CHD3 / ATP-dependent chromatin remodeler CHD3 · IHC design guide

Design Immunohistochemistry for CHD3

Plan chromogenic CHD3 IHC in paraffin sections using the catalog antibody at 1:100 as a starting dilution (datasheet: M03200 IHC images). Assess nuclear and cytoplasmic staining, comparing strongly stained urothelial cells in urinary bladder with lower-signal cell populations (HPA tissue IHC).

Evidence assembled Oct 2026 · For research use; verify linked source records and product datasheet before use

Immunohistochemistry protocol sheet for CHD3 (IHC for CHD3): expected localisation Nuclear and cytoplasmic tissue staining (HPA tissue IHC), antibody M03200, validated IHC image, and IHC protocol steps — Printable **CHD3** IHC protocol sheet — expected localisation Nuclear and cytoplasmic tissue staining (HPA tissue IHC), antibody M03200, controls and protocol steps. Open the full CHD3 IHC guide →

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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 tissue staining (HPA tissue IHC)
	Staining pattern	Nuclear and cytoplasmic staining with variable intensity (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 paraffin-section fixation consistent (standard IHC practice; not target-specific)
	Caveat	Cell-type staining ranges from high to undetected (HPA tissue IHC)
	Regulation	Expression regulator not specified (UniProt)
	Isoform / epitope	3 isoforms; epitope coverage is unknown (UniProt)

Section 1

Recommended CHD3 IHC & IF Protocols

The catalog antibody’s IHC-P protocol is followed by one published CHD3 protocol for paraffin sections (PMC3654872).

Recommended immunohistochemistry (IHC-P) protocol parameters
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 protocol reports retrieval without specifying its conditions (PMC3654872).

Section 2

What Is the Expected CHD3 Staining Pattern?

CHD3 is a nuclear chromatin remodeler that can also localize to centrosomes (UniProt Q12873: localization and function). In paraffin sections, expect staining in selected neuronal, glandular, endothelial, Sertoli, and urothelial cells, with nuclear and cytoplasmic expression reported across tissues (HPA: tissue IHC, Supported reliability). CHD3 has no transmembrane segment (UniProt Q12873: topology).

What am I looking at on my slide?
Nuclear staining in cerebral cortex neurons and fallopian tube glandular cells.	This fits the expected compartment and cells: both populations show high CHD3 staining (HPA: tissue IHC). Compare cell types within the section; widespread expression does not mean every cell should stain equally (UniProt Q12873: widely expressed; HPA: tissue IHC).
Staining appears only along cell membranes, without a discernible nuclear component.	A membrane-only pattern conflicts with the reported nuclear and cytoplasmic tissue profile and nuclear localization (HPA: tissue IHC; UniProt Q12873: localization). CHD3 has no transmembrane segment (UniProt Q12873: topology). Treat this pattern as suspect until controls support it.
Strong signal appears in appendix non-germinal center cells or bone marrow hematopoietic cells.	Those specific populations were not detected in the HPA tissue survey (HPA: tissue IHC). Check for cross-reactivity or endogenous detection activity before interpreting the signal as CHD3; an HPA observation is a reference pattern, not an absolute biological exclusion.
A diffuse brown haze obscures both nuclei and tissue boundaries.	When staining lacks recognizable cellular localization, it cannot establish the reported CHD3 pattern (HPA: tissue IHC). Nonspecific antibody binding, residual detection activity, or inadequate washing are general IHC possibilities; inspect a negative reagent control and the counterstain (general IHC practice).
There is no signal in a well-preserved cerebral cortex neuronal population.	Neurons were high in the HPA cerebral cortex sample (HPA: tissue IHC). First check the staining run and tissue preservation with appropriate controls (general IHC practice). A negative result in one specimen does not by itself establish CHD3 absence.

💡Expected CHD3 appearanceCall a result positive when identifiable nuclei in an HPA-high cell population stain clearly, allowing the reported cytoplasmic component, while diffuse haze or isolated membrane-only color remains suspect (HPA: tissue IHC; UniProt Q12873: localization and topology).

How each factor affects the staining
Cell population and reference tissue	CHD3 is widely expressed, yet HPA staining varies by cell type (UniProt Q12873: tissue specificity; HPA: tissue IHC). High-reference examples include salivary gland glandular cells and bladder urothelial cells; low-reference examples include small-intestine enterocytes and breast glandular cells (HPA: tissue IHC).
Antibody evidence	The tissue IHC profile has Supported reliability, with medium consistency between staining and RNA data; HPA043368 is Supported for IHC (HPA: tissue IHC and antibody validation). Interpret an individual stain alongside controls and morphology rather than assuming every reported intensity will reproduce in every specimen (general IHC practice).
Subcellular localization	UniProt places CHD3 in nuclei and PML bodies and reports centrosome association; HPA describes general nuclear and cytoplasmic tissue expression (UniProt Q12873: localization; HPA: tissue IHC). Thus cytoplasmic signal alone needs context, while a clean nuclear component is a useful reference.
Isoforms and modified residues	UniProt lists three isoforms and multiple phosphorylation sites (UniProt Q12873: isoforms and modified residues). The supplied sources give no epitope map for the catalog antibody, so they do not establish whether isoform choice or phosphorylation changes this IHC stain.
Antigen retrieval	Retrieval conditions are a general paraffin-section optimization variable (general IHC practice). Neither supplied source establishes CHD3-specific retrieval sensitivity; compare any candidate condition against the same positive-reference tissue and controls rather than attributing a change to CHD3 chemistry.
IF/ICC Q: Where should fluorescence appear?	A: Mainly in nucleoplasm and nucleoli (HPA: ICC-IF, supported); centriolar-satellite localization is uncertain (HPA: ICC-IF). This is an IF localization reference, not an IHC protocol choice.

Why is my staining missing, weak or wrong?
Situation	Likely cause	Next action
No staining in a positive-reference section	A failed reagent or detection step is possible (general IHC practice); neuronal cells in cerebral cortex were high in the HPA survey (HPA: tissue IHC).	Check the run control, reagent sequence, detection chemistry, and counterstained tissue integrity (general IHC practice); repeat with an HPA-high cell population (HPA: tissue IHC).
Only cytoplasmic color is visible	HPA reports a cytoplasmic component, but UniProt also places CHD3 in nuclei (HPA: tissue IHC; UniProt Q12873: localization).	Inspect nuclear boundaries and the matched controls before scoring; compare with an HPA-high population for a nuclear component (general IHC practice; HPA: tissue IHC).
Every cell stains equally strongly	Uniform signal obscures HPA's cell-type differences and may reflect nonspecific binding or detection background (HPA: tissue IHC; general IHC practice).	Review a negative reagent control and optimize blocking, washing, or detection conditions if background is present (general IHC practice).
Brown haze persists outside recognizable cells	Nonspecific binding or residual detection activity can produce poorly localized color (general IHC practice).	Compare with a negative reagent control, then review blocking and wash conditions; score only signal assignable to intact cells (general IHC practice).
A presumed negative tissue shows scattered positive cells	HPA 'not detected' entries apply to named populations, not necessarily every cell in an organ (HPA: tissue IHC).	Identify the stained cell type before calling the tissue discordant; compare the same population with its HPA reference and check controls (HPA: tissue IHC; general IHC practice).
Signal varies between specimens of the same tissue	HPA rates the tissue IHC evidence Supported with medium staining–RNA consistency, and its reported levels are cell-type specific (HPA: tissue IHC).	Compare matched cell populations and run controls, document staining location and intensity, and avoid assigning a fixation-specific CHD3 effect without evidence (HPA: tissue IHC; general IHC practice).

Source: UniProt Q12873 Human Protein Atlas tissue Human Protein Atlas subcellular

Experiment evidence

IHC & IF images showing CHD3 staining

IHC analysis of CHD3 using anti-CHD3 antibody (M03200). CHD3 was detected in a paraffin-embedded section of human pancrease 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 1:100 rabbit anti-CHD3 Antibody (M03200) 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.

M03200 · IHCIHC analysis of CHD3 using anti-CHD3 antibody (M03200). CHD3 was detected in a paraffin-embedded section of human pancrease cancer tissue. H

IHC analysis of CHD3 using anti-CHD3 antibody (M03200). CHD3 was detected in a paraffin-embedded section of human bladder 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 1:100 rabbit anti-CHD3 Antibody (M03200) 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.

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.

← swipe / scroll for more images →

Real IHC / IF data behind the staining-pattern expectations in this section.

Sample controls for CHD3 IHC & IF

🧪Run fallopian tube first and require staining in glandular cells (HPA: High in fallopian tube glandular cells); use cerebellum granular-layer cells as the negative comparison (HPA: Not detected in cerebellum granular-layer cells). On the positive slide, adjacent non-glandular cells can serve as internal negative cells only if they remain unstained; their CHD3 status is not specified in the supplied HPA rows (HPA: fallopian tube glandular-cell row).

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 a no-primary, secondary-only control, a rabbit isotype control matched to the primary’s clonality, and a CHD3-knockout biological control where available (caption: rabbit anti-CHD3 primary; standard IHC practice). Quench endogenous peroxidase and check for tissue background before scoring the HRP/DAB signal (caption: HRP/DAB detection; standard IHC practice).

⚠️Feasibility: The selected M03200 paraffin-section caption reports heat retrieval in EDTA at pH 8.0 and a 1:100 primary dilution, but its fixative and a target-specific fixation window or fixation effect are unreported (M03200 tissue-IHC caption). Retrieval is documented in that example; its necessity for every specimen is unreported (M03200 tissue-IHC caption). The supplied evidence does not establish whether frozen sections or IF are easier; if assessing fallopian tube by fluorescence, check tissue autofluorescence before interpreting signal (HPA: fallopian tube glandular cells High; standard IF 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, cell compartment, controls and scoring before interpreting chromogenic signal.

How should I retrieve CHD3 when nuclear staining is weak?

Start with heat-mediated antigen retrieval in EDTA at pH 8.0 for the catalog antibody (datasheet M03200). Keep section thickness, heating, cooling and primary incubation consistent across the first comparison, because retrieval changes can otherwise be confused with detection changes (standard IHC practice). The selected paraffin-section example used 1:100 primary antibody overnight at 4°C after retrieval (datasheet M03200). If staining remains weak, test a longer heat exposure on adjacent sections alongside the original condition, and judge improvement by nuclear detail and background in the same cell populations (standard IHC practice).

Could fixation explain weak or uneven CHD3 staining?

CHD3-specific fixation sensitivity is unknown: the selected paraffin-section caption does not state its fixative (datasheet M03200). Record each block’s fixative and processing history where available, then compare sections processed together so fixation is not confounded with retrieval or detection (standard IHC practice). If staining varies within a section, inspect morphology and compare well-preserved areas before increasing the 1:100 primary concentration used in the selected example (datasheet M03200; standard IHC practice). Use a consistently stained control section in the same run, and treat any apparent fixation effect as a testable explanation rather than a property established for CHD3 (standard IHC practice).

How do I assess cytoplasmic CHD3 without dismissing nuclear staining?

Score nuclear and cytoplasmic signal separately, since tissue IHC reports both compartments for CHD3 (HPA: general nuclear and cytoplasmic expression). Nuclear staining fits CHD3’s chromatin-remodeling role, while centrosome association provides a reason to examine discrete extranuclear signal carefully (UniProt Q12873 function and subcellular location). In each compartment, compare staining with matched negative-control sections and intact cell morphology before calling a focal deposit positive (standard IHC practice). Record the fraction of cells with convincing nuclear staining and describe any cytoplasmic pattern independently; a diffuse brown haze should not be counted as centrosomal localisation without suitable spatial evidence (standard IHC practice).

Can epitope or isoform differences explain discordant CHD3 staining?

CHD3 has 3 reported isoforms and multiple modified residues, including phosphoserines at positions 79, 308 and 324 (UniProt Q12873 isoforms and modified residues). The supplied product caption does not identify the antibody’s epitope, so it cannot establish which isoforms or modification states the chromogenic signal represents (datasheet M03200). Keep retrieval and detection matched when comparing sections, and check the antibody’s documented immunogen or epitope before assigning a discrepancy to splicing (standard IHC practice). Report results as CHD3 immunoreactivity unless isoform-specific recognition has been demonstrated with an appropriate control; morphology and compartment alone cannot identify an isoform (standard IHC practice).

How should I plan IF follow-up to a chromogenic CHD3 result?

Use IF as a follow-up to the paraffin-section IHC result, and validate staining conditions separately before comparing signal between methods (standard IF/IHC practice). CHD3 is mainly reported in nucleoplasm and nucleoli in subcellular imaging, with an uncertain centriolar-satellite location (HPA: subcellular summary). Multiplex a CHD3 channel with a validated marker for the cell type being assessed, and choose a fluorophore channel after checking that section’s autofluorescence (standard IF practice). Because CHD3 has no transmembrane segment, use controlled permeabilisation to reach intracellular epitopes; titrate it while preserving nuclei and cell boundaries, and include single-label controls for channel bleed-through (UniProt Q12873 topology; standard IF practice).

What should I change when DAB obscures CHD3-positive nuclei?

First inspect a no-primary control and apply an appropriate endogenous-peroxidase block before HRP and DAB detection (standard IHC practice). The selected paraffin-section example used 10% goat serum blocking, 1:100 primary antibody overnight at 4°C, and a peroxidase-conjugated secondary for 30 minutes at 37°C (datasheet M03200). If background persists, compare shorter chromogen development and a primary-antibody titration on adjacent sections while keeping retrieval at EDTA pH 8.0 (datasheet M03200; standard IHC practice). Judge the change by preservation of interpretable nuclear detail, since a darker field alone does not establish more CHD3 staining (standard IHC practice).

How should I quantify CHD3 across heterogeneous tissue sections? ⚠ ANSWER MARKED FOR VERIFICATION

Define the cell population and region before scoring, then record nuclear CHD3 as percent-positive cells and staining intensity; an H-score can combine those observations (standard IHC practice). Report cytoplasmic signal separately because tissue IHC describes both nuclear and cytoplasmic expression (HPA: general nuclear and cytoplasmic expression). Normalise counts to the number of eligible, intact cells in each region, or report positive-cell density per mm² of evaluated tissue when cell boundaries are unreliable (standard IHC practice). Use identical retrieval, DAB development, counterstain and scoring thresholds across compared sections, and exclude damaged edges and necrotic areas before calculating a summary (standard IHC practice).

How can I distinguish plausible CHD3 staining from tissue artefact?

Look for reproducible intracellular staining in intact cells: CHD3 is a nuclear chromatin regulator, while tissue IHC also reports cytoplasmic expression (UniProt Q12873 function; HPA: general nuclear and cytoplasmic expression). High staining in fallopian-tube glandular cells and low staining in pancreatic exocrine glandular cells are reported patterns, but neither alone validates an individual section (HPA: tissue IHC). Treat staining concentrated at section edges, in necrotic material or in a no-primary control as suspect, and check the endogenous-peroxidase block when DAB appears broadly (standard IHC practice). Confirm a proposed positive pattern with morphology, the expected cell population and a consistently processed control section before interpreting a biological difference (standard IHC practice).

Boster reagents

Best CHD3 / ATP-dependent chromatin remodeler CHD3 IHC Antibodies

M03200 has IHC images from paraffin sections of human, mouse, and rat tissue (M03200 IHC captions). IF/ICC is listed for both antibodies, but no IF images are supplied (catalog applications and IF images).

Real IHC data

Anti-CHD3 Rabbit Monoclonal Antibody

Cat # M03200

View product →

M03200 is the only SKU with a rendering card (cards payload). Its IHC captions show paraffin sections of human pancreas and bladder cancer tissue and mouse and rat bladder cancer tissue (M03200 IHC captions).

Which to pick: Choose M03200 for tissue IHC: its own captions document EDTA pH 8 retrieval and 1:100 primary antibody overnight at 4°C on paraffin sections; the fixative is unreported (M03200 IHC captions). For IF/ICC, both rabbit monoclonals are listed at 1:50–1:200, but neither has a supplied IF image (catalog host, applications, IF dilutions, and IF images). Choose M03200 for cross-species work because it lists human, mouse, and rat reactivity, while M03200-1 lists human only (catalog reactivity).

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.