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PER3 / Period circadian protein homolog 3 · IHC design guide
Design Immunohistochemistry for PER3
Plan PER3 IHC in paraffin sections around the general cytoplasmic tissue pattern (HPA tissue IHC). Start with the catalog antibody’s 1:50–1:200 IHC dilution (datasheet), and record sampling time when comparing staining because PER3 participates in circadian regulation (UniProt).
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 | Cytoplasmic tissue staining (HPA tissue IHC); nuclear transit (UniProt) | |
| Staining pattern | General cytoplasmic staining (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 | Keep fixation consistent across sections. (standard IHC practice; not target-specific) | |
| Caveat | Low staining–RNA consistency; verify the pattern (HPA tissue IHC) | |
| Regulation | Circadian timing can affect expression (UniProt) | |
| Isoform / epitope | 2 isoforms; epitope impact is unknown (UniProt) |
Section 1
Recommended PER3 IHC & IF Protocols
The catalog antibody’s IHC-P protocol (datasheet) is accompanied by four published PER3 IHC protocols (PMC4206725; PMC12644904; PMC11439802; 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 HIER 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 appear mainly in the cytoplasm, with possible nuclear staining because it can enter the nucleus through binding clock partners (UniProt P56645). HPA reports general cytoplasmic tissue staining, including high staining in several glandular, hematopoietic and neural cell populations (HPA tissue IHC). PER3 has no transmembrane segment (UniProt P56645 topology). Interpret this pattern cautiously: HPA rates its tissue IHC evidence Approved, with low staining–RNA consistency and external verification pending (HPA tissue IHC).
| Cytoplasmic staining in adrenal glandular cells, bronchial respiratory epithelial cells or bone marrow hematopoietic cells. | This matches HPA's reported High staining in those populations and its general cytoplasmic profile (HPA tissue IHC). Compare staining with cell morphology and a matched control; HPA's Approved rating carries a low staining–RNA consistency caveat (HPA tissue IHC). |
| Cytoplasmic staining with a nuclear component in otherwise plausible positive cells. | Nuclear PER3 is biologically plausible: UniProt places PER3 in both compartments and describes nuclear entry through binding PER1, PER2, CRY1 or CRY2 (UniProt P56645). Judge the nuclear signal alongside cytoplasmic staining and controls; HPA describes the overall tissue pattern as cytoplasmic (HPA tissue IHC). |
| Predominantly cell-surface, extracellular or structure-shaped staining without convincing intracellular signal. | That distribution conflicts with the reported cytoplasmic pattern (HPA tissue IHC) and PER3's lack of a transmembrane segment (UniProt P56645 topology). Treat it as suspect; check an adjacent section and a no-primary control before assigning PER3 localisation. |
| Strong staining in adipocytes, especially when expected cell populations lack signal. | HPA lists adipocytes as Low, while reporting High staining in several other cell populations (HPA tissue IHC). This mismatch raises concern for nonspecific staining or endogenous detection activity; it does not establish that every stained adipocyte is a false positive. |
| No detectable staining in a tissue and cell population listed as High by HPA. | A negative section is inconclusive: HPA's tissue observations have low staining–RNA consistency and await external verification (HPA tissue IHC). First assess section quality, control performance and the IHC workflow; avoid calling the specimen PER3-negative from one failed stain. |
💡Expected PER3 appearanceA convincing positive is mainly cytoplasmic staining in the relevant cells, with High staining reported in selected HPA populations and possible nuclear signal (HPA tissue IHC; UniProt P56645); isolated surface or extracellular colour is suspect given PER3's intracellular localisation and lack of a transmembrane segment (UniProt P56645).
| Cell population and tissue | HPA reports High staining in adrenal and breast glandular cells, bronchial respiratory epithelial cells, bone marrow hematopoietic cells and selected brain cells, but Low staining in adipocytes (HPA tissue IHC). Score the intended cell population rather than treating the entire section as uniformly positive. |
| Compartment and clock partners | PER3 is mainly cytoplasmic and can translocate to the nucleus through binding PER1, PER2, CRY1 or CRY2 (UniProt P56645). Record cytoplasmic and nuclear staining separately; a nuclear component alone does not establish altered PER3 expression. |
| Circadian timing | PER3 participates in the circadian clock, whose components show approximately 24-hour rhythms (UniProt P56645). If comparing specimens collected at different times, record collection time and avoid attributing an intensity difference to disease or treatment without considering timing. |
| Strength of tissue evidence | HPA calls the tissue IHC profile Approved, reports low consistency between staining and RNA expression, and says external verification is pending; its listed antibody HPA019530 is IHC Approved (HPA tissue IHC; HPA antibodies). Use controls and confirm unexpected patterns before interpreting them biologically. |
| IF/ICC: should the pattern match? | HPA reports supported cytosolic localisation by ICC-IF, consistent with the main cytoplasmic expectation in tissue IHC (HPA subcellular; HPA tissue IHC). UniProt also allows nuclear PER3 through partner binding (UniProt P56645); compare compartment patterns without assuming identical intensities across applications. |
| Situation | Likely cause | Next action |
|---|---|---|
| No signal in an HPA High cell population. | The run may lack detectable signal, or the selected tissue pattern may not reproduce; HPA notes low staining–RNA consistency (HPA tissue IHC). | Check a positive control on the same run, then review the catalog antibody's IHC-P dilution, antigen retrieval and detection steps. These are general IHC checks, not evidence that PER3 has a known retrieval requirement. |
| Strong nuclear staining with little or no cytoplasmic staining. | Nuclear entry is possible (UniProt P56645), but a predominantly nuclear slide differs from HPA's general cytoplasmic tissue profile (HPA tissue IHC). | Score compartments separately, compare with a plausible positive tissue and examine the no-primary control. If the pattern persists, describe it as unexpected rather than assigning a mechanism from staining alone. |
| Colour extends across stroma, empty spaces or section edges. | The distribution does not resemble intracellular PER3 (HPA tissue IHC; UniProt P56645); general IHC causes include nonspecific reagent deposition or uneven detection. | Inspect morphology and no-primary control staining, then review blocking, washes and chromogen development as general IHC workflow checks. Exclude noncellular colour from PER3 scoring. |
| Many unrelated cell types stain similarly, including strong adipocyte staining. | HPA reports Low staining in adipocytes and High staining in selected populations (HPA tissue IHC). Broad colour could reflect nonspecific binding or endogenous detection activity. | Compare the no-primary and appropriate detection controls, assess endogenous enzyme blocking if using enzyme detection, and score each cell population separately. Controls distinguish detection background from antibody-associated staining. |
| Comparable sections show different staining intensity. | Collection timing could contribute because PER3 belongs to the circadian clock (UniProt P56645); differences in cell composition or staining runs can also affect an IHC comparison. | Record collection time, compare the same cell population, and include a common control across runs. Do not infer a biological change from intensity alone, especially given HPA's low staining–RNA consistency (HPA tissue IHC). |
| A crisp membrane-like outline dominates the stain. | A membrane-dominant pattern conflicts with HPA's cytoplasmic profile and PER3's lack of a transmembrane segment (HPA tissue IHC; UniProt P56645 topology). | Check whether the outline remains in the no-primary control, review morphology under the counterstain, and repeat with an appropriate control if needed. Do not score the outline as confirmed PER3. |
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 breast tissue first and expect glandular cells to stain (HPA: High in breast glandular cells). HPA detects PER3 in all 44 scored tissues, so use no-primary and isotype controls in place of a negative tissue; any stromal cells without staining should show only background signal, but should not be assumed to be PER3-negative (HPA: no negative tissue rows).
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 control and a host- and isotype-matched nonimmune IgG control; use PER3 knockout material or a validated peptide block as a biological specificity control. Quench endogenous peroxidase for chromogenic IHC, and check endogenous biotin if using avidin–biotin detection (caption: Goat Anti-Rabbit IgG-biotin followed by avidin-peroxidase).
⚠️Feasibility: Paraffin-section IHC is documented for the selected antibody at 1:50, but the caption does not report a fixative, and no target-specific fixation window or effect is reported (caption: paraffin-embedded rectum carcinoma; fixative unreported). Retrieval dependency is unreported, so optimize antigen retrieval empirically. HPA reports cytosolic ICC-IF localisation, but the supplied evidence does not establish that IF or frozen sections are easier; assess background from breast tissue and the chosen detection system on the control slide (HPA: Cytosol supported; HPA: High in breast glandular cells).
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, compartment patterns, controls, and circadian sampling context.
How should I retrieve PER3 in paraffin sections when staining is weak?
Use Tris-EDTA pH 9.0 heat-induced epitope retrieval at 95–98 °C for 20 min (page retrieval setting). Keep section thickness, heating, cooling, and antibody incubation consistent across the comparison before changing retrieval conditions (standard IHC practice). If staining remains weak, compare a modestly shorter and longer heating time on matched sections, watching for tissue damage or increased background (standard IHC practice). Include a no-primary control and a section with an expected cytoplasmic pattern; PER3 is mainly cytoplasmic, although it can enter nuclei (UniProt P56645 localisation). Record the retrieval condition beside each score so a brighter slide is not mistaken for higher biological expression (standard IHC practice).
Can fixation explain weak or patchy PER3 staining?
Target-specific PER3 sensitivity to fixation is unknown from the supplied evidence; the selected paraffin-section caption does not state its fixative (A01835 tissue-IHC caption). Record the fixative, time before fixation, fixation duration, and processing history for each specimen before comparing staining (standard IHC practice). On matched material, compare sections processed under the same documented conditions and keep retrieval and detection constant (standard IHC practice). Examine whether patchiness follows folds, tears, or poorly preserved regions, and exclude those areas from scoring (standard IHC practice). Do not infer a PER3 fixation preference from its phosphorylation sites or from tissue staining patterns (UniProt P56645 modified residues; HPA tissue IHC).
Should PER3 stain cytoplasm, nuclei, or both?
Expect predominantly cytoplasmic staining, with possible nuclear staining because PER3 can translocate through binding PER1, PER2, CRY1, or CRY2 (UniProt P56645 localisation). A selected paraffin-section image reports cytoplasmic and nuclear staining in human rectum carcinoma tissue at 1:50 (A01835 tissue-IHC caption). HPA describes general cytoplasmic tissue expression and a supported cytosol location in cell images (HPA tissue IHC; HPA subcellular). Score nuclear and cytoplasmic signal separately against a clear counterstain, using the same thresholds across sections (standard IHC practice). If staining is exclusively nuclear or follows section edges, review controls and morphology before treating it as altered PER3 trafficking (standard IHC practice; UniProt P56645 localisation).
What can I conclude if this antibody stains only some PER3-positive cells?
PER3 has 2 annotated isoforms, but the supplied antibody evidence does not map its epitope to either one (UniProt P56645 isoforms; A01835 tissue-IHC caption). Its PAS domains span residues 121–188 and 262–328, and phosphorylation is annotated at several sites, including 919 (UniProt P56645 domains; modified residues). Those annotations alone cannot establish isoform recognition or an effect of phosphorylation on staining (UniProt P56645 isoforms; modified residues). Check epitope documentation and, if available, compare an independently validated antibody on adjacent sections using matched scoring (standard IHC practice). Describe discordant staining as antibody-dependent until specificity and epitope coverage are established (standard IHC practice).
How can IF help assess a disputed PER3 IHC pattern?
Use IF as a separate assessment of localisation, since PER3 is mainly cytoplasmic but can also enter nuclei (UniProt P56645 localisation). Multiplex PER3 with an established marker for the cell population under examination and a nuclear counterstain, checking each channel separately (standard IF practice). Choose a fluorophore in a channel with low autofluorescence for the specimen, and include unstained and secondary-only controls (standard IF practice). PER3 has no transmembrane segment, so permeabilisation should provide access to intracellular epitopes; its exact antibody epitope is not supplied (UniProt P56645 topology; A01835 tissue-IHC caption). Keep any IF fixation choice separate from the paraffin-section image, whose fixative was not reported (A01835 tissue-IHC caption).
How do I reduce diffuse brown staining without losing PER3 signal?
First inspect the no-primary control: the selected image used PBS instead of primary antibody and an avidin–peroxidase detection system (A01835 tissue-IHC caption). Block endogenous peroxidase before chromogen development and assess whether endogenous biotin contributes signal when using avidin-based detection (standard IHC practice; A01835 tissue-IHC caption). Titrate primary antibody around a documented starting condition only on comparable sections; the selected image reports 1:50, without establishing that dilution for every specimen (A01835 tissue-IHC caption; standard IHC practice). Adjust blocking, washes, and DAB development consistently while preserving a readable cytoplasmic signal (standard IHC practice; UniProt P56645 localisation). Exclude precipitate, folds, and necrotic regions when assessing residual staining (standard IHC practice).
How should I quantify PER3 across tissue sections? ⚠ ANSWER MARKED FOR VERIFICATION
Define the cell population and anatomical region before scoring, then report the percentage of positive cells and staining intensity for each compartment separately (standard IHC practice; UniProt P56645 localisation). An H-score can combine intensity categories 0–3 with their cell percentages to yield 0–300; apply one threshold set to the entire series (standard IHC practice). For spatial analyses, report positive-cell density per mm² of viable, evaluated tissue and normalise counts to that same area (standard IHC practice). Keep exposure to detection reagents, section handling, and sampling time consistent because PER3 participates in circadian regulation (standard IHC practice; UniProt P56645 function). Report cytoplasmic and nuclear results separately rather than collapsing a possible localisation shift into one score (UniProt P56645 localisation; standard IHC practice).
When is a PER3-positive IHC pattern convincing?
A convincing pattern shows signal in intact cells, predominantly in cytoplasm, with any nuclear component assessed separately (UniProt P56645 localisation; standard IHC practice). The selected paraffin-section image shows both compartments in human rectum carcinoma, but its PBS no-primary control supports interpretation only for that illustrated preparation (A01835 tissue-IHC caption). Treat edge staining, necrotic debris, and signal reproduced in a no-primary control as artefact candidates, especially with peroxidase detection (standard IHC practice; A01835 tissue-IHC caption). Check cell identity against morphology or an appropriate marker before assigning signal to a cell population (standard IHC practice). Interpret tissue differences cautiously: HPA reports low consistency between antibody staining and RNA expression and pending external verification (HPA tissue IHC).
Boster reagents
Best PER3 / Period circadian protein homolog 3 IHC Antibodies
A01835 has IHC data from paraffin-embedded human rectum carcinoma (catalog IHC image caption); Human, Mouse, and Rat reactivity is listed (catalog reactivity). No IF data is supplied (catalog).
Real IHC data
Anti-Per3 (P2) Antibody
Cat # A01835
A01835 is listed for IHC and WB in Human, Mouse, and Rat samples (catalog applications and reactivity). Its IHC image shows nuclear and cytoplasmic staining in paraffin-embedded human rectum carcinoma at 1:50, with a PBS primary-antibody omission control (catalog IHC image caption).
Which to pick: For tissue IHC, choose A01835: it is a rabbit antibody listed for IHC at 1:50–1:200, with its own paraffin-section image at 1:50 (catalog host, applications, dilution, and IHC image caption). The caption does not report a fixative (catalog IHC image caption). No SKU in this payload lists IF/ICC, so there is no IF/ICC pick; A01835 lists Human, Mouse, and Rat reactivity, but its supplied IHC image documents only human tissue (catalog applications, reactivity, and IHC image caption).
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 Cytoplasmic tissue staining (HPA tissue IHC); nuclear transit (UniProt). 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: Keep fixation consistent across sections. (standard IHC practice; not target-specific); Caveat: Low staining–RNA consistency; verify the pattern (HPA tissue IHC); Isoform / epitope: 2 isoforms; epitope impact is unknown (UniProt); Regulation: Circadian timing can affect expression (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.