MATR3 / Matrin-3 · IHC design guide

Design Immunohistochemistry for MATR3

Plan paraffin IHC for MATR3 using its nuclear tissue pattern (HPA tissue IHC) and the catalog antibody’s 1–2 μg/ml starting range (datasheet A02931-2). Compare nuclear staining across consistently fixed sections, keeping HPA’s cross-gene staining caution in mind (HPA tissue IHC).

Evidence assembled Oct 2026 · For research use; verify linked source records and product datasheet before use
Immunohistochemistry protocol sheet for MATR3 (IHC for MATR3): expected localisation Nuclear staining in tissue (HPA tissue IHC), antibody A02931-2, validated IHC image, and IHC protocol steps
Printable MATR3 IHC protocol sheet — expected localisation Nuclear staining in tissue (HPA tissue IHC), antibody A02931-2, controls and protocol steps. Open the full MATR3 IHC guide →

MATR3 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 Nuclear staining in tissue (HPA tissue IHC)
Staining pattern Nuclei across many tissue cell types (HPA tissue IHC)
Antigen retrieval EDTA pH 8.0 HIER, heat-mediated (datasheet A02931-2)
Positive control ⓘ Adipose tissue+4 more · see all
Negative control ⓘ None in HPA (detected in all 45 tissues); use no-primary + isotype controls
Important caveats
Reasons your staining may differ from the expected pattern.
Fixation Keep fixation conditions consistent across sections. (standard IHC practice; not target-specific)
Caveat Staining may reflect proteins from other genes (HPA tissue IHC)
Regulation Low tissue specificity (HPA tissue RNA)
Isoform / epitope Two isoforms; epitope differences are unspecified (UniProt)
Section 1

Recommended MATR3 IHC & IF Protocols

The catalog antibody’s IHC-P protocol is accompanied by published MATR3 IHC protocols for mouse spinal cord and muscle, renal tissue, and human entorhinal cortex (PMC6299607; PMC9952985; PMC7603783).

Recommended immunohistochemistry (IHC-P) protocol parameters
SampleParaffin-embedded human breast cancer tissue; fixative not specified (datasheet A02931-2)
FixationImage fixative and duration unreported (datasheet A02931-2); verify before use.
Sectioning4–5 µm sections on charged slides (standard)
DeparaffinisationXylene, graded ethanol series to water (standard)
Antigen retrievalHeat retrieval: EDTA pH 8.0 (datasheet A02931-2); 20 min, 95–100 °C (standard)
Peroxidase block3% H2O2, 10 min, room temperature (standard)
Blocking10% goat serum (datasheet A02931-2)
Primary antibodyRabbit anti-MATR3, 1-2 μg/ml (datasheet A02931-2)
Primary incubationOvernight at 4 °C (datasheet A02931-2)
DetectionHRP-conjugated secondary, DAB chromogen (datasheet A02931-2)
CounterstainHematoxylin, blue, dehydrate and mount (standard)
Expected resultMATR3-positive staining in adipocytes of adipose tissue (HPA tissue IHC: High). HPA tissue profile: Ubiquitous nuclear expression. No signal in the no-primary control.
💡Decision noteStart with EDTA pH 8.0 heat retrieval for the catalog antibody (datasheet A02931-2). Use citrate pH 6.0 when reproducing the published antibody protocols (PMC6299607; PMC7603783).
Section 2

What Is the Expected MATR3 Staining Pattern?

MATR3 is a nuclear matrix protein with no transmembrane segment (UniProt P43243: subcellular location and topology). Expect nuclear staining across many cell types, including adipocytes, glandular cells, hematopoietic cells, and neurons (HPA tissue IHC: ubiquitous nuclear expression; High in the listed cells). Interpret this expectation cautiously: HPA rates the tissue pattern Supported, reports medium agreement with RNA data, and warns that the staining targets proteins from more than one gene (HPA tissue IHC).

What am I looking at on my slide?
Distinct nuclear chromogen in tissue cells, with limited staining outside nuclei.This matches the reported ubiquitous nuclear pattern (HPA tissue IHC) and nuclear matrix location (UniProt P43243). Nuclear staining in listed High examples—adipocytes, adrenal glandular cells, bone marrow hematopoietic cells, or caudate neurons—is a useful positive check (HPA tissue IHC). The pattern supports interpretation but does not, by itself, establish antibody specificity (HPA tissue IHC: multiple-gene caution).
Predominantly cytoplasmic, membranous, or extracellular staining while nuclei remain faint.The dominant compartment conflicts with the expected nuclear location (UniProt P43243; HPA tissue IHC). Review morphology and detection controls before calling it MATR3. A stained section alone cannot distinguish antibody binding to another protein from nonspecific chromogen deposition; the HPA multiple-gene warning makes that distinction especially relevant (HPA tissue IHC).
Strong signal confined to an unexpected cell population while nearby expected nuclei are unstained.Check whether the apparent cell identity and nuclear boundaries are correct. HPA describes broad nuclear expression and lists several High cell populations (HPA tissue IHC), but supplies no negative tissue or cell population. An isolated unexpected pattern raises cross-reactivity or endogenous detection activity as possibilities; it is not proof of either. Compare a negative detection control and another validated antibody when available (general IHC practice).
Haze or granular chromogen covers nuclei and surrounding tissue alike.Diffuse deposit obscures the compartment needed to interpret MATR3 (UniProt P43243: nuclear matrix; HPA tissue IHC: nuclear expression). Excess detection background, inadequate washing, or endogenous enzyme activity are general chromogenic IHC possibilities. Assess the no-primary control and preserve visible nuclear counterstain before scoring cells (general IHC practice).
No convincing nuclear signal in a listed High tissue and no widespread background.A technical false negative is possible, particularly if internal tissue morphology or the control section is poor (general IHC practice). HPA lists High staining in adipocytes, adrenal glandular cells, bone marrow hematopoietic cells, and caudate neurons (HPA tissue IHC). Confirm that the expected cell type is present, then review the antibody's IHC-P instructions and positive control; HPA levels do not establish a target-specific fixation effect.
💡Expected MATR3 appearanceCall a convincing positive result when tissue cells show clearly bounded nuclear staining, readily visible in an HPA-listed High cell population (HPA tissue IHC); dominant cytoplasmic or tissue-wide diffuse deposit is inconsistent with the reported nuclear location (UniProt P43243; HPA tissue IHC).
How each factor affects the staining
Compartment and tissue distributionMATR3 is assigned to the nuclear matrix (UniProt P43243); HPA reports ubiquitous nuclear tissue staining and low tissue RNA specificity (HPA tissue IHC). Use nuclear location and the identity of cells in the section together; broad tissue positivity alone is a weak specificity check.
Strength of tissue evidenceThe tissue profile is Supported, with medium agreement between antibody staining and RNA expression, and a warning that staining targets proteins from more than one gene (HPA tissue IHC). Treat an otherwise plausible nuclear pattern as supported, not uniquely attributable to MATR3 without further validation.
Antibody validationThree listed antibodies have Supported IHC status: HPA036564, HPA036565, and CAB033552 (HPA antibodies). No listed antibody has an IHC Enhanced designation in this payload (HPA antibodies). Confirm which antibody produced a reference image before comparing its pattern with the catalog antibody.
IF/ICC Q&A: what location should be expected?The HPA ICC-IF location is approved nucleoplasm, with images from A-431, U-251MG, and U2OS; HPA also warns that the antibodies target proteins from multiple genes (HPA subcellular). Nuclear fluorescence is compatible with that record. This IF/ICC observation does not define an IHC-P staining protocol.
Why is my staining missing, weak or wrong?
SituationLikely causeNext action
Expected nuclei are blank in an HPA-listed High tissue.Target-specific fixation effects are not established by the supplied assay evidence. Verify with a matched IHC source before attributing a result to fixation.Verify tissue morphology and the listed High cells, then check the positive control and catalog antibody's IHC-P instructions. Review retrieval and detection conditions as general IHC workflow variables.
Chromogen is mainly cytoplasmic or membranous.That distribution conflicts with nuclear matrix localization and the nuclear tissue profile (UniProt P43243; HPA tissue IHC). Misread cell boundaries or nonspecific staining may contribute (general IHC practice).Inspect nuclear counterstain and a no-primary control. Score only a reproducible nuclear pattern; if the discrepancy persists, compare another IHC-supported antibody (HPA antibodies).
Only an unusual cell population stains strongly.HPA reports ubiquitous nuclear expression but provides no negative cell population here; cross-reactivity or endogenous detection activity remains possible (HPA tissue IHC; general IHC practice).Identify the stained cells morphologically, check the no-primary control, and compare an independent IHC-supported antibody if available (HPA antibodies). Avoid declaring the population MATR3-specific from this pattern alone.
The whole section has diffuse brown background.Nonspecific reagent binding, insufficient washing, or endogenous peroxidase are general chromogenic IHC causes; diffuse deposit cannot be read as nuclear MATR3 (general IHC practice; UniProt P43243).Check a no-primary control, review blocking and washes, and verify the detection system's endogenous-activity control (general IHC practice). Reassess nuclear localization after background is controlled.
Nuclear staining is too strong to distinguish individual cells.Excess chromogen or high antibody concentration can obscure nuclear boundaries in chromogenic IHC (general IHC practice). Intensity alone cannot overcome HPA's multiple-gene caution (HPA tissue IHC).Follow the catalog antibody's IHC-P dilution guidance and optimize detection development with a counterstain that leaves nuclei readable (general IHC practice). Score localization only where cell boundaries remain clear.
A nuclear pattern differs between antibodies.The supplied antibodies are IHC Supported, while HPA flags possible staining of proteins from multiple genes (HPA antibodies; HPA tissue IHC). Different patterns therefore require scrutiny rather than averaging.Compare matched tissue regions and controls, document each antibody separately, and restrict conclusions to the reproducible nuclear pattern (general IHC practice; UniProt P43243).

Sample controls for MATR3 IHC & IF

🧪Run breast tissue first and look for nuclear staining in adipocytes (HPA: High in breast adipocytes; UniProt P43243: nuclear matrix). HPA detects MATR3 in all 45 scored tissues, so there is no supported negative tissue or established negative cell population within the positive slide; cells lacking nuclear signal should be judged against no-primary and isotype controls (HPA: no negative rows; HPA: detected in all 45 scored tissues).
Positive control tissue: Adipose tissue (Adipocytes, HPA High)
Negative control tissue: None in HPA: MATR3 is detected in all 45 scored tissues. Use a no-primary (secondary-only) and an isotype control instead.
ICC-IF cell lines (HPA subcellular resource): HPA ICC-IF images show MATR3 in A-431, U-251MG, U2OS, with annotated localisation: Nucleoplasm (approved) (HPA subcellular).
Technical controls: Include a no-primary, secondary-only slide, a concentration-matched rabbit IgG isotype control, and a MATR3 knockout specimen or validated peptide-block control (caption: rabbit anti-MATR3 antibody). Quench endogenous peroxidase before chromogenic detection and inspect adipose-rich areas for nonspecific background (caption: peroxidase secondary and DAB; HPA: breast adipocytes High).
⚠️Feasibility: A target-specific fixation window or fixation effect is unreported, and the selected A02931-2 caption does not state a fixative (caption: fixative not stated). Its paraffin-section example uses heat retrieval in EDTA at pH 8.0 and 2 μg/ml primary antibody overnight at 4°C, providing an IHC starting point without establishing that retrieval is required for every specimen (caption: breast cancer tissue IHC). Frozen-section or IF ease relative to paraffin IHC is unreported; in breast adipose tissue, lipid extraction during paraffin processing can leave clear adipocyte spaces, so score nuclei rather than empty vacuoles (HPA: High in breast adipocytes; standard paraffin histology).

HPA tissue IHC evidence for MATR3

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.

Positive expression · recommended positive controls

TissueCell typeLevelEvidenceSource
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 →

Undetected expression · recommended negative controls

TissueCell typeLevelEvidenceSource
None in HPA: MATR3 is detected in all 45 scored tissues. Use a no-primary (secondary-only) and an isotype control instead.
Section 3

Advanced MATR3 IHC Tips

Troubleshoot chromogenic MATR3 staining in paraffin sections by checking nuclear localisation, retrieval conditions and assay controls before comparing staining scores.

What should I change when MATR3 staining is weak after antigen retrieval?
Start with heat-mediated retrieval in EDTA at pH 8.0 (datasheet A02931-2). The selected paraffin-section image used this retrieval before incubation with 2 μg/ml primary antibody overnight at 4°C, providing a documented starting condition for this antibody (datasheet A02931-2). If nuclear staining remains weak, compare retrieval heating and cooling conditions on adjacent sections while keeping antibody concentration, detection and development constant (standard IHC practice). Include a section processed without primary antibody to check whether stronger retrieval also raises background (standard IHC practice). Judge improvement by nuclear signal and tissue preservation together, since MATR3 is assigned to the nuclear matrix (UniProt P43243 localisation).
Could fixation be masking MATR3 in my paraffin sections?
Target-specific fixation sensitivity is unknown because the selected paraffin-section caption does not state a fixative (datasheet A02931-2). Record the fixative and fixation duration for each specimen, then compare sections processed and stained together before attributing differences to MATR3 abundance (standard IHC practice). Keep retrieval at EDTA pH 8.0 for the initial comparison because that is the documented condition for this antibody (datasheet A02931-2). If staining varies between blocks, examine tissue preservation, nuclear morphology and staining in internal control cells on the same slide (standard IHC practice). Neither the reported nuclear location nor phosphorylation annotations establish how fixation affects this epitope (UniProt P43243 localisation and modified residues).
Where should convincing MATR3 staining appear in tissue sections?
Look primarily for staining within intact nuclei: MATR3 is assigned to the nuclear matrix, and HPA reports ubiquitous nuclear tissue staining (UniProt P43243 localisation; HPA tissue IHC). HPA additionally places it in the nucleoplasm by ICC/IF, with a caution that the antibodies target proteins from multiple genes (HPA subcellular). Compare nuclei within the same tissue compartment and check that the chromogenic signal aligns with nuclear counterstain rather than surrounding cytoplasm (standard IHC practice). In breast sections, adipocytes provide a reported high-staining cell population for comparison (HPA: High in breast adipocytes). Treat predominantly cytoplasmic or extracellular staining as a reason to investigate specificity and section artefacts before scoring it as MATR3 (UniProt P43243 localisation; standard IHC practice).
Can epitope location explain discordant MATR3 staining between antibodies?
MATR3 has 2 annotated isoforms, so an antibody’s epitope and isoform coverage matter when comparing nuclear staining across reagents (UniProt P43243 isoforms; standard IHC practice). The supplied caption identifies the tested antibody as A02931-2 but does not identify its epitope, leaving isoform recognition unresolved for that reagent (datasheet A02931-2). MATR3 contains RNA recognition motifs at residues 398–473 and 496–571, alongside annotated modified residues, which are useful coordinates when an epitope sequence becomes available (UniProt P43243 domains and modified residues). Compare antibody documentation and staining in matched sections before assigning discordance to isoform expression (standard IHC practice). Do not interpret a negative chromogenic result as loss of a particular isoform without epitope-specific evidence (UniProt P43243 isoforms; standard IHC practice).
How should I assess MATR3 by IF alongside this chromogenic IHC guide?
Use the separate IF/ICC guide to plan fluorescent staining; this page’s documented antibody workflow is paraffin-section chromogenic IHC (datasheet A02931-2). For multiplex IF, pair MATR3 with a marker identifying the expected cell population, such as neuronal cells in caudate, where HPA reports high staining (HPA: High in caudate neuronal cells; standard IF practice). Choose spectrally separated fluorophores and consider a far-red channel when tissue autofluorescence obscures shorter wavelengths (standard IF practice). Because MATR3 is nuclear and has no transmembrane segment, include a permeabilisation step that permits antibody access to nuclear epitopes (UniProt P43243 localisation and topology; standard IF practice). Check single-label and no-primary controls before interpreting overlap, without transferring the IHC caption’s processing conditions to IF (standard IF practice; datasheet A02931-2).
How can I reduce diffuse or nonspecific chromogenic background?
First compare the stained section with a no-primary control and inspect whether colour follows nuclei or spreads through stroma and damaged areas (standard IHC practice; UniProt P43243 localisation). The documented paraffin-section workflow used 10% goat serum blocking, 2 μg/ml primary antibody overnight at 4°C, and a peroxidase-conjugated secondary for 30 minutes at 37°C (datasheet A02931-2). Keep those conditions recorded while changing one suspected background source at a time, such as blocking, washing or primary concentration (standard IHC practice). Include a peroxidase-blocking step and monitor DAB development, especially if the no-primary section develops colour (standard chromogenic IHC practice). Preserve nuclear counterstain visibility so diffuse brown signal cannot be mistaken for MATR3-positive nuclei (standard IHC practice; UniProt P43243 localisation).
How should I quantify MATR3 staining across paraffin sections? ⚠ ANSWER MARKED FOR VERIFICATION
Define the tissue compartment and count only intact, interpretable nuclei because MATR3 is a nuclear-matrix protein and HPA describes nuclear tissue staining (UniProt P43243 localisation; HPA tissue IHC). Report the percentage of positive nuclei and, when intensity grading is reproducible, an H-score calculated from the proportions at each intensity level (standard IHC scoring practice). Normalise each result to the number of eligible nuclei in that compartment, using the same positivity threshold and DAB development conditions across sections (standard IHC scoring practice). For spatial comparisons, positive nuclei per mm² can supplement the percentage, with viable tissue area defined consistently (standard IHC scoring practice). Record the antibody and retrieval condition, including EDTA pH 8.0, so scores remain traceable to this assay (datasheet A02931-2; standard IHC practice).
How do I distinguish true MATR3 signal from tissue artefact?
Prioritise staining that follows intact nuclei across viable tissue, consistent with MATR3’s nuclear-matrix assignment and HPA’s ubiquitous nuclear pattern (UniProt P43243 localisation; HPA tissue IHC). Check suspicious cytoplasmic deposits, section edges and necrotic regions against neighbouring preserved tissue before calling them positive (standard IHC interpretation practice). A no-primary control helps identify detection-system colour, including residual endogenous enzyme signal in a peroxidase and DAB assay (standard chromogenic IHC practice; datasheet A02931-2). Compare the expected cell population within the section; HPA reports high staining in breast adipocytes, but its tissue profile carries a cross-gene antibody caution (HPA tissue IHC). If nuclear staining and controls disagree, report the result as uncertain rather than assigning a biological change in MATR3 (standard IHC interpretation practice).
Boster reagents

Best MATR3 / Matrin-3 IHC Antibodies

Both antibodies have paraffin-section IHC images from human breast cancer tissue; A02931-2 also has an IF image from A549 cells (catalog image captions). Human, Mouse and Rat are listed as reactive species (catalog reactivity).

Real IHC data IHC analysis of MATR3 using anti-MATR3 antibody (A02931-2). MATR3 was detected in a paraffin-embedded section of human breast cancer tissue. Heat mediated antigen retrieval was performed in EDTA buffer (pH 8.0, epitope retrieval solution). The tissue section was blocked with 10% goat serum. The tissue section was then incubated with 2 μg/ml rabbit anti-MATR3 Antibody (A02931-2) overnight at 4°C. Peroxidase Conjugated Goat Anti-rabbit IgG was used as secondary antibody and incubated for 30 minutes at 37°C. The tissue section was developed using HRP Conjugated Rabbit IgG Super Vision Assay Kit (Catalog # SV0002) with DAB as the chromogen.
Anti-MATR3 Antibody ®
Cat # A02931-2
Real IHC data IHC analysis of MATR3 using anti-MATR3 antibody (M02931-1). MATR3 was detected in a paraffin-embedded section of human breast cancer tissue. Heat mediated antigen retrieval was performed in EDTA buffer (pH 8.0, epitope retrieval solution). The tissue section was blocked with 10% goat serum. The tissue section was then incubated with 1:50 rabbit anti-MATR3 Antibody (M02931-1) overnight at 4°C. Peroxidase Conjugated Goat Anti-rabbit IgG was used as secondary antibody and incubated for 30 minutes at 37°C. The tissue section was developed using HRP Conjugated Rabbit IgG Super Vision Assay Kit (Catalog # SV0002) with DAB as the chromogen.
Anti-Matrin 3 Rabbit Monoclonal Antibody
Cat # M02931-1

A02931-2 has IHC images from human breast cancer, rectum adenocarcinoma, placenta and testicular germ cell tumor sections, plus an IF image from A549 cells (A02931-2 image captions). M02931-1 has an IHC image from human breast cancer tissue; IF/ICC is listed as an application, but no IF image is supplied (M02931-1 catalog applications and image captions).

Which to pick: For tissue IHC, A02931-2 has images across more sample types; both SKUs have paraffin-section images using EDTA pH 8.0 retrieval, and neither caption reports the fixative (catalog IHC image captions). For IF/ICC, A02931-2 has an A549 IF image, while M02931-1 is a rabbit monoclonal with IF/ICC listed but no IF image (catalog IF image captions; M02931-1 catalog clone and applications). Both list Human, Mouse and Rat reactivity, though the supplied IHC images show human tissue only (catalog reactivity and IHC image captions).

Each figure is that product's own IHC / IF validation image from its datasheet.

References

  1. UniProt Consortium. UniProt entry P43243 (MATR3_HUMAN, Matrin-3).
  2. Human Protein Atlas. MATR3 tissue IHC expression (reliability: Supported).
  3. Human Protein Atlas. MATR3 subcellular location (ICC-IF): Localized to the nucleoplasm. Caution: Based on antibodies targeting proteins from multiple genes..
  4. Human Protein Atlas. MATR3 antibody validation summary (3 antibodies).
  5. Analysis of spinal and muscle pathology in transgenic mice overexpressing wild-type and ALS-linked mutant MATR3. Acta neuropathologica communications 2018 — PMC6299607.
  6. Low Expression of MATR3 Is Associated with Poor Survival in Clear Cell Renal Cell Carcinoma. Biomedicines 2023 — PMC9952985.
  7. RNA dependent suppression of C9orf72 ALS/FTD associated neurodegeneration by Matrin-3. Acta neuropathologica communications 2020 — PMC7603783.
  8. Inner nuclear protein Matrin-3 coordinates cell differentiation by stabilizing chromatin architecture. Nature communications 2021 — PMC8556400.
  9. PubMed PMID:9872452 — UniProt-cited evidence.
  10. PubMed PMID:10931946 — UniProt-cited evidence.
  11. PubMed PMID:14702039 — UniProt-cited evidence.