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GATM / Glycine amidinotransferase, mitochondrial · IHC design guide
Design Immunohistochemistry for GATM
Plan chromogenic GATM IHC in paraffin sections using kidney tubules, hepatocytes and pancreatic exocrine cells as high-staining references (HPA tissue IHC). Assess granular cytoplasmic staining while considering GATM’s annotated mitochondrial inner-membrane localisation (HPA tissue IHC; UniProt).
Evidence assembled Oct 2026 · For research use; verify linked source records and product datasheet before use
GATM Immunohistochemistry Experimental Design Guide
Expected localisation, validated protocols, controls and antibodies — the at-a-glance facts below, then the full design guide.
Must know before staining
| Expected localisation | Granular cytoplasm in kidney, liver and pancreas (HPA tissue IHC) | |
| Staining pattern | Granular cytoplasm in tubules, hepatocytes and exocrine cells (HPA tissue IHC) | |
| Antigen retrieval | EDTA pH 8.0 HIER, heat-mediated (datasheet A02754-1) | |
| Positive control | Kidney+4 more · see all | |
| Negative control | Adipose tissue+4 more · see all |
Important caveats
Reasons your staining may differ from the expected pattern.
| Fixation | Matched tissue-IHC evidence does not establish the fixation claim. Validate the specimen-specific method before use. (selected-SKU IHC image A02754-1) | |
| Caveat | Antibody staining and RNA show medium consistency (HPA tissue IHC) | |
| Regulation | Highest tissue expression is in kidney (UniProt) | |
| Isoform / epitope | 3 isoforms; the mature chain starts at residue 44 (UniProt) |
Section 1
Recommended GATM IHC & IF Protocols
The catalog antibody’s IHC-P protocol is paired with four published GATM IHC protocols from lung, cholangiocarcinoma, renal carcinoma and glioblastoma specimens (PMC9513582; PMC11408786; PMC9139776; PMC10842612).
| Sample | Paraffin-embedded human breast cancer tissue; fixative not specified (datasheet A02754-1) |
| Fixation | Image fixative and duration unreported (datasheet A02754-1); 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 A02754-1); 20 min, 95–100 °C (standard) |
| Peroxidase block | 3% H2O2, 10 min, room temperature (standard) |
| Blocking | 10% goat serum (datasheet A02754-1) |
| Primary antibody | Rabbit anti-GATM, 2-5 μg/ml (datasheet A02754-1) |
| Primary incubation | Overnight at 4 °C (datasheet A02754-1) |
| Detection | HRP-conjugated secondary, DAB chromogen (datasheet A02754-1) |
| Counterstain | Hematoxylin, blue, dehydrate and mount (standard) |
| Expected result | GATM-positive staining in cells in tubules of kidney (HPA tissue IHC: High). HPA tissue profile: Granular cytoplasmic expression in several different tissue types, mainly in kidney, liver and pancreas. No signal in the no-primary control. |
💡Decision noteStart with heat-mediated EDTA pH 8.0 retrieval for the catalog antibody (datasheet A02754-1); published protocols also report citrate or pH 6 retrieval (PMC11408786; PMC10842612).
Section 2
What Is the Expected GATM Staining Pattern?
GATM should appear as granular cytoplasmic staining in kidney tubule cells, hepatocytes and pancreatic exocrine glandular cells (HPA tissue IHC). Its mitochondrial inner-membrane association, probably on the outer side, and cytoplasmic localization fit this pattern; no transmembrane segment is annotated (UniProt P50440 topology). HPA rates tissue IHC reliability Enhanced, while reporting medium consistency between staining and RNA expression (HPA tissue IHC).
| Granular cytoplasmic staining in kidney tubule cells, hepatocytes or pancreatic exocrine glandular cells. | This matches the reported high-staining cell populations (HPA tissue IHC). Score intensity and the fraction of stained cells within the identified population, with the tissue context recorded; HPA's High category describes its observations, not a required intensity for every section (HPA tissue IHC; general IHC practice). |
| Predominantly nuclear staining, or a sharply outlined plasma-membrane pattern with little cytoplasmic signal. | That distribution conflicts with the reported granular cytoplasmic tissue pattern and supported mitochondrial IF localization (HPA tissue IHC; HPA ICC-IF). Review controls and staining conditions before assigning it to GATM; UniProt also annotates cytoplasm and inner-membrane association, but no transmembrane segment (UniProt P50440 topology). |
| Prominent staining in a cell population reported as not detected, such as adipocytes or bone-marrow hematopoietic cells. | HPA reports no detection in those sampled populations (HPA tissue IHC). Check cell identity and a negative control: unexpected color may reflect cross-reactivity or endogenous detection activity (general IHC practice). A single discrepancy does not establish a new GATM-positive population or prove the cause of staining. |
| Weak, diffuse color across cells and extracellular spaces, without a granular cytoplasmic pattern. | This is difficult to distinguish from nonspecific background and does not match HPA's reported GATM pattern (HPA tissue IHC). Compare the distribution with a known-positive section and a control for detection background; assess the whole slide before calling faint color positive (general IHC practice). |
| No visible signal in kidney tubules, hepatocytes or pancreatic exocrine glandular cells. | These are HPA High populations, so an entirely blank result calls for a technical check before a biological conclusion (HPA tissue IHC; general IHC practice). Confirm that the expected cells are present and that the positive control and detection reagents worked; HPA's Enhanced reliability does not guarantee staining in every preparation (HPA tissue IHC). |
💡Expected GATM appearanceCall the result consistent with GATM when kidney tubule cells, hepatocytes or pancreatic exocrine cells show predominantly granular cytoplasmic staining, commonly strong in HPA examples; isolated nuclear color or uniform diffuse background is suspect (HPA tissue IHC; general IHC practice).
| Tissue and cell population | HPA reports High staining in kidney tubule cells, hepatocytes and pancreatic exocrine cells; several other populations are Medium or Low, and some are not detected (HPA tissue IHC). Compare like cell types when judging an unfamiliar section; absence from a listed negative population is more informative than whole-organ color. |
| Location and topology | GATM is annotated in cytoplasm and at the mitochondrial inner membrane, probably attached to its outer side, with no transmembrane segment (UniProt P50440 topology). This supports an intracellular interpretation but cannot resolve mitochondrial membrane position by chromogenic tissue IHC alone (general IHC practice). |
| Antibody and tissue evidence | The listed antibody HPA026077 has Enhanced IHC validation, and the overall tissue profile has Enhanced reliability with medium agreement between staining and RNA data (HPA antibodies; HPA tissue IHC). Use those ratings to weigh an observed pattern; they do not identify the cause of an unexpected stain. |
| Protein forms and epitope inference | UniProt lists three isoforms and a mature chain spanning residues 44–423 (UniProt P50440). The supplied record gives no antibody epitope or isoform-specific IHC result, so a staining difference cannot be assigned to isoform recognition or processing from these annotations alone. |
| IF/ICC: What pattern is expected? | A mitochondrial pattern is the supported ICC-IF localization, with images listed for RT-4, Rh30 and U2OS; HPA026077 has Supported ICC status (HPA ICC-IF; HPA antibodies). Interpret that as localization evidence for the separate IF/ICC application, not an intensity standard for paraffin-section chromogenic IHC. |
| Situation | Likely cause | Next action |
|---|---|---|
| Known-positive tissue is completely blank. | A missing or inactive staining step is possible; HPA reports High signal in kidney tubule cells, hepatocytes and pancreatic exocrine cells (HPA tissue IHC; general IHC practice). | Check that the expected cells are in the section, then review primary antibody, detection reagents and chromogen with a working positive control; review retrieval conditions as general paraffin-IHC practice. |
| Signal is weak in an expected High cell population. | The result differs from HPA's reported level, but that alone does not identify a GATM-specific fixation or epitope problem (HPA tissue IHC). | Compare the same cell type with a positive control; review antibody dilution, retrieval and detection conditions under general IHC practice. No target-specific fixation sensitivity is supplied. |
| Color covers much of the section without cellular detail. | Diffuse background can obscure the granular cytoplasmic pattern reported by HPA (HPA tissue IHC; general IHC practice). | Inspect a negative control, then review blocking, wash steps and detection background as general IHC practice. Reassess only after the expected cells and their cytoplasmic pattern can be distinguished. |
| Strong signal appears mainly in nuclei or along cell surfaces. | Those dominant compartments disagree with HPA's granular cytoplasmic tissue pattern and supported mitochondrial ICC-IF location (HPA tissue IHC; HPA ICC-IF). | Confirm the cells and section quality, compare a known-positive tissue and negative control, and review staining specificity before scoring the unusual compartment as GATM (general IHC practice). |
| Adipocytes or bone-marrow hematopoietic cells appear strongly positive. | HPA reports these sampled cell populations as not detected; cross-reactivity or endogenous detection activity are possible explanations, not established diagnoses (HPA tissue IHC; general IHC practice). | Verify cell identity and compare appropriate negative controls with a known-positive tissue. Record the discrepancy without treating the unexpected color alone as proof of GATM expression. |
| A negative control develops chromogen color. | Color in a control without the primary antibody points toward background in the detection workflow (general IHC practice). | Review blocking and detection steps, including possible endogenous activity, and resolve control staining before interpreting weak tissue signal (general IHC practice). |
Experiment evidence
IHC & IF images showing GATM staining
A02754-1 · IHCIHC analysis of GATM using anti-GATM antibody (A02754-1). GATM was detected in a paraffin-embedded section of human breast cancer tissue. He
A02754-1 · IHCIHC analysis of GATM using anti-GATM antibody (A02754-1). GATM was detected in a paraffin-embedded section of human pancreas cancer tissue.
A02754-1 · IFIF analysis of GATM using anti-GATM antibody (A02754-1). GATM was detected in a paraffin-embedded section of human breast cancer tissue. Hea
HPA · Cerebral cortexHuman Protein Atlas IHC, Cerebral cortex. Source: https://www.proteinatlas.org/ENSG00000171766-GATM/tissue/cerebral+cortex#imid_6546536
HPA · ColonHuman Protein Atlas IHC, Colon. Source: https://www.proteinatlas.org/ENSG00000171766-GATM/tissue/colon#imid_6549702
HPA · LiverHuman Protein Atlas IHC, Liver. Source: https://www.proteinatlas.org/ENSG00000171766-GATM/tissue/liver#imid_6549711
HPA · PancreasHuman Protein Atlas IHC, Pancreas. Source: https://www.proteinatlas.org/ENSG00000171766-GATM/tissue/pancreas#imid_6549662
HPA · ICC-IF RT-4Human Protein Atlas immunofluorescence, RT-4, antibody HPA026077; green = GATM, blue = nucleus, red = microtubules.
HPA · ICC-IF RT-4Human Protein Atlas immunofluorescence, RT-4, antibody HPA026077; green = GATM, blue = nucleus, red = microtubules.
← swipe / scroll for more images →
Real IHC / IF data behind the staining-pattern expectations in this section.
Sample controls for GATM IHC & IF
🧪Run kidney first: cells in tubules should stain (HPA: High in kidney tubule cells). Use adipose tissue as the negative tissue (HPA: Not detected in adipocytes); on the kidney slide, assess background in cells lacking tubular staining without assuming a particular kidney cell type is GATM-negative.
Positive control tissue: Kidney (Cells in tubules, HPA High)
Negative control tissue: Adipose tissue (HPA Not detected)
ICC-IF cell lines (HPA subcellular resource): HPA ICC-IF images show GATM in RT-4, Rh30, U2OS, with annotated localisation: Mitochondria (supported) (HPA subcellular).
Technical controls: Include a no-primary (secondary-only) slide, a rabbit IgG isotype control matched to the primary antibody, and GATM-knockout tissue if available; peptide blocking is an alternative only if the antibody’s immunizing peptide is available (caption: rabbit anti-GATM antibody). For kidney, block endogenous peroxidase before HRP detection and assess tissue autofluorescence if using IF (standard IHC/IF practice; caption: HRP/DAB detection).
⚠️Feasibility: A target-specific fixation window or fixation effect is unreported, and the selected A02754-1 paraffin-section caption does not state the fixative (caption: fixative not stated). The caption reports heat-mediated retrieval in EDTA at pH 8.0, but does not establish whether GATM staining depends on that retrieval method; HPA reports mitochondrial localization in ICC-IF, without evidence that frozen sections or IF are easier (caption: EDTA retrieval; HPA: Mitochondria, supported). Kidney tubular autofluorescence can complicate IF interpretation, so assess it with an unstained section (standard IF practice).
HPA tissue IHC evidence for GATM
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.
Positive expression · recommended positive controls
| Tissue | Cell type | Level | Evidence | Source |
|---|---|---|---|---|
| Kidney | Cells in tubules | High | Protein (IHC) | HPA → |
| Liver | Hepatocytes | High | Protein (IHC) | HPA → |
| Pancreas | Exocrine glandular cells | High | Protein (IHC) | HPA → |
| Cerebellum | Granular cells - cytoplasm/membrane | Medium | Protein (IHC) | HPA → |
| Cerebral cortex | Glial cells | Medium | Protein (IHC) | HPA → |
Undetected expression · recommended negative controls
| Tissue | Cell type | Level | Evidence | Source |
|---|---|---|---|---|
| Adipose tissue | Adipocytes | Not detected | Protein (IHC) | HPA → |
| Appendix | Glandular cells | Not detected | Protein (IHC) | HPA → |
| Bone marrow | Hematopoietic cells | Not detected | Protein (IHC) | HPA → |
| Breast | Adipocytes | Not detected | Protein (IHC) | HPA → |
| Bronchus | Respiratory epithelial cells | Not detected | Protein (IHC) | HPA → |
Section 3
Advanced GATM IHC Tips
Troubleshoot GATM staining in paraffin sections by checking retrieval, controls, cell type and subcellular pattern before scoring chromogenic signal.
Which retrieval conditions should I start with for GATM IHC?
Start with heat-mediated retrieval in EDTA at pH 8.0 for paraffin sections (datasheet A02754-1). The selected tissue-IHC example used this retrieval before 10% goat serum blocking and 2 μg/ml primary antibody overnight at 4°C (datasheet A02754-1). If signal is weak, check that heating, cooling and section handling were consistent across runs before changing retrieval conditions (standard IHC practice). Compare a kidney tubular-cell control with a no-primary control on the same run, because high tubular expression provides a useful expected pattern (HPA: High in kidney tubular cells; standard IHC practice). Excessively harsh retrieval can compromise morphology and make granular cytoplasmic staining difficult to judge (standard IHC practice).
How should I troubleshoot inconsistent staining after fixation?
GATM-specific sensitivity to fixation is unknown from the supplied evidence; the selected paraffin-section caption does not report a fixative (datasheet A02754-1: fixative not stated). Record each specimen’s fixative and fixation duration, then compare sections processed with the same retrieval and detection conditions (standard IHC practice). Include a kidney control in each run and assess morphology alongside granular cytoplasmic signal in tubular cells (HPA: High in kidney tubular cells; HPA: granular cytoplasmic expression; standard IHC practice). If staining differs between specimens, examine fixation records and section quality before attributing the difference to GATM biology (standard IHC practice). Do not infer fixation sensitivity from GATM’s mitochondrial location or modified residues (UniProt P50440: localization and modified residues).
Where should a convincing GATM stain appear in tissue sections?
Expect granular cytoplasmic staining rather than a uniform nuclear pattern in tissue IHC (HPA: granular cytoplasmic expression). This appearance is compatible with mitochondrial localization, although chromogenic light microscopy alone cannot resolve which side of the inner membrane contains the antigen (HPA: mitochondria supported; UniProt P50440: probably attached to the outer side of the inner membrane; standard IHC practice). Use kidney tubular cells, hepatocytes and pancreatic exocrine glandular cells as high-expression reference populations (HPA: High in these cells). Review cellular boundaries and adjacent unstained structures before assigning puncta to a cell (standard IHC practice). Strong nuclear-only staining warrants checking retrieval, antibody concentration and no-primary controls before assigning it to GATM (HPA: granular cytoplasmic expression; standard IHC practice).
Could isoforms or processing explain discordant GATM staining?
GATM has 3 annotated isoforms, but the supplied antibody caption does not map its epitope to any of them (UniProt P50440: isoforms 1–3; datasheet A02754-1). The precursor has 423 residues and an annotated mature chain spanning residues 44–423; epitope accessibility therefore cannot be inferred without antibody mapping (UniProt P50440: processing; standard IHC practice). UniProt lists phosphoserines at residues 46 and 49 and acetyllysine at 385, without evidence here that these modifications alter this antibody’s IHC signal (UniProt P50440: modified residues; datasheet A02754-1). For discordant cases, compare matched controls and request epitope information before proposing an isoform-specific explanation (standard IHC practice).
How can I investigate GATM localization by multiplex IF?
Use IF as a separate localization experiment and compare its pattern with granular cytoplasmic IHC staining (HPA: granular cytoplasmic expression; standard IF practice). Multiplex GATM with a marker identifying the cell population under study, then assess whether signal falls in those cells; kidney tubular cells are a high-expression reference (HPA: High in kidney tubular cells; standard IF practice). Choose spectrally separated fluorophores after checking tissue autofluorescence in unstained sections, and include single-label controls to evaluate bleed-through (standard IF practice). Because GATM is probably attached to the outer side of the mitochondrial inner membrane and has no transmembrane segment, optimize permeabilisation for access to that compartment while preserving mitochondrial structure (UniProt P50440: topology and localization; standard IF practice).
What should I check when GATM DAB staining is diffuse?
First distinguish granular cytoplasmic signal from diffuse chromogen deposition by reviewing a no-primary control beside the test section (HPA: granular cytoplasmic expression; standard IHC practice). The selected paraffin-section example used 10% goat serum blocking, 2 μg/ml primary antibody overnight at 4°C, and a peroxidase-linked detection system with DAB (datasheet A02754-1). Check peroxidase blocking and secondary-only background, then adjust washing or primary concentration if nonspecific color persists (standard chromogenic IHC practice). Inspect tissue folds, section edges and damaged areas separately from intact cell populations, since uneven reagent access can distort staining (standard IHC practice). Compare kidney tubular cells with no-primary controls before calling weak diffuse color positive (HPA: High in kidney tubular cells; standard IHC practice).
How should I quantify GATM across stained sections? ⚠ ANSWER MARKED FOR VERIFICATION
Define the cell population and compartment before scoring, since GATM is reported as granular cytoplasmic staining in tissue IHC (HPA: granular cytoplasmic expression; standard IHC practice). For an H-score, grade cytoplasmic intensity and multiply each grade by its percentage of cells, reporting the scoring bins used (standard IHC practice). Alternatively, report the percentage of positive cells or positive-cell density per mm² within the same annotated tissue compartment (standard IHC practice). Normalize to eligible intact cells or analyzed compartment area, and keep section processing, imaging and positivity thresholds consistent across cases (standard IHC practice). Use kidney tubular cells as a run control rather than as a universal denominator for other tissues (HPA: High in kidney tubular cells; standard IHC practice).
When is GATM staining more likely to be artefactual?
A credible positive pattern is granular and cytoplasmic in the expected cell population, with kidney tubular cells, hepatocytes and pancreatic exocrine glandular cells providing high-expression references (HPA: granular cytoplasmic expression; HPA: High in these cells). Nuclear-only or evenly diffuse staining conflicts with that reported tissue pattern and needs control review (HPA: granular cytoplasmic expression; standard IHC practice). Exclude section-edge color, necrotic regions and deposits that also appear in no-primary or secondary-only controls (standard chromogenic IHC practice). Check endogenous peroxidase blocking when DAB color persists without primary antibody (standard chromogenic IHC practice). The selected breast-cancer section demonstrates staining with this antibody, but its paraffin-section caption alone does not establish which cell populations express GATM there (datasheet A02754-1).
Boster reagents
Best GATM / Glycine amidinotransferase, mitochondrial IHC Antibodies
A02754-1 has IHC images from human breast and pancreas cancer sections and rat kidney sections, plus an IF image from a human breast cancer section (catalog image captions).
Real IHC data
Anti-GATM Antibody ®
Cat # A02754-1
A02754-1 was demonstrated by IHC on paraffin sections of human breast cancer, human pancreas cancer, and rat kidney (IHC image captions). The same SKU was demonstrated by IF on a paraffin section of human breast cancer (IF image caption).
Which to pick: Choose A02754-1 for paraffin section IHC; its caption reports EDTA retrieval at pH 8.0, 2 μg/ml primary antibody, and HRP/DAB detection, but does not report the fixative (IHC image caption). For IF, A02754-1 has a paraffin section image at 5 μg/ml; ICC validation is unreported (IF image caption; catalog applications). For work across species, A02754-1 lists human, mouse, and rat reactivity, while its IHC images cover human and rat tissue; the host is rabbit and clonality is unreported (catalog reactivity and host; IHC image captions).
Each figure is that product's own IHC / IF validation image from its datasheet.
References
- UniProt Consortium. UniProt entry P50440 (GATM_HUMAN, Glycine amidinotransferase, mitochondrial).
- Human Protein Atlas. GATM tissue IHC expression (reliability: Enhanced).
- Human Protein Atlas. GATM subcellular location (ICC-IF): Localized to the mitochondria..
- Human Protein Atlas. GATM antibody validation summary (1 antibodies).
- Reprogramming alternative macrophage polarization by GATM-mediated endogenous creatine synthesis: A potential target for HDM-induced asthma treatment. Frontiers in immunology 2022 — PMC9513582.
- A novel biomarker GATM suppresses proliferation and malignancy of cholangiocarcinoma cells by modulating the JNK/c-Jun signalling pathways. Heliyon 2024 — PMC11408786.
- Molecular Subtypes Based on Genomic and Transcriptomic Features Correlate with the Responsiveness to Immune Checkpoint Inhibitors in Metastatic Clear Cell Renal Cell Carcinoma. Cancers 2022 — PMC9139776.
- Myeloid cell-derived creatine in the hypoxic niche promotes glioblastoma growth. Cell metabolism 2024 — PMC10842612.
- PubMed PMID:8313955 — UniProt-cited evidence.
- PubMed PMID:14702039 — UniProt-cited evidence.
- PubMed PMID:16572171 — UniProt-cited evidence.
Immunohistochemistry protocol sheet for GATM (Glycine amidinotransferase, mitochondrial). Expected localisation Granular cytoplasm in kidney, liver and pancreas (HPA tissue IHC). Antigen retrieval: EDTA pH 8.0 HIER, heat-mediated (datasheet A02754-1). Validated IHC antibody: A02754-1 at 2-5 μg/ml (the product's own IHC validation image is shown). Controls (HPA): positive Kidney (Cells in tubules); negative Adipose tissue. IHC-P workflow on paraffin sections; fixative unspecified. Protocol steps: 1. Sample: Paraffin-embedded human breast cancer tissue; fixative not specified (datasheet A02754-1); 2. Fixation: Image fixative and duration unreported (datasheet A02754-1); verify before use.; 3. Sectioning: 4–5 µm sections on charged slides (standard); 4. Deparaffinisation: Xylene, graded ethanol series to water (standard); 5. Antigen retrieval: Heat retrieval: EDTA pH 8.0 (datasheet A02754-1); 20 min, 95–100 °C (standard); 6. Peroxidase block: 3% H2O2, 10 min , room temperature (standard); 7. Blocking: 10% goat serum (datasheet A02754-1); 8. Primary antibody: Rabbit anti-GATM, 2-5 μg/ml (datasheet A02754-1); 9. Primary incubation: Overnight at 4 °C (datasheet A02754-1). Watch for: Fixation: Matched tissue-IHC evidence does not establish the fixation claim. Validate the specimen-specific method before use. (selected-SKU IHC image A02754-1); Caveat: Antibody staining and RNA show medium consistency (HPA tissue IHC); Isoform / epitope: 3 isoforms; the mature chain starts at residue 44 (UniProt); Regulation: Highest tissue expression is in kidney (UniProt). Evidence: UniProt P50440, HPA tissue IHC · Enhanced, HPA ICC-IF · mitochondria., Datasheet A02754-1, PMC9513582, PMC11408786. QR code links to https://www.bosterbio.com/bosterbio-gene-info-cards/GATM/immunohistochemistry-ihc-guide.