associated colour from background produced by the detection system (standard IHC practice). The selected image used 10% goat-serum blocking, 1 μg/ml primary antibody overnight at 4°C, and biotin-based DAB detection (caption PB9804). For a peroxidase-based workflow, assess endogenous peroxidase blocking and any background from the chosen detection chemistry before changing retrieval (standard IHC practice). Titrate primary antibody and compare wash conditions on matched sections if the control is clean but staining remains diffuse (standard IHC practice). Preserve a readable nuclear signal, the expected dominant compartment, when judging the adjustment (UniProt Q96AY2 localisation).

How should I quantify EME1 IHC when nuclear intensity varies across a section? ⚠ ANSWER MARKED FOR VERIFICATION

Define the sampled regions and exclude folds, damaged edges and necrotic areas before scoring (standard IHC practice). Because EME1 is predominantly nuclear, score the percentage of positive nuclei and nuclear intensity separately, or combine them as an H-score using a prespecified threshold (UniProt Q96AY2 localisation; standard IHC practice). Normalise positive-cell counts to all evaluable nuclei in the same compartment, or report positive nuclei per mm² with the sampled area stated (standard IHC practice). Keep retrieval, detection and image-acquisition settings consistent across compared sections (standard IHC practice). Report cell populations separately when composition differs, since a section-wide average can reflect cellular mix (standard IHC practice).

What evidence helps distinguish true EME1 staining from artefact in tissue IHC?

Give most weight to reproducible nuclear staining with preserved morphology, consistent with EME1's nuclear annotation and nucleoplasmic subcellular profile (UniProt Q96AY2 localisation; HPA subcellular). Treat membrane-only colour, edge-concentrated staining, necrotic regions or signal reproduced in a primary-omission control as reasons to investigate artefact (UniProt Q96AY2 topology; standard IHC practice). Cell identity alone is a weak specificity test because the HPA tissue profile describes ubiquitous nuclear expression (HPA tissue IHC). Check endogenous enzyme or detection-system background when DAB colour appears independently of the primary antibody (standard IHC practice). Interpret tissue differences cautiously: the HPA tissue assessment reports low consistency between staining and RNA data, pending external verification (HPA tissue IHC).

Boster reagents

Best EME1 / Structure-specific endonuclease subunit EME1 IHC Antibodies

PB9804 has real EME1 IHC images from human lung cancer and rat intestine paraffin sections (catalog IHC captions); ICC is listed, but no IF image is supplied (catalog applications and images).

Real IHC data

Anti-EME1 Antibody ®

Cat # PB9804

View product →

PB9804 was demonstrated on human lung cancer and rat intestine paraffin sections (catalog IHC captions). PB9804 lists IHC, IHC-F and ICC applications and human and rat reactivity; no IF image is supplied (catalog applications, reactivity and images).

Which to pick: Choose PB9804 for paraffin-section IHC: its images show citrate retrieval and chromogenic detection in human lung cancer and rat intestine sections (catalog IHC captions). For IF/ICC, PB9804 lists ICC, but no IF image is supplied (catalog applications and images). It is also the listed human-and-rat option (catalog reactivity); the IHC captions do not report the fixative (catalog IHC captions).

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

References

UniProt Consortium. UniProt entry Q96AY2 (EME1_HUMAN, Structure-specific endonuclease subunit EME1).
Human Protein Atlas. EME1 tissue IHC expression (reliability: Supported).
Human Protein Atlas. EME1 subcellular location (ICC-IF): Mainly localized to the nucleoplasm..
Human Protein Atlas. EME1 antibody validation summary (3 antibodies).
Gastroesophageal junction adenocarcinoma displays abnormalities in homologous recombination and nucleotide excision repair. Lung Cancer (Auckland, N.Z.) 2014 — PMC5217507.
LncRNA-EME1 enhances BRCA1 recruitment and alters repair of DNA damage in cervical cancer radioresistance. Non-coding RNA research 2026 — PMC12528910.
Essential meiotic structure-specific endonuclease1 (EME1) promotes malignant features in gastric cancer cells via the Akt/GSK3B/CCND1 pathway. Bioengineered 2021 — PMC8810030.
Comprehensive analysis to identify a novel PTEN-associated ceRNA regulatory network as a prognostic biomarker for lung adenocarcinoma. Frontiers in oncology 2022 — PMC9449356.
PubMed PMID:14702039 — UniProt-cited evidence.
PubMed PMID:15489334 — UniProt-cited evidence.
PubMed PMID:12686547 — UniProt-cited evidence.