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- Table of Contents
This guide pairs HPA’s general cytoplasmic tissue pattern with a paraffin IHC protocol for PIK3R1 (HPA tissue IHC; datasheet A00318-1). Start the IHC-validated antibody at 2 μg/ml overnight at 4°C, and score strongly staining cell populations such as lung macrophages separately (datasheet A00318-1; HPA tissue IHC).
Expected localisation, validated protocols, controls and antibodies — the at-a-glance facts below, then the full design guide.
| Expected localisation | General cytoplasmic staining (HPA tissue IHC) | |
| Staining pattern | Cytoplasmic staining across diverse cell types (HPA tissue IHC) | |
| Antigen retrieval | EDTA pH 8.0 HIER, heat-mediated (datasheet A00318-1) | |
| Positive control | Bone marrow+4 more · see all | |
| Negative control | None in HPA (detected in all 45 tissues); use no-primary + isotype controls |
| Fixation | Keep fixation consistent across sections (standard IHC practice; not target-specific) | |
| Caveat | Lung macrophages stain strongly; score cell types separately (HPA tissue IHC) | |
| Regulation | Tissue-dependent isoform 2 expression (UniProt) | |
| Isoform / epitope | Five isoforms; check cytoplasmic epitope coverage (UniProt) |
The catalog antibody’s IHC protocol (datasheet A00318-1) is paired with a published human hepatocellular carcinoma protocol (PMC6264640).
| Sample | Paraffin-embedded human lung cancer tissue; fixative not specified (datasheet A00318-1) |
| Fixation | Image fixative and duration unreported (datasheet A00318-1); 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 A00318-1); 20 min, 95–100 °C (standard) |
| Peroxidase block | 3% H2O2, 10 min, room temperature (standard) |
| Blocking | 10% goat serum (datasheet A00318-1) |
| Primary antibody | Rabbit anti-PIK3R1, 2-5 μg/ml (datasheet A00318-1) |
| Primary incubation | Overnight at 4 °C (datasheet A00318-1) |
| Detection | Streptavidin-biotin complex (SABC), DAB chromogen (datasheet A00318-1) |
| Counterstain | Hematoxylin, blue, dehydrate and mount (standard) |
| Expected result | PIK3R1-positive staining in hematopoietic cells of bone marrow (HPA tissue IHC: High). HPA tissue profile: General cytoplasmic expression. No signal in the no-primary control. |
PIK3R1 is a cytoplasmic protein with no transmembrane segment (UniProt P27986: subcellular location and topology). In paraffin tissue sections, expect mainly cytoplasmic staining across several cell types, including neuronal cells, cardiomyocytes, lung macrophages and placental trophoblastic cells (HPA: general cytoplasmic expression; High in those cell types). HPA rates the tissue IHC pattern Approved, with medium consistency between staining and RNA expression (HPA: tissue IHC reliability).
| Cytoplasmic staining in lung macrophages or heart cardiomyocytes, with identifiable cell boundaries. | This fits the reported compartment and two reported High cell populations (UniProt P27986: Cytoplasm; HPA: High in lung macrophages and heart cardiomyocytes). Compare intensity within the same staining run; a High HPA category is a reference pattern, not a numeric intensity cutoff. |
| Predominantly nuclear staining, or membrane-only staining with little cytoplasmic signal. | Treat this as a localisation discrepancy and investigate an artefact before scoring it as PIK3R1 (UniProt P27986: Cytoplasm; HPA: general cytoplasmic expression). PIK3R1 can be recruited toward activated receptors at the plasma membrane, so some peripheral signal alone does not prove an error (UniProt P27986: function). |
| Strong staining assigned to an unexpected cell population while expected positive cells are clear. | Check cell identity and the staining controls; cross-reactivity or endogenous chromogenic detection activity may explain the contrast (general IHC practice). HPA reports Low staining in liver cholangiocytes, smooth muscle cells and soft tissue fibroblasts, rather than universal absence (HPA: tissue IHC). |
| Uniform chromogen over cells and surrounding tissue, with cell outlines hard to distinguish. | This diffuse background does not establish the reported cytoplasmic pattern (HPA: general cytoplasmic expression). Assess the no-primary control, blocking and detection steps to distinguish nonspecific reagent signal from cell-associated staining (general IHC practice). |
| No convincing cytoplasmic signal in a section containing a reported High cell population. | Treat the run as unresolved until an on-run positive control and tissue preservation are checked (general IHC practice). HPA lists High staining in bone marrow hematopoietic cells, cerebral cortex neuronal cells and other specified populations, but its Approved rating has only medium RNA-to-staining consistency (HPA: tissue IHC). |
| Tissue and cell selection | HPA reports High staining in cerebellar molecular-layer cells, fallopian tube glandular cells, lymph-node germinal-center cells and placental trophoblastic cells (HPA: tissue IHC). Its RNA specificity is Low across tissues, so tissue-wide RNA expression alone does not identify which cells should show the strongest chromogen (HPA: RNA specificity and tissue IHC). |
| Antibody evidence | HPA001216 and CAB004268 each have Approved IHC status (HPA: antibody validation). The tissue profile itself is Approved with medium staining-to-RNA consistency (HPA: tissue IHC reliability). Use those ratings to set confidence; they do not guarantee that every cell or specimen will reproduce a High category. |
| Isoform coverage | UniProt lists five PIK3R1 isoforms and reports isoforms 2 and 4 at protein level in skeletal muscle (UniProt P27986: isoforms and tissue specificity). Without an antibody epitope map in the supplied evidence, the observed IHC pattern cannot be assigned to one isoform or assumed to detect all five. |
| Compartment and receptor recruitment | The baseline annotation is Cytoplasm, with no transmembrane segment (UniProt P27986: location and topology). SH2-mediated binding to activated tyrosine kinases can recruit the p110-containing complex toward the plasma membrane (UniProt P27986: function). Interpret peripheral accentuation alongside, rather than in place of, the expected cytoplasmic pattern. |
| IF/ICC Q: what pattern is supported? | A cytosolic pattern is the supported IF/ICC expectation (HPA: Cytosol, approved). HPA001216 has Approved ICC status, and HPA lists images from A-431, U-251MG, U2OS, ASC52telo, RPTEC/TERT1 and serum-starved hTERT-RPE1 cells (HPA: subcellular record and antibody validation). |
| Situation | Likely cause | Next action |
|---|---|---|
| Known-positive cells show no chromogen. | The run may have failed at retrieval, primary staining or detection (general IHC practice); absence alone cannot identify which step failed. | Review an on-run positive control, retrieval record and detection controls before calling the specimen negative (general IHC practice). Use a reported High population as a reference, such as lung macrophages (HPA: tissue IHC). |
| Signal appears mainly nuclear. | The distribution conflicts with the annotated cytoplasmic pattern (UniProt P27986: Cytoplasm; HPA: general cytoplasmic expression). | Check morphology and a no-primary control, then compare with a reported positive cell population (general IHC practice; HPA: tissue IHC). Do not score nuclear-only staining as the expected pattern. |
| Chromogen is widespread, including areas between cells. | Diffuse deposition may reflect nonspecific detection or endogenous enzyme activity (general chromogenic IHC practice). | Inspect the no-primary control and the assay's blocking and endogenous-activity controls; adjust the staining workflow only after locating the background source (general IHC practice). |
| An unexpected cell type stains more strongly than a reported High population. | Cell misidentification, cross-reactivity or detection background are possibilities (general IHC practice); HPA levels describe observed populations, not a universal rank order (HPA: tissue IHC). | Recheck cell morphology and controls, and compare another reported High population in the same run where available (general IHC practice; HPA: tissue IHC). |
| Mostly peripheral staining appears in otherwise positive cells. | PIK3R1 can associate with activated receptor signalling at the plasma membrane, although its annotated location is cytoplasmic (UniProt P27986: function and location). | Assess whether cytoplasmic staining is also present and whether the signal follows cell boundaries; investigate membrane-only staining as a localisation discrepancy (HPA: general cytoplasmic expression; general IHC practice). |
| Staining differs between specimens or antibodies. | HPA reports medium consistency between tissue staining and RNA expression, and the supplied evidence does not establish isoform recognition for either antibody (HPA: tissue IHC reliability; UniProt P27986: five isoforms). | Compare the same named cell population and controls across runs, record the antibody used, and avoid assigning the difference to an isoform without epitope evidence (general IHC practice; UniProt P27986: isoforms). |
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.
| Tissue | Cell type | Level | Evidence | Source |
|---|---|---|---|---|
| Bone marrow | Hematopoietic cells | High | Protein (IHC) | HPA → |
| Cerebellum | Cells in molecular layer | High | Protein (IHC) | HPA → |
| Cerebral cortex | Neuronal cells | High | Protein (IHC) | HPA → |
| Fallopian tube | Glandular cells | High | Protein (IHC) | HPA → |
| Heart muscle | Cardiomyocytes | High | Protein (IHC) | HPA → |
| Tissue | Cell type | Level | Evidence | Source |
|---|---|---|---|---|
| None in HPA: PIK3R1 is detected in all 45 scored tissues. Use a no-primary (secondary-only) and an isotype control instead. | ||||
Troubleshoot PIK3R1 staining in paraffin sections by checking retrieval, compartment, cell identity, and controls before comparing signal intensity across samples.
Catalog antibodies have IHC images from human and mouse tissues and IF images from cells (catalog image captions); listed reactivity includes human, mouse and rat (catalog reactivity).
A00318-1 shows paraffin sections of human lung cancer and mouse brain (catalog IHC captions); M00318-3 shows mouse testis and human placenta (catalog IHC captions); A00318Y463 and A00318Y467 show paraffin sections of human breast carcinoma (catalog IHC captions). A00318Y607 shows IF in BV2 cells, while M00318-2 has IF images with no sample identified (catalog IF captions); both list human, mouse and rat reactivity (catalog reactivity).
Which to pick: For tissue IHC, choose A00318-1: its paraffin-section caption documents EDTA retrieval at pH 8.0 and primary antibody at 2 μg/ml overnight at 4°C (A00318-1 IHC caption); the fixative is unreported (A00318-1 IHC caption). For IF/ICC, choose M00318-2 if a rabbit monoclonal is preferred: it lists both applications and has IF images, though their sample is unidentified (M00318-2 catalog applications and IF captions). For cross-species tissue work, A00318-1 lists human, mouse and rat reactivity, with IHC images from human and mouse tissue; its captions do not document rat tissue staining (A00318-1 catalog reactivity and IHC captions).