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CCNA1 / Cyclin-A1 · IHC design guide
Design Immunohistochemistry for CCNA1
Plan CCNA1 chromogenic IHC in paraffin sections using ciliated-cell staining in bronchus and fallopian tube as tissue references (HPA tissue IHC). Compare the nuclear expectation (UniProt) with observed staining, and titrate the IHC-validated antibody at 1:50–1:200 (datasheet: A03889-3).
Evidence assembled Oct 2026 · For research use; verify linked source records and product datasheet before use
CCNA1 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 | Nucleus expected (UniProt); ciliary rootlets observed (HPA tissue IHC) | |
| Staining pattern | Bronchial ciliated cell bodies and fallopian ciliary rootlets stain (HPA tissue IHC) | |
| Antigen retrieval | Tris-EDTA pH 9.0 HIER, 95–98 °C, 20 min (rule: nuclear antigen) | |
| Positive control | Bronchus+2 more · see all | |
| Negative control | Adipose tissue+4 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 | Nuclear expectation diverges from ciliary-rootlet staining (UniProt; HPA tissue IHC) | |
| Regulation | Very high expression in testis (UniProt) | |
| Isoform / epitope | 3 isoforms; no processing annotated (UniProt) |
Section 1
Recommended CCNA1 IHC & IF Protocols
The catalog antibody’s IHC-P protocol is paired with published CCNA1 staining protocols for gastric cancer and head and neck squamous cell carcinoma (PMC4598091; PMC3404904).
| Sample | Paraffin-embedded human breast carcinoma tissue; fixative not specified (datasheet A03889-3) |
| Fixation | Image fixative and duration unreported (datasheet A03889-3); 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-CCNA1, 1:50-1:200 (datasheet A03889-3) |
| 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 | CCNA1-positive staining in ciliated cells (cell body) of bronchus (HPA tissue IHC: High). HPA tissue profile: Expression in mainly in testis. 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); compare the published retrieval methods if staining is weak.
Section 2
What Is the Expected CCNA1 Staining Pattern?
CCNA1 is a nuclear protein with no transmembrane segment (UniProt P78396). In tissue IHC, expect low staining in testis pachytene spermatocytes and high staining in bronchial ciliated cell bodies; HPA also reports high staining at fallopian tube ciliary rootlets (HPA tissue IHC). Tissue IHC reliability is Enhanced, with medium consistency between staining and RNA expression (HPA tissue IHC). The rootlet observation needs care because it differs from the reported nuclear localisation (UniProt P78396; HPA subcellular ICC-IF).
| Nuclear staining in pachytene spermatocytes, even if faint (HPA tissue IHC; UniProt P78396). | This fits the reported low testis IHC signal and nuclear localisation (HPA tissue IHC; UniProt P78396). Assess the named cells rather than treating uniformly strong staining throughout testis as the expected pattern (HPA tissue IHC). |
| Strong staining in bronchial ciliated cell bodies (HPA tissue IHC). | The cell type and high signal match the tissue observation (HPA tissue IHC). Check whether signal is nuclear, since HPA's tissue entry specifies the cell body but does not resolve its subcellular pattern; nucleoplasm and nuclear bodies are approved ICC-IF locations (HPA tissue IHC; HPA subcellular ICC-IF). |
| Predominantly diffuse cytoplasmic staining, or staining confined to ciliary rootlets (HPA tissue IHC). | Diffuse cytoplasmic staining conflicts with reported nuclear localisation (UniProt P78396; HPA subcellular ICC-IF). Rootlet staining is reported as high in fallopian tube, but its apparent compartment differs from those localisation records; assess it separately before calling it specific CCNA1 (HPA tissue IHC; UniProt P78396; HPA subcellular ICC-IF). |
| Strong staining in cells listed as not detected, such as adipocytes or bone marrow hematopoietic cells (HPA tissue IHC). | This disagrees with the cited tissue observations and raises possible cross-reactivity or endogenous detection activity (HPA tissue IHC; standard IHC practice). Compare a reagent-omission control and the expected cell distribution before scoring it as CCNA1 (standard IHC practice). |
| No discernible staining in a selected positive tissue, or color spread across most of the section (HPA tissue IHC; standard IHC practice). | Absent signal in testis alone is inconclusive because pachytene spermatocyte staining is reported as low; bronchial ciliated cell bodies offer a reported high-signal comparison (HPA tissue IHC). Widespread color obscuring cell boundaries suggests background rather than a readable localisation pattern (standard IHC practice). |
💡Expected CCNA1 appearanceScore a supported positive as nuclear signal in a relevant cell, allowing low intensity in testis pachytene spermatocytes and checking high-signal bronchial ciliated cell bodies; diffuse stain across unrelated cells is suspicious, while reported fallopian tube rootlet staining requires separate interpretation (UniProt P78396; HPA tissue IHC; HPA subcellular ICC-IF).
| Tissue and cell selection (HPA tissue IHC) | Testis pachytene spermatocytes are reported low, bronchial ciliated cell bodies high, and several listed cell types not detected; use the specific cell population when judging whether a section behaves as expected (HPA tissue IHC). |
| Compartment and topology (UniProt P78396; HPA subcellular ICC-IF) | UniProt places CCNA1 in the nucleus and reports no transmembrane segment; approved ICC-IF locations are nucleoplasm and nuclear bodies (UniProt P78396; HPA subcellular ICC-IF). These records support a nuclear cross-check but do not resolve the tissue rootlet observation (HPA tissue IHC). |
| Antibody evidence by application (HPA antibodies; HPA tissue IHC) | HPA077614 has Enhanced IHC validation, whereas HPA060646 has Approved ICC status and no listed IHC status (HPA antibodies). The overall tissue reliability is Enhanced despite medium staining–RNA consistency; do not transfer an ICC approval to an IHC interpretation (HPA tissue IHC; HPA antibodies). |
| Isoforms and processing (UniProt P78396) | Three isoforms are listed, with no annotated signal peptide, propeptide or glycosylation sites (UniProt P78396). The supplied records give no epitope location or isoform-specific IHC pattern, so they cannot predict which isoform an individual stain detects (UniProt P78396). |
| IF/ICC cross-check (HPA subcellular ICC-IF) | What should an IF/ICC comparison show? Approved localisation is nucleoplasm and nuclear bodies, with images listed for PC-3, Rh30 and U2OS (HPA subcellular ICC-IF). Use that location as a comparison, while interpreting tissue IHC against its own cell-specific observations (HPA tissue IHC). |
| Situation | Likely cause | Next action |
|---|---|---|
| Testis section appears entirely negative (HPA tissue IHC). | The reported signal in pachytene spermatocytes is low, so a negative-looking field may miss the relevant cells or a subtle signal (HPA tissue IHC). | Confirm pachytene spermatocytes are present and inspect nuclei; compare a bronchial section containing ciliated cells, reported high, while checking the general IHC detection controls (HPA tissue IHC; standard IHC practice). |
| Ciliated cells stain, but only at fallopian tube ciliary rootlets (HPA tissue IHC). | High rootlet staining is reported in tissue IHC, yet nuclear localisation is reported by UniProt and ICC-IF; the records do not explain the difference (HPA tissue IHC; UniProt P78396; HPA subcellular ICC-IF). | Record rootlet and nuclear staining separately; compare appropriate reagent-omission controls and another reported positive cell population before interpreting the rootlet signal as specific (HPA tissue IHC; standard IHC practice). |
| Broad cytoplasmic signal obscures nuclei (UniProt P78396; HPA subcellular ICC-IF). | The pattern differs from reported nuclear localisation and may reflect nonspecific staining or background in the IHC workflow (UniProt P78396; HPA subcellular ICC-IF; standard IHC practice). | Review the counterstain and control section, then check blocking, antibody concentration and detection settings using general IHC practice; no CCNA1-specific dilution or retrieval condition is supplied (standard IHC practice). |
| Strong staining appears in listed negative cells (HPA tissue IHC). | Adipocytes and bone marrow hematopoietic cells are reported as not detected, so cross-reactivity or endogenous detection activity is possible (HPA tissue IHC; standard IHC practice). | Compare a primary-antibody-omission control and inspect whether color follows the expected cells and nuclear compartment; address endogenous detection activity if the control also develops color (standard IHC practice; HPA tissue IHC; UniProt P78396). |
| Brown color is widespread even where cell structure is hard to distinguish (standard IHC practice). | Diffuse chromogen can arise from general staining background or endogenous detection activity; the appearance alone cannot identify which (standard IHC practice). | Check reagent-omission controls, blocking and chromogen development, then reassess localisation against the counterstain and HPA's named cell populations (standard IHC practice; HPA tissue IHC). |
| A positive section loses signal after a workflow change (standard IHC practice). | Target-specific fixation effects are not established by the supplied assay evidence. Verify with a matched IHC source before attributing a result to fixation. | Compare matched sections and document the changed retrieval, antibody and detection steps; verify the assay controls before assigning the loss to CCNA1 biology (standard IHC practice). |
Experiment evidence
IHC & IF images showing CCNA1 staining
A03889-3 · IHCImmunohistochemistry (IHC) analyzes of Cyclin A (W250) pAb in paraffin-embedded human breast carcinoma tissue at 1:100.
HPA · Cerebral cortexHuman Protein Atlas IHC, Cerebral cortex. Source: https://www.proteinatlas.org/ENSG00000133101-CCNA1/tissue/cerebral+cortex#imid_20568811
HPA · ColonHuman Protein Atlas IHC, Colon. Source: https://www.proteinatlas.org/ENSG00000133101-CCNA1/tissue/colon#imid_20568753
HPA · LiverHuman Protein Atlas IHC, Liver. Source: https://www.proteinatlas.org/ENSG00000133101-CCNA1/tissue/liver#imid_20568754
HPA · KidneyHuman Protein Atlas IHC, Kidney. Source: https://www.proteinatlas.org/ENSG00000133101-CCNA1/tissue/kidney#imid_20568755
HPA · ICC-IF PC-3Human Protein Atlas immunofluorescence, PC-3, antibody HPA060646; green = CCNA1, blue = nucleus, red = microtubules.
HPA · ICC-IF PC-3Human Protein Atlas immunofluorescence, PC-3, antibody HPA060646; green = CCNA1, blue = nucleus, red = microtubules.
← swipe / scroll for more images →
Real IHC / IF data behind the staining-pattern expectations in this section.
Sample controls for CCNA1 IHC & IF
🧪Run bronchus first and look for staining in ciliated cell bodies (HPA: bronchus ciliated cells [cell body], High). Use adipose tissue as the negative tissue, with adipocytes lacking detectable staining (HPA: adipose tissue adipocytes, Not detected); on the bronchus slide, use cells without the ciliated-cell-body staining pattern as internal background comparators, without assigning them a negative HPA call.
Positive control tissue: Bronchus (Ciliated cells (cell body), HPA High)
Negative control tissue: Adipose tissue (HPA Not detected)
ICC-IF cell lines (HPA subcellular resource): HPA ICC-IF images show CCNA1 in PC-3, Rh30, U2OS, with annotated localisation: Nucleoplasm (approved), Nuclear bodies (approved) (HPA subcellular).
Technical controls: Include a no-primary, secondary-only control; an isotype or normal-IgG control matched to the primary antibody’s host species and clonality; and a CCNA1 knockout control or peptide competition when a matching immunizing peptide is available (standard IHC practice). For chromogenic bronchus IHC, block endogenous peroxidase and check for staining in inflammatory cells that could confound interpretation (standard IHC practice).
⚠️Feasibility: A target-specific fixation window and the effect of antigen retrieval are unreported in the supplied evidence; optimize retrieval for the IHC-validated antibody (selected SKU A03889-3 caption: paraffin-embedded human breast carcinoma at 1:100). The selected-SKU caption does not report a fixative, and it does not establish fixation (selected SKU A03889-3 caption: fixative not stated). The evidence does not establish that frozen sections or IF are easier; for IF, assess signal in the nucleoplasm and nuclear bodies while checking bronchial tissue autofluorescence (HPA: approved nucleoplasm and nuclear bodies; standard IF practice). The selected A03889-3 tissue-IHC caption documents paraffin sections, but does not specify the fixative (selected-SKU IHC image A03889-3).
HPA tissue IHC evidence for CCNA1
Comprehensive Human Protein Atlas IHC scoring per tissue (reliability: Enhanced — 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 |
|---|---|---|---|---|
| Bronchus | Ciliated cells (cell body) | High | Protein (IHC) | HPA → |
| Fallopian tube | Ciliated cells (ciliary rootlets) | High | Protein (IHC) | HPA → |
| Nasopharynx | Ciliated cells (cell body) | Medium | Protein (IHC) | HPA → |
Undetected expression · recommended negative controls
| Tissue | Cell type | Level | Evidence | Source |
|---|---|---|---|---|
| Adipose tissue | Adipocytes | Not detected | Protein (IHC) | HPA → |
| Adrenal gland | Glandular cells | Not detected | Protein (IHC) | HPA → |
| Appendix | Glandular cells | Not detected | Protein (IHC) | HPA → |
| Bone marrow | Hematopoietic cells | Not detected | Protein (IHC) | HPA → |
| Breast | Adipocytes | Not detected | Protein (IHC) | HPA → |
Section 3
Advanced CCNA1 IHC Tips
Troubleshoot CCNA1 staining in paraffin sections by checking retrieval, nuclear localisation, controls and cell-specific scoring (UniProt P78396; HPA subcellular).
What retrieval conditions should I start with for CCNA1 in paraffin sections?
Start with Tris-EDTA at pH 9.0, heated to 95–98 °C for 20 min (page retrieval rule: nuclear antigen). Allow sections to cool in retrieval buffer, then compare staining with a no-primary control and a section processed alongside it (standard IHC practice). Score nuclear signal separately from diffuse cytoplasmic colour because CCNA1 is nuclear and has no transmembrane segment (UniProt P78396). If signal remains weak, change one retrieval variable at a time while keeping antibody concentration and detection conditions fixed (standard IHC practice). The selected paraffin-section caption reports 1:100 antibody dilution but gives no retrieval method (caption A03889-3).
Could fixation be causing weak or uneven CCNA1 staining?
Target-specific fixation sensitivity is unknown: the selected paraffin-section caption does not report a fixative (caption A03889-3). Record the fixative, fixation duration and processing history for each specimen before comparing staining across sections (standard IHC practice). For a controlled comparison, process matched sections through the same Tris-EDTA pH 9.0 retrieval at 95–98 °C for 20 min (page retrieval rule: nuclear antigen). Then check whether weak nuclear staining tracks with processing history while the no-primary control remains clear (standard IHC practice). Do not assign that pattern to a CCNA1-specific fixation effect without a direct comparison (standard IHC practice).
How should I assess cytoplasmic or punctate staining?
Assess nuclear staining first: CCNA1 is annotated in the nucleus, and HPA localises it to the nucleoplasm and nuclear bodies (UniProt P78396; HPA subcellular). Nuclear puncta can therefore be plausible, but judge them against nuclear counterstain and the surrounding tissue pattern (HPA subcellular; standard IHC practice). CCNA1 has no transmembrane segment or annotated signal peptide, so prominent membrane outlining warrants a specificity check (UniProt P78396). Compare that pattern with the no-primary control and an independently validated antibody, if available (standard IHC practice). Record cytoplasmic colour separately from nuclear positivity until those checks support its interpretation (standard IHC practice).
Can this antibody distinguish CCNA1 isoforms in tissue sections?
Do not assign an isoform from staining alone: the record lists 3 CCNA1 isoforms, while the selected tissue caption does not identify an epitope (UniProt P78396; caption A03889-3). Request the antibody's immunogen sequence or mapped epitope and compare it with the isoform sequences before making an isoform-specific claim (standard IHC practice). CCNA1 has no annotated glycosylation sites or modified residues in the supplied record, which does not establish how fixation or retrieval affects this antibody's epitope (UniProt P78396). Document the clone or reagent identifier alongside the retrieval condition when comparing sections (standard IHC practice). Interpret positive nuclei as CCNA1 staining without an isoform label unless specificity is demonstrated (standard IHC practice).
How can I investigate CCNA1 by multiplex IF?
Treat IF as a separate application requiring its own antibody validation; the selected caption documents paraffin-section IHC at 1:100 (caption A03889-3). For testis, pair CCNA1 with a validated marker of pachytene spermatocytes and assess signal within counterstained nuclei (HPA tissue IHC: low in pachytene spermatocytes; UniProt P78396). Image an unstained section first, then choose a fluorophore channel with little tissue autofluorescence and include single-label controls for multiplexing (standard IF practice). Because the expected epitope is intracellular and CCNA1 lacks a transmembrane segment, optimise permeabilisation to allow nuclear antibody access (UniProt P78396; standard IF practice). Compare nuclear patterns with HPA's nucleoplasm and nuclear-body localisation (HPA subcellular).
What should I check when the chromogenic stain looks diffuse?
Run a no-primary section to identify colour produced by the detection system, and block endogenous peroxidase before DAB development (standard chromogenic IHC practice). Titrate the antibody around the caption's 1:100 condition while holding retrieval and development time constant (caption A03889-3; standard IHC practice). Add an appropriate protein block and check whether staining falls outside nuclei, since CCNA1 is nuclear (standard IHC practice; UniProt P78396). Inspect tissue edges, folds and damaged regions separately because they can distort background assessment (standard IHC practice). Use the same exposure and development conditions when comparing controls with test sections (standard IHC practice).
How should I quantify CCNA1 staining across samples? ⚠ ANSWER MARKED FOR VERIFICATION
Define the cell population and tissue area before scoring, then count counterstained nuclei as the denominator for nuclear positivity (standard IHC practice; UniProt P78396). Report the percentage of positive nuclei and, if intensity is reproducible, an H-score using intensity categories 0–3 multiplied by their respective percentages (standard IHC practice). For spatial comparisons, report positive-nucleus density per mm² of viable tissue and state any regions excluded from analysis (standard IHC practice). Keep retrieval, antibody dilution, DAB development and scoring thresholds consistent across the comparison (standard IHC practice). Record cell type because HPA reports different staining levels among sampled cell populations (HPA tissue IHC).
How can I distinguish credible CCNA1 positivity from artefact?
Give greatest weight to staining in intact nuclei, including plausible nucleoplasmic or nuclear-body patterns (UniProt P78396; HPA subcellular). Check whether the stained cells fit the sampled tissue: HPA reports high signal in bronchial ciliated cells, low signal in testicular pachytene spermatocytes and no detection in adipose adipocytes (HPA tissue IHC). Treat strong edge-only colour, necrotic-region staining or signal reproduced in a no-primary section as possible artefact (standard IHC practice). Review endogenous peroxidase blocking when DAB appears outside the expected compartment (standard chromogenic IHC practice). HPA rates tissue evidence as Enhanced while reporting medium agreement between staining and RNA data, so interpret discordant cases cautiously (HPA tissue IHC).
Boster reagents
Best CCNA1 / Cyclin-A1 IHC Antibodies
Real IHC data show human paraffin-embedded breast carcinoma tissue (A03889-3 image caption); IF/ICC data show PC-3 cells (PB9485 IF caption). Both antibodies list Human, Mouse, and Rat reactivity (catalog reactivity).
Real IHC data
Anti-Cyclin A (W250) CCNA1 Antibody
Cat # A03889-3
The rendered card is A03889-3, with IHC demonstrated on paraffin-embedded human breast carcinoma tissue at 1:100 (A03889-3 image caption). PB9485 has IF/ICC data from PC-3 cells but has no IHC card here (PB9485 IF caption; catalog applications).
Which to pick: Choose A03889-3 for paraffin-section IHC because its own image documents that preparation; the fixative is unreported (A03889-3 image caption). Choose PB9485 for IF/ICC because its cell image documents that application (PB9485 IF caption). Both list Human, Mouse, and Rat reactivity, while the supplied images document human samples only (catalog reactivity; A03889-3 image caption; PB9485 IF caption).
Each figure is that product's own IHC / IF validation image from its datasheet.
References
- UniProt Consortium. UniProt entry P78396 (CCNA1_HUMAN, Cyclin-A1).
- Human Protein Atlas. CCNA1 tissue IHC expression (reliability: Enhanced).
- Human Protein Atlas. CCNA1 subcellular location (ICC-IF): Localized to the nucleoplasm and nuclear bodies..
- Human Protein Atlas. CCNA1 antibody validation summary (2 antibodies).
- Exclusive Association of p53 Mutation with Super-High Methylation of Tumor Suppressor Genes in the p53 Pathway in a Unique Gastric Cancer Phenotype. PloS one 2015 — PMC4598091.
- Cyclin A1 shows age-related expression in benign tonsils, HPV16-dependent overexpression in HNSCC and predicts lower recurrence rate in HNSCC independently of HPV16. BMC cancer 2012 — PMC3404904.
- MCT1 governs a metabolic checkpoint at pachytene during spermatogenesis. Research square 2026 — PMC13142633.
- MCT1 governs a metabolic checkpoint at pachytene during spermatogenesis. bioRxiv : the preprint server for biology 2026 — PMC13131624.
- PubMed PMID:9041194 — UniProt-cited evidence.
- PubMed PMID:14702039 — UniProt-cited evidence.
- PubMed PMID:15057823 — UniProt-cited evidence.
Immunohistochemistry protocol sheet for CCNA1 (Cyclin-A1). Expected localisation Nucleus expected (UniProt); ciliary rootlets observed (HPA tissue IHC). Antigen retrieval: Tris-EDTA pH 9.0 HIER, 95–98 °C, 20 min (rule: nuclear antigen). Validated IHC antibody: A03889-3 at 1:50-1:200 (the product's own IHC validation image is shown). Controls (HPA): positive Bronchus (Ciliated cells (cell body)); negative Adipose tissue. IHC-P workflow on paraffin sections; fixative unspecified. Protocol steps: 1. Sample: Paraffin-embedded human breast carcinoma tissue; fixative not specified (datasheet A03889-3); 2. Fixation: Image fixative and duration unreported (datasheet A03889-3); 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-CCNA1, 1:50-1:200 (datasheet A03889-3); 9. Primary incubation: Overnight at 4 °C (standard). Watch for: Fixation: Keep fixation consistent across sections. (standard IHC practice; not target-specific); Caveat: Nuclear expectation diverges from ciliary-rootlet staining (UniProt; HPA tissue IHC); Isoform / epitope: 3 isoforms; no processing annotated (UniProt); Regulation: Very high expression in testis (UniProt). Evidence: UniProt P78396, HPA tissue IHC · Enhanced, HPA ICC-IF · nucleoplasm and nuclear bodies., Datasheet A03889-3, PMC4598091, PMC3404904. QR code links to https://www.bosterbio.com/bosterbio-gene-info-cards/CCNA1/immunohistochemistry-ihc-guide.