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- Table of Contents
Plan FEN1 staining in paraffin sections around the nuclear signal seen in highly proliferative cells (HPA tissue IHC). Compare with a low-signal tissue control and assess nuclear staining across cell populations (HPA tissue IHC).
Expected localisation, validated protocols, controls and antibodies — the at-a-glance facts below, then the full design guide.
| Expected localisation | Nuclear staining in tissue; nucleolar enrichment is a molecular expectation (HPA tissue IHC; UniProt) | |
| Staining pattern | Nuclear signal in highly proliferative cells (HPA tissue IHC) | |
| Antigen retrieval | EDTA pH 8.0 HIER, heat-mediated (datasheet M01484-3) | |
| Positive control | Adrenal gland+4 more · see all | |
| Negative control | Heart muscle+3 more · see all |
| Fixation | Keep fixation consistent across sections. (standard IHC practice; not target-specific) | |
| Caveat | Cardiomyocytes may be unstained (HPA tissue IHC) | |
| Regulation | Enriched in highly proliferative cells (HPA tissue IHC) | |
| Isoform / epitope | 2 isoforms, FEN1 and FENMIT; epitope coverage unknown (UniProt) |
The catalog antibody protocol uses heat retrieval in EDTA pH 8.0 (datasheet M01484-3). The published IHC protocols below cover osteosarcoma and hepatocellular carcinoma (PMC8504935; PMC8771828; PMC7201445).
| Sample | Paraffin-embedded human bladder epithelial carcinoma tissue; fixative not specified (datasheet M01484-3) |
| Fixation | Image fixative and duration unreported (datasheet M01484-3); 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 M01484-3); 20 min, 95–100 °C (standard) |
| Peroxidase block | 3% H2O2, 10 min, room temperature (standard) |
| Blocking | 10% goat serum (datasheet M01484-3) |
| Primary antibody | Mouse monoclonal (clone 6F3F2) anti-FEN1, 2 μg/ml (datasheet M01484-3) |
| Primary incubation | Overnight at 4 °C (datasheet M01484-3) |
| Detection | HRP-conjugated secondary, DAB chromogen (datasheet M01484-3) |
| Counterstain | Hematoxylin, blue, dehydrate and mount (standard) |
| Expected result | FEN1-positive staining in glandular cells of adrenal gland (HPA tissue IHC: High). HPA tissue profile: Nuclear expression in highly proliferative cells in most tissues. No signal in the no-primary control. |
FEN1 should stain nuclei, especially in highly proliferative cells across most tissues (HPA tissue IHC: Enhanced). UniProt places FEN1 in the nucleolus and nucleoplasm, also annotates mitochondria, and reports no transmembrane segment (UniProt P39748). Interpret chromogenic staining by both compartment and cell type: HPA reports high staining in lymph node germinal center cells and bone marrow hematopoietic cells, while cardiomyocytes are not detected (HPA tissue IHC).
| Distinct nuclear staining in germinal center cells, with weaker or absent staining in surrounding cells (HPA tissue IHC). | This fits the reported nuclear pattern in highly proliferative cells and high staining in lymph node germinal centers (HPA tissue IHC). Judge the stained cell population, not the whole section: variation between neighboring cells can be expected from the HPA profile, so a uniformly positive field is not required. |
| Predominantly cytoplasmic or membranous color, with little convincing nuclear staining. | That distribution conflicts with the principal nuclear pattern in tissue IHC (HPA tissue IHC) and with the absence of a transmembrane segment (UniProt P39748). UniProt also annotates mitochondria, so extranuclear signal alone cannot prove an artefact; compare a known nuclear-positive tissue and reassess detection background before assigning it to FEN1. |
| Strong staining in cardiomyocytes or skeletal myocytes, or uniformly strong staining across unrelated cell types. | HPA reports FEN1 as not detected in cardiomyocytes and skeletal myocytes, while its overall tissue profile emphasizes highly proliferative cells (HPA tissue IHC). Confirm which cells carry the color; unexpected staining warrants checks for antibody cross-reactivity and endogenous detection activity (general IHC practice). |
| Diffuse color covers nuclei, cytoplasm, and surrounding tissue without clear cell boundaries. | This cannot establish the nuclear FEN1 pattern reported by HPA (HPA tissue IHC). Review a negative detection control, blocking, washing, and chromogen development to locate nonspecific or endogenous signal (general IHC practice); do not score diffuse background as FEN1-positive cells. |
| No nuclear signal in germinal center cells or bone marrow hematopoietic cells. | Both populations have high FEN1 staining in HPA tissue IHC (HPA tissue IHC). An entirely blank result in a suitable positive section calls for a workflow check, including antibody preparation, antigen retrieval, and detection controls (general IHC practice), before interpreting the sample as FEN1-negative. |
| Nuclear compartment | HPA tissue IHC describes nuclear expression, while UniProt places FEN1 in nucleoli and nucleoplasm and notes movement toward the nucleoplasm after DNA damage (HPA tissue IHC; UniProt P39748). Do not require every positive nucleus to display a separately resolved nucleolus in a chromogenic section (general IHC practice). |
| Cell population and tissue choice | High staining in colon glandular cells and lymph node germinal center cells contrasts with FEN1 not being detected in cardiomyocytes (HPA tissue IHC). Choose and score the named cell population rather than using all cells in either tissue as a single positive or negative control. |
| Antibody evidence | HPA marks tissue IHC reliability as Enhanced and lists Enhanced IHC validation for HPA006748 and CAB002262 (HPA tissue IHC; HPA antibodies). That supports the reported pattern; it does not establish the staining behavior of an unspecified catalog antibody under the reader’s staining conditions. |
| Isoforms and mitochondrial annotation | UniProt lists two isoforms and a mitochondrial location alongside nuclear locations (UniProt P39748). The supplied record gives no antibody epitope or isoform-specific IHC pattern, so it cannot determine which isoform an unexpected extranuclear signal represents or validate that signal by location alone. |
| IF/ICC Q&A: where should signal appear? | Mainly in the nucleoplasm, with additional nucleolar signal (HPA subcellular ICC-IF: supported). This is an IF/ICC localization answer; tissue IHC interpretation still follows the nuclear pattern and cell populations reported for sections (HPA tissue IHC). |
| Fixation sensitivity | Target-specific fixation sensitivity is unreported in the supplied UniProt and HPA records. Record the fixation and retrieval conditions used for comparisons (general IHC practice), without attributing a change in FEN1 staining to fixation from these sources. |
| Situation | Likely cause | Next action |
|---|---|---|
| A putative positive section shows no nuclear color. | The expected cell population may be absent, or an antibody, retrieval, or detection step may have failed (HPA tissue IHC; general IHC practice). | Locate germinal center cells or bone marrow hematopoietic cells, both reported High (HPA tissue IHC); then check reagent preparation, retrieval, and detection with suitable controls (general IHC practice). |
| Color is mostly cytoplasmic or along cell borders. | The dominant pattern is inconsistent with HPA nuclear tissue staining; FEN1 has no transmembrane segment, although UniProt also annotates mitochondria (HPA tissue IHC; UniProt P39748). | Compare a known nuclear-positive population and a negative detection control before assigning the extranuclear color to FEN1 (HPA tissue IHC; general IHC practice). |
| Cardiomyocytes or skeletal myocytes stain strongly. | Those cells are reported as not detected in HPA tissue IHC; cross-reactivity or endogenous detection activity is possible (HPA tissue IHC; general IHC practice). | Confirm cell identity and compare antibody-omission and detection controls; reassess specificity if the unexpected cellular signal persists (general IHC practice). |
| The entire section has a diffuse brown cast. | Unresolved background can obscure the nuclear pattern needed for interpretation (HPA tissue IHC; general IHC practice). | Inspect negative controls, blocking and washing, then adjust detection or chromogen development as indicated by those controls (general IHC practice). |
| Only scattered cells stain in an otherwise weak tissue section. | HPA describes nuclear expression in highly proliferative cells rather than uniform staining of every cell in most tissues (HPA tissue IHC). | Map the positive nuclei to their cell types and compare a named High population before calling the section technically weak (HPA tissue IHC; general IHC practice). |
| An IF/ICC image appears more nucleoplasmic than nucleolar. | HPA reports nucleoplasm as the main IF/ICC location and nucleoli as an additional location (HPA subcellular ICC-IF). | Assess whether signal remains nuclear; use the separate IF/ICC guide for its workflow, and use the HPA tissue IHC pattern when scoring paraffin sections (HPA subcellular ICC-IF; HPA tissue IHC). |
Comprehensive Human Protein Atlas IHC scoring per tissue (reliability: Enhanced — High 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 |
|---|---|---|---|---|
| Adrenal gland | Glandular cells | High | Protein (IHC) | HPA → |
| Bone marrow | Hematopoietic cells | High | Protein (IHC) | HPA → |
| Colon | Glandular cells | High | Protein (IHC) | HPA → |
| Duodenum | Glandular cells | High | Protein (IHC) | HPA → |
| Endometrium | Glandular cells | High | Protein (IHC) | HPA → |
| Tissue | Cell type | Level | Evidence | Source |
|---|---|---|---|---|
| Heart muscle | Cardiomyocytes | Not detected | Protein (IHC) | HPA → |
| Skeletal muscle | Myocytes | Not detected | Protein (IHC) | HPA → |
| Smooth muscle | Smooth muscle cells | Not detected | Protein (IHC) | HPA → |
| Soft tissue | Fibroblasts | Not detected | Protein (IHC) | HPA → |
Troubleshoot FEN1 staining in paraffin sections by checking retrieval, nuclear localisation, controls and cell specific scoring before interpreting chromogenic signal.
Three anti-FEN1 antibodies have IHC images from human paraffin sections and IF/ICC images from cultured cells (catalog image captions). Their listed reactivity covers human, mouse and, for two antibodies, rat (catalog applications/reactivity).
M01484-3 has an IHC image from human bladder epithelial carcinoma, and M01484-4 has one from human liver cancer; both list IHC and IF/ICC applications and have IF images from MCF-7 cells (catalog image captions; catalog applications). A01484-1 has an IHC image from human liver cancer and IF images from U20S cells and human intestinal cancer tissue (catalog image captions).
Which to pick: For tissue IHC, choose by the matching paraffin-section example: M01484-3 for bladder epithelial carcinoma, or M01484-4 or A01484-1 for liver cancer (each SKU’s IHC image caption). For IF/ICC, all three list those applications and have corresponding images; choose the rabbit antibody A01484-1 or a mouse monoclonal, M01484-3 or M01484-4, according to the host species needed for your staining panel (catalog host, clone, applications and IF image captions). For mouse or rat work, A01484-1 and M01484-3 list both species, while M01484-4 lists mouse only; the IHC captions describe paraffin sections but do not report the fixative (catalog reactivity; each SKU’s IHC image caption).