COL4A3 / Collagen alpha-3(IV) chain · IHC design guide

Design Immunohistochemistry for COL4A3

Plan paraffin-section COL4A3 IHC around cytoplasmic staining and extracellular positivity (HPA tissue IHC). The catalog antibody A01755-3 has an IHC-P range of 2–5 μg/ml (datasheet A01755-3).

Evidence assembled Oct 2026 · For research use; verify linked source records and product datasheet before use
Immunohistochemistry protocol sheet for COL4A3 (IHC for COL4A3): expected localisation Cytoplasmic and extracellular tissue staining (HPA tissue IHC), antibody A01755-3, validated IHC image, and IHC protocol steps
Printable COL4A3 IHC protocol sheet — expected localisation Cytoplasmic and extracellular tissue staining (HPA tissue IHC), antibody A01755-3, controls and protocol steps. Open the full COL4A3 IHC guide →

COL4A3 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 Cytoplasmic and extracellular tissue staining (HPA tissue IHC)
Staining pattern Cytoplasmic staining with extracellular positivity in several tissues (HPA tissue IHC)
Antigen retrieval EDTA pH 8.0 HIER, heat-mediated (datasheet A01755-3)
Positive control ⓘ Appendix+4 more · see all
Negative control ⓘ Adipose tissue+4 more · see all
Important caveats
Reasons your staining may differ from the expected pattern.
Fixation Keep fixation consistent across 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 A01755-3)
Caveat Secreted COL4A3 may stain beyond its producing cells (UniProt)
Regulation Staining intensity varies by tissue (HPA tissue IHC)
Isoform / epitope 5 isoforms; processed tumstatin makes epitope location relevant (UniProt)
Section 1

Recommended COL4A3 IHC & IF Protocols

The catalog antibody’s IHC-P protocol (datasheet: A01755-3) is followed by published COL4A3 protocols for lung adenocarcinoma and mouse inner ear sections (PMC13452252; PMC7619435).

Recommended immunohistochemistry (IHC-P) protocol parameters
SampleParaffin-embedded human gastric cancer tissue; fixative not specified (datasheet A01755-3)
FixationImage fixative and duration unreported (datasheet A01755-3); 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 A01755-3); 20 min, 95–100 °C (standard)
Peroxidase block3% H2O2, 10 min, room temperature (standard)
Blocking10% goat serum (datasheet A01755-3)
Primary antibodyRabbit anti-COL4A3, 2-5 μg/ml (datasheet A01755-3)
Primary incubationOvernight at 4 °C (datasheet A01755-3)
DetectionStreptavidin-biotin complex (SABC), DAB chromogen (datasheet A01755-3)
CounterstainHematoxylin, blue, dehydrate and mount (standard)
Expected resultCOL4A3-positive staining in glandular cells of appendix (HPA tissue IHC: Medium). HPA tissue profile: Cytoplasmic expression and extracellular positivity in several tissues. No signal in the no-primary control.
💡Decision noteStart with heat-mediated EDTA at pH 8.0 for the catalog antibody (datasheet: A01755-3); the mouse inner ear study used a different retrieval method (PMC7619435).
Section 2

What Is the Expected COL4A3 Staining Pattern?

COL4A3 is a secreted, non-transmembrane collagen of extracellular basement membranes, including the glomerular basement membrane (UniProt Q01955: location and topology). In tissue IHC, HPA reports cytoplasmic expression and extracellular positivity across several tissues, with medium staining in specified epithelial and trophoblastic cells (HPA tissue IHC: Approved; tissue profile). Interpret cellular staining alongside the extracellular pattern and tissue context.

What am I looking at on my slide?
Extracellular staining follows basement membrane structures, with cytoplasmic staining in cells represented among HPA positives.This fits COL4A3's matrix location (UniProt Q01955: location) and HPA's reported cytoplasmic and extracellular tissue pattern (HPA tissue IHC: Approved). HPA lists medium staining in appendix glandular cells, for example; it does not assign every listed tissue a compartment-specific pattern (HPA tissue IHC: appendix and profile).
Strong nuclear staining dominates while the expected extracellular and cytoplasmic patterns are absent.Nuclear dominance conflicts with the reported tissue pattern and secreted protein location (HPA tissue IHC: profile; UniProt Q01955: location). Treat it as a possible artefact until a known-positive section, omission control, and staining workflow have been checked (standard IHC practice).
Strong staining appears in adipocytes or adrenal glandular cells.Those cells are listed as not detected, so prominent cellular signal needs scrutiny for cross-reactivity or endogenous detection activity (HPA tissue IHC: adipose tissue and adrenal gland; standard IHC practice). Their cell-level negatives do not establish that every basement membrane in those tissues lacks COL4A3 (HPA tissue IHC: listed cell types).
A broad brown haze covers cells and stroma without a discernible anatomical pattern.The haze cannot be confidently assigned to COL4A3's reported cytoplasmic and extracellular distribution (HPA tissue IHC: profile). Uneven reagent deposition, inadequate washing, or endogenous detection activity are general IHC possibilities; compare controls before scoring it as positive (standard IHC practice).
No staining appears in a well-preserved appendix glandular-cell control.HPA reports medium staining in those cells, making complete absence a reason to inspect assay performance (HPA tissue IHC: appendix glandular cells, Medium). A negative result alone cannot identify whether retrieval, antibody application, detection, or specimen quality failed (standard IHC practice).
💡Expected COL4A3 appearanceCall the IHC result positive when anatomically coherent extracellular staining and/or cytoplasmic staining in HPA-listed cells is visible, with medium cellular staining plausible in appendix glandular cells; isolated strong nuclear signal or uniform brown haze is suspect (UniProt Q01955: location; HPA tissue IHC: profile and appendix, Medium; standard IHC practice).
How each factor affects the staining
Protein location and processingCOL4A3 has a signal peptide at residues 1–28 and no transmembrane segment; the chain spans residues 29–1670 (UniProt Q01955: processing and topology). A cytoplasmic IHC signal can coexist with extracellular deposition, as HPA reports both, but the record does not establish the fraction retained within cells (HPA tissue IHC: profile).
Antibody validationThe listed rabbit polyclonal HPA042064 has IHC status Approved (HPA antibodies: HPA042064). HPA's tissue reliability is also Approved; neither label here establishes that every specimen or unexpected cell-level signal is specific (HPA tissue IHC: reliability; HPA antibodies: HPA042064). Use appropriate controls when interpreting exceptions (standard IHC practice).
Tissue and isoform contextFive isoforms are listed, and UniProt reports different expression across tissues and studies (UniProt Q01955: isoforms and tissue specificity). For example, UniProt reports conflicting kidney comparisons with COL4A4 and differing pancreatic findings; avoid turning any single tissue or study into a universal intensity threshold (UniProt Q01955: tissue specificity).
Epitope coverageUniProt places the collagen IV NC1 domain at residues 1445–1669 and identifies tumstatin at 1426–1670 (UniProt Q01955: domains and processing). The supplied antibody record gives no epitope location, so it cannot establish which forms this assay recognizes or whether a particular processing event changes staining (HPA antibodies: HPA042064).
IF/ICC Q&A: Can intracellular COL4A3 staining be expected?Yes: HPA reports mainly vesicular localisation, with additional endoplasmic reticulum localisation, in its ICC-IF record; images are listed for HeLa and U2OS (HPA subcellular: approved locations and image cell lines). This answers localisation for IF/ICC; it does not supply an IF protocol or override tissue IHC interpretation (HPA subcellular; HPA tissue IHC: profile).
Why is my staining missing, weak or wrong?
SituationLikely causeNext action
The positive-control appendix lacks detectable glandular-cell staining.HPA records medium staining in appendix glandular cells; the absent signal could reflect an assay or specimen problem, but the record does not identify a target-specific cause (HPA tissue IHC: appendix, Medium).Check section integrity, antibody application, retrieval, detection reagents, and the positive-control run before interpreting study samples (standard IHC practice). Do not assume a COL4A3-specific fixation effect; none is supplied here.
The slide shows diffuse brown haze with little anatomical detail.This differs from interpretable cytoplasmic or extracellular positivity (HPA tissue IHC: profile). Background may arise from insufficient washing or endogenous detection activity in a chromogenic assay (standard IHC practice).Review the no-primary control, wash steps, blocking, and detection chemistry; score only signal that resolves into a reproducible tissue pattern (standard IHC practice).
Nuclei stain strongly across multiple tissues.Dominant nuclear staining is discordant with extracellular COL4A3 and HPA's tissue IHC profile (UniProt Q01955: location; HPA tissue IHC: profile). The appearance alone cannot distinguish nonspecific binding from a detection problem (standard IHC practice).Compare a known-positive section and omission control in the same run, then review reagent concentration and detection background before assigning specificity (standard IHC practice).
Adipocytes show strong cellular staining.HPA lists adipocytes in adipose tissue as not detected, so strong cellular signal is unexpected; this cell-level observation says nothing definitive about nearby basement membranes (HPA tissue IHC: adipose tissue).Check whether signal belongs to adipocytes or adjacent extracellular structures, then compare the omission control and an HPA-listed positive cell population (HPA tissue IHC: profile and positive list; standard IHC practice).
A kidney section gives a weaker or different pattern than anticipated.UniProt places COL4A3 in glomerular and tubular basement membranes but reports differing kidney expression comparisons across studies; this payload gives no HPA kidney IHC intensity grade (UniProt Q01955: location and tissue specificity; HPA tissue IHC: supplied list).Judge anatomical localisation and run quality before using intensity alone as a failure criterion; confirm the assay against an HPA-listed medium-positive tissue where available (UniProt Q01955: location; HPA tissue IHC: positive list; standard IHC practice).
Cellular staining is present but extracellular staining is difficult to resolve.HPA reports both cytoplasmic and extracellular positivity across tissues without specifying their proportions in each listed cell type (HPA tissue IHC: profile). Weak anatomical detail or excess background can hinder compartment assignment (standard IHC practice).Review morphology and counterstain, compare with the omission control, and record cellular and extracellular staining separately; avoid inferring absent COL4A3 solely from an unresolved extracellular pattern (HPA tissue IHC: profile; standard IHC practice).

Sample controls for COL4A3 IHC & IF

🧪Run appendix first: its glandular cells have medium COL4A3 staining (HPA: Appendix, glandular cells, Medium). Use adrenal gland as the negative tissue (HPA: Adrenal gland, glandular cells, Not detected); on the appendix slide, assess non-glandular cells as internal background controls while allowing for extracellular basement-membrane staining adjacent to cells (UniProt Q01955: basement-membrane localization).
Positive control tissue: Appendix (Glandular cells, HPA Medium)
Negative control tissue: Adipose tissue (HPA Not detected)
ICC-IF cell lines (HPA subcellular resource): HPA ICC-IF images show COL4A3 in HeLa, U2OS, with annotated localisation: Vesicles (approved) (HPA subcellular).
Technical controls: Include a no-primary, secondary-only control and a host- and class-matched rabbit isotype control (selected IHC caption: rabbit primary antibody). A validated COL4A3 knockout specimen or peptide competition can provide a biological specificity control; for the DAB and biotin-based detection described in the caption, check endogenous peroxidase and biotin background in appendix (selected IHC caption: SABC/DAB detection).
⚠️Feasibility: The selected A01755-3 paraffin-section caption reports heat-mediated retrieval in EDTA at pH 8.0, but does not state the fixative; a target-specific fixation window or fixation effect is unreported (selected IHC caption). Retrieval is part of that demonstrated IHC procedure, but the supplied evidence does not establish whether frozen sections or IF would be easier (selected IHC caption; HPA: HeLa and U2OS ICC-IF images). In appendix, distinguish basement-membrane signal from staining assigned to glandular cells, since COL4A3 is an extracellular basement-membrane protein (UniProt Q01955: subcellular location; HPA: Appendix, glandular cells, Medium).

HPA tissue IHC evidence for COL4A3

Comprehensive Human Protein Atlas IHC scoring per tissue (reliability: Approved — At least one protein variant secreted, tissue location of RNA and protein might differ and correlation is complex.). 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
Appendix Glandular cells Medium Protein (IHC) HPA →
Cervix Glandular cells Medium Protein (IHC) HPA →
Gallbladder Glandular cells Medium Protein (IHC) HPA →
Placenta Trophoblastic cells Medium Protein (IHC) HPA →
Skin Keratinocytes Medium Protein (IHC) HPA →

Undetected expression · recommended negative controls

TissueCell typeLevelEvidenceSource
Adipose tissue Adipocytes Not detected Protein (IHC) HPA →
Adrenal gland Glandular cells Not detected Protein (IHC) HPA →
Bone marrow Hematopoietic cells Not detected Protein (IHC) HPA →
Breast Adipocytes Not detected Protein (IHC) HPA →
Caudate Glial cells Not detected Protein (IHC) HPA →
Section 3

Advanced COL4A3 IHC Tips

Troubleshoot COL4A3 staining in paraffin section chromogenic IHC, using the catalog antibody’s documented workflow and compartment aware controls.

What should I change when COL4A3 staining is weak after antigen retrieval?
Start with heat mediated retrieval in EDTA at pH 8.0 (datasheet A01755-3). The documented paraffin section workflow then used 2 μg/ml primary antibody overnight at 4°C, so confirm those conditions before changing retrieval (caption A01755-3). Compare a known staining section in the same run and check whether basement membrane signal is continuous rather than judging intensity alone (UniProt Q01955 localisation; standard IHC practice). If staining remains weak, compare a second retrieval condition on adjacent sections while holding detection and development constant, and reject conditions that increase diffuse background (standard IHC practice).
Could fixation explain weak or uneven COL4A3 staining in my paraffin sections?
The selected paraffin section caption does not report its fixative, so COL4A3 specific fixation sensitivity is unknown (caption A01755-3). Record the actual fixative, fixation duration, tissue thickness, and processing history for each section before comparing staining between samples (standard IHC practice). Run differently processed sections with the same EDTA pH 8.0 retrieval and the same antibody incubation to isolate processing effects (datasheet A01755-3; standard IHC practice). If a prolonged fixation condition gives weaker signal, treat that as a result of your paired comparison, then confirm preserved morphology and specific basement membrane staining before changing the workflow (standard IHC practice; UniProt Q01955 localisation).
How should I evaluate cytoplasmic staining when I expect basement membrane COL4A3?
Prioritise linear extracellular staining along an anatomically identifiable basement membrane, because mature COL4A3 is secreted into extracellular matrix and basement membranes (UniProt Q01955 localisation). HPA also reports cytoplasmic expression and extracellular positivity across tissues, so cytoplasmic signal alone cannot establish deposited collagen (HPA tissue IHC). Compare cellular and extracellular compartments separately on the same section, and inspect whether the signal follows intact tissue structures rather than cut edges or debris (standard IHC practice). For kidney sections, examine glomerular and tubular basement membrane patterns in context; UniProt places COL4A3 with COL4A4 and COL4A5 in both locations (UniProt Q01955 localisation).
Why might an antibody miss deposited COL4A3 despite detectable cellular staining?
Check the antibody’s mapped epitope and documented isoform coverage before treating absent matrix staining as protein loss; those details are not supplied for this antibody (catalog antibody information supplied). COL4A3 has 5 listed isoforms, a signal peptide at residues 1–28, and an NC1 domain at 1445–1669 (UniProt Q01955). The NC1 region participates in the collagen IV network, so epitope accessibility in deposited matrix may differ from that in intracellular material (UniProt Q01955 subunit; standard IHC practice). Compare retrieval conditions on adjacent sections and use a separately validated epitope reagent, if available, before assigning a negative result to an isoform (standard IHC practice).
How can IF help resolve whether chromogenic COL4A3 staining is correctly localised?
Use IF as an independent localisation check, while keeping the documented paraffin section IHC conditions as the reference for this page (caption A01755-3). Multiplex COL4A3 with a validated marker of the expected cell type and compare its signal with the adjacent basement membrane, where secreted COL4A3 is expected (UniProt Q01955 localisation; standard IF practice). Select fluorophores after measuring tissue autofluorescence in unstained controls, and include single stain controls when assessing overlap (standard IF practice). Because COL4A3 has no transmembrane segment, choose permeabilisation according to whether the antibody recognises intracellular precursor or extracellular deposited protein; the supplied evidence does not map its epitope (UniProt Q01955 topology; standard IF practice).
How do I distinguish COL4A3 signal from chromogenic background?
Compare the stained section with a no primary control and inspect whether DAB follows intact basement membrane contours (UniProt Q01955 localisation; standard IHC practice). The documented workflow uses biotinylated secondary antibody, streptavidin biotin detection, and DAB, so include detection system controls when background appears in both tissue and control sections (caption A01755-3; standard IHC practice). Confirm that peroxidase blocking and washing are adequate, then adjust blocking or primary antibody concentration one variable at a time (standard IHC practice). The caption used 10% goat serum and 2 μg/ml primary antibody; treat these as starting conditions rather than proof that every tissue has low background (caption A01755-3).
What is a defensible way to quantify COL4A3 IHC across sections? ⚠ ANSWER MARKED FOR VERIFICATION
Define the anatomical region and score extracellular basement membrane staining separately from cytoplasmic staining, since both patterns are reported but represent different compartments (HPA tissue IHC; UniProt Q01955 localisation). For cellular staining, report percentage positive cells and intensity or an H score; for deposited matrix, measure positive length or area per mm² of evaluable tissue (standard IHC practice). Normalise matrix signal to basement membrane length or another prespecified anatomical denominator rather than total image area when tissue composition differs (standard IHC practice). Use the same retrieval, imaging, threshold, and exclusion rules across sections, with blinded review of ambiguous regions (standard IHC practice).
When should I distrust a strong COL4A3 positive IHC result?
Distrust staining confined to nuclei or unrelated tissue edges when the proposed finding is deposited COL4A3, which is a secreted basement membrane component (UniProt Q01955 localisation; standard IHC practice). Review the cell type and tissue context: HPA reports medium glandular cell staining in stomach, whereas its tissue profile also describes extracellular positivity (HPA tissue IHC). Exclude necrotic areas, folds, and cut edge accentuation, and compare a no primary control for endogenous enzyme or detection system signal (standard IHC practice). A convincing result should preserve plausible anatomy, reproduce across sections, and show the expected compartment under the same EDTA pH 8.0 retrieval workflow (UniProt Q01955 localisation; datasheet A01755-3; standard IHC practice).
Boster reagents

Best COL4A3 / Collagen alpha-3(IV) chain IHC Antibodies

Both antibodies have IHC images from human paraffin sections (catalog: A01755-1, A01755-3); A01755-1 also has an IF image from COS7 cells (catalog: A01755-1 IF image caption).

Real IHC data IHC analysis of COL4A3 using anti-COL4A3 antibody (A01755-3). COL4A3 was detected in a paraffin-embedded section of human gastric 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-COL4A3 Antibody (A01755-3) overnight at 4°C. Biotinylated goat anti-rabbit IgG was used as secondary antibody and incubated for 30 minutes at 37°C. The tissue section was developed using Strepavidin-Biotin-Complex (SABC) (Catalog # SA1022) with DAB as the chromogen.
Anti-COL4A3 Antibody
Cat # A01755-3
Real IHC data Immunohistochemistry analysis of paraffin-embedded human brain tissue, using Collagen IV alpha3 Antibody. The picture on the right is blocked with the synthesized peptide.
Anti-Collagen alpha-3(IV) chain COL4A3 Antibody
Cat # A01755-1

A01755-3 has IHC images from human gastric, rectal, renal and skin cancer paraffin sections (A01755-3 IHC image captions). A01755-1 has an IHC image from a human brain paraffin section and an IF image from COS7 cells (A01755-1 image captions).

Which to pick: For tissue IHC, choose A01755-3 when its documented workflow fits: the human gastric cancer paraffin section used EDTA retrieval at pH 8.0 and 2 μg/ml primary antibody (A01755-3 IHC image caption). For IF/ICC planning, choose A01755-1 because IF is listed and shown in COS7 cells; ICC is not separately listed (A01755-1 applications and IF image caption). A01755-1 also lists Human and Mouse reactivity, while A01755-3 lists Human and is polyclonal (catalog: reactivity; A01755-3 dilution_raw); neither IHC caption reports the fixative (A01755-1 and A01755-3 IHC image captions).

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

References

  1. UniProt Consortium. UniProt entry Q01955 (CO4A3_HUMAN, Collagen alpha-3(IV) chain).
  2. Human Protein Atlas. COL4A3 tissue IHC expression (reliability: Approved).
  3. Human Protein Atlas. COL4A3 subcellular location (ICC-IF): Mainly localized to vesicles. In addition localized to the endoplasmic reticulum..
  4. Human Protein Atlas. COL4A3 antibody validation summary (1 antibodies).
  5. Characterization of Ocular Morphology in Col4a3-/- Mice as a Murine Model for Alport Syndrome. Translational vision science & technology 2024 — PMC11268448.
  6. A single-nucleus transcriptomic characterization of EGFR G719X/S768I double-mutant lung adenocarcinoma identifies an immunosuppressive niche defined by COL4A3-CD44 interaction. Translational oncology 2026 — PMC13452252.
  7. An Overlapping Case of Alport Syndrome and Thin Basement Membrane Disease. Journal of clinical medicine research 2016 — PMC5012249.
  8. Low level of expression of known deafness genes Kcne1, Kcnj10 or Col4a3 is sufficient to maintain hearing in mice. Hearing research 2025 — PMC7619435.
  9. PubMed PMID:8083201 — UniProt-cited evidence.
  10. PubMed PMID:11134255 — UniProt-cited evidence.
  11. PubMed PMID:15815621 — UniProt-cited evidence.