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- Table of Contents
Plan FOXP1 IHC on paraffin sections around the expected nuclear staining pattern (HPA tissue IHC). Use the catalog antibody’s documented IHC conditions (datasheet A00723) and score nuclear staining across cells (standard IHC practice).
Expected localisation, validated protocols, controls and antibodies — the at-a-glance facts below, then the full design guide.
| Expected localisation | Nuclear in most tissue cells (HPA tissue IHC) | |
| Staining pattern | Nuclear staining across most cell types (HPA tissue IHC) | |
| Antigen retrieval | EDTA pH 8.0 HIER, heat-mediated (datasheet A00723) | |
| Positive control | Appendix+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 | Staining may reflect proteins from more than one gene (HPA tissue IHC) | |
| Regulation | Isoform 8 occurs in embryonic stem cells (UniProt) | |
| Isoform / epitope | Seven isoforms; check which the antibody epitope covers (UniProt) |
The catalog antibody uses heat-mediated EDTA retrieval for IHC-P (datasheet: A00723). Published protocols cover paraffin-embedded extrahepatic cholangiocarcinoma tissues (PMC6489656) and mouse whole-brain sections (PMC4920670).
| Sample | Paraffin-embedded human mammary cancer tissue; fixative not specified (datasheet A00723) |
| Fixation | Image fixative and duration unreported (datasheet A00723); 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 A00723); 20 min, 95–100 °C (standard) |
| Peroxidase block | 3% H2O2, 10 min, room temperature (standard) |
| Blocking | 10% goat serum (datasheet A00723) |
| Primary antibody | Rabbit anti-FOXP1, 2μg/ml (datasheet A00723) |
| Primary incubation | Overnight at 4 °C (datasheet A00723) |
| Detection | Streptavidin-biotin complex (SABC), DAB chromogen (datasheet A00723) |
| Counterstain | Hematoxylin, blue, dehydrate and mount (standard) |
| Expected result | FOXP1-positive staining in endocrine cells of appendix (HPA tissue IHC: High). HPA tissue profile: Nuclear expression in most cells. No signal in the no-primary control. |
FOXP1 should appear in nuclei, outside nucleoli (UniProt Q9H334: nucleus; absent from nucleolus); it has no transmembrane segment (UniProt Q9H334: topology). In paraffin-section IHC, HPA reports nuclear expression in most cells, with high staining in several epithelial, endocrine, hematopoietic and neuronal cell groups (HPA: tissue IHC). Treat that distribution as a guide: HPA rates the tissue result Supported, with medium consistency between staining and RNA data and a caution that the assay targets protein from more than one gene (HPA: tissue IHC reliability).
| Distinct nuclear chromogen in glandular cells of breast or respiratory epithelial cells of bronchus, with identifiable counterstained tissue architecture (HPA: High in these cell groups). | This matches the expected compartment and documented high-staining cells (UniProt Q9H334: nucleus; HPA: tissue IHC). Score the proportion and intensity of stained nuclei within each identified cell group. HPA's Supported rating and multi-gene-target caution limit claims that every positive nucleus represents FOXP1 alone (HPA: tissue IHC reliability). |
| Predominantly cytoplasmic, membranous or nucleolar signal, with little nuclear signal. | That distribution conflicts with the reported FOXP1 location (UniProt Q9H334: nucleus, absent from nucleolus; HPA: nucleoplasm). Check whether the chromogen follows pigment, tissue edges or background, then reassess detection and antibody specificity. Compartment mismatch alone identifies an unreliable result; it does not establish which technical step failed. |
| Strong staining confined to an unexpected cell group while the documented cells in the same section lack nuclear signal. | Recheck cell identity and compartment before calling the stain positive. HPA reports nuclear expression in most cells and low tissue specificity, so an unlisted cell type is not automatically negative (HPA: tissue IHC). An isolated off-pattern result can reflect cross-reactivity or endogenous detection activity; HPA also cautions that its assay targets protein from more than one gene (HPA: reliability). |
| Diffuse chromogen over nuclei, cytoplasm and extracellular tissue, with no clear nuclear boundaries. | This is background rather than a scorable nuclear pattern (UniProt Q9H334: nucleus; HPA: tissue IHC). Inspect the no-primary control for detection-related signal and the section for residual reagent or tissue pigment. Interpret intensity only after distinct nuclei can be separated from background. |
| No nuclear signal in a documented high-staining control, such as bone marrow hematopoietic cells or breast glandular cells (HPA: High). | The run is inconclusive until the control works. Confirm that the intended cells are present, then review the catalog antibody's IHC-P conditions, retrieval, dilution and detection as general workflow checks. HPA's high designation describes observed staining; it does not establish FOXP1-specific fixation sensitivity (HPA: tissue IHC). |
| Compartment and scoring | FOXP1 is nuclear and excluded from nucleoli (UniProt Q9H334: subcellular location). Score stained nuclei within identified cell groups; do not count diffuse color as equivalent nuclear staining. |
| Choice of tissue control | HPA reports High staining in appendix endocrine cells, bone marrow hematopoietic cells, breast glandular cells and bronchial respiratory epithelial cells (HPA: tissue IHC). Its Low entries, including hippocampal neuronal cells and liver cholangiocytes, are weak comparators, not validated negative controls (HPA: tissue IHC). |
| Antibody interpretation | Two listed antibodies have Supported IHC status (HPA: HPA003876 and CAB011501). The tissue profile has medium staining–RNA consistency and a multi-gene-target caution (HPA: reliability); agreement with location and controls strengthens interpretation but does not prove unique FOXP1 recognition. |
| Isoforms and epitope coverage | UniProt lists seven FOXP1 isoforms (UniProt Q9H334: isoforms 1, 3, 4, 5, 6, 7, 8). No antibody epitope or isoform coverage is supplied here, so differences between specimens cannot be assigned to a particular isoform from staining alone. |
| IF/ICC Q&A: where should signal appear? | In IF/ICC, expect nucleoplasmic localization (HPA: subcellular ICC-IF, Nucleoplasm supported). HPA lists images from A-431, U-251MG, U2OS and KOLF2.1J (HPA: subcellular ICC-IF). This localization cross-check supplies no IF/ICC protocol for this IHC-P guide. |
| Situation | Likely cause | Next action |
|---|---|---|
| The high-staining tissue control has no nuclear chromogen (HPA: tissue IHC). | The target cell group may be absent, or a general IHC step may have underperformed; these data do not identify a FOXP1-specific fixation effect. | Verify the cell group on the counterstain, then compare the run with the catalog antibody's IHC-P instructions for retrieval, dilution and detection. Repeat with a documented high-staining control. |
| Signal is mainly cytoplasmic or nucleolar. | The compartment conflicts with FOXP1's reported nuclear, non-nucleolar location (UniProt Q9H334: subcellular location). | Check nuclear morphology and tissue pigment; compare a no-primary control and an established high-staining control before interpreting the suspect signal. |
| Broad brown haze obscures nuclear boundaries. | Excess background can arise from general blocking, washing, detection or chromogen conditions; the pattern cannot be scored as nuclear FOXP1. | Inspect the no-primary control, optimize blocking and washes, and adjust detection conditions using the catalog IHC-P guidance. Reassess only clearly delimited nuclei. |
| Unexpected cells stain strongly while documented cells do not. | Cell identification may be wrong, or staining may reflect cross-reactivity or endogenous detection activity. HPA reports broad nuclear expression and cautions about multi-gene targeting (HPA: tissue IHC reliability). | Identify the cells on the counterstain, assess whether signal is nuclear, and check a no-primary control. Avoid declaring an unlisted cell group negative solely from HPA's examples. |
| Only faint staining appears in hippocampal neuronal cells or liver cholangiocytes. | HPA lists these cell groups as Low, so faint signal can fit the reported tissue pattern (HPA: tissue IHC). | Compare nuclear localization and background against a documented High control before changing assay conditions. Do not use a Low entry as a proven negative control. |
| Replicate sections or antibodies give different nuclear fractions. | HPA rates the tissue profile Supported with medium staining–RNA consistency and warns of multi-gene targeting (HPA: reliability); the supplied data cannot assign discordance to an isoform or fixation effect. | Score the same identified cell group across sections and check each antibody's control pattern and IHC-P instructions. Report unresolved differences without assigning a molecular cause. |
Comprehensive Human Protein Atlas IHC scoring per tissue (reliability: Supported — Medium consistency between antibody staining and RNA expression data. Caution, targets protein from more than one gene.). 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 |
|---|---|---|---|---|
| Appendix | Endocrine 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 → |
| Caudate | Neuronal cells | High | Protein (IHC) | HPA → |
| Tissue | Cell type | Level | Evidence | Source |
|---|---|---|---|---|
| None in HPA: FOXP1 is detected in all 45 scored tissues. Use a no-primary (secondary-only) and an isotype control instead. | ||||
Troubleshoot FOXP1 staining in paraffin sections by checking retrieval, nuclear localisation, antibody specificity and cell-based scoring before interpreting chromogenic signal.
Anti-FOXP1 antibodies have IHC images from human paraffin sections and rectal cancer tissue, plus an IF image from HeLa cells (catalog image captions). Listed reactivity includes human, monkey, mouse and rat (catalog applications and reactivity).
A00723 has IHC images from human mammary and rectal cancer paraffin sections; A00723-1 has IHC images from human thymus paraffin sections and paraffin-section, paraffin-embedded lung tissue (catalog image captions). PA1593 has an IHC-P image from human rectal cancer tissue, while M00723 has an IF image from HeLa cells (catalog image captions).
Which to pick: For tissue IHC, choose A00723 when its documented EDTA pH 8 retrieval and 2 μg/ml incubation suit the experiment; its mammary and rectal cancer captions specify paraffin sections but do not report the fixative (A00723 image captions). A00723-1 offers a human IHC-P dilution range of 1:50–1:100 (catalog: A00723-1); its thymus image uses 1:25 on a paraffin section with fixative unreported, while its separate lung caption specifies fixation (A00723-1 image captions). For IF/ICC, choose rabbit monoclonal M00723, shown in HeLa cells at 1:50 (catalog: M00723; M00723 image caption); for broader listed species reactivity in tissue IHC, consider A00723, with human, monkey, mouse and rat reactivity listed but IHC images shown only in human tissue (catalog: A00723; A00723 image captions). The selected A00723 tissue-IHC caption documents paraffin sections, but does not specify the fixative (selected-SKU IHC image A00723).