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- Table of Contents
Plan CPSF6 paraffin IHC around the nuclear staining observed across tissues (HPA tissue IHC). This guide covers fixation consistency, antibody selection, detection and nuclear scoring (standard IHC practice).
Expected localisation, validated protocols, controls and antibodies — the at-a-glance facts below, then the full design guide.
| Expected localisation | Ubiquitous nuclear tissue staining (HPA tissue IHC) | |
| Staining pattern | Nuclear staining across diverse cell types (HPA tissue IHC) | |
| Antigen retrieval | EDTA pH 8.0 HIER, heat-mediated (datasheet A04551-1) | |
| Positive control | Adipose tissue+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 | Antibody staining and RNA show medium consistency (HPA tissue IHC) | |
| Regulation | Low tissue specificity (HPA tissue RNA) | |
| Isoform / epitope | 3 isoforms; epitope coverage is unknown (UniProt) |
The catalog antibody’s IHC-P protocol (datasheet A04551-1) is presented alongside two published CPSF6 paraffin-section IHC protocols (PMC11234225; PMC5514498).
| Sample | Paraffin-embedded human liver cancer tissue; fixative not specified (datasheet A04551-1) |
| Fixation | Image fixative and duration unreported (datasheet A04551-1); 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 A04551-1); 20 min, 95–100 °C (standard) |
| Peroxidase block | 3% H2O2, 10 min, room temperature (standard) |
| Blocking | 10% goat serum (datasheet A04551-1) |
| Primary antibody | Rabbit anti-CPSF6, 2-5 μg/ml (datasheet A04551-1) |
| Primary incubation | Overnight at 4 °C (datasheet A04551-1) |
| Detection | Streptavidin-biotin complex (SABC), DAB chromogen (datasheet A04551-1) |
| Counterstain | Hematoxylin, blue, dehydrate and mount (standard) |
| Expected result | CPSF6-positive staining in adipocytes of adipose tissue (HPA tissue IHC: High). HPA tissue profile: Ubiquitous nuclear expression. No signal in the no-primary control. |
CPSF6 should stain predominantly in nuclei across many cell types, including adipocytes, hematopoietic cells and glandular cells reported as High by HPA (HPA tissue IHC: ubiquitous nuclear expression; High in these cells). Nucleoplasmic and speckled nuclear signal fits its known distribution; CPSF6 can also shuttle through the cytoplasm (UniProt Q16630: subcellular location). It has no transmembrane segment (UniProt Q16630: topology). HPA rates the tissue IHC pattern Supported, with medium agreement between staining and RNA data (HPA tissue IHC: reliability).
| Nuclear chromogen appears in many cells, with clear signal in adipocytes or hematopoietic cells. | This fits the broad nuclear pattern and reported High staining in those cells (HPA tissue IHC). Compare cells within the same section before scoring intensity; a High HPA call is a reference pattern, not a calibrated intensity threshold. |
| Cytoplasmic staining dominates while nuclei are faint or blank. | Predominantly cytoplasmic IHC conflicts with the reported ubiquitous nuclear pattern (HPA tissue IHC). CPSF6 does shuttle between nucleus and cytoplasm (UniProt Q16630), so some cytoplasmic signal alone is inconclusive. Check nuclear preservation, background and control staining before calling the distribution biological. |
| Strong staining appears chiefly in a cell population while the expected High population is unstained. | Review cell identification and possible cross-reactivity or endogenous detection activity (general IHC practice). HPA reports High staining in specified populations but supplies no negative cell populations here (HPA tissue IHC); an unlisted cell type cannot be declared CPSF6-negative from this record. |
| Chromogen coats tissue broadly, obscuring nuclear boundaries. | A diffuse deposit cannot establish CPSF6 localization. Excess background may reflect nonspecific antibody binding, detection activity or inadequate washing (general IHC practice). Judge a positive result only where stained nuclei can be distinguished from surrounding tissue. |
| No nuclear signal is visible in bone marrow hematopoietic cells or adrenal glandular cells. | Both are reported High by HPA, so absence warrants a run-level check (HPA tissue IHC). Review the positive control, antibody and detection reagents, and retrieval conditions (general IHC practice). A single blank section does not establish absent CPSF6 expression. |
| Nuclear distribution | The primary scoring compartment is the nucleus (HPA tissue IHC: ubiquitous nuclear expression). UniProt also places CPSF6 in nucleoplasm and nuclear speckles (UniProt Q16630); routine chromogenic sections may not resolve individual speckles (general microscopy practice). |
| Shuttling and cell-cycle distribution | CPSF6 shuttles between nucleus and cytoplasm, and its speckle and paraspeckle distribution varies during the cell cycle (UniProt Q16630). Interpret modest compartment variation against the dominant tissue IHC pattern, without treating every cytoplasmic trace as failure (HPA tissue IHC). |
| Isoforms and epitope coverage | Three isoforms are listed (UniProt Q16630). The supplied record gives no antibody epitope or isoform-specific IHC performance, so this evidence cannot predict which isoforms the catalog antibody detects or explain a negative section. |
| Antibody validation | The listed antibody HPA039973 is Supported for IHC and Enhanced for ICC (HPA antibodies). The tissue pattern has medium agreement with RNA expression (HPA tissue IHC); use the reported pattern as a reference, while evaluating the actual section and controls. |
| IF/ICC Q&A | Where should signal appear in IF/ICC? In nucleoplasm and nuclear speckles (HPA subcellular ICC-IF: both enhanced); UniProt also reports speckles and cytoplasmic shuttling (UniProt Q16630). This localization answer does not establish an IF/ICC protocol or dilution. |
| Situation | Likely cause | Next action |
|---|---|---|
| Known High tissue gives no nuclear stain. | The run may have failed at primary incubation, retrieval or detection (general IHC practice); HPA reports High staining in bone marrow hematopoietic cells (HPA tissue IHC). | Check an on-run positive control and reagent sequence; review the catalog antibody's IHC-P instructions before adjusting retrieval or antibody concentration (general IHC practice). |
| Cytoplasm is stronger than nuclei throughout the section. | This departs from the reported nuclear tissue pattern (HPA tissue IHC), although CPSF6 can shuttle (UniProt Q16630); diffuse background remains a possible explanation (general IHC practice). | Inspect whether nuclei are intact and separately stained, then compare the positive and negative controls and reduce nonspecific background using standard IHC optimization (general IHC practice). |
| Brown deposit is diffuse or follows tissue edges. | Nonspecific binding, drying or uneven reagent coverage can create misleading chromogen deposition (general IHC practice). | Review section handling, blocking, wash coverage and development time; score only interpretable cellular staining with a nuclear location (general IHC practice; HPA tissue IHC: nuclear pattern). |
| Signal appears in the no-primary control. | The primary antibody cannot account for that control's staining; endogenous detection activity or detection-reagent background is possible (general IHC practice). | Check the detection chemistry and its appropriate endogenous-activity block, then repeat the control alongside the test section (general IHC practice). |
| Only an unlisted cell population stains strongly. | Cell identification, cross-reactivity or local background may explain the mismatch (general IHC practice); the supplied HPA extract lists no negative populations (HPA tissue IHC). | Confirm morphology and staining compartment, compare a reported High population on the same run, and avoid calling the unlisted cells false positive solely because they are unlisted. |
| Nuclear stain varies between adjacent cells. | CPSF6 nuclear substructure distribution can vary with the cell cycle (UniProt Q16630); staining variation may also reflect section or detection variability (general IHC practice). | Score the fraction of clearly stained nuclei and their intensity within each cell population, and compare technical controls before assigning biological meaning (general IHC practice). |
Comprehensive Human Protein Atlas IHC scoring per tissue (reliability: Supported — 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.
| Tissue | Cell type | Level | Evidence | Source |
|---|---|---|---|---|
| Adipose tissue | Adipocytes | High | Protein (IHC) | HPA → |
| Adrenal gland | Glandular cells | High | Protein (IHC) | HPA → |
| Appendix | Glandular cells | High | Protein (IHC) | HPA → |
| Bone marrow | Hematopoietic cells | High | Protein (IHC) | HPA → |
| Breast | Adipocytes | High | Protein (IHC) | HPA → |
| Tissue | Cell type | Level | Evidence | Source |
|---|---|---|---|---|
| None in HPA: CPSF6 is detected in all 45 scored tissues. Use a no-primary (secondary-only) and an isotype control instead. | ||||
Use the documented paraffin-section conditions as a starting point, then assess nuclear staining, tissue controls, and background before interpreting CPSF6 signal.
Anti-CPSF6 antibodies have IHC images from human paraffin sections (catalog IHC captions) and IF/ICC images from MCF-7 and U20S cells (catalog IF captions); both list human, monkey, mouse and rat reactivity (catalog applications/reactivity).
A04551-1 has IHC images from human liver cancer and appendiceal adenocarcinoma paraffin sections and an IF/ICC image from MCF-7 cells (A04551-1 image captions). M04551 has IHC images from human squamous cell carcinoma, cervical cancer, colorectal adenocarcinoma and ovarian cancer paraffin sections and an IF/ICC image from U20S cells (M04551 image captions).
Which to pick: For paraffin-section IHC, choose A04551-1 for its human liver cancer example or M04551 for its human squamous cell carcinoma example; each caption reports EDTA retrieval at pH 8.0, while neither reports the fixative (A04551-1 IHC caption; M04551 IHC caption). For IF/ICC, both have cell images at 5 μg/ml; A04551-1 is rabbit-hosted with an MCF-7 image, while M04551 is mouse-hosted clone 3F11E1 with a U20S image (catalog host/clone; A04551-1 IF caption; M04551 IF caption). For cross-species planning, both list human, mouse, rat and monkey reactivity, but their stated IHC-P dilutions cover human, mouse and rat, and their IF/ICC dilutions cover human (catalog reactivity; catalog dilution_raw).