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SLIRP / SRA stem-loop-interacting RNA-binding protein, mitochondrial · IHC design guide
Design Immunohistochemistry for SLIRP
Plan chromogenic SLIRP IHC in paraffin sections around the granular cytoplasmic tissue pattern (HPA tissue IHC). Use the catalog antibody at 2–5 μg/ml (datasheet A08297-1) and kidney tubules as a positive staining reference (HPA tissue IHC).
Evidence assembled Oct 2026 · For research use; verify linked source records and product datasheet before use
SLIRP 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 | Granular cytoplasm in tissue (HPA tissue IHC); predominantly mitochondrial, with some nuclear localisation (UniProt) | |
| Staining pattern | Granular cytoplasm; high in kidney tubules and glandular cells (HPA tissue IHC) | |
| Antigen retrieval | EDTA pH 8.0 HIER, heat-mediated (datasheet A08297-1) | |
| Positive control | Adrenal gland+4 more · see all | |
| Negative control | Liver+3 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 and RNA show medium agreement (HPA tissue IHC) | |
| Regulation | No specific regulator reported (UniProt) | |
| Isoform / epitope | 2 isoforms; epitope coverage is unknown (UniProt) |
Section 1
Recommended SLIRP IHC & IF Protocols
The catalog antibody uses heat-mediated EDTA pH 8.0 retrieval (datasheet A08297-1). One published testis IHC protocol provides additional staining details (PMC3744554).
| Sample | Paraffin-embedded human colon cancer tissue; fixative not specified (datasheet A08297-1) |
| Fixation | Image fixative and duration unreported (datasheet A08297-1); 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 A08297-1); 20 min, 95–100 °C (standard) |
| Peroxidase block | 3% H2O2, 10 min, room temperature (standard) |
| Blocking | 10% goat serum (datasheet A08297-1) |
| Primary antibody | Rabbit anti-SLIRP, 2-5 μg/ml (datasheet A08297-1) |
| Primary incubation | Overnight at 4 °C (datasheet A08297-1) |
| Detection | HRP-conjugated secondary, DAB chromogen (datasheet A08297-1) |
| Counterstain | Hematoxylin, blue, dehydrate and mount (standard) |
| Expected result | SLIRP-positive staining in glandular cells of adrenal gland (HPA tissue IHC: High). HPA tissue profile: General cytoplasmic expression with a granular pattern. No signal in the no-primary control. |
💡Decision noteStart with heat-mediated EDTA pH 8.0 retrieval (datasheet A08297-1); the published testis protocol also used EDTA pH 8.0 (PMC3744554).
Section 2
What Is the Expected SLIRP Staining Pattern?
Expect predominantly granular cytoplasmic SLIRP staining, consistent with its mainly mitochondrial location (HPA tissue IHC: granular cytoplasmic profile; UniProt Q9GZT3: predominantly mitochondrial). Kidney tubular cells, adrenal glandular cells and lymph node germinal center cells are useful high-staining examples (HPA tissue IHC: High). A smaller nuclear fraction is possible (UniProt Q9GZT3: some nuclear localization). Interpret tissue results with caution because antibody staining and RNA expression show medium consistency (HPA tissue IHC: Approved reliability). SLIRP has no transmembrane segment (UniProt Q9GZT3: topology).
| Granular cytoplasmic staining in kidney tubular cells or adrenal glandular cells, with clear cell boundaries. | This fits the reported high staining in these cells and the general granular cytoplasmic profile (HPA tissue IHC: High; granular cytoplasmic). The pattern is compatible with predominantly mitochondrial SLIRP (UniProt Q9GZT3: subcellular location), although chromogenic IHC alone does not prove organelle identity. |
| Strong, exclusively nuclear staining with little granular cytoplasmic signal. | Check specificity before calling this the expected pattern: a nuclear fraction is reported, but SLIRP is predominantly mitochondrial (UniProt Q9GZT3: subcellular location). Mitochondrial localization is supported by ICC-IF (HPA subcellular: supported). Nuclear signal alone therefore needs independent confirmation. |
| Prominent staining in liver cholangiocytes, smooth muscle cells or soft tissue fibroblasts. | These cells were not detected in the supplied tissue survey (HPA tissue IHC: Not detected). Treat unexpected staining as a possible detection artefact or cross-reactivity; check morphology and controls before assigning SLIRP positivity. The survey is a reference pattern, not proof that every specimen must be negative. |
| Broad, even colour over cells, stroma or empty areas, without discernible cytoplasmic granules. | This differs from the reported granular cytoplasmic profile (HPA tissue IHC: general profile). Diffuse deposit can arise from background or endogenous detection activity under standard chromogenic IHC conditions; inspect a no-primary control and the distribution of precipitate before scoring. |
| No staining in a kidney section that contains intact tubular cells. | Kidney tubular cells are reported as High (HPA tissue IHC: kidney). A blank result calls for a technical check before a biological conclusion: confirm tissue preservation and run the IHC-validated antibody with an appropriate positive control (HPA HPA020291: IHC Approved). |
💡Expected SLIRP appearanceCall a positive result when high-staining reference cells show distinct granular cytoplasmic signal (HPA tissue IHC: High; granular cytoplasmic), while diffuse deposit or dominant nuclear-only colour is suspect (UniProt Q9GZT3: predominantly mitochondrial).
| Cellular compartment | Score cytoplasmic granularity first (HPA tissue IHC: general profile). A limited nuclear component can be plausible (UniProt Q9GZT3: some nuclear localization); nuclear-only staining requires a specificity check. |
| Choice of reference cells | Use reported High populations, such as kidney tubular cells or lymph node germinal center cells (HPA tissue IHC: High). Low-staining lung macrophages are a weaker visual reference (HPA tissue IHC: Low). |
| Antibody evidence | The listed antibody HPA020291 is IHC Approved and ICC Supported (HPA antibodies: HPA020291). Tissue staining has medium consistency with RNA expression (HPA tissue IHC: reliability); interpret an unusual pattern with that limit in mind. |
| IF/ICC Q: Where should fluorescence appear? | A: Predominantly at mitochondria (HPA subcellular: Mitochondria, supported; UniProt Q9GZT3: predominantly mitochondrial). This is an interpretation cue; IF/ICC has its own guide. |
| Isoforms and target features | Two isoforms and an RRM spanning residues 19–103 are annotated (UniProt Q9GZT3: isoforms; domain). The supplied evidence does not map the antibody epitope, so isoform coverage and retrieval requirements cannot be inferred. |
| Situation | Likely cause | Next action |
|---|---|---|
| High-staining reference cells have no visible signal. | A run failure is possible when kidney tubular cells remain blank despite their reported High staining (HPA tissue IHC: kidney). The supplied sources do not identify a SLIRP-specific retrieval condition. | For general IHC troubleshooting, verify the positive control, reagent order, primary antibody application, detection reagents and counterstain; then review the assay's documented retrieval conditions before changing them. |
| The whole section has diffuse colour or a coloured edge. | Background staining or pooled reagent is possible under standard chromogenic IHC practice; this appearance lacks the reported granular cytoplasmic profile (HPA tissue IHC: general profile). | Review a no-primary control, washing, blocking and section drying as general IHC checks. Score cells only where morphology and discrete cytoplasmic staining are interpretable. |
| Only nuclei stain strongly. | A nuclear SLIRP fraction is reported, but a nuclear-only pattern conflicts with its predominant mitochondrial localization (UniProt Q9GZT3: subcellular location; HPA subcellular: mitochondria supported). | Compare the same run with a high-staining tissue reference (HPA tissue IHC: kidney tubular cells, High) and review the no-primary control. Seek independent localization evidence before accepting nuclear-only positivity. |
| Liver cholangiocytes or smooth muscle cells look strongly positive. | These populations were Not detected in the tissue survey (HPA tissue IHC: liver cholangiocytes; smooth muscle cells). Cross-reactivity or endogenous detection activity is possible, but the stain alone cannot distinguish them. | Check the no-primary control and tissue morphology, then compare with a reported High cell population on the same run (HPA tissue IHC: kidney tubular cells, High). Report unresolved staining as unexpected. |
| A low-staining population looks negative. | Low reported signal may be hard to distinguish from background in chromogenic IHC (HPA tissue IHC: lung macrophages, Low; salivary glandular cells, Low). A negative visual call there is weaker evidence than a blank High reference. | Confirm assay performance in a reported High population (HPA tissue IHC: adrenal glandular cells, High). Interpret the low population against local background and avoid treating an undetectable signal as proof of absence. |
| Granules are present, but the counterstain makes their cellular location unclear. | The expected profile is granular cytoplasmic (HPA tissue IHC: general profile), so poor separation of colour from morphology limits compartment scoring under standard IHC practice. | For general IHC workflow, inspect a lighter counterstain or detection development on a repeat section. Score only cells in which cytoplasm and nucleus can be separated reliably. |
Experiment evidence
IHC & IF images showing SLIRP staining
A08297-1 · IHCIHC analysis of SLIRP using anti-SLIRP antibody (A08297-1). SLIRP was detected in a paraffin-embedded section of human colon cancer tissue.
A08297-1 · IHCIHC analysis of SLIRP using anti-SLIRP antibody (A08297-1). SLIRP was detected in a paraffin-embedded section of human stomach cancer tissue
A08297-1 · IFIF analysis of SLIRP using anti-SLIRP antibody (A08297-1). SLIRP was detected in an immunocytochemical section of A549 cells. Enzyme antigen
HPA · Cerebral cortexHuman Protein Atlas IHC, Cerebral cortex. Source: https://www.proteinatlas.org/ENSG00000119705-SLIRP/tissue/cerebral+cortex#imid_5327504
HPA · ColonHuman Protein Atlas IHC, Colon. Source: https://www.proteinatlas.org/ENSG00000119705-SLIRP/tissue/colon#imid_5327438
HPA · LiverHuman Protein Atlas IHC, Liver. Source: https://www.proteinatlas.org/ENSG00000119705-SLIRP/tissue/liver#imid_5327423
HPA · KidneyHuman Protein Atlas IHC, Kidney. Source: https://www.proteinatlas.org/ENSG00000119705-SLIRP/tissue/kidney#imid_5327432
HPA · ICC-IF A-431Human Protein Atlas immunofluorescence, A-431, antibody HPA020291; green = SLIRP, blue = nucleus, red = microtubules.
HPA · ICC-IF A-431Human Protein Atlas immunofluorescence, A-431, antibody HPA020291; green = SLIRP, blue = nucleus, red = microtubules.
← swipe / scroll for more images →
Real IHC / IF data behind the staining-pattern expectations in this section.
Sample controls for SLIRP IHC & IF
🧪Run colon first: its glandular cells should stain (HPA: High in colon glandular cells). Use smooth muscle cells as the negative tissue comparison (HPA: Not detected in smooth muscle cells); any independently verified negative cells on the colon slide should show counterstain and background, without specific DAB staining.
Positive control tissue: Adrenal gland (Glandular cells, HPA High)
Negative control tissue: Liver (HPA Not detected)
ICC-IF cell lines (HPA subcellular resource): HPA ICC-IF images show SLIRP in A-431, SiHa, U2OS, Sperm, with annotated localisation: Mitochondria (supported) (HPA subcellular).
Technical controls: Include a no-primary, secondary-only slide; a concentration-matched nonimmune rabbit IgG isotype control matched to the primary antibody’s clonality; and SLIRP-knockout material as a biological negative (selected tissue-IHC caption: rabbit anti-SLIRP antibody). Block endogenous peroxidase before DAB detection and assess nonspecific background in the colon section (selected tissue-IHC caption: HRP/DAB detection).
⚠️Feasibility: Heat-mediated retrieval in EDTA at pH 8.0 was used on a paraffin-embedded colon cancer section (selected tissue-IHC caption); whether SLIRP staining depends on that retrieval condition is unreported. A target-specific fixation window and fixation effect are unreported, and the exact selected-SKU caption does not state the fixative (selected tissue-IHC caption: fixative not stated). HPA supports mitochondrial localization by ICC-IF (HPA subcellular: mitochondria supported), but the supplied evidence does not establish that frozen sections or tissue IF are easier than paraffin IHC; inspect colon sections for luminal debris and uneven DAB background during scoring (standard IHC practice).
HPA tissue IHC evidence for SLIRP
Comprehensive Human Protein Atlas IHC scoring per tissue (reliability: Approved — Medium 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 |
|---|---|---|---|---|
| Adrenal gland | Glandular cells | High | Protein (IHC) | HPA → |
| Appendix | Glandular cells | High | Protein (IHC) | HPA → |
| Cerebral cortex | Neuronal cells | High | Protein (IHC) | HPA → |
| Colon | Glandular cells | High | Protein (IHC) | HPA → |
| Duodenum | Glandular cells | High | Protein (IHC) | HPA → |
Undetected expression · recommended negative controls
| Tissue | Cell type | Level | Evidence | Source |
|---|---|---|---|---|
| Liver | Cholangiocytes | Not detected | Protein (IHC) | HPA → |
| Smooth muscle | Smooth muscle cells | Not detected | Protein (IHC) | HPA → |
| Soft tissue | Fibroblasts | Not detected | Protein (IHC) | HPA → |
| Spleen | Cells in red pulp | Not detected | Protein (IHC) | HPA → |
Section 3
Advanced SLIRP IHC Tips
These answers troubleshoot chromogenic SLIRP IHC in paraffin sections; the immunofluorescence entry addresses the separate IF/ICC application.
Which retrieval condition should I try first for SLIRP IHC?
Start with heat-mediated antigen retrieval in EDTA at pH 8.0 (datasheet A08297-1). The selected antibody detected SLIRP in a paraffin section of human colon cancer after this retrieval, followed by 10% goat serum blocking and 2 μg/ml primary antibody overnight at 4°C (datasheet A08297-1). If staining is weak, compare a carefully controlled alternative retrieval condition on serial sections while keeping antibody concentration and detection constant (general IHC practice). Assess both signal and tissue morphology: stronger diffuse color is unconvincing when the expected granular cytoplasmic pattern is lost (HPA: general cytoplasmic expression with a granular pattern).
Could fixation explain weak or uneven SLIRP staining?
SLIRP-specific fixation sensitivity is unknown: the selected image describes a paraffin section but does not state its fixative (datasheet A08297-1). Record the fixative, fixation duration, tissue thickness, and processing history for each specimen so differences can be assessed alongside staining (general IHC practice). Compare matched sections processed with the same EDTA pH 8.0 retrieval and 2 μg/ml primary antibody conditions before changing several steps together (datasheet A08297-1; general IHC practice). If morphology or staining varies across a section, inspect processing and section integrity before attributing the variation to SLIRP abundance (general IHC practice).
What staining pattern is plausible for SLIRP in tissue sections?
Expect predominantly granular cytoplasmic staining in chromogenic tissue IHC, consistent with the reported tissue pattern and mitochondrial localisation (HPA: general cytoplasmic expression with a granular pattern; UniProt Q9GZT3: predominantly mitochondrial). Assess granules within intact cells, using a nuclear counterstain to distinguish cytoplasmic signal from nuclear color (general IHC practice). A smaller nuclear fraction is biologically plausible because SLIRP can be recruited to nuclear receptor target promoters (UniProt Q9GZT3: nuclear fraction and promoter recruitment). Interpret isolated strong nuclear staining cautiously, especially when cytoplasmic granules are absent, and compare it with controls and adjacent well-preserved cells (HPA: mitochondrial localisation supported; general IHC practice).
Could isoforms or epitope accessibility alter the IHC result?
SLIRP has 2 annotated isoforms and an RNA recognition motif spanning residues 19–103 (UniProt Q9GZT3: isoforms and RRM). The supplied product caption does not identify the recognized epitope or establish whether this antibody detects both isoforms (datasheet A08297-1). Keep EDTA pH 8.0 retrieval and the 2 μg/ml primary condition consistent when comparing specimens, since accessibility can change with tissue processing (datasheet A08297-1; general IHC practice). Annotated phosphorylation at residues 15, 101, and 102 does not, by itself, establish altered antibody binding; resolve unexpected patterns with epitope documentation or an independent antibody when available (UniProt Q9GZT3: modified residues; general IHC practice).
How should I assess SLIRP by multiplex IF/ICC?
For the separate IF/ICC application, pair SLIRP with a mitochondrial marker and, in tissue, a marker identifying the cell population being scored (HPA: mitochondrial localisation supported; general IF practice). Select fluorophores after checking tissue autofluorescence and image single-label controls before interpreting overlap (general IF practice). SLIRP is intracellular and lacks an annotated transmembrane segment, but the supplied record does not define the antibody epitope's membrane-facing side (UniProt Q9GZT3: localisation and topology; datasheet A08297-1). Optimise permeabilisation for antibody access to that epitope, checking whether mitochondrial structure and the expected granular signal remain intact (HPA: mitochondrial localisation supported; general IF practice).
How can I reduce diffuse or granular IHC background?
First compare stained sections with a no-primary control to identify color arising from the detection system or tissue rather than the primary antibody (general IHC practice). The selected workflow used 10% goat serum blocking, 2 μg/ml primary antibody overnight at 4°C, and DAB detection (datasheet A08297-1). If background persists, review washing, blocking, primary concentration, peroxidase blocking, and DAB development one variable at a time (general IHC practice). Preserve the distinction between nonspecific diffuse color and the reported granular cytoplasmic pattern; inspect tissue folds, edges, and damaged regions separately (HPA: tissue staining pattern; general IHC practice).
How should I quantify heterogeneous SLIRP staining? ⚠ ANSWER MARKED FOR VERIFICATION
Define the cell population and region before scoring, then record the percentage of positive cells and an intensity-weighted H-score for chromogenic SLIRP staining (general IHC practice). For spatial comparisons, report positive-cell density per mm² of viable tissue or the proportion of positive cells within the chosen compartment (general IHC practice). Normalise counts to viable tissue area or eligible cell number, and keep retrieval, imaging, color thresholds, and counterstain consistent across sections (general IHC practice). Score granular cytoplasmic and nuclear staining separately because SLIRP is predominantly mitochondrial but can have a nuclear fraction (UniProt Q9GZT3: subcellular localisation).
When is SLIRP staining convincing rather than artefactual?
A convincing result shows granular cytoplasmic staining in intact cells and agrees with controls processed in the same run (HPA: general cytoplasmic expression with a granular pattern; general IHC practice). Colon glandular cells are reported as high-staining, whereas smooth muscle cells are reported as not detected; use cell identity when interpreting neighboring structures (HPA: colon glandular cells high; smooth muscle cells not detected). Treat edge staining, necrotic regions, and color persisting in a no-primary control as potential artefacts, including endogenous peroxidase activity (general IHC practice). Nuclear staining can be plausible, but strong nuclear-only color warrants corroboration because SLIRP is predominantly mitochondrial (UniProt Q9GZT3: subcellular localisation).
Boster reagents
Best SLIRP / SRA stem-loop-interacting RNA-binding protein, mitochondrial IHC Antibodies
A08297-1 has IHC data from human paraffin-embedded colon and stomach cancer sections and IF data from those sections and A549 cells (catalog image captions).
Real IHC data
Anti-SLIRP Antibody ®
Cat # A08297-1
A08297-1 is listed for human IHC, IF and ICC (catalog applications and reactivity). Its IHC captions show human paraffin-embedded colon and stomach cancer sections; its IF captions show those sections and A549 cells (catalog image captions).
Which to pick: Choose A08297-1 for human paraffin-section IHC; its IHC captions document both tissues, while the fixative is unreported (catalog IHC image captions). The same SKU is listed for IF/ICC and has IF images from tissue sections and A549 cells (catalog applications and IF image captions). No cross-species choice is supported because the catalog lists human reactivity only (catalog reactivity).
Each figure is that product's own IHC / IF validation image from its datasheet.
References
- UniProt Consortium. UniProt entry Q9GZT3 (SLIRP_HUMAN, SRA stem-loop-interacting RNA-binding protein, mitochondrial).
- Human Protein Atlas. SLIRP tissue IHC expression (reliability: Approved).
- Human Protein Atlas. SLIRP subcellular location (ICC-IF): Localized to the mitochondria..
- Human Protein Atlas. SLIRP antibody validation summary (1 antibodies).
- Loss of the nuclear receptor corepressor SLIRP compromises male fertility. PloS one 2013 — PMC3744554.
- LRPPRC regulates redox homeostasis via the circANKHD1/FOXM1 axis to enhance bladder urothelial carcinoma tumorigenesis. Redox biology 2021 — PMC8645923.
- PubMed PMID:16762838 — UniProt-cited evidence.
- PubMed PMID:12508121 — UniProt-cited evidence.
- PubMed PMID:15489334 — UniProt-cited evidence.
Immunohistochemistry protocol sheet for SLIRP (SRA stem-loop-interacting RNA-binding protein, mitochondrial). Expected localisation Granular cytoplasm in tissue (HPA tissue IHC); predominantly mitochondrial, with some nuclear localisation (UniProt). Antigen retrieval: EDTA pH 8.0 HIER, heat-mediated (datasheet A08297-1). Validated IHC antibody: A08297-1 at 2-5 μg/ml (the product's own IHC validation image is shown). Controls (HPA): positive Adrenal gland (Glandular cells); negative Liver. IHC-P workflow on paraffin sections; fixative unspecified. Protocol steps: 1. Sample: Paraffin-embedded human colon cancer tissue; fixative not specified (datasheet A08297-1); 2. Fixation: Image fixative and duration unreported (datasheet A08297-1); 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 A08297-1); 20 min, 95–100 °C (standard); 6. Peroxidase block: 3% H2O2, 10 min , room temperature (standard); 7. Blocking: 10% goat serum (datasheet A08297-1); 8. Primary antibody: Rabbit anti-SLIRP, 2-5 μg/ml (datasheet A08297-1); 9. Primary incubation: Overnight at 4 °C (datasheet A08297-1). Watch for: Fixation: Keep fixation consistent across sections (standard IHC practice; not target-specific); Caveat: Staining and RNA show medium agreement (HPA tissue IHC); Isoform / epitope: 2 isoforms; epitope coverage is unknown (UniProt); Regulation: No specific regulator reported (UniProt). Evidence: UniProt Q9GZT3, HPA tissue IHC · Approved, HPA ICC-IF · mitochondria., Datasheet A08297-1, PMC3744554. QR code links to https://www.bosterbio.com/bosterbio-gene-info-cards/SLIRP/immunohistochemistry-ihc-guide.