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SNRPA / U1 small nuclear ribonucleoprotein A · IHC design guide
Design Immunohistochemistry for SNRPA
Plan SNRPA paraffin-section IHC around the broad nuclear staining reported in tissues (HPA tissue IHC). Use the IHC-validated antibody’s documented conditions and compare staining across samples with consistent fixation.
Evidence assembled Oct 2026 · For research use; verify linked source records and product datasheet before use
SNRPA 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 across tissues (HPA tissue IHC) | |
| Staining pattern | Broad nuclear staining across tissue cell types (HPA tissue IHC) | |
| Antigen retrieval | EDTA pH 8.0 HIER, heat-mediated (datasheet A08780-2) | |
| Positive control | Caudate+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 paraffin-section fixation consistent across samples. (standard IHC practice; not target-specific) | |
| Caveat | Vaginal squamous cells show low staining (HPA tissue IHC) | |
| Regulation | Low tissue specificity (HPA tissue RNA) | |
| Isoform / epitope | 0 isoforms annotated; chain spans residues 2–282 (UniProt) |
Section 1
Recommended SNRPA IHC & IF Protocols
The catalog antibody protocol uses EDTA pH 8.0 heat retrieval (datasheet A08780-2). The published SNRPA IHC protocols below provide tissue preparation, staining, and detection details where reported (cited PMC methods).
| Sample | Paraffin-embedded human appendix adenocarcinoma tissue; fixative not specified (datasheet A08780-2) |
| Fixation | Image fixative and duration unreported (datasheet A08780-2); verify before use. |
| Sectioning | 4–5 µm sections on charged slides (standard) |
| Deparaffinisation | Xylene, graded ethanol series to water (standard) |
| Antigen retrieval | Heat retrieval: EDTA pH 8.0 (datasheet A08780-2); 20 min, 95–100 °C (standard) |
| Peroxidase block | 3% H2O2, 10 min, room temperature (standard) |
| Blocking | 10% goat serum (datasheet A08780-2) |
| Primary antibody | Rabbit anti-SNRPA, 2-5 μg/ml (datasheet A08780-2) |
| Primary incubation | Overnight at 4 °C (datasheet A08780-2) |
| Detection | HRP-conjugated secondary, DAB chromogen (datasheet A08780-2) |
| Counterstain | Hematoxylin, blue, dehydrate and mount (standard) |
| Expected result | SNRPA-positive staining in neuronal cells of caudate (HPA tissue IHC: High). HPA tissue profile: Ubiquitous nuclear expression. No signal in the no-primary control. |
💡Decision noteStart with EDTA pH 8.0 heat retrieval for the catalog antibody (datasheet A08780-2); the published protocols report citrate or Tris/EDTA retrieval for their own antibodies (PMC12102793; PMC9290672).
Section 2
What Is the Expected SNRPA Staining Pattern?
SNRPA should stain nuclei, consistent with its nuclear localisation and lack of a transmembrane segment (UniProt P09012: subcellular location and topology). HPA describes ubiquitous nuclear expression with Supported tissue IHC reliability, meaning high consistency between antibody staining and RNA expression (HPA tissue IHC). Expect nuclear staining across many cell types, with particularly high staining in the specific cells listed by HPA; intensity need not be uniform across tissues (HPA tissue IHC).
| Distinct nuclear chromogen in kidney tubular cells, with nuclei distinguishable from surrounding cytoplasm. | This fits the expected compartment and a documented high staining cell population (UniProt P09012: nucleus; HPA tissue IHC: High in kidney tubular cells). Judge the pattern in identifiable cells, rather than treating all brown tissue as positive. |
| Predominantly cytoplasmic, membranous, or extracellular colour with little nuclear staining. | That distribution conflicts with the reported nuclear location and absence of a transmembrane segment (UniProt P09012: location and topology). Treat it as a suspect IHC pattern and assess background, detection, and tissue morphology before assigning it to SNRPA. |
| Strong colour in an unexpected cell population while the documented cells lack clear nuclear staining. | The mismatch warrants checking antibody cross-reactivity or endogenous detection activity (general IHC practice). HPA reports ubiquitous nuclear expression, so an unlisted cell type alone does not prove a false positive; compare compartment and local cell identity together (HPA tissue IHC). |
| Diffuse colour over nuclei, cytoplasm, and tissue spaces, without crisp cell boundaries. | The distribution is difficult to score as specific nuclear staining (UniProt P09012: nucleus). Diffuse signal can reflect nonspecific binding or detection background; inspect controls and chromogen development before interpreting intensity (general IHC practice). |
| No nuclear signal in an adequately preserved kidney section containing identifiable tubular cells. | This is discordant with HPA's high tubular cell staining (HPA tissue IHC: Kidney, Cells in tubules, High). First check section quality and assay controls; the supplied sources do not establish a SNRPA specific fixation or retrieval failure. |
💡Expected SNRPA appearanceCall a result positive when identifiable cells show predominantly nuclear chromogen, including strong staining in an HPA high population such as kidney tubular cells (UniProt P09012: nucleus; HPA tissue IHC: Kidney, High); isolated cytoplasmic or diffuse colour is suspect (general IHC practice).
| Compartment used for scoring | Score nuclei: UniProt places SNRPA in the nucleus, and HPA reports supported nucleoplasmic localisation by ICC-IF (UniProt P09012: location; HPA subcellular). Cytoplasmic colour alone does not match either observation. |
| Cell and tissue choice | HPA reports high staining in kidney tubular cells, lung alveolar type I cells, and several listed brain cell populations, but low staining in vaginal squamous epithelial cells (HPA tissue IHC). Use the documented cell population when comparing sections. |
| Strength of tissue evidence | The tissue IHC profile has Supported reliability and low RNA tissue specificity (HPA tissue IHC). These support a broadly nuclear expectation, while the listed High and Low observations remain cell specific rather than universal intensity standards. |
| Antibody evidence by application | HPA lists IHC as Supported for HPA046440 and CAB004652; HPA054834 has ICC Supported without an IHC status (HPA antibodies). Apply an antibody's stated evidence to its own application; the supplied record gives no catalog dilution or IHC protocol. |
| IF/ICC: what localisation should appear? | Expect nucleoplasmic fluorescence: HPA reports supported nucleoplasmic localisation and images in A-431, U-251MG, and U2OS cells (HPA subcellular). This is an interpretation reference for IF/ICC, not an IHC protocol or a claim of equal antibody performance. |
| Target specific preparation sensitivity | No target specific fixation or antigen retrieval effect is supplied (UniProt P09012; HPA tissue IHC). Select and assess retrieval through the IHC assay's controls (general IHC practice); do not infer fixation sensitivity from topology, modifications, or tissue staining level. |
| Situation | Likely cause | Next action |
|---|---|---|
| Kidney tubular nuclei show no chromogen. | The result conflicts with a documented high staining population (HPA tissue IHC: Kidney, Cells in tubules, High); the cause cannot be assigned from this record. | Confirm tubules and preserved nuclei, then inspect positive control performance, antibody application, detection reagents, and retrieval conditions (general IHC practice). Do not assume a SNRPA specific fixation effect. |
| Colour is mainly cytoplasmic or membranous. | The compartment conflicts with nuclear SNRPA and its lack of a transmembrane segment (UniProt P09012: location and topology); background or cross-reactivity is possible (general IHC practice). | Compare a reagent control and an HPA documented positive cell population; score only convincing nuclear signal, then reassess blocking and detection background (HPA tissue IHC; general IHC practice). |
| The whole section is diffusely brown. | Diffuse colour obscures the nuclear pattern expected for SNRPA (UniProt P09012: nucleus). Nonspecific binding, endogenous detection activity, or excessive chromogen development can cause broad colour (general IHC practice). | Inspect the reagent control, check endogenous activity blocking appropriate to the detection chemistry, and review antibody concentration and chromogen development (general IHC practice). |
| An unexpected cell population stains strongly. | Cross-reactivity or endogenous detection activity is possible (general IHC practice), but HPA's ubiquitous nuclear profile means cell identity alone cannot establish an artefact (HPA tissue IHC). | Verify cell identity and nuclear localisation; compare documented high staining cells and reagent controls before rejecting the result (HPA tissue IHC; general IHC practice). |
| A vaginal squamous epithelial sample looks weak beside kidney tubules. | HPA reports low staining in vaginal squamous epithelial cells and high staining in kidney tubular cells (HPA tissue IHC). That difference can be consistent with the reported profile. | Assess each cell population against its own expected level and confirm that the kidney control stains nuclei; avoid calling the lower level a technical failure solely from this comparison (HPA tissue IHC). |
| Two antibody results disagree, or ICC images appear clearer than the IHC section. | HPA records application specific statuses: two antibodies have IHC Supported, while HPA054834 has ICC Supported without an IHC status (HPA antibodies). Different application evidence does not resolve an IHC discrepancy. | Check the exact antibody identity and IHC validation status, then compare nuclear patterns using the same tissue and appropriate assay controls (HPA antibodies; general IHC practice). |
Experiment evidence
IHC & IF images showing SNRPA staining
A08780-2 · IHCIHC analysis of U1A/SNRPA using anti-U1A/SNRPA antibody (A08780-2). U1A/SNRPA was detected in a paraffin-embedded section of human appendix
A08780-2 · IHCIHC analysis of U1A/SNRPA using anti-U1A/SNRPA antibody (A08780-2). U1A/SNRPA was detected in a paraffin-embedded section of human breast ca
A08780-2 · IFIF analysis of U1A/SNRPA and Tubulin beta using anti-U1A/SNRPA antibody (A08780-2) and anti-Tubulin beta antibody (M05613-4). U1A/SNRPA and
HPA · Cerebral cortexHuman Protein Atlas IHC, Cerebral cortex. Source: https://www.proteinatlas.org/ENSG00000077312-SNRPA/tissue/cerebral+cortex#imid_16711011
HPA · ColonHuman Protein Atlas IHC, Colon. Source: https://www.proteinatlas.org/ENSG00000077312-SNRPA/tissue/colon#imid_16710953
HPA · LiverHuman Protein Atlas IHC, Liver. Source: https://www.proteinatlas.org/ENSG00000077312-SNRPA/tissue/liver#imid_16710938
HPA · KidneyHuman Protein Atlas IHC, Kidney. Source: https://www.proteinatlas.org/ENSG00000077312-SNRPA/tissue/kidney#imid_16710947
HPA · ICC-IF A-431Human Protein Atlas immunofluorescence, A-431, antibody CAB004652; green = SNRPA, blue = nucleus, red = microtubules.
HPA · ICC-IF A-431Human Protein Atlas immunofluorescence, A-431, antibody CAB004652; green = SNRPA, blue = nucleus, red = microtubules.
← swipe / scroll for more images →
Real IHC / IF data behind the staining-pattern expectations in this section.
Sample controls for SNRPA IHC & IF
🧪Run kidney first and assess nuclear staining in tubular cells (HPA: High in kidney tubular cells; UniProt P09012: nucleus). HPA detects SNRPA in all 45 scored tissues, so use no-primary and isotype controls instead of a negative tissue; no cell type on the kidney slide is established as antigen-negative, and unstained nuclei should be recorded without treating them as an internal negative (HPA: no negative rows).
Positive control tissue: Caudate (Neuronal cells, HPA High)
Negative control tissue: None in HPA: SNRPA 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 SNRPA in A-431, U-251MG, U2OS, with annotated localisation: Nucleoplasm (supported) (HPA subcellular).
Technical controls: Include a no-primary, secondary-only slide and a concentration-matched nonimmune rabbit IgG control, since the catalog primary is rabbit IgG (selected A08780-2 caption: rabbit antibody). If available, compare a matched SNRPA knockout sample as a biological negative; for kidney sections, block endogenous peroxidase before HRP/DAB detection and assess endogenous biotin if using biotin-based detection (standard IHC practice; selected A08780-2 caption: HRP/DAB).
⚠️Feasibility: A target-specific fixation window or fixation effect is unreported, and the selected A08780-2 paraffin-section caption does not state the fixative (selected A08780-2 caption). That caption uses heat retrieval in EDTA at pH 8.0, a starting condition for IHC rather than proof that retrieval is required (selected A08780-2 caption). Whether frozen sections or IF are easier is unreported; IF/ICC images show nucleoplasmic localization in A-431, U-251MG and U2OS (HPA subcellular), while kidney sections warrant checks for endogenous peroxidase and biotin background in chromogenic IHC (standard IHC practice).
HPA tissue IHC evidence for SNRPA
Comprehensive Human Protein Atlas IHC scoring per tissue (reliability: Supported — High 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 |
|---|---|---|---|---|
| Caudate | Neuronal cells | High | Protein (IHC) | HPA → |
| Cerebellum | Cells in molecular layer | High | Protein (IHC) | HPA → |
| Cerebral cortex | Glial cells | High | Protein (IHC) | HPA → |
| Hippocampus | Glial cells | High | Protein (IHC) | HPA → |
| Kidney | Cells in tubules | High | Protein (IHC) | HPA → |
Undetected expression · recommended negative controls
| Tissue | Cell type | Level | Evidence | Source |
|---|---|---|---|---|
| None in HPA: SNRPA is detected in all 45 scored tissues. Use a no-primary (secondary-only) and an isotype control instead. | ||||
Section 3
Advanced SNRPA IHC Tips
Use nuclear localisation and matched tissue controls to troubleshoot SNRPA staining in paraffin sections (UniProt P09012; HPA: ubiquitous nuclear expression).
What should I change when nuclear SNRPA staining is weak after retrieval?
Start with heat-mediated retrieval in EDTA at pH 8.0 for paraffin sections (datasheet A08780-2). The selected image used this retrieval, followed by 10% goat serum blocking and 2 μg/ml primary antibody overnight at 4°C (datasheet A08780-2). If nuclear signal remains weak, check that sections reached the intended retrieval temperature and compare a controlled change in heating time while keeping detection conditions constant (standard IHC practice). Interpret any gain against nuclear staining in a reference section, since SNRPA is nuclear and the tissue profile is broadly nuclear (UniProt P09012; HPA: ubiquitous nuclear expression).
Could fixation explain absent SNRPA staining in my paraffin sections?
Target-specific fixation sensitivity is unknown: the selected paraffin-section caption does not state a fixative (datasheet A08780-2). Record the specimen's actual fixation history and compare sections processed together before attributing a failed stain to fixation (standard IHC practice). Run the documented EDTA pH 8.0 retrieval and 2 μg/ml primary incubation overnight at 4°C on a reference section from the same processing batch (datasheet A08780-2). If the reference stains but the test section does not, assess tissue preservation and processing records; nuclear staining is the expected compartment, but it does not establish fixation sensitivity (UniProt P09012; standard IHC practice).
How should I assess cytoplasmic staining when SNRPA is expected in nuclei?
Prioritise staining within intact nuclei because SNRPA is nuclear and the supported subcellular location is the nucleoplasm (UniProt P09012; HPA: nucleoplasm, supported). Assess chromogen against a nuclear counterstain and examine whether the apparent cytoplasmic signal surrounds stained nuclei or also appears in cell-free areas (standard IHC practice). SNRPA has no transmembrane segment, so membrane outlining is not an expected localisation pattern (UniProt P09012 topology). If cytoplasmic or membrane staining dominates, inspect blocking, secondary-only controls and section morphology before scoring; the selected paraffin image establishes a staining method, not evidence for another compartment (datasheet A08780-2; standard IHC practice).
Could epitope access or modification alter the SNRPA staining pattern?
The supplied record lists 0 isoforms and places SNRPA's RNA recognition motifs at residues 10–89 and 208–282 (UniProt P09012). It also lists modified residues, including phosphothreonine 131 and methylarginine 152, but the catalog antibody's epitope is not specified (UniProt P09012; datasheet A08780-2). Do not assign a staining difference to an isoform or modification without epitope-mapping evidence; compare retrieval and antibody incubation under otherwise matched conditions (standard IHC practice). If signal changes, confirm that the improvement remains nuclear and reproducible in a reference section, rather than treating stronger DAB deposition alone as specificity (UniProt P09012; standard IHC practice).
How can IF help assess a puzzling SNRPA IHC localisation pattern?
On the separate IF/ICC workflow, assess SNRPA within nuclei using a nuclear counterstain; nucleoplasmic localisation is supported independently (HPA: nucleoplasm, supported). Multiplex with a marker identifying the cell population under study and keep channels separable, so cell identity and nuclear signal can be assessed together (standard IF practice). Choose a fluorophore channel after checking tissue autofluorescence and include single-channel controls when evaluating bleed-through (standard IF practice). Because SNRPA has no transmembrane segment and is nuclear, permeabilisation must permit antibody access to the nuclear compartment; optimise that step for the IF specimen and antibody (UniProt P09012 topology; standard IF practice).
What should I check when DAB obscures nuclear SNRPA staining?
Compare stained sections with a primary-omission control to identify deposition from the detection system, and inspect unstained tissue for pigment (standard IHC practice). The selected paraffin-section workflow used 10% goat serum blocking, a peroxidase-conjugated secondary incubated for 30 minutes at 37°C, and DAB development (datasheet A08780-2). Include a peroxidase-blocking step and control DAB development time as general chromogenic IHC measures, especially if diffuse brown signal masks nuclei (standard IHC practice). Reassess specificity by asking whether staining resolves to intact nuclei; supported SNRPA localisation is nucleoplasmic (HPA: nucleoplasm, supported).
How should I quantify SNRPA staining across paraffin sections? ⚠ ANSWER MARKED FOR VERIFICATION
Define the tissue region and eligible cells before scoring, then record the percentage of nuclei positive for SNRPA and a nuclear intensity score (standard IHC practice). An H-score can combine the percentage at each intensity level, whereas positive nuclei per mm² is useful when cell density varies; state which measure you used (standard IHC practice). Normalise counts to the number of eligible, intact nuclei or sampled tissue area, and use matched retrieval, chromogen development and counterstaining across sections (standard IHC practice). Report cell populations separately when morphology permits, because HPA describes broadly nuclear expression rather than a single exclusive positive population (HPA: ubiquitous nuclear expression).
How do I distinguish genuine SNRPA signal from staining artefacts?
A credible positive pattern is nuclear in intact cells, consistent with SNRPA's nuclear annotation and supported nucleoplasmic localisation (UniProt P09012; HPA: nucleoplasm, supported). Do not require one exclusive positive cell type: HPA reports ubiquitous nuclear expression and low tissue specificity, with staining intensity varying among listed cell populations (HPA: tissue IHC profile). Examine tissue edges, necrotic areas and poorly preserved cells for disproportionate DAB, and compare a primary-omission control to identify detection-system staining (standard IHC practice). Treat dominant membrane or diffuse cell-free staining as suspect, and check the nuclear counterstain and morphology before calling a section positive (UniProt P09012 topology; standard IHC practice).
Boster reagents
Best SNRPA / U1 small nuclear ribonucleoprotein A IHC Antibodies
The catalog antibody has paraffin-section IHC images from human tumors and an IF image from human cells (catalog: A08780-2 image captions); its listed reactivity includes human, mouse, and rat (catalog: A08780-2 reactivity).
Real IHC data
Anti-U1A/SNRPA Antibody ®
Cat # A08780-2
A08780-2 has IHC images from human paraffin sections and IF images from human A549 cells and an intestinal cancer section (catalog: A08780-2 image captions). M08780-1 lists IF/ICC among its applications and human, mouse, and rat reactivity, but provides no IHC or IF image (catalog: M08780-1 applications, reactivity, image captions).
Which to pick: Choose A08780-2 for tissue IHC: it lists IHC for human, mouse, and rat at 2–5 μg/ml (catalog: A08780-2 dilution data), and its own IHC captions document EDTA retrieval at pH 8.0 in human paraffin sections; the fixative is unreported (catalog: A08780-2 IHC image captions). For IF/ICC, A08780-2 has its own IF images and a listed 5 μg/ml concentration (catalog: A08780-2 IF image captions and dilution data); M08780-1 is a rabbit monoclonal, clone 18S46, with listed IF/ICC use at 1:50–1:200 but no supplied IF image (catalog: M08780-1 clone, applications, dilution data, image captions). For mouse or rat tissue IHC, A08780-2 is the listed option, although its supplied IHC images show human sections (catalog: A08780-2 dilution data and IHC image captions).
Each figure is that product's own IHC / IF validation image from its datasheet.
References
- UniProt Consortium. UniProt entry P09012 (SNRPA_HUMAN, U1 small nuclear ribonucleoprotein A).
- Human Protein Atlas. SNRPA tissue IHC expression (reliability: Supported).
- Human Protein Atlas. SNRPA subcellular location (ICC-IF): Localized to the nucleoplasm..
- Human Protein Atlas. SNRPA antibody validation summary (3 antibodies).
- LncRNA CASC19 promotes the growth and glycolysis of colorectal cancer cells and tumor metastasis in mice. BMC cancer 2025 — PMC12053857.
- The novel tRNA-derived fragment, tiRNA-Met, inhibits the malignant progression of triple-negative breast cancer by regulating RANBP3L via a targeted interaction with SNRPA. Cellular & molecular biology letters 2025 — PMC12102793.
- Elevated Small Nuclear Ribonucleoprotein Polypeptide an Expression Correlated With Poor Prognosis and Immune Infiltrates in Patients With Hepatocellular Carcinoma. Frontiers in oncology 2022 — PMC9290672.
- LINC01088 promotes the growth and invasion of glioma cells through regulating small nuclear ribonucleoprotein polypeptide A transcription. Bioengineered 2022 — PMC9162022.
- PubMed PMID:1831431 — UniProt-cited evidence.
- PubMed PMID:2962859 — UniProt-cited evidence.
- PubMed PMID:15489334 — UniProt-cited evidence.
Immunohistochemistry protocol sheet for SNRPA (U1 small nuclear ribonucleoprotein A). Expected localisation Nuclear staining across tissues (HPA tissue IHC). Antigen retrieval: EDTA pH 8.0 HIER, heat-mediated (datasheet A08780-2). Validated IHC antibody: A08780-2 at 2-5 μg/ml (the product's own IHC validation image is shown). Controls (HPA): positive Caudate (Neuronal cells); negative None in HPA (detected in all 45 tissues); use no-primary + isotype controls. IHC-P workflow on paraffin sections; fixative unspecified. Protocol steps: 1. Sample: Paraffin-embedded human appendix adenocarcinoma tissue; fixative not specified (datasheet A08780-2); 2. Fixation: Image fixative and duration unreported (datasheet A08780-2); 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 retrieval: EDTA pH 8.0 (datasheet A08780-2); 20 min, 95–100 °C (standard); 6. Peroxidase block: 3% H2O2, 10 min , room temperature (standard); 7. Blocking: 10% goat serum (datasheet A08780-2); 8. Primary antibody: Rabbit anti-SNRPA, 2-5 μg/ml (datasheet A08780-2); 9. Primary incubation: Overnight at 4 °C (datasheet A08780-2). Watch for: Fixation: Keep paraffin-section fixation consistent across samples. (standard IHC practice; not target-specific); Caveat: Vaginal squamous cells show low staining (HPA tissue IHC); Isoform / epitope: 0 isoforms annotated; chain spans residues 2–282 (UniProt); Regulation: Low tissue specificity (HPA tissue RNA). Evidence: UniProt P09012, HPA tissue IHC · Supported, HPA ICC-IF · nucleoplasm., Datasheet A08780-2, PMC12053857, PMC12102793. QR code links to https://www.bosterbio.com/bosterbio-gene-info-cards/SNRPA/immunohistochemistry-ihc-guide.