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- Table of Contents
Plan SHMT1 chromogenic IHC in paraffin sections using cytoplasmic staining in hepatocytes and kidney tubule cells as positive references (HPA tissue IHC). Interpret nuclear signal in light of cell cycle dependent localization (UniProt).
Expected localisation, validated protocols, controls and antibodies — the at-a-glance facts below, then the full design guide.
| Expected localisation | Cytoplasmic tissue staining (HPA tissue IHC); nuclear location (UniProt) | |
| Staining pattern | Cytoplasmic staining in hepatocytes and kidney tubule cells (HPA tissue IHC) | |
| Antigen retrieval | EDTA pH 8.0 HIER, heat-mediated (datasheet M02944) | |
| Positive control | Appendix+4 more · see all | |
| Negative control | Adipose tissue+4 more · see all |
| Fixation | Keep fixation consistent across paraffin sections. (standard IHC practice; not target-specific) | |
| Caveat | Cell cycle dependent nuclear localization may shift the pattern (UniProt) | |
| Regulation | Nuclear retention during S and G2/M phases (UniProt) | |
| Isoform / epitope | 4 isoforms; epitope differences are unspecified (UniProt) |
The catalog antibody’s IHC-P protocol (datasheet: M02944) is followed by four published SHMT1 IHC protocols (PMC10728000; PMC12683878; PMC11724956; PMC6373090).
| Sample | Paraffin-embedded human liver cancer tissue; fixative not specified (datasheet M02944) |
| Fixation | Image fixative and duration unreported (datasheet M02944); 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 M02944); 20 min, 95–100 °C (standard) |
| Peroxidase block | 3% H2O2, 10 min, room temperature (standard) |
| Blocking | 10% goat serum (datasheet M02944) |
| Primary antibody | Mouse monoclonal (clone 9C7) anti-SHMT1, 2μg/ml (datasheet M02944) |
| Primary incubation | Overnight at 4 °C (datasheet M02944) |
| Detection | Streptavidin-biotin complex (SABC), DAB chromogen (datasheet M02944) |
| Counterstain | Hematoxylin, blue, dehydrate and mount (standard) |
| Expected result | SHMT1-positive staining in glandular cells of appendix (HPA tissue IHC: High). HPA tissue profile: Cytoplasmic expression in several tissues. No signal in the no-primary control. |
SHMT1 should stain mainly the cytoplasm of kidney tubular cells, hepatocytes and several glandular cell populations; spermatogonia also show high staining (HPA tissue IHC). Nuclear staining can occur, although cytosolic localization has stronger support in ICC-IF (UniProt P34896; HPA subcellular). SHMT1 has no transmembrane segment (UniProt P34896 topology). HPA rates tissue IHC reliability Enhanced, with medium consistency between antibody staining and RNA expression (HPA tissue IHC).
| Clear cytoplasmic staining in kidney tubules or hepatocytes, with identifiable cell borders. | This matches high staining in both cell populations (HPA tissue IHC) and SHMT1's cytoplasmic localization (UniProt P34896). Compare cells within the same section before judging intensity: HPA levels describe observed cell populations, not a required shade or staining threshold for every specimen (HPA tissue IHC). |
| Some nuclei stain along with the cytoplasm; or staining appears only as a crisp membrane outline. | Nuclear signal can be plausible because SHMT1 enters the nucleus during the cell cycle (UniProt P34896); HPA reports additional nucleoplasmic ICC-IF localization as uncertain (HPA subcellular). A membrane-only pattern conflicts with the reported compartments and lack of a transmembrane segment (UniProt P34896 topology); investigate it as possible artefact. |
| Strong chromogen appears in adipocytes or cardiomyocytes while expected positive cells remain weak. | HPA reports SHMT1 as not detected in those cell populations (HPA tissue IHC). The mismatch raises concern for nonspecific antibody binding or endogenous detection activity; it does not prove either cause. Review tissue morphology, antibody controls and detection-only controls before interpreting these cells as SHMT1 positive (general IHC practice). |
| Color covers stroma, blank spaces and many unrelated cells, obscuring cell boundaries. | Diffuse deposition cannot establish the cell-restricted cytoplasmic pattern reported across several tissues (HPA tissue IHC). Assess background with a control lacking primary antibody, then review blocking, washes and detection chemistry (general IHC practice). A clean-looking field alone does not establish antibody specificity (general IHC practice). |
| Kidney tubules and hepatocytes show no convincing signal despite interpretable tissue morphology. | Both are high-staining reference populations in HPA tissue IHC (HPA tissue IHC), so their simultaneous absence makes a technical failure plausible. Check the IHC-validated antibody's stated paraffin-section conditions and the run's positive control (general IHC practice). HPA's Enhanced rating supports the reported pattern but does not guarantee every specimen will stain (HPA tissue IHC). |
| Choice of reference tissue | Kidney tubules and hepatocytes are high-staining examples; adipocytes and cardiomyocytes are reported not detected (HPA tissue IHC). Use the named cell populations when comparing sections, since a tissue contains more than one cell type (general IHC practice). |
| Compartment and cell-cycle context | SHMT1 is cytoplasmic and nuclear; nuclear import and enrichment during S and G2/M phases are reported (UniProt P34896). Nuclear staining therefore needs cell context and cannot be rejected solely for being nuclear (UniProt P34896). |
| Antibody evidence | HPA023314 and HPA078682 each have Enhanced IHC validation (HPA antibodies). Tissue reliability is also Enhanced, but staining and RNA show medium consistency (HPA tissue IHC). Treat an unexpected pattern as a finding to verify, not as automatic proof of expression. |
| Isoforms and epitope coverage | Four SHMT1 isoforms are listed (UniProt P34896). The supplied record gives no antibody epitope or isoform coverage, so it cannot predict whether the catalog antibody detects every isoform or explain an apparent negative by isoform choice. |
| IF/ICC Q: Where should fluorescence appear? | A: Mainly in cytosol; additional nucleoplasm is reported with uncertain support (HPA subcellular). This informs localization checks only: ICC-IF images do not supply an IHC-P protocol or establish the expected chromogenic intensity in tissue sections (HPA subcellular; HPA tissue IHC). |
| Situation | Likely cause | Next action |
|---|---|---|
| No signal in a kidney section. | The sampled cells may not include intact tubules, or the IHC run may have failed; tubule cells are high staining in HPA (HPA tissue IHC). | Confirm tubule morphology and inspect a concurrently processed positive control; then check the catalog antibody's IHC-P instructions and detection reagents (general IHC practice). |
| Nuclei stain more strongly than cytoplasm. | Nuclear SHMT1 is biologically plausible, with cell-cycle-linked localization reported (UniProt P34896), but nonspecific nuclear signal remains possible (general IHC practice). | Compare the pattern across cells and sections, and inspect controls before scoring it; HPA's additional nucleoplasmic ICC-IF location has uncertain support (HPA subcellular). |
| Only cell membranes have sharp staining. | That distribution conflicts with cytoplasm/nucleus localization and the absence of a transmembrane segment (UniProt P34896 topology). | Review morphology and detection-only controls; repeat with an independently validated IHC antibody if available (general IHC practice; HPA antibodies: two Enhanced IHC antibodies). |
| Brown deposit appears without the primary antibody. | The primary antibody cannot account for that control's deposit; endogenous detection activity or detection-reagent background is possible (general IHC practice). | Check the enzyme and chromogen system, its appropriate endogenous-activity control and blocking steps, then repeat the control alongside the specimen (general IHC practice). |
| Diffuse staining hides differences between listed high and not-detected cells. | Background or excessive detection signal may obscure the cell-specific pattern reported by HPA (HPA tissue IHC; general IHC practice). | Compare a primary-omission control, review washes and blocking, and adjust the assay using the catalog antibody's IHC-P instructions (general IHC practice). |
| An HPA not-detected population stains reproducibly. | HPA's designation describes its observed assay result, not an absolute absence of protein in every specimen (HPA tissue IHC). The new staining could also be nonspecific (general IHC practice). | Record the exact cell type and compartment, compare a known high-staining population, and seek independent antibody or orthogonal evidence before assigning SHMT1 expression (HPA tissue IHC; general IHC practice). |
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.
| Tissue | Cell type | Level | Evidence | Source |
|---|---|---|---|---|
| Appendix | Glandular cells | High | Protein (IHC) | HPA → |
| Duodenum | Glandular cells | High | Protein (IHC) | HPA → |
| Epididymis | Glandular cells | High | Protein (IHC) | HPA → |
| Kidney | Cells in tubules | High | Protein (IHC) | HPA → |
| Liver | Hepatocytes | High | Protein (IHC) | HPA → |
| Tissue | Cell type | Level | Evidence | Source |
|---|---|---|---|---|
| Adipose tissue | Adipocytes | Not detected | Protein (IHC) | HPA → |
| Adrenal gland | Glandular cells | Not detected | Protein (IHC) | HPA → |
| Caudate | Glial cells | Not detected | Protein (IHC) | HPA → |
| Cerebellum | Cells in granular layer | Not detected | Protein (IHC) | HPA → |
| Heart muscle | Cardiomyocytes | Not detected | Protein (IHC) | HPA → |
Troubleshoot SHMT1 staining in paraffin sections by checking retrieval, compartment, cell type, detection background and scoring against the supplied IHC evidence.
The catalog shows SHMT1 IHC in a human paraffin-embedded liver cancer section (M02944 image caption) and IF/ICC in A431 cells (A02944-1 image caption); both antibodies list Human, Monkey, Mouse and Rat reactivity (catalog).
M02944 is listed for IHC and IF/ICC, with its own IHC figure showing a human paraffin-embedded liver cancer section (catalog; M02944 image caption). A02944-1 is listed for IHC and IF/ICC, with its own IF figure showing A431 cells (catalog; A02944-1 image caption).
Which to pick: For tissue IHC, choose the mouse monoclonal M02944 (clone 9C7): its own caption documents chromogenic staining of a paraffin-embedded human liver cancer section; the fixative is unreported (catalog; M02944 image caption). For IF/ICC, choose the rabbit A02944-1, whose own figure documents staining in A431 cells at 5 μg/mL (catalog; A02944-1 image caption). For cross-species work, both list Human, Monkey, Mouse and Rat reactivity, while the cited figures show human samples (catalog; M02944 image caption; A02944-1 image caption).