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SSR3 / Translocon-associated protein subunit gamma · IHC design guide
Design Immunohistochemistry for SSR3
Use this guide to plan SSR3 staining in paraffin sections and interpret its general cytoplasmic tissue pattern (HPA tissue IHC). Its ER membrane location provides molecular context (UniProt), while medium agreement between staining and RNA warrants careful interpretation (HPA tissue IHC).
Evidence assembled Oct 2026 · For research use; verify linked source records and product datasheet before use
SSR3 Immunohistochemistry Experimental Design Guide
Expected localisation, validated protocols, controls and antibodies — the at-a-glance facts below, then the full design guide.
Must know before staining
| Expected localisation | Cytoplasmic tissue staining; ER membrane location (HPA tissue IHC; UniProt) | |
| Staining pattern | Cytoplasmic staining in glandular and hematopoietic cells (HPA tissue IHC) | |
| Antigen retrieval | EDTA pH 8.0 HIER, heat-mediated (datasheet PA1796) | |
| Positive control | Adipose tissue+4 more · see all | |
| Negative control | None in HPA (detected in all 43 tissues); use no-primary + isotype controls |
Important caveats
Reasons your staining may differ from the expected pattern.
| Fixation | Matched tissue-IHC evidence does not establish the fixation claim. Validate the specimen-specific method before use. (selected-SKU IHC image PA1796) | |
| Caveat | Staining and RNA show only medium consistency (HPA tissue IHC) | |
| Regulation | No specific expression regulator reported (UniProt) | |
| Isoform / epitope | 2 isoforms; lumenal versus cytoplasmic epitope unknown (UniProt) |
Section 1
Recommended SSR3 IHC & IF Protocols
The catalog antibody’s IHC protocol uses EDTA pH 8.0 heat retrieval (datasheet PA1796). One published mouse tumor IHC protocol provides additional staining details (PMC10191221).
| Sample | Paraffin-embedded human breast cancer tissue; fixative not specified (datasheet PA1796) |
| Fixation | Image fixative and duration unreported (datasheet PA1796); 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 PA1796); 20 min, 95–100 °C (standard) |
| Peroxidase block | 3% H2O2, 10 min, room temperature (standard) |
| Blocking | 10% goat serum (datasheet PA1796) |
| Primary antibody | Rabbit anti-SSR3, 2-5μg/ml (datasheet PA1796) |
| Primary incubation | Overnight at 4 °C (datasheet PA1796) |
| Detection | HRP-conjugated secondary, DAB chromogen (datasheet PA1796) |
| Counterstain | Hematoxylin, blue, dehydrate and mount (standard) |
| Expected result | SSR3-positive staining in adipocytes of adipose tissue (HPA tissue IHC: High). HPA tissue profile: General cytoplasmic expression. No signal in the no-primary control. |
💡Decision noteTry EDTA pH 8.0 heat retrieval first (datasheet PA1796); the published protocol does not specify retrieval conditions (PMC10191221).
Section 2
What Is the Expected SSR3 Staining Pattern?
SSR3 is a four-pass endoplasmic reticulum (ER) membrane protein (UniProt Q9UNL2 topology). In paraffin-section IHC, expect predominantly cytoplasmic staining, consistent with the tissue survey (HPA: general cytoplasmic expression). Glandular cells in colon, duodenum, cervix and epididymis are useful high-staining examples (HPA: High in each). Interpret intensity cautiously: HPA rates tissue IHC Approved, with medium consistency between staining and RNA expression (HPA: reliability description).
| Cytoplasmic staining in colon or duodenal glandular cells. | This fits the reported high-staining cell types (HPA: High in colon and duodenal glandular cells). ER membrane localisation makes intracellular staining plausible (UniProt Q9UNL2 topology); chromogenic IHC alone does not prove that each stained structure is ER. |
| Predominantly nuclear or cell-surface staining, with little cytoplasmic signal. | Treat a compartment shift as suspect: the tissue pattern is generally cytoplasmic (HPA: tissue IHC profile), while SSR3 is assigned to the ER membrane (UniProt Q9UNL2 subcellular location). Review morphology, controls and detection conditions before assigning the signal to SSR3. |
| Strong signal in vaginal squamous cells or smooth muscle cells. | Those cells are reported as low staining (HPA: Vagina, squamous epithelial cells; smooth muscle, smooth muscle cells). Unexpected strong signal may reflect nonspecific antibody binding or endogenous detection activity (standard IHC practice); compare with a matched detection control. |
| Broad haze or precipitate across cells and empty areas. | A field-wide signal is difficult to reconcile with the reported cell-associated cytoplasmic pattern (HPA: tissue IHC profile). Check background in a control processed without primary antibody, then review blocking, washes and chromogen development (standard IHC practice). |
| No staining in glandular cells of a well-preserved colon section. | Colon glandular cells are reported as high staining (HPA: Colon, glandular cells). A negative result warrants a check of the antibody, retrieval and detection run (standard IHC practice). The HPA rating is Approved with medium RNA–staining consistency, so a single section is not an absolute biological standard (HPA: reliability description). |
💡Expected SSR3 appearanceCall a positive result when glandular cells show clear cytoplasmic staining in a high-staining reference tissue such as colon or duodenum (HPA: High in glandular cells; general cytoplasmic expression); dominant nuclear, cell-surface or uniform field-wide color is suspect against that pattern (UniProt Q9UNL2 ER membrane location; standard IHC practice).
| ER location and membrane topology | SSR3 has four transmembrane segments, with short cytoplasmic regions and lumenal regions (UniProt Q9UNL2 topology). An ER-associated target can appear cytoplasmic by chromogenic IHC (standard IHC interpretation); the topology does not establish which epitope the antibody recognises. |
| Reference tissue and cell type | High staining is reported in adipocytes, bone-marrow hematopoietic cells and several glandular epithelia (HPA: tissue IHC). Vaginal squamous cells, muscle cells and chondrocytes are listed as low (HPA: tissue IHC). These are useful comparisons, not guaranteed positive or negative controls for every specimen. |
| Strength of IHC evidence | The listed rabbit polyclonal antibody HPA014906 is IHC Approved (HPA: antibody validation). The tissue survey describes medium consistency with RNA expression (HPA: reliability description). Neither statement establishes antibody-specific ER colocalisation or identical staining in every sample. |
| Isoforms and epitope coverage | Two isoforms are listed (UniProt Q9UNL2 isoforms 1 and 2). The supplied evidence does not map the IHC antibody epitope to either isoform, so isoform-specific staining or a predicted change in intensity cannot be assigned. |
| ICC-IF evidence | The subcellular entry summarizes location as Membrane but supplies no main location or cell-line ICC-IF images (HPA: subcellular record). Use the ER assignment as a localisation hypothesis for IF (UniProt Q9UNL2); this record does not validate an IF staining pattern. |
| Fixation and retrieval evidence | Target-specific fixation sensitivity and an SSR3 retrieval condition are unreported in the supplied UniProt and HPA records. Retrieval may be checked against tissue controls as general paraffin-section IHC practice; do not infer a specific fixation effect from topology or tissue staining. |
| Situation | Likely cause | Next action |
|---|---|---|
| A high-staining reference tissue gives no signal. | A failed detection step, unsuitable antibody conditions or tissue processing are possible (standard IHC practice); colon glandular cells are a reported high-staining reference (HPA: Colon). | Confirm tissue morphology and a working detection control, then check the antibody instructions and compare retrieval conditions on adjacent sections (standard IHC practice). Do not assign an SSR3-specific fixation cause from these sources. |
| The entire section is uniformly brown. | Background from the detection system, insufficient blocking or excessive chromogen development is possible (standard IHC practice). Uniform color lacks the reported cytoplasmic cell pattern (HPA: tissue IHC profile). | Inspect a section run without primary antibody; adjust the relevant blocking, washing or chromogen step according to that control (standard IHC practice). |
| Signal is strongest in nuclei or on the outer cell edge. | The dominant compartment conflicts with general cytoplasmic tissue staining (HPA: tissue IHC profile) and ER membrane assignment (UniProt Q9UNL2). Artefact or nonspecific binding is possible (standard IHC practice). | Compare a high-staining reference section with a matched detection control; score SSR3 only where cell-associated cytoplasmic staining is credible (HPA: tissue IHC profile; standard IHC practice). |
| Vaginal squamous cells stain as strongly as the positive reference. | Vaginal squamous cells are reported as low staining (HPA: Vagina), whereas colon glandular cells are high (HPA: Colon). Strong equal signal may indicate background or antibody cross-reactivity (standard IHC practice). | Compare sections processed in the same run, including a control without primary antibody; assess cell-specific staining after background is accounted for (standard IHC practice). |
| Intensity varies among otherwise comparable sections. | Section handling, retrieval or development can vary between IHC runs (standard IHC practice). HPA reports medium consistency between staining and RNA expression, so intensity alone is a limited biological readout (HPA: reliability description). | Process reference and study sections together, keep development and scoring consistent, and interpret differences alongside tissue morphology (standard IHC practice). |
| An IF image is requested to confirm the IHC pattern. | The supplied HPA subcellular record has no cell-line ICC-IF images or specified main location (HPA: subcellular record). It cannot establish an SSR3 IF reference pattern. | Use the separate IF/ICC guide for assay design. For localisation interpretation, treat ER membrane residence as the UniProt assignment (UniProt Q9UNL2), without claiming IF validation from this record. |
Experiment evidence
IHC & IF images showing SSR3 staining
PA1796 · IHCIHC analysis of SSR3 using anti-SSR3 antibody (PA1796). SSR3 was detected in a paraffin-embedded section of human breast cancer tissue. Heat
PA1796 · IHCIHC analysis of SSR3 using anti-SSR3 antibody (PA1796). SSR3 was detected in a paraffin-embedded section of human placenta tissue. Heat medi
PA1796 · IFICC analysis of SSR3 using anti-SSR3 antibody (PA1796). SSR3 was detected in immunocytochemical section of HELA cell. Enzyme antigen retriev
HPA · Cerebral cortexHuman Protein Atlas IHC, Cerebral cortex. Source: https://www.proteinatlas.org/ENSG00000114850-SSR3/tissue/cerebral+cortex#imid_3815448
HPA · ColonHuman Protein Atlas IHC, Colon. Source: https://www.proteinatlas.org/ENSG00000114850-SSR3/tissue/colon#imid_3815382
HPA · LiverHuman Protein Atlas IHC, Liver. Source: https://www.proteinatlas.org/ENSG00000114850-SSR3/tissue/liver#imid_3815391
HPA · KidneyHuman Protein Atlas IHC, Kidney. Source: https://www.proteinatlas.org/ENSG00000114850-SSR3/tissue/kidney#imid_3815376
← swipe / scroll for more images →
Real IHC / IF data behind the staining-pattern expectations in this section.
Sample controls for SSR3 IHC & IF
🧪Run colon first and look for staining in its glandular cells (HPA: High in colon glandular cells). HPA lists no negative tissue and detects SSR3 in all 43 scored tissues (HPA: no negative rows); use no-primary and isotype controls for the negative comparison, and treat any cells on the positive slide that show only counterstain as internally nonstaining without assuming they lack SSR3.
Positive control tissue: Adipose tissue (Adipocytes, HPA High)
Negative control tissue: None in HPA: SSR3 is detected in all 43 scored tissues. Use a no-primary (secondary-only) and an isotype control instead.
ICC-IF cell lines (HPA subcellular resource): HPA carries no ICC-IF cell line for SSR3; derive a cell-line control from the positive tissue's cell type (Adipocytes) and confirm it by RNA or western blot first.
Technical controls: Include a no-primary, secondary-only slide and a concentration-matched rabbit IgG isotype control, since the catalog antibody is rabbit-derived (PA1796 tissue-IHC caption: rabbit anti-SSR3); a validated SSR3 knockout sample provides a biological negative. Quench endogenous peroxidase before chromogenic detection and check background in colon sections (standard IHC practice).
⚠️Feasibility: No target-specific fixation window or fixation effect is reported, and the selected PA1796 paraffin-section caption does not state a fixative (PA1796 tissue-IHC caption: fixative unreported). That caption uses heat-mediated EDTA retrieval at pH 8.0, but does not establish that retrieval is required (PA1796 tissue-IHC caption: EDTA pH 8.0). SSR3 is an ER membrane protein (UniProt Q9UNL2: subcellular location); the supplied evidence does not establish that frozen sections or IF are easier, and colon background should be assessed with the negative controls.
HPA tissue IHC evidence for SSR3
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 |
|---|---|---|---|---|
| Adipose tissue | Adipocytes | High | Protein (IHC) | HPA → |
| Bone marrow | Hematopoietic cells | High | Protein (IHC) | HPA → |
| Cerebellum | GLUC cells - cytoplasm/membrane | High | Protein (IHC) | HPA → |
| Cervix | Glandular cells | High | Protein (IHC) | HPA → |
| Colon | Glandular cells | High | Protein (IHC) | HPA → |
Undetected expression · recommended negative controls
| Tissue | Cell type | Level | Evidence | Source |
|---|---|---|---|---|
| None in HPA: SSR3 is detected in all 43 scored tissues. Use a no-primary (secondary-only) and an isotype control instead. | ||||
Section 3
Advanced SSR3 IHC Tips
Troubleshoot SSR3 staining in paraffin sections by checking retrieval, cellular compartment, controls and scoring before interpreting signal intensity.
How should I retrieve SSR3 in paraffin sections when staining is weak?
Start with heat-mediated retrieval in EDTA at pH 8.0 (datasheet PA1796). The selected paraffin-section example then used 2 μg/ml primary antibody overnight at 4°C, so keep those conditions consistent while comparing retrieval runs (datasheet PA1796). If signal remains weak, adjust heating duration in small increments on matched sections and watch for tissue damage or increased background (standard IHC practice). Because SSR3 has 4 membrane-spanning segments and short exposed loops, epitope accessibility may depend on the antibody’s binding site; the supplied evidence does not identify that site (UniProt Q9UNL2 topology; datasheet PA1796). Include a positive control section in each run to distinguish a retrieval problem from weak expression in the test specimen (standard IHC practice).
Can I adjust fixation to improve SSR3 staining in paraffin sections?
Target-specific fixation sensitivity for SSR3 is unknown from the supplied evidence; the selected image describes a paraffin-embedded section but does not state its fixative (datasheet PA1796). Record the specimen’s fixative, fixation duration and processing history before attributing weak staining to antibody performance (standard IHC practice). Compare matched sections processed consistently, then assess whether EDTA retrieval at pH 8.0 restores interpretable staining without damaging morphology (datasheet PA1796; standard IHC practice). Do not infer fixation tolerance from the reported tissue staining profile or from SSR3’s membrane topology and phosphorylation sites (HPA tissue IHC; UniProt Q9UNL2 topology and modified residues). Use the same processing conditions for specimens whose staining intensity will be compared quantitatively (standard IHC practice).
What SSR3 staining pattern should I accept as plausible?
Expect a cytoplasmic pattern compatible with the endoplasmic reticulum membrane, while recognizing that chromogenic IHC does not resolve individual membrane compartments (UniProt Q9UNL2 subcellular location; HPA tissue IHC; standard IHC practice). HPA describes general cytoplasmic expression, and its subcellular summary says membrane without an available main location (HPA tissue IHC; HPA subcellular). Evaluate signal in intact cells against the counterstain and tissue architecture, rather than calling isolated DAB deposits intracellular staining (standard IHC practice). Strong nuclear-only signal should prompt checks of the antibody, detection controls and morphology because the supplied localisation evidence does not support a nuclear assignment (UniProt Q9UNL2 subcellular location; standard IHC practice). Compare candidate positive areas with a concurrently stained control section before assigning a new compartment (standard IHC practice).
Could isoforms or membrane topology explain discordant SSR3 staining?
SSR3 has 2 annotated isoforms, but the supplied evidence does not map the catalog antibody’s epitope or establish which isoforms it detects (UniProt Q9UNL2 isoforms; datasheet PA1796). Its 4 transmembrane segments separate lumenal regions at residues 1–27 and 77–135 from short cytoplasmic regions at 49–54 and 158–163 (UniProt Q9UNL2 topology). Therefore, access to a particular epitope may differ after processing and retrieval; do not assign that mechanism without epitope information (UniProt Q9UNL2 topology; standard IHC practice). Document retrieval and primary-antibody conditions when comparing sections, and investigate discordance with an independently validated antibody whose epitope is known (standard IHC practice). Report isoform-specific staining only if the antibody’s isoform recognition has been established independently (standard IHC practice).
How can I use IF to investigate an ambiguous IHC pattern?
Use IF as a separate validation experiment, since the supplied PA1796 example establishes paraffin-section chromogenic IHC conditions rather than an IF procedure (datasheet PA1796). Multiplex SSR3 with a marker for the expected cell population, such as glandular cells in the documented colon example, and check cellular overlap before comparing it with DAB staining (HPA tissue IHC; standard IF practice). Choose a fluorophore in a channel with low measured tissue autofluorescence, using an unstained section to establish that baseline (standard IF practice). Select permeabilisation after identifying the antibody epitope: access requirements may differ for the lumenal 77–135 region and cytoplasmic 158–163 loop (UniProt Q9UNL2 topology; standard IF practice). Keep IF findings distinct from the antibody’s documented IHC conditions when reporting conclusions (datasheet PA1796).
What should I check when SSR3 DAB staining looks diffuse?
Compare a no-primary control with the test section to identify signal from the detection system or endogenous peroxidase (standard IHC practice). The selected example used 10% goat serum for blocking and a peroxidase-conjugated secondary followed by DAB; these are documented image conditions, not proof that background is absent in every specimen (datasheet PA1796). Apply a peroxidase block and inspect sections for pigment, precipitate and staining concentrated at folds or edges (standard IHC practice). Titrate the primary from the documented 2 μg/ml condition if both the expected cellular signal and background are strong (datasheet PA1796; standard IHC practice). Judge residual staining against intact-cell morphology and the expected cytoplasmic distribution (HPA tissue IHC; standard IHC practice).
How should I score SSR3 IHC across specimens? ⚠ ANSWER MARKED FOR VERIFICATION
Define the cell population and compartment before scoring; HPA reports general cytoplasmic staining with differing levels among sampled cell populations (HPA tissue IHC). For comparable sections, record the percentage of positive eligible cells and staining intensity, then calculate an H-score using the same scoring rules throughout (standard IHC practice). If spatial abundance is the question, report positive-cell density per mm² of viable tissue and identify the area used as the denominator (standard IHC practice). Normalize comparisons to the same cell type, viable area, staining batch and exposure to retrieval and detection conditions (standard IHC practice). Keep the documented 2 μg/ml antibody condition consistent across scoring batches, and use blinded or agreed scoring thresholds (datasheet PA1796; standard IHC practice).
How do I distinguish true SSR3 staining from artefact?
A plausible positive is intracellular staining in intact cells with a cytoplasmic distribution compatible with SSR3’s endoplasmic reticulum membrane location (HPA tissue IHC; UniProt Q9UNL2 subcellular location). Compare the stained cell population with the tissue context: HPA reports high staining in colon glandular cells, while its listed squamous epithelial cells of the vagina show low staining (HPA tissue IHC). Treat nuclear-only deposits, section-edge enhancement and signal over necrotic material as reasons to inspect morphology and controls before assigning positivity (UniProt Q9UNL2 subcellular location; standard IHC practice). A no-primary control and appropriate peroxidase blocking help reveal detection-system signal or endogenous enzyme activity that can mimic DAB positivity (standard IHC practice). HPA rates its tissue staining approved with medium agreement to RNA data, so corroborate unexpected patterns independently (HPA tissue IHC).
Boster reagents
Best SSR3 / Translocon-associated protein subunit gamma IHC Antibodies
PA1796 has paraffin-section IHC images from human breast cancer, placenta, lung cancer and mouse cerebral cortex, plus IF images from human placenta and mouse and rat brain (catalog image captions).
Real IHC data
Anti-SSR3 Antibody ®
Cat # PA1796
PA1796 is the sole card; its IHC images show paraffin sections of human breast cancer, placenta and lung cancer, and mouse cerebral cortex (PA1796 IHC captions). Its IF images show human placenta and mouse and rat brain; an ICC image shows HELA cells with DAB detection (PA1796 IF/ICC captions).
Which to pick: Choose PA1796 for tissue IHC in paraffin sections: its IHC captions document EDTA pH 8.0 retrieval, 2 μg/ml primary antibody and DAB detection (PA1796 IHC captions). PA1796 also supports IF and ICC, with images for each application (PA1796 application list and IF/ICC captions). Human, Monkey, Mouse and Rat are listed as reactive, while the pictured tissue IHC covers Human and Mouse; the fixative and clonality are unreported (PA1796 reactivity list, IHC captions and clone field).
Each figure is that product's own IHC / IF validation image from its datasheet.
References
- UniProt Consortium. UniProt entry Q9UNL2 (SSRG_HUMAN, Translocon-associated protein subunit gamma).
- Human Protein Atlas. SSR3 tissue IHC expression (reliability: Approved).
- Human Protein Atlas. SSR3 subcellular location (ICC-IF): Membrane.
- Human Protein Atlas. SSR3 antibody validation summary (1 antibodies).
- Translocon-associated Protein Subunit SSR3 Determines and Predicts Susceptibility to Paclitaxel in Breast Cancer and Glioblastoma. Clinical cancer research : an official journal of the American Association for Cancer Research 2022 — PMC10191221.
- PubMed PMID:14702039 — UniProt-cited evidence.
- PubMed PMID:16641997 — UniProt-cited evidence.
- PubMed PMID:15489334 — UniProt-cited evidence.
Immunohistochemistry protocol sheet for SSR3 (Translocon-associated protein subunit gamma). Expected localisation Cytoplasmic tissue staining; ER membrane location (HPA tissue IHC; UniProt). Antigen retrieval: EDTA pH 8.0 HIER, heat-mediated (datasheet PA1796). Validated IHC antibody: PA1796 at 2-5μg/ml (the product's own IHC validation image is shown). Controls (HPA): positive Adipose tissue (Adipocytes); negative None in HPA (detected in all 43 tissues); use no-primary + isotype controls. IHC-P workflow on paraffin sections; fixative unspecified. Protocol steps: 1. Sample: Paraffin-embedded human breast cancer tissue; fixative not specified (datasheet PA1796); 2. Fixation: Image fixative and duration unreported (datasheet PA1796); 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 PA1796); 20 min, 95–100 °C (standard); 6. Peroxidase block: 3% H2O2, 10 min , room temperature (standard); 7. Blocking: 10% goat serum (datasheet PA1796); 8. Primary antibody: Rabbit anti-SSR3, 2-5μg/ml (datasheet PA1796); 9. Primary incubation: Overnight at 4 °C (datasheet PA1796). Watch for: Fixation: Matched tissue-IHC evidence does not establish the fixation claim. Validate the specimen-specific method before use. (selected-SKU IHC image PA1796); Caveat: Staining and RNA show only medium consistency (HPA tissue IHC); Isoform / epitope: 2 isoforms ; lumenal versus cytoplasmic epitope unknown (UniProt); Regulation: No specific expression regulator reported (UniProt). Evidence: UniProt Q9UNL2, HPA tissue IHC · Approved, HPA ICC-IF · Membrane, Datasheet PA1796, PMC10191221. QR code links to https://www.bosterbio.com/bosterbio-gene-info-cards/SSR3/immunohistochemistry-ihc-guide.