This website uses cookies to ensure you get the best experience on our website.
- Table of Contents
CHD3 / ATP-dependent chromatin remodeler CHD3 · IHC design guide
Design Immunohistochemistry for CHD3
Plan CHD3 IHC in paraffin sections using nuclear and cytoplasmic staining as the tissue reference (HPA tissue IHC). This guide covers a high-staining control in bladder urothelial cells (HPA tissue IHC), antibody titration at 1:50–1:200 (datasheet M03200), and compartment-aware scoring.
Evidence assembled Oct 2026 · For research use; verify linked source records and product datasheet before use
CHD3 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 and cytoplasmic staining (HPA tissue IHC) | |
| Staining pattern | General nuclear and cytoplasmic staining (HPA tissue IHC) | |
| Antigen retrieval | EDTA pH 8.0 HIER, heat-mediated (datasheet M03200) | |
| Positive control | Cerebral cortex+4 more · see all | |
| Negative control | Appendix+4 more · see all |
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 and RNA show medium consistency (HPA tissue IHC) | |
| Regulation | Widely expressed (UniProt) | |
| Isoform / epitope | 3 isoforms; check whether the epitope is shared (UniProt) |
Section 1
Recommended CHD3 IHC & IF Protocols
The catalog antibody’s IHC-P protocol is accompanied by one published CHD3 IHC method using SCM muscle sections (PMC3654872: Methods).
| Sample | Paraffin-embedded human pancrease cancer tissue; fixative not specified (datasheet M03200) |
| Fixation | Image fixative and duration unreported (datasheet M03200); 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 M03200); 20 min, 95–100 °C (standard) |
| Peroxidase block | 3% H2O2, 10 min, room temperature (standard) |
| Blocking | 10% goat serum (datasheet M03200) |
| Primary antibody | Rabbit monoclonal (clone 17C46) anti-CHD3, 1:50-1:200 (datasheet M03200) |
| Primary incubation | Overnight at 4 °C (datasheet M03200) |
| Detection | HRP-conjugated secondary, DAB chromogen (datasheet M03200) |
| Counterstain | Hematoxylin, blue, dehydrate and mount (standard) |
| Expected result | CHD3-positive staining in neuronal cells of cerebral cortex (HPA tissue IHC: High). HPA tissue profile: General nuclear and cytoplasmic expression. No signal in the no-primary control. |
💡Decision noteStart with heat-mediated EDTA retrieval at pH 8.0 (datasheet: M03200); the published SCM method reports retrieval without specifying its buffer (PMC3654872: Methods).
Section 2
What Is the Expected CHD3 Staining Pattern?
CHD3 is mainly nuclear, with reported nucleoplasm and nucleoli localization; HPA tissue IHC also describes general nuclear and cytoplasmic staining (UniProt Q12873 localization; HPA subcellular; HPA tissue IHC). Expect staining in appropriate cells across many tissues, with intensity varying by cell type (UniProt Q12873: widely expressed; HPA tissue IHC: low tissue specificity). HPA rates its tissue IHC pattern Supported, with medium consistency between staining and RNA data (HPA tissue IHC: Supported). CHD3 has no transmembrane segment (UniProt Q12873 topology).
| Nuclear staining in neuronal cells of cerebral cortex or glandular cells of fallopian tube, with some cytoplasmic staining. | This fits HPA's High staining in those cell types and its general nuclear and cytoplasmic IHC profile (HPA tissue IHC: High; HPA tissue IHC profile). Assess the intended cells, since intensity differs across tissues and cell populations (HPA tissue IHC). |
| Strong, exclusively membranous staining, or a uniform extracellular deposit, without convincing nuclear signal. | This is discordant with CHD3's reported localization and lack of a transmembrane segment (UniProt Q12873 localization and topology; HPA subcellular). Treat it as a possible detection artefact; check a known-positive section and detection controls before assigning CHD3 positivity. |
| Strong staining mainly in bone marrow hematopoietic cells or heart cardiomyocytes. | HPA reports CHD3 as Not detected in those particular cell types, so review cell identification and consider cross-reactivity or endogenous detection activity (HPA tissue IHC: Not detected). Their result does not establish that every cell in either tissue must be negative. |
| Diffuse color covers the section, including spaces between cells and a no-primary control. | This does not define a CHD3 compartment. In chromogenic IHC, nonspecific reagent binding or endogenous enzyme activity can produce background (standard IHC practice). Compare controls and reagent distribution before interpreting weak cellular staining. |
| No discernible signal in cerebral cortex neuronal cells or fallopian tube glandular cells. | These are HPA High cell-type examples (HPA tissue IHC: High). A blank result calls for review of tissue identity, antibody and detection controls, retrieval conditions, and section quality (standard IHC practice); it alone does not prove CHD3 absence. |
💡Expected CHD3 appearanceCall positive when the intended cells show convincing nuclear staining, allowing cytoplasmic staining where present, with High examples in cerebral cortex neurons and fallopian tube glandular cells (UniProt Q12873 localization; HPA tissue IHC: High and general nuclear/cytoplasmic profile); isolated membrane staining or diffuse deposits are suspect (UniProt Q12873 topology; standard IHC practice).
| Tissue and cell-type selection | HPA calls tissue RNA specificity Low and reports CHD3 widely across tissues, yet its IHC levels vary by cell type (HPA tissue IHC; UniProt Q12873 tissue specificity). Pair a High example with a cell type reported Not detected; do not treat an entire tissue as a uniform control. |
| IHC antibody evidence | HPA043368 is Supported for IHC, while the supplied HPA status for that antibody has no ICC rating (HPA antibodies: HPA043368). HPA's overall tissue IHC reliability is Supported with medium RNA concordance, so compare the observed compartment and cell type with controls (HPA tissue IHC reliability). |
| IF/ICC Q&A: where should CHD3 appear? | Mainly in nucleoplasm and nucleoli (HPA subcellular: supported); centriolar satellites are an additional uncertain location (HPA subcellular). HPA076524 has Supported ICC validation (HPA antibodies: HPA076524). The IF/ICC guide covers that application; these observations are not an IHC-P protocol. |
| Isoforms and epitope interpretation | UniProt lists three CHD3 isoforms, but the supplied record does not map antibody epitopes to them (UniProt Q12873 isoforms). A differing stain cannot be assigned to a particular isoform from this evidence; consult the antibody's documented immunogen and validation before making that claim. |
| Processing and membrane expectations | UniProt lists a single CHD3 chain, no signal peptide or propeptide, and no transmembrane segment (UniProt Q12873 processing and topology). The record supplies no processing or shedding basis for an extracellular staining pattern; assess such color as a possible artefact. |
| Situation | Likely cause | Next action |
|---|---|---|
| Expected High cells are blank. | The observed result conflicts with HPA's High examples, but the image alone cannot identify the failed step (HPA tissue IHC: cerebral cortex neurons; fallopian tube glandular cells). | Confirm cell identity and tissue integrity; inspect the IHC-validated antibody's documented conditions, retrieval, and detection controls (standard IHC practice). Do not infer a CHD3-specific fixation effect from HPA staining levels. |
| Only a bright membrane rim appears. | CHD3 has no transmembrane segment, and its reported locations are mainly nuclear with some cytoplasmic or centrosomal association (UniProt Q12873 topology and localization; HPA tissue IHC). | Check adjacent morphology and no-primary control, then compare with a known-positive section (standard IHC practice). Score the rim cautiously unless a convincing expected compartment is also present. |
| A reported Not detected cell type stains strongly. | The result disagrees with that HPA cell-type observation; cross-reactivity or endogenous chromogenic activity is possible (HPA tissue IHC: Not detected; standard IHC practice). | Verify the cell type. For enzyme-based detection, review appropriate no-primary and endogenous-enzyme controls; assess whether staining remains in the expected nuclear compartment (standard IHC practice; UniProt Q12873 localization). |
| Color spreads across tissue and empty spaces. | Diffuse deposition can reflect background from reagents or endogenous enzyme activity rather than a cellular CHD3 pattern (standard IHC practice). | Compare no-primary and positive-control sections, review blocking and washing, and interpret only resolved cellular staining (standard IHC practice). |
| Signal is faint across all tested cell types. | HPA reports Low as well as High staining in different cell types; uniformly weak results also leave assay performance uncertain (HPA tissue IHC: Low and High). | Use a reported High cell type as a performance check and follow the catalog antibody's IHC-P conditions when available; evaluate retrieval and detection with controls (HPA tissue IHC: High; standard IHC practice). |
| Nucleolar or satellite-like puncta are difficult to assign. | HPA supports nucleoplasm and nucleoli in ICC-IF but labels centriolar satellites uncertain; tissue IHC reports a broader nuclear and cytoplasmic profile (HPA subcellular; HPA tissue IHC). | Score the dominant IHC compartment and identified cell type. Do not require satellite puncta for a positive IHC call, or use ICC-IF localization alone to validate a chromogenic deposit (HPA subcellular; HPA tissue IHC). |
Experiment evidence
IHC & IF images showing CHD3 staining
M03200 · IHCIHC analysis of CHD3 using anti-CHD3 antibody (M03200). CHD3 was detected in a paraffin-embedded section of human pancrease cancer tissue. H
M03200 · IHCIHC analysis of CHD3 using anti-CHD3 antibody (M03200). CHD3 was detected in a paraffin-embedded section of human bladder cancer tissue. Hea
HPA · Cerebral cortexHuman Protein Atlas IHC, Cerebral cortex. Source: https://www.proteinatlas.org/ENSG00000170004-CHD3/tissue/cerebral+cortex#imid_14555512
HPA · ColonHuman Protein Atlas IHC, Colon. Source: https://www.proteinatlas.org/ENSG00000170004-CHD3/tissue/colon#imid_14542830
HPA · LiverHuman Protein Atlas IHC, Liver. Source: https://www.proteinatlas.org/ENSG00000170004-CHD3/tissue/liver#imid_14542847
HPA · KidneyHuman Protein Atlas IHC, Kidney. Source: https://www.proteinatlas.org/ENSG00000170004-CHD3/tissue/kidney#imid_14542840
HPA · ICC-IF REHHuman Protein Atlas immunofluorescence, REH, antibody HPA076524; green = CHD3, blue = nucleus, red = microtubules.
HPA · ICC-IF REHHuman Protein Atlas immunofluorescence, REH, antibody HPA076524; green = CHD3, blue = nucleus, red = microtubules.
← swipe / scroll for more images →
Real IHC / IF data behind the staining-pattern expectations in this section.
Sample controls for CHD3 IHC & IF
🧪Run cerebral cortex first: neuronal cells should stain strongly (HPA: High in cerebral cortex neuronal cells). Use cerebellum granular-layer cells as a negative comparison (HPA: Not detected); on the positive slide, cells without specific CHD3 staining should show counterstain alone, but should be treated as background references rather than validated biological negatives (standard IHC practice).
Positive control tissue: Cerebral cortex (Neuronal cells, HPA High)
Negative control tissue: Appendix (HPA Not detected)
ICC-IF cell lines (HPA subcellular resource): HPA ICC-IF images show CHD3 in REH, SiHa, U2OS, KOLF2.1J, with annotated localisation: Nucleoplasm (supported), Nucleoli (supported) (HPA subcellular).
Technical controls: Include no-primary or secondary-only controls, a concentration-matched rabbit isotype control for the rabbit catalog antibody, and CHD3 knockout tissue or a peptide-block control if a matching peptide is available (selected-SKU caption: rabbit anti-CHD3; standard IHC practice). Quench endogenous peroxidase and check cerebral cortex pigment against the control slides when interpreting DAB staining (selected-SKU caption: HRP/DAB detection; standard IHC practice).
⚠️Feasibility: A target-specific fixation window and fixation effect are unreported, and the selected-SKU paraffin-section caption does not state a fixative (selected-SKU caption: fixative unreported). The documented tissue-IHC procedure uses heat retrieval in EDTA at pH 8.0; this establishes a working retrieval condition, not that retrieval is universally required (selected-SKU caption). HPA reports ICC-IF localization in the nucleoplasm and nucleoli, but the supplied evidence does not establish that frozen sections or IF are easier than paraffin IHC; cerebral cortex pigment should be distinguished from DAB signal (HPA: supported nucleoplasm and nucleoli; standard IHC practice).
HPA tissue IHC evidence for CHD3
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.
Positive expression · recommended positive controls
| Tissue | Cell type | Level | Evidence | Source |
|---|---|---|---|---|
| Cerebral cortex | Neuronal cells | High | Protein (IHC) | HPA → |
| Endometrium | Glandular cells | Low | Protein (IHC) | HPA → |
| Fallopian tube | Glandular cells | High | Protein (IHC) | HPA → |
| Gallbladder | Glandular cells | High | Protein (IHC) | HPA → |
| Salivary gland | Glandular cells | High | Protein (IHC) | HPA → |
Undetected expression · recommended negative controls
| Tissue | Cell type | Level | Evidence | Source |
|---|---|---|---|---|
| Appendix | Non-germinal center cells | Not detected | Protein (IHC) | HPA → |
| Bone marrow | Hematopoietic cells | Not detected | Protein (IHC) | HPA → |
| Cerebellum | Cells in granular layer | Not detected | Protein (IHC) | HPA → |
| Duodenum | Endocrine cells | Not detected | Protein (IHC) | HPA → |
| Heart muscle | Cardiomyocytes | Not detected | Protein (IHC) | HPA → |
Section 3
Advanced CHD3 IHC Tips
Troubleshoot CHD3 staining in paraffin sections by checking retrieval, compartment-specific signal, controls, and cell-level scoring.
Which retrieval conditions should I try first for weak CHD3 staining?
Start with heat-mediated retrieval in EDTA at pH 8.0 for the catalog antibody (datasheet M03200). The selected paraffin-section image used that retrieval before incubation with antibody at 1:100 overnight at 4°C (caption M03200). If staining is weak, compare heating and cooling conditions across matched sections while keeping antibody dilution and detection constant (standard IHC practice). Score signal in nuclei and surrounding cytoplasm separately, because both compartments appear in tissue IHC (HPA: general nuclear and cytoplasmic expression). Include a no-primary control to distinguish gained CHD3 signal from retrieval-associated background (standard IHC practice).
How should I troubleshoot CHD3 staining when fixation history is uncertain?
The selected image identifies a paraffin-embedded section but does not report its fixative, so CHD3-specific fixation sensitivity remains unknown (caption M03200). Record the fixative and fixation duration for each specimen, then compare sections processed and stained together (standard IHC practice). Begin with the reported EDTA retrieval at pH 8.0 and 1:100 antibody incubation overnight at 4°C when assessing the catalog method (caption M03200). If specimens differ in staining, examine preservation, edge staining, and matched control tissue before assigning the difference to CHD3 abundance (standard IHC practice). Do not use tissue staining patterns to infer a fixation requirement.
Should CHD3 staining be confined to the nucleus?
Assess nuclear staining first, but record cytoplasmic staining separately: tissue IHC reports both nuclear and cytoplasmic expression (HPA: tissue IHC profile). Nucleoplasm and nucleoli are supported locations in subcellular imaging, while centriolar-satellite localization is uncertain (HPA: subcellular). CHD3 also associates with centrosomes in interphase and mitosis (UniProt Q12873; PubMed:17626165). A small perinuclear focus therefore needs morphological and control-based assessment before interpretation; diffuse chromogen deposits alone do not establish centrosomal CHD3 (standard IHC practice). Compare compartment patterns in the same cell type across matched sections, using no-primary staining to assess nonspecific deposits (standard IHC practice).
Could CHD3 isoforms or epitope accessibility explain uneven staining?
CHD3 has 3 annotated isoforms, but the supplied catalog caption does not specify the antibody epitope or isoform coverage (UniProt Q12873; caption M03200). Its two chromo domains occupy residues 494–594 and 631–673, and its helicase regions begin at residue 748 (UniProt Q12873). These domain coordinates cannot establish which isoforms the antibody detects without an epitope map (UniProt Q12873; caption M03200). Compare matched sections under the reported EDTA pH 8.0 retrieval and document cell-specific nuclear and cytoplasmic patterns (datasheet M03200; HPA: tissue IHC profile). If an epitope map becomes available, check its sequence against each isoform before attributing staining differences to splicing (standard IHC practice).
How can I assess CHD3 by IF alongside the paraffin-section IHC result?
Treat IF as a separate assay and pair CHD3 with a validated marker for the expected cell type, such as a neuronal marker when examining cerebral-cortex neuronal cells (HPA: High in cerebral-cortex neuronal cells; standard IF practice). Choose fluorophores in channels with low specimen autofluorescence and include single-label and no-primary controls when multiplexing (standard IF practice). CHD3 has no transmembrane segment and is mainly nucleoplasmic and nucleolar in subcellular images, so permeabilize sufficiently for intracellular epitope access (UniProt Q12873 topology; HPA: subcellular). Optimize permeabilization on matched specimens because the catalog epitope is unspecified (caption M03200). Compare nuclear and cytoplasmic IF patterns with the compartments scored by chromogenic IHC, without treating fluorescence intensity as directly equivalent to DAB intensity (HPA: tissue IHC profile; standard IF/IHC practice).
What should I check when CHD3 DAB staining appears diffuse?
Run a no-primary section to assess secondary-reagent binding and endogenous peroxidase, and apply a peroxidase block before HRP/DAB detection (standard IHC practice). The selected image used 10% goat serum blocking, a rabbit primary at 1:100 overnight at 4°C, and peroxidase-linked detection with DAB (caption M03200). Compare background in matched sections while changing one blocking, washing, or detection variable at a time (standard IHC practice). Evaluate whether diffuse color obscures nuclear boundaries, since CHD3 has reported nuclear and cytoplasmic tissue staining (HPA: tissue IHC profile). Check section edges and damaged regions separately before calling widespread color a positive result (standard IHC practice).
How should I quantify CHD3 staining across samples? ⚠ ANSWER MARKED FOR VERIFICATION
Define cell types and compartments before scoring, since CHD3 tissue IHC includes nuclear and cytoplasmic expression (HPA: tissue IHC profile). For chromogenic sections, report the percentage of positive cells and a nuclear H-score based on intensity categories 0–3; score cytoplasm separately (standard IHC practice). If counting localized positive cells, report density per mm² of evaluable tissue and exclude necrotic or damaged regions consistently (standard IHC practice). Normalize counts to the relevant cell population or intact tissue area, and compare sections stained in the same run (standard IHC practice). Record thresholds, counterstain quality, and no-primary background so differences can be audited (standard IHC practice).
How can I distinguish convincing CHD3 positivity from staining artefact?
Look for reproducible staining within intact cells and assess its nuclear and cytoplasmic distribution, which is reported for CHD3 tissue IHC (HPA: tissue IHC profile). A nuclear pattern is consistent with its supported nucleoplasmic and nucleolar locations, but compartment agreement alone does not prove antibody specificity (HPA: subcellular; standard IHC practice). Compare the stained cell type with the intended reference: cerebral-cortex neuronal cells show high staining, whereas cerebellar granular-layer cells are reported as not detected (HPA: tissue IHC). Discount edge-restricted color, necrotic deposits, and signal reproduced in a no-primary control; inspect endogenous peroxidase before interpreting DAB (standard IHC practice). Resolve unexpected compartments or cell types with an independent antibody or orthogonal assay when available (standard IHC practice).
Boster reagents
Best CHD3 / ATP-dependent chromatin remodeler CHD3 IHC Antibodies
CHD3 has paraffin-section IHC images for human, mouse and rat samples (M03200 IHC captions); IF/ICC is listed for both antibodies, but no IF images are supplied (catalog applications and image alts).
Real IHC data
Anti-CHD3 Rabbit Monoclonal Antibody
Cat # M03200
M03200 has IHC images from paraffin-embedded human pancreas and bladder cancer, mouse bladder cancer, and rat bladder cancer sections; IHC and IF/ICC are listed applications (M03200 IHC captions; catalog applications). M03200-1 lists human reactivity and IHC and IF/ICC applications, but has no supplied IHC or IF image (catalog reactivity, applications and image alts).
Which to pick: For paraffin-section IHC, choose M03200 because its own captions document staining in human, mouse and rat samples (M03200 IHC captions). For IF/ICC, both M03200 and M03200-1 list the applications, but neither has a supplied IF image; M03200-1 is limited to listed human reactivity (catalog applications, reactivity and image alts). For cross-species IHC, choose rabbit monoclonal M03200, whose listed reactivity and IHC captions cover human, mouse and rat; the fixative is unreported in those captions (catalog host, clone and reactivity; M03200 IHC captions).
Each figure is that product's own IHC / IF validation image from its datasheet.
References
- UniProt Consortium. UniProt entry Q12873 (CHD3_HUMAN, ATP-dependent chromatin remodeler CHD3).
- Human Protein Atlas. CHD3 tissue IHC expression (reliability: Supported).
- Human Protein Atlas. CHD3 subcellular location (ICC-IF): Mainly localized to the nucleoplasm and nucleoli. In addition localized to the centriolar satellites..
- Human Protein Atlas. CHD3 antibody validation summary (2 antibodies).
- Integrative analysis of congenital muscular torticollis: from gene expression to clinical significance. BMC medical genomics 2013 — PMC3654872.
- PubMed PMID:9688266 — UniProt-cited evidence.
- PubMed PMID:16625196 — UniProt-cited evidence.
- PubMed PMID:9326634 — UniProt-cited evidence.
Immunohistochemistry protocol sheet for CHD3 (ATP-dependent chromatin remodeler CHD3). Expected localisation Nuclear and cytoplasmic staining (HPA tissue IHC). Antigen retrieval: EDTA pH 8.0 HIER, heat-mediated (datasheet M03200). Validated IHC antibody: M03200 at 1:50-1:200 (the product's own IHC validation image is shown). Controls (HPA): positive Cerebral cortex (Neuronal cells); negative Appendix. IHC-P workflow on paraffin sections; fixative unspecified. Protocol steps: 1. Sample: Paraffin-embedded human pancrease cancer tissue; fixative not specified (datasheet M03200); 2. Fixation: Image fixative and duration unreported (datasheet M03200); 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 M03200); 20 min, 95–100 °C (standard); 6. Peroxidase block: 3% H2O2, 10 min , room temperature (standard); 7. Blocking: 10% goat serum (datasheet M03200); 8. Primary antibody: Rabbit monoclonal (clone 17C46) anti-CHD3, 1:50-1:200 (datasheet M03200); 9. Primary incubation: Overnight at 4 °C (datasheet M03200). Watch for: Fixation: Keep fixation conditions consistent across sections. (standard IHC practice; not target-specific); Caveat: Staining and RNA show medium consistency (HPA tissue IHC); Isoform / epitope: 3 isoforms; check whether the epitope is shared (UniProt); Regulation: Widely expressed (UniProt). Evidence: UniProt Q12873, HPA tissue IHC · Supported, HPA ICC-IF · Mainly localized to the nucleoplasm and nucleoli. In addition…, Datasheet M03200, PMC3654872. QR code links to https://www.bosterbio.com/bosterbio-gene-info-cards/CHD3/immunohistochemistry-ihc-guide.