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- Table of Contents
Plan XRCC5 chromogenic IHC in paraffin sections using its observed widespread nuclear tissue staining as a reference (HPA tissue IHC). The guide covers fixation consistency, staining controls and nuclear scoring, including the reported lack of signal in liver cholangiocytes (HPA tissue IHC).
Expected localisation, validated protocols, controls and antibodies — the at-a-glance facts below, then the full design guide.
| Expected localisation | Nuclear tissue staining (HPA tissue IHC); nucleolar and chromosomal locations are annotated (UniProt) | |
| Staining pattern | Widespread nuclear staining across tissue cell types (HPA tissue IHC) | |
| Antigen retrieval | EDTA pH 8.0 HIER, heat-mediated (datasheet PA1641) | |
| Positive control | Appendix+4 more · see all | |
| Negative control | Liver |
| Fixation | Keep fixation consistent across paraffin sections (standard IHC practice; not target-specific); Matched tissue-IHC evidence does not establish the fixation claim. Validate the specimen-specific method before use. (selected-SKU IHC image PA1641) | |
| Caveat | Liver cholangiocytes show no detected signal (HPA tissue IHC) | |
| Regulation | Low tissue specificity (HPA tissue RNA) | |
| Isoform / epitope | No annotated isoforms; chain spans residues 2–732 (UniProt) |
The catalog antibody’s IHC-P protocol uses EDTA pH 8.0 retrieval (datasheet: PA1641). Four published XRCC5 IHC workflows provide sample-specific comparisons (PMC5648251; PMC8762376; PMC5354834; PMC6137920).
| Sample | Paraffin-embedded human intestinal cancer tissue; fixative not specified (datasheet PA1641) |
| Fixation | Image fixative and duration unreported (datasheet PA1641); 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 PA1641); 20 min, 95–100 °C (standard) |
| Peroxidase block | 3% H2O2, 10 min, room temperature (standard) |
| Blocking | 10% goat serum (datasheet PA1641) |
| Primary antibody | Rabbit anti-XRCC5, 0.5-1μg/ml (datasheet PA1641) |
| Primary incubation | Overnight at 4 °C (datasheet PA1641) |
| Detection | Streptavidin-biotin complex (SABC), DAB chromogen (datasheet PA1641) |
| Counterstain | Hematoxylin, blue, dehydrate and mount (standard) |
| Expected result | XRCC5-positive staining in endocrine cells of appendix (HPA tissue IHC: High). HPA tissue profile: Ubiquitous nuclear expression. No signal in the no-primary control. |
XRCC5 is a nuclear protein associated with the nucleolus and chromosomes (UniProt P13010: subcellular location). In paraffin-section IHC, expect widespread nuclear staining; HPA describes ubiquitous nuclear expression with Supported reliability and medium consistency between antibody staining and RNA expression (HPA: tissue IHC). XRCC5 has no transmembrane segment, so a membrane-rim pattern is unexpected (UniProt P13010: topology). Judge intensity against the cell types documented in the tissue being examined (HPA: tissue IHC).
| Distinct nuclear staining in breast glandular cells or bone-marrow hematopoietic cells (HPA: High in each cell type). | This matches documented high-staining examples and XRCC5’s nuclear location (HPA: tissue IHC; UniProt P13010: subcellular location). Compare nuclei with nearby tissue structure and the run controls before calling intensity, since HPA’s IHC reliability is Supported with medium staining–RNA consistency (HPA: tissue IHC). |
| Predominantly membrane-rim or diffuse cytoplasmic staining, with little nuclear signal. | The compartment conflicts with XRCC5’s nuclear annotation and lack of a transmembrane segment (UniProt P13010: subcellular location and topology). Treat it as a possible nonspecific or detection artefact, then review the primary-antibody omission control and staining distribution (general IHC practice). |
| Strong staining appears in liver cholangiocytes while nuclei in documented high-staining cells are weak. | HPA reports cholangiocytes as Not detected, whereas several other cell types are High (HPA: tissue IHC). This mismatch raises possible cross-reactivity or endogenous detection activity; it does not prove either cause or establish that all liver cells lack XRCC5 (HPA: tissue IHC; general IHC practice). |
| Chromogen covers extracellular spaces, section edges, or nuclei and cytoplasm indiscriminately. | That distribution does not resolve the reported nuclear pattern (HPA: tissue IHC; UniProt P13010: subcellular location). Diffuse deposit can reflect background from detection reagents or staining conditions; assess a primary-antibody omission control and inspect tissue morphology (general IHC practice). |
| No nuclear signal in a breast glandular-cell or bone-marrow hematopoietic-cell section. | Both are documented High examples, so a blank result warrants a run-control check (HPA: tissue IHC). Check tissue preservation, retrieval, primary-antibody use, and detection reagents as general IHC workflow checks; the supplied sources do not establish XRCC5-specific fixation sensitivity (general IHC practice). |
| Tissue and cell selection (HPA: tissue IHC) | HPA reports High staining in appendix endocrine cells, breast glandular cells, bone-marrow hematopoietic cells, and other listed examples; adipocytes are Low and liver cholangiocytes Not detected (HPA: tissue IHC). Score the named cell population rather than treating an entire organ as uniformly positive or negative (general IHC practice). |
| Compartment and molecular form (UniProt P13010) | Nuclear, nucleolar, and chromosome locations are annotated; no transmembrane segment, signal peptide, propeptide, or isoforms are listed (UniProt P13010: subcellular location, topology, processing, isoforms). These facts support nuclear interpretation but do not predict epitope accessibility or a particular retrieval condition (UniProt P13010; general IHC practice). |
| IHC antibody evidence (HPA: antibodies) | HPA lists IHC as Supported for HPA025813 and CAB004468; HPA064685 has no listed IHC status (HPA: antibodies). Those entries describe the named antibodies, not every XRCC5 reagent, and HPA’s tissue-level Supported rating carries medium staining–RNA consistency (HPA: antibodies and tissue IHC). |
| Endogenous detection activity (general IHC practice) | Chromogenic detection can produce signal unrelated to primary-antibody binding if endogenous activity or nonspecific reagent binding is insufficiently controlled (general IHC practice). A primary-antibody omission control helps identify detection background; a positive nuclear pattern and suitable tissue control are still needed to interpret XRCC5 staining (general IHC practice; HPA: tissue IHC). |
| IF/ICC Q: Where should XRCC5 appear? (HPA: subcellular ICC-IF) | A: Mainly in the nucleoplasm; HPA marks that location Supported (HPA: subcellular ICC-IF). UniProt also annotates nucleus, nucleolus, and chromosome (UniProt P13010: subcellular location). This is an interpretation cue for IF/ICC images, not an IF/ICC protocol or an IHC detection setting. |
| Situation | Likely cause | Next action |
|---|---|---|
| Documented High tissue has no nuclear staining (HPA: tissue IHC). | The run may have failed at tissue handling, retrieval, primary-antibody application, or chromogenic detection (general IHC practice); no XRCC5-specific fixation effect is reported in the supplied sources. | Verify the run with a documented High cell population and check each recorded IHC step and reagent control (HPA: tissue IHC; general IHC practice). Do not infer that retrieval or fixation is the XRCC5-specific cause without direct evidence. |
| Nuclei are visible but chromogen is mainly cytoplasmic or membranous. | That pattern conflicts with nuclear XRCC5 and its lack of a transmembrane segment (UniProt P13010: subcellular location and topology). Nonspecific staining is one possible explanation (general IHC practice). | Compare with a primary-antibody omission control, examine morphology, and repeat with an IHC-supported antibody if available (general IHC practice; HPA: antibodies). Score nuclear staining separately from off-compartment deposit. |
| Liver cholangiocytes stain strongly despite weak staining in a documented High control. | HPA records cholangiocytes as Not detected and the selected control as High (HPA: tissue IHC). Cross-reactivity or endogenous chromogenic activity is possible, but the pattern alone cannot identify the mechanism (general IHC practice). | Review the omission control and cell identification; compare with an independently IHC-supported XRCC5 antibody where feasible (general IHC practice; HPA: antibodies). Avoid calling every liver cell negative based on the cholangiocyte entry. |
| Brown deposit spreads across stroma, edges, or most cellular compartments. | The distribution obscures the nuclear pattern expected for XRCC5 (HPA: tissue IHC; UniProt P13010: subcellular location). Detection background or excess chromogen development can produce diffuse deposit (general IHC practice). | Inspect the primary-antibody omission control and review blocking, washing, detection, and development records (general IHC practice). Interpret only nuclei that remain distinct from background and match the tissue’s documented cell pattern (HPA: tissue IHC). |
| A low-signal adipocyte field is interpreted as a failed run. | HPA lists adipocytes as Low, so weak staining there alone is a poor failure criterion (HPA: tissue IHC). A field may also contain other cell types requiring separate identification (general IHC practice). | Use a documented High population in the same run to judge performance, then score adipocytes as their own cell population (HPA: tissue IHC; general IHC practice). Do not turn Low into an expected absence of protein. |
| An IF/ICC image shows nucleoplasmic staining, but the paraffin IHC result is unclear. | Nucleoplasm is the Supported ICC-IF location, while tissue IHC has its own Supported reliability assessment (HPA: subcellular ICC-IF and tissue IHC). The two applications provide different evidence. | Use the IF/ICC image to check compartment expectations only; resolve the IHC call with an IHC-supported antibody, tissue control, morphology, and chromogenic controls (HPA: antibodies and tissue IHC; 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 |
|---|---|---|---|---|
| Appendix | Endocrine cells | High | Protein (IHC) | HPA → |
| Bone marrow | Hematopoietic cells | High | Protein (IHC) | HPA → |
| Breast | Glandular cells | High | Protein (IHC) | HPA → |
| Caudate | Glial cells | High | Protein (IHC) | HPA → |
| Cerebellum | Cells in granular layer | High | Protein (IHC) | HPA → |
| Tissue | Cell type | Level | Evidence | Source |
|---|---|---|---|---|
| Liver | Cholangiocytes | Not detected | Protein (IHC) | HPA → |
Troubleshoot XRCC5 staining in paraffin sections by checking retrieval, nuclear localisation, controls and cell-level scoring before interpreting chromogenic signal.
Anti-XRCC5 antibodies have IHC images from human paraffin sections and IF images from cells and tissue (catalog captions: PA1641, PB9464, M01275); PB9464 also lists Mouse and Rat reactivity (catalog: PB9464).
PA1641 shows IHC in paraffin-embedded human intestinal cancer and IF in A549 cells and paraffin-embedded human intestinal cancer (catalog captions: PA1641); PB9464 shows IHC in paraffin-embedded human lung cancer and IF in U20S cells (catalog captions: PB9464). M01275 shows IHC in paraffin-embedded human colon and lists IF/ICC among its applications, although no IF image is supplied (catalog: M01275).
Which to pick: For tissue IHC, choose PA1641 for the pictured human intestinal cancer section, PB9464 for the pictured human lung cancer section, or rabbit monoclonal M01275 for the pictured human colon section; each is paraffin-embedded, and none of these captions reports the fixative (catalog IHC captions: PA1641, PB9464, M01275; catalog: M01275 clone FAE-24). For IF/ICC, PA1641 has IF images in A549 cells and human intestinal cancer tissue, while PB9464 has an IF image in U20S cells (catalog IF captions: PA1641, PB9464). For cross-species planning, PB9464 lists Human, Mouse, and Rat reactivity, although its pictured paraffin IHC uses human tissue (catalog: PB9464; catalog IHC caption: PB9464).