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PER3 / Period circadian protein homolog 3 · IHC design guide
Design Immunohistochemistry for PER3
Plan PER3 chromogenic IHC in paraffin sections around the reported cytoplasmic tissue pattern (HPA tissue IHC) and the catalog antibody’s 1:50–1:200 dilution range (datasheet). Record collection times because PER3 participates in circadian rhythms (UniProt), and verify staining independently given its low agreement with RNA expression (HPA tissue IHC).
Evidence assembled Oct 2026 · For research use; verify linked source records and product datasheet before use
PER3 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 | General cytoplasmic tissue staining (HPA tissue IHC) | |
| Staining pattern | Cytoplasmic staining across tissue cell types (HPA tissue IHC) | |
| Antigen retrieval | Tris-EDTA pH 9.0 HIER, 95–98 °C, 20 min (rule: nuclear antigen) | |
| Positive control | Adrenal gland+4 more · see all | |
| Negative control | None in HPA (detected in all 44 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 A01835) | |
| Caveat | Staining has low agreement with RNA; verify independently (HPA tissue IHC) | |
| Regulation | Clock-linked expression may vary with time (UniProt) | |
| Isoform / epitope | 2 isoforms; check whether the epitope is shared (UniProt) |
Section 1
Recommended PER3 IHC & IF Protocols
The catalog antibody IHC-P protocol is accompanied by 3 published PER3 IHC protocols (PMC4206725; PMC12644904; PMC11743850).
| Sample | Paraffin-embedded human rectum carcinoma tissue; fixative not specified (datasheet A01835) |
| Fixation | Image fixative and duration unreported (datasheet A01835); verify before use. |
| Sectioning | 4–5 µm sections on charged slides (standard) |
| Deparaffinisation | Xylene, graded ethanol series to water (standard) |
| Antigen retrieval | Heat-induced epitope retrieval in Tris-EDTA buffer, pH 9.0, 20 min at 95–98 °C (standard rule: nuclear antigen) |
| Peroxidase block | 3% H2O2, 10 min, room temperature (standard) |
| Blocking | 10% normal serum of the secondary host, 30 min, room temperature (standard) |
| Primary antibody | Rabbit anti-PER3, 1:50-1:200 (datasheet A01835) |
| Primary incubation | Overnight at 4 °C (standard) |
| Detection | HRP-polymer secondary, DAB chromogen 5–10 min (standard) |
| Counterstain | Hematoxylin, blue, dehydrate and mount (standard) |
| Expected result | PER3-positive staining in glandular cells of adrenal gland (HPA tissue IHC: High). HPA tissue profile: General cytoplasmic expression. No signal in the no-primary control. |
💡Decision noteStart with Tris-EDTA pH 9.0 retrieval at 95–98 °C for 20 min (page retrieval rule); citrate pH 6.0 is a published alternative (PMC4206725).
Section 2
What Is the Expected PER3 Staining Pattern?
PER3 should stain mainly in the cytoplasm, with possible nuclear signal when it translocates with clock partners; it has no transmembrane segment (UniProt P56645). HPA reports general cytoplasmic tissue staining and supported cytosolic IF localisation (HPA tissue IHC; HPA subcellular). High IHC staining is reported in selected glandular, hematopoietic and neural cells (HPA tissue IHC). Treat the pattern as provisional: HPA rates its IHC evidence Approved but reports low agreement with RNA data and pending external verification (HPA tissue IHC).
| Cytoplasmic chromogen in adrenal or appendix glandular cells, with some cells stronger than others (HPA tissue IHC). | This fits PER3's mainly cytoplasmic localisation and the High staining reported for those cell types (UniProt P56645; HPA tissue IHC). Judge the pattern within identifiable cells; a dark field alone does not establish cell-specific staining (general IHC practice). |
| Cytoplasmic staining with a nuclear component in otherwise credible positive cells (UniProt P56645). | Nuclear PER3 is plausible because PER3 can enter the nucleus through binding PER1, PER2, CRY1 or CRY2 (UniProt P56645). HPA's supported IF location is cytosol, so nuclear staining alone needs careful control review (HPA subcellular; general IHC practice). |
| Predominantly membrane, luminal or extracellular deposit instead of cell-associated cytoplasm (UniProt P56645; HPA tissue IHC). | That distribution conflicts with the reported localisation and lack of a transmembrane segment (UniProt P56645; HPA tissue IHC). Check whether the deposit persists when the primary antibody is omitted before interpreting it as PER3 (general IHC practice). |
| Strong signal chiefly in a cell population outside the annotated positive cells (HPA tissue IHC). | HPA's cell-specific observations cannot validate that new pattern; cross-reactivity or endogenous detection activity is possible (HPA tissue IHC; general IHC practice). A blank control and an independently supported assay can help distinguish those explanations (general IHC practice). |
| No cell-associated signal in an adequately represented High-staining HPA tissue (HPA tissue IHC). | Consider a failed staining run alongside biological or sampling variation; HPA's Approved IHC result remains pending external verification (HPA tissue IHC; general IHC practice). Compare controls and cell identity before calling the specimen PER3-negative (general IHC practice). |
💡Expected PER3 appearanceA credible positive is mainly cytoplasmic chromogen in identifiable cells such as adrenal or appendix glandular cells, where HPA reports High staining; isolated membrane or luminal colour is suspect (UniProt P56645; HPA tissue IHC; general IHC practice).
| Compartment and processing (UniProt P56645) | PER3 is mainly cytoplasmic, can translocate to the nucleus, and has no transmembrane segment or signal peptide (UniProt P56645). Interpret discrete cytoplasmic staining first; a membrane-only pattern needs investigation (UniProt P56645; general IHC practice). |
| Isoforms and epitope information (UniProt P56645) | UniProt lists 2 isoforms and phosphorylation sites, but the supplied record does not map this antibody's epitope (UniProt P56645). It cannot predict which isoforms or phosphorylation states the stain detects. |
| Timing (UniProt P56645) | PER3 participates in an approximately 24-hour clock mechanism (UniProt P56645). Record collection time when comparing specimens; the supplied evidence gives no tissue-specific IHC peak or expected intensity by hour. |
| Strength of tissue evidence (HPA tissue IHC; HPA antibodies) | The listed antibody has IHC status Approved, while HPA reports low agreement between staining and RNA expression and pending external verification (HPA antibodies; HPA tissue IHC). High is an observed staining level, not an independently verified specificity claim. |
| Low-staining comparison (HPA tissue IHC) | HPA lists adipocytes in adipose tissue as Low and supplies no negative tissue here (HPA tissue IHC). Use adipose staining as a relative comparison, not a required blank control (HPA tissue IHC; general IHC practice). |
| IF/ICC Q: What localisation should I expect? (HPA subcellular) | A: HPA supports cytosolic localisation in ICC-IF images from A-431, U-251MG and U2OS; UniProt also permits nuclear localisation (HPA subcellular; UniProt P56645). This observation does not establish an IF protocol for paraffin IHC. |
| Situation | Likely cause | Next action |
|---|---|---|
| No stain in adrenal or appendix glandular cells expected to be High (HPA tissue IHC). | The run may have failed, the relevant cells may be absent, or this specimen may differ from HPA's observations (HPA tissue IHC; general IHC practice). | Confirm the cell type and review a known positive section, detection reagents and the antibody's stated IHC use before revising the interpretation (general IHC practice). |
| Colour covers the section, including spaces between cells (general IHC practice). | Diffuse deposit can reflect excess background or nonspecific detection rather than PER3 localisation (general IHC practice; UniProt P56645). | Compare a primary-omission control; review blocking, washing and chromogen development in the same run (general IHC practice). |
| Signal appears chiefly at cell borders or in lumens (general IHC practice). | That pattern does not match mainly cytoplasmic PER3 or HPA's general cytoplasmic IHC profile (UniProt P56645; HPA tissue IHC). | Check a primary-omission section and cell morphology; require reproducible intracellular staining before scoring PER3-positive cells (general IHC practice). |
| Only nuclei stain in the cells being assessed (general IHC practice). | Nuclear entry is biologically possible, but HPA's supported IF localisation is cytosol (UniProt P56645; HPA subcellular). | Review the matching cytoplasm, a positive tissue section and omission control; report nuclear-only staining as uncertain if specificity remains unresolved (general IHC practice). |
| Adipocytes show colour despite their Low HPA staining annotation (HPA tissue IHC). | Low does not mean absent; background or a specimen-dependent signal could also explain the colour (HPA tissue IHC; general IHC practice). | Compare intensity with identified High-staining cells and the omission control; do not score adipose as a validated negative tissue (HPA tissue IHC; general IHC practice). |
| A new cell type stains strongly while annotated High-staining cells do not (HPA tissue IHC). | Cross-reactivity, endogenous detection activity or a run problem remains possible; HPA reports limited agreement with RNA data (HPA tissue IHC; general IHC practice). | Check primary-omission and positive sections, then seek independent confirmation before assigning the new cell pattern to PER3 (general IHC practice; HPA tissue IHC). |
Experiment evidence
IHC & IF images showing PER3 staining
A01835 · IHCImmunohistochemistry (IHC) analyzes of Per3 (P2) pAb in paraffin-embedded human rectum carcinoma tissue at 1:50.showing cytoplasmic and nucl
HPA · Cerebral cortexHuman Protein Atlas IHC, Cerebral cortex. Source: https://www.proteinatlas.org/ENSG00000049246-PER3/tissue/cerebral+cortex#imid_5107844
HPA · ColonHuman Protein Atlas IHC, Colon. Source: https://www.proteinatlas.org/ENSG00000049246-PER3/tissue/colon#imid_5107778
HPA · LiverHuman Protein Atlas IHC, Liver. Source: https://www.proteinatlas.org/ENSG00000049246-PER3/tissue/liver#imid_5107779
HPA · KidneyHuman Protein Atlas IHC, Kidney. Source: https://www.proteinatlas.org/ENSG00000049246-PER3/tissue/kidney#imid_5107772
HPA · ICC-IF A-431Human Protein Atlas immunofluorescence, A-431, antibody HPA019530; green = PER3, blue = nucleus, red = microtubules.
HPA · ICC-IF A-431Human Protein Atlas immunofluorescence, A-431, antibody HPA019530; green = PER3, blue = nucleus, red = microtubules.
← swipe / scroll for more images →
Real IHC / IF data behind the staining-pattern expectations in this section.
Sample controls for PER3 IHC & IF
🧪Run bone marrow first; hematopoietic cells should stain because HPA scores them High for PER3 (HPA: bone marrow hematopoietic cells, High). HPA detects PER3 in all 44 scored tissues, so use no-primary and isotype controls for the negative comparison; cells outside the hematopoietic compartment should show only background in those controls, but the supplied data do not establish a PER3-negative internal cell type (HPA: no negative tissue rows; PER3 detected in all 44 scored tissues).
Positive control tissue: Adrenal gland (Glandular cells, HPA High)
Negative control tissue: None in HPA: PER3 is detected in all 44 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 PER3 in A-431, U-251MG, U2OS, with annotated localisation: Cytosol (supported) (HPA subcellular).
Technical controls: Include a no-primary, secondary-only slide and a host-matched polyclonal IgG isotype control; a PER3 knockout sample, if available, provides a biological specificity control (standard IHC practice). Quench endogenous peroxidase and check unstained bone marrow for pigment or chromogen-like background, especially in myeloid cells (standard IHC practice).
⚠️Feasibility: A PER3-specific fixation window or fixation effect is unreported, and the selected A01835 paraffin-section caption does not state its fixative (selected SKU tissue-IHC caption). Antigen-retrieval dependence is also unreported; optimize retrieval against the controls rather than infer it from staining location (supplied target/application evidence). The paraffin-section caption supports an IHC starting point, while HPA shows cytosolic ICC-IF signal in A-431, U-251MG and U2OS; neither source establishes that frozen sections or IF are easier, and endogenous peroxidase in bone marrow myeloid cells can complicate chromogenic scoring (selected SKU tissue-IHC caption; HPA: subcellular ICC-IF; standard IHC practice).
HPA tissue IHC evidence for PER3
Comprehensive Human Protein Atlas IHC scoring per tissue (reliability: Approved — 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 |
|---|---|---|---|---|
| Adrenal gland | Glandular cells | High | Protein (IHC) | HPA → |
| Appendix | Glandular cells | High | Protein (IHC) | HPA → |
| Bone marrow | Hematopoietic cells | High | Protein (IHC) | HPA → |
| Breast | Glandular cells | High | Protein (IHC) | HPA → |
| Bronchus | Respiratory epithelial cells | High | Protein (IHC) | HPA → |
Undetected expression · recommended negative controls
| Tissue | Cell type | Level | Evidence | Source |
|---|---|---|---|---|
| None in HPA: PER3 is detected in all 44 scored tissues. Use a no-primary (secondary-only) and an isotype control instead. | ||||
Section 3
Advanced PER3 IHC Tips
Troubleshoot PER3 chromogenic IHC in paraffin sections by checking retrieval, staining compartment, controls, and the limits of the available antibody evidence.
How should I retrieve PER3 in paraffin sections when staining is weak?
Start with Tris-EDTA pH 9.0 heat-induced retrieval at 95–98 °C for 20 min (page retrieval setting). Allow sections to cool in retrieval buffer, then compare the suspected weak section with a concurrently processed positive section and a no-primary control (standard IHC practice). If staining remains weak, optimize heating and cooling first; only then trial a different buffer or pH as a documented fallback, keeping detection conditions constant (standard IHC practice). Score cytoplasmic and nuclear signal separately because PER3 is mainly cytoplasmic but can enter nuclei through binding other clock proteins (UniProt P56645 localisation).
Could fixation explain inconsistent PER3 staining across paraffin blocks?
PER3-specific fixation sensitivity is unknown from the supplied evidence; the selected A01835 paraffin-section caption does not state a fixative (A01835 caption). Record fixation type and duration for each block, and compare blocks with similar processing before changing retrieval or antibody concentration (standard IHC practice). Underfixation can compromise tissue morphology, while excessive fixation can mask epitopes in routine IHC; neither outcome establishes a PER3-specific effect here (standard IHC practice). Use the same positive tissue and no-primary control in each run, then assess whether variation tracks block processing, cell compartment, or the staining run (standard IHC practice).
Should PER3 staining be cytoplasmic, nuclear, or both?
Expect mainly cytoplasmic staining, with possible nuclear signal because PER3 can translocate to nuclei through binding PER1, PER2, CRY1, or CRY2 (UniProt P56645 localisation). The selected A01835 paraffin-section image reports cytoplasmic and nuclear staining in human rectum carcinoma at 1:50 (A01835 caption). Assess both compartments against morphology and a no-primary control; diffuse staining outside intact cells should prompt a check of section quality and detection background (standard IHC practice). Report cytoplasmic and nuclear scores separately rather than treating a change in compartment as a change in total abundance (standard IHC practice).
How can isoforms or epitope accessibility affect PER3 IHC?
PER3 has 2 annotated isoforms and a 1–1201 amino-acid canonical chain, so document which sequence the antibody recognizes before claiming isoform coverage (UniProt P56645 isoforms and processing). Its PAS regions span residues 121–188 and 262–328, with a PAC region at 337–380; phosphorylation is annotated at 919, 994, and 1053 (UniProt P56645 domains and modified residues). Without a supplied epitope map, staining differences cannot be assigned to a particular isoform or modification (supplied antibody evidence). Compare retrieval conditions and controls on adjacent sections, and describe the result as PER3 immunoreactivity unless specificity for an isoform has been established (standard IHC practice).
How should I adapt the PER3 question to multiplex IF?
For a separate IF experiment, pair PER3 with a marker identifying the expected cell type, selected for the tissue under study, and include single-stain controls for each channel (standard IF practice). Choose fluorophores and acquisition settings after examining unstained tissue autofluorescence; place the weaker signal in a channel with a clear separation from that background (standard IF practice). PER3 has no transmembrane segment and is reported in cytoplasm and nucleus, so test permeabilisation that permits antibody access to intracellular epitopes while preserving cell boundaries (UniProt P56645 topology and localisation; standard IF practice). The A01835 paraffin-section caption supplies IHC evidence and no IF fixation or permeabilisation conditions (A01835 caption).
What should I check when PER3 IHC shows widespread background?
Run a no-primary section alongside the test section; the A01835 image used PBS in place of primary antibody and a biotin-linked secondary followed by avidin-peroxidase (A01835 caption). If both sections stain, inspect endogenous peroxidase activity, nonspecific secondary binding, and, for biotin-based detection, endogenous biotin before changing the primary antibody (standard IHC practice). Apply an appropriate peroxidase block and protein block, then compare shorter chromogen development and thorough washes on matched sections (standard IHC practice). Keep genuine PER3 signal tied to intact-cell cytoplasm or nuclei; a uniform precipitate across empty spaces and tissue surfaces warrants investigation as background (UniProt P56645 localisation; standard IHC practice).
How can I score PER3 staining without confusing compartments or tissue composition? ⚠ ANSWER MARKED FOR VERIFICATION
Define the cell population and regions before scoring, exclude damaged areas, and apply one threshold to all slides in the comparison (standard IHC practice). Report the percentage of positive cells and a compartment-specific H-score, using intensity grades 0–3 and a possible score of 0–300 (standard IHC practice). Normalize cell counts to the number of evaluable cells of the same type, or report positive-cell density per mm² of evaluable tissue, rather than comparing raw counts across unequal areas (standard IHC practice). Record sampling or collection time when available because PER3 participates in circadian regulation, and avoid interpreting one section as a rhythm measurement (UniProt P56645 function).
How do I distinguish plausible PER3 staining from artefact?
A plausible PER3 pattern follows intact-cell cytoplasm, with nuclear staining possible, and agrees with the cell identities established by tissue morphology (UniProt P56645 localisation; standard IHC practice). HPA reports general cytoplasmic expression and high staining in several listed cell populations, but flags low consistency with RNA data and pending external verification (HPA tissue IHC). Treat staining confined to section edges, necrotic zones, or spaces outside cells as suspect, and compare it with the no-primary control for detection-system artefacts (standard IHC practice). Check endogenous peroxidase when chromogen appears in both controls and test sections; a compartment match alone cannot establish antibody specificity (standard IHC practice).
Boster reagents
Best PER3 / Period circadian protein homolog 3 IHC Antibodies
A01835 has an IHC image from paraffin-embedded human rectum carcinoma (image caption) and lists Human, Mouse and Rat reactivity (catalog: reactivity). No IF data are supplied (catalog: IF images absent).
Real IHC data
Anti-Per3 (P2) Antibody
Cat # A01835
A01835 will render with its IHC image from paraffin-embedded human rectum carcinoma stained at 1:50 (image caption). Its listed applications are IHC and WB, and its listed reactivity is Human, Mouse and Rat (catalog: applications; reactivity).
Which to pick: Choose A01835 for paraffin-section IHC: its own caption documents human rectum carcinoma staining, calls the antibody pAb, and does not report a fixative (image caption). For cross-species IHC, A01835 lists Mouse and Rat reactivity, although its IHC image shows human tissue only (catalog: reactivity; image caption). No IF/ICC SKU is supported here because A01835 lists IHC and WB only and has no IF image or dilution (catalog: applications; IF images and dilution absent).
Each figure is that product's own IHC / IF validation image from its datasheet.
References
- UniProt Consortium. UniProt entry P56645 (PER3_HUMAN, Period circadian protein homolog 3).
- Human Protein Atlas. PER3 tissue IHC expression (reliability: Approved).
- Human Protein Atlas. PER3 subcellular location (ICC-IF): Localized to the cytosol..
- Human Protein Atlas. PER3 antibody validation summary (1 antibodies).
- PER3, a novel target of miR-103, plays a suppressive role in colorectal cancer in vitro. BMB reports 2014 — PMC4206725.
- PER3 suppresses lung adenocarcinomatous cell proliferation/migration through activating AMPK/mTOR pathway. Scientific reports 2025 — PMC12644904.
- Uncovering the Penile Clock: Expression of Molecular Clock Proteins in Human Penile Cavernous Tissue. The world journal of men's health 2024 — PMC11439802.
- PER3 suppresses tumor metastasis of oral squamous cell carcinoma by promoting HIF-1α degradation. Translational oncology 2025 — PMC11743850.
- PubMed PMID:11306557 — UniProt-cited evidence.
- PubMed PMID:16710414 — UniProt-cited evidence.
- PubMed PMID:23186163 — UniProt-cited evidence.
Immunohistochemistry protocol sheet for PER3 (Period circadian protein homolog 3). Expected localisation General cytoplasmic tissue staining (HPA tissue IHC). Antigen retrieval: Tris-EDTA pH 9.0 HIER, 95–98 °C, 20 min (rule: nuclear antigen). Validated IHC antibody: A01835 at 1:50-1:200 (the product's own IHC validation image is shown). Controls (HPA): positive Adrenal gland (Glandular cells); negative None in HPA (detected in all 44 tissues); use no-primary + isotype controls. IHC-P workflow on paraffin sections; fixative unspecified. Protocol steps: 1. Sample: Paraffin-embedded human rectum carcinoma tissue; fixative not specified (datasheet A01835); 2. Fixation: Image fixative and duration unreported (datasheet A01835); 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-induced epitope retrieval in Tris-EDTA buffer, pH 9.0 , 20 min at 95–98 °C…; 6. Peroxidase block: 3% H2O2, 10 min , room temperature (standard); 7. Blocking: 10% normal serum of the secondary host, 30 min , room temperature (standard); 8. Primary antibody: Rabbit anti-PER3, 1:50-1:200 (datasheet A01835); 9. Primary incubation: Overnight at 4 °C (standard). Watch for: Fixation: Matched tissue-IHC evidence does not establish the fixation claim. Validate the specimen-specific method before use. (selected-SKU IHC image A01835); Caveat: Staining has low agreement with RNA; verify independently (HPA tissue IHC); Isoform / epitope: 2 isoforms; check whether the epitope is shared (UniProt); Regulation: Clock-linked expression may vary with time (UniProt). Evidence: UniProt P56645, HPA tissue IHC · Approved, HPA ICC-IF · cytosol., Datasheet A01835, PMC4206725, PMC12644904. QR code links to https://www.bosterbio.com/bosterbio-gene-info-cards/PER3/immunohistochemistry-ihc-guide.