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CHD2 / ATP-dependent chromatin remodeler CHD2 · IHC design guide
Design Immunohistochemistry for CHD2
Plan CHD2 paraffin-section IHC around variable nuclear staining in most tissues (HPA tissue IHC). The guide covers staining with the IHC-validated antibody and assessment of nuclear signal against controls (datasheet A04079; standard IHC practice).
Evidence assembled Oct 2026 · For research use; verify linked source records and product datasheet before use
CHD2 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 | Variable nuclear staining in most tissues (HPA tissue IHC) | |
| Staining pattern | Variable nuclear signal across most tissue types (HPA tissue IHC) | |
| Antigen retrieval | Citrate pH 6 HIER, heat-mediated (datasheet A04079) | |
| Positive control | Cerebellum+4 more · see all | |
| Negative control | Adipose tissue+1 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) | |
| Caveat | Skeletal myocytes may be unstained (HPA tissue IHC) | |
| Regulation | Variable levels by tissue (HPA tissue IHC) | |
| Isoform / epitope | 3 isoforms; epitope coverage is unspecified (UniProt) |
Section 1
Recommended CHD2 IHC & IF Protocols
The catalog antibody protocol provides the starting conditions (datasheet: A04079); one published CHD2 IHC study reports the sample and animal details shown below (PMC9700024).
| Sample | Paraffin-embedded rat brain tissue; fixative not specified (datasheet A04079) |
| Fixation | Image fixative and duration unreported (datasheet A04079); verify before use. |
| Sectioning | 4–5 µm sections on charged slides (standard) |
| Deparaffinisation | Xylene, graded ethanol series to water (standard) |
| Antigen retrieval | Heat retrieval: Citrate pH 6, 20 min (datasheet A04079) |
| Peroxidase block | 3% H2O2, 10 min, room temperature (standard) |
| Blocking | 10% goat serum (datasheet A04079) |
| Primary antibody | Rabbit anti-CHD2, 0.5-1μg/ml (datasheet A04079) |
| Primary incubation | Overnight at 4 °C (datasheet A04079) |
| Detection | Streptavidin-biotin complex (SABC), DAB chromogen (datasheet A04079) |
| Counterstain | Hematoxylin, blue, dehydrate and mount (standard) |
| Expected result | CHD2-positive staining in cells in granular layer of cerebellum (HPA tissue IHC: High). HPA tissue profile: Nuclear expression at variable levels in most tissue types. No signal in the no-primary control. |
💡Decision noteStart with heat-mediated citrate retrieval at pH 6 (datasheet: A04079); the published excerpt does not specify retrieval conditions (PMC9700024).
Section 2
What Is the Expected CHD2 Staining Pattern?
CHD2 should appear chiefly as nuclear staining in paraffin-section IHC (UniProt O14647: nucleus; HPA tissue IHC: nuclear expression). Expect variable staining across most tissues, with high signal reported in cerebellar granular-layer cells, cortical and hippocampal neurons, and selected glandular cells (HPA tissue IHC). HPA rates its tissue-IHC reliability Enhanced, while noting medium consistency with RNA expression (HPA tissue IHC). CHD2 has no transmembrane segment (UniProt O14647: topology).
| Distinct nuclear chromogen in the expected cells, with neighboring cells showing different intensities. | This fits CHD2's nuclear localization and HPA's variable tissue pattern (UniProt O14647: nucleus; HPA tissue IHC). Compare the relevant cell population, rather than treating uniform staining throughout a section as the expected result (HPA tissue IHC: variable levels). |
| Predominantly cytoplasmic or membrane-like staining, with little nuclear signal. | Question target attribution: the expected IHC pattern is nuclear and CHD2 lacks a transmembrane segment (HPA tissue IHC; UniProt O14647: topology). HPA reports additional Golgi and vesicle signal by ICC-IF, so that observation alone does not validate a cytoplasmic IHC pattern (HPA subcellular ICC-IF). |
| Strong staining in adipocytes or skeletal myocytes while expected nuclei are weak. | HPA reports CHD2 as not detected in those two cell populations (HPA tissue IHC). Consider antibody cross-reactivity or endogenous chromogenic detection activity, then check controls; an isolated stained cell does not establish tissue-wide CHD2 expression (general IHC practice). |
| Broad haze or chromogen over nuclei, cytoplasm and extracellular areas. | The distribution obscures the expected nuclear readout (UniProt O14647: nucleus; HPA tissue IHC). Nonspecific antibody binding, insufficient blocking or washing, or detection background are possible causes; use controls to distinguish them before scoring nuclei (general IHC practice). |
| No nuclear signal in cerebellar granular-layer cells or cortical neurons. | These are reported high-staining populations, so a blank result warrants an assay check (HPA tissue IHC: High). Review section identity and positive-control performance, then assess retrieval, antibody incubation and chromogenic detection as general workflow variables (general IHC practice). |
💡Expected CHD2 appearanceCall a result positive when nuclear staining is clear in the relevant cells and can be high in HPA-reported positive populations; predominant membrane-like staining or indiscriminate chromogen is suspect (UniProt O14647: nucleus and topology; HPA tissue IHC: High and variable levels; general IHC practice: background assessment).
| Tissue and cell choice | HPA reports high staining in cerebellar granular-layer cells, cortical and hippocampal neurons, endometrial, epididymal and seminal-vesicle glandular cells, and testicular Sertoli cells (HPA tissue IHC). Adrenal glandular cells are medium; adipocytes and skeletal myocytes are not detected (HPA tissue IHC). |
| Strength of the tissue evidence | HPA calls the overall tissue-IHC result Enhanced but describes medium consistency between antibody staining and RNA expression (HPA tissue IHC). Its listed antibodies differ in IHC validation: HPA060744 is Enhanced and HPA060960 is Supported (HPA antibodies). |
| Isoforms and epitope interpretation | UniProt lists 3 CHD2 isoforms and chromo and helicase domains (UniProt O14647). The supplied evidence gives no antibody epitope, so it cannot establish which isoforms a particular IHC reagent detects or predict staining from domain position (UniProt O14647; HPA antibodies). |
| Processing and modifications | Target-specific fixation effects are not established by the supplied assay evidence. Verify with a matched IHC source before attributing a result to fixation. |
| IF/ICC Q&A: should the signal be exclusively nuclear? | HPA calls nucleoplasm the approved main ICC-IF location and also reports approved nucleoli, Golgi and vesicle locations (HPA subcellular ICC-IF). Use that as an IF interpretation note; the paraffin-section IHC expectation remains nuclear expression at variable levels (HPA tissue IHC). |
| Situation | Likely cause | Next action |
|---|---|---|
| Expected nuclei are blank in a high-staining tissue. | A failed assay step or an incorrect section is possible; HPA reports high staining in the specified positive cells (HPA tissue IHC; general IHC practice). | Verify tissue and cell identity, then review the positive control, retrieval, antibody incubation and detection run (general IHC practice). The supplied sources give no CHD2-specific retrieval setting or fixation effect (HPA tissue IHC; UniProt O14647). |
| Most chromogen is outside nuclei. | Background or off-target binding may dominate the slide; CHD2's expected tissue-IHC localization is nuclear (general IHC practice; HPA tissue IHC). | Compare with a negative reagent control and the positive tissue, and score nuclear signal separately from diffuse stain (general IHC practice; HPA tissue IHC). |
| Unexpectedly strong adipocyte or skeletal-myocyte staining. | Cross-reactivity or endogenous detection activity is plausible because HPA lists those cells as not detected (HPA tissue IHC; general IHC practice). | Check controls for antibody-independent chromogen and compare an expected positive cell population in the same run (general IHC practice; HPA tissue IHC). |
| The whole section has a brown haze. | Nonspecific binding, endogenous chromogenic activity or inadequate washing can raise background (general IHC practice). | Review blocking, washing and detection controls before increasing antibody concentration or calling weak nuclei positive (general IHC practice). |
| One tissue stains less strongly than another. | CHD2 levels vary by tissue and cell type; low staining is reported in several epithelial and glandular populations (HPA tissue IHC). | Identify and compare the same relevant cell population across sections, with a high-staining positive tissue in the run (HPA tissue IHC; general IHC practice). |
| Two antibodies yield different apparent patterns. | The listed reagents have different IHC validation ratings, and HPA reports medium staining-to-RNA consistency overall (HPA antibodies; HPA tissue IHC). | Compare nuclear localization and controls for each reagent before attributing disagreement to CHD2 biology; neither the epitope nor a CHD2-specific fixation response is supplied (HPA tissue IHC; HPA antibodies; UniProt O14647). |
Experiment evidence
IHC & IF images showing CHD2 staining
A04079 · IHCIHC analysis of CHD2 using anti-CHD2 antibody (A04079). CHD2 was detected in paraffin-embedded section of rat brain tissue . Heat mediated a
A04079 · IHCIHC analysis of CHD2 using anti-CHD2 antibody (A04079). CHD2 was detected in paraffin-embedded section of mouse brain tissue . Heat mediated
HPA · Cerebral cortexHuman Protein Atlas IHC, Cerebral cortex. Source: https://www.proteinatlas.org/ENSG00000173575-CHD2/tissue/cerebral+cortex#imid_16832467
HPA · ColonHuman Protein Atlas IHC, Colon. Source: https://www.proteinatlas.org/ENSG00000173575-CHD2/tissue/colon#imid_16832385
HPA · LiverHuman Protein Atlas IHC, Liver. Source: https://www.proteinatlas.org/ENSG00000173575-CHD2/tissue/liver#imid_16832386
HPA · KidneyHuman Protein Atlas IHC, Kidney. Source: https://www.proteinatlas.org/ENSG00000173575-CHD2/tissue/kidney#imid_16832379
HPA · ICC-IF Rh30Human Protein Atlas immunofluorescence, Rh30, antibody HPA060744; green = CHD2, blue = nucleus, red = microtubules.
HPA · ICC-IF Rh30Human Protein Atlas immunofluorescence, Rh30, antibody HPA060744; green = CHD2, blue = nucleus, red = microtubules.
← swipe / scroll for more images →
Real IHC / IF data behind the staining-pattern expectations in this section.
Sample controls for CHD2 IHC & IF
🧪Run cerebellum first and score staining in cells of its granular layer (HPA: High in cells in the cerebellar granular layer). Use skeletal muscle myocytes as the negative tissue (HPA: Not detected in skeletal muscle myocytes); on the cerebellar slide, use cells lacking nuclear chromogen as internal background comparators without assigning a named cell type as CHD2 negative (UniProt O14647: nucleus; standard IHC practice).
Positive control tissue: Cerebellum (Cells in granular layer, HPA High)
Negative control tissue: Adipose tissue (HPA Not detected)
ICC-IF cell lines (HPA subcellular resource): HPA ICC-IF images show CHD2 in Rh30, SiHa, U2OS, RPTEC/TERT1, hTERT-RPE1 (serum starved), with annotated localisation: Nucleoplasm (approved) (HPA subcellular).
Technical controls: Include a no-primary, secondary-only control, an isotype control matched to the primary antibody’s host species and clonality, and a validated CHD2 knockout specimen as a biological negative (standard IHC practice). For chromogenic detection, quench endogenous peroxidase and check for endogenous biotin when using the caption’s avidin–biotin detection method (A04079 tissue-IHC caption: SABC with DAB).
⚠️Feasibility: A target-specific fixation window and fixation effect are unreported, and the selected-SKU rat brain caption does not state its fixative (A04079 tissue-IHC caption). The caption reports heat retrieval in citrate buffer at pH 6 for 20 minutes, but does not establish that CHD2 staining depends on that retrieval condition (A04079 tissue-IHC caption). The supplied evidence does not establish whether frozen sections or IF are easier; in brain tissue, assess pigment and other background before scoring nuclear chromogen (UniProt O14647: nucleus; standard IHC practice).
HPA tissue IHC evidence for CHD2
Comprehensive Human Protein Atlas IHC scoring per tissue (reliability: Enhanced — Medium consistency between antibody staining and RNA expression data.). Rows are taken directly from the HPA tissue chart — click any row's HPA link to view the source.
Positive expression · recommended positive controls
| Tissue | Cell type | Level | Evidence | Source |
|---|---|---|---|---|
| Cerebellum | Cells in granular layer | High | Protein (IHC) | HPA → |
| Cerebral cortex | Neuronal cells | High | Protein (IHC) | HPA → |
| Endometrium | Glandular cells | High | Protein (IHC) | HPA → |
| Epididymis | Glandular cells | High | Protein (IHC) | HPA → |
| Hippocampus | Neuronal cells | High | Protein (IHC) | HPA → |
Section 3
Advanced CHD2 IHC Tips
Troubleshoot CHD2 staining by checking nuclear localisation, tissue context, and controls alongside the catalog antibody’s paraffin-section IHC conditions.
What retrieval should I try first when CHD2 nuclear staining is weak?
Start with heat-mediated citrate retrieval at pH 6 for 20 minutes (datasheet A04079; caption A04079). The catalog antibody produced CHD2 staining in a paraffin-embedded rat brain section after that treatment, although the caption does not state the fixative (caption A04079). Check a known positive cell population, such as cerebral cortex neurons, before increasing retrieval intensity (HPA tissue IHC: High in cerebral cortex neuronal cells; standard IHC practice). If nuclei remain weak, compare a longer heating interval or an alternative retrieval buffer on adjacent sections while holding antibody and detection conditions constant (standard IHC practice). Record tissue damage and background alongside nuclear signal when selecting the final condition (standard IHC practice).
Could fixation explain weak or patchy CHD2 staining in paraffin sections?
CHD2-specific fixation sensitivity is unknown because the selected paraffin-section caption does not report a fixative (caption A04079). Record the fixative, fixation duration, section age, and processing history for affected blocks, then compare sections processed together (standard IHC practice). Use the documented citrate pH 6 retrieval for 20 minutes as a starting point while assessing those variables (datasheet A04079; caption A04079). Evaluate preserved nuclear morphology and a positive control on each run; damaged or poorly preserved tissue can make a negative result difficult to interpret (standard IHC practice). Do not assign patchiness to a CHD2-specific fixation effect without a controlled comparison (standard IHC practice).
How should I investigate CHD2 staining outside nuclei?
Expect predominantly nuclear staining in tissue sections because CHD2 is annotated as nuclear and tissue IHC shows variable nuclear expression (UniProt O14647: nucleus; HPA tissue IHC: nuclear expression). Compare the signal with a nuclear counterstain and inspect individual cells at high magnification before scoring (standard IHC practice). HPA subcellular imaging places CHD2 mainly in the nucleoplasm, with additional nucleolar, Golgi, and vesicular localisation, so an occasional nonnuclear pattern needs context (HPA subcellular). Diffuse cytoplasmic DAB without convincing nuclei warrants checks of secondary-only controls, tissue edges, and detection background (standard IHC practice). Score nuclear staining separately from any other compartment and document the distinction (standard IHC practice).
Can isoforms or epitope accessibility explain discordant CHD2 IHC results?
CHD2 has 3 annotated isoforms, but the supplied evidence does not locate this antibody’s epitope or establish isoform coverage (UniProt O14647: isoforms 1, 2, 3; caption A04079). Confirm the antibody’s immunogen and whether its sequence is retained in the isoforms relevant to your specimen before attributing discordance to splicing (standard IHC practice). CHD2 contains chromodomains and helicase domains, and several annotated phosphorylation sites; these features alone do not establish altered IHC recognition (UniProt O14647: domains and modified residues). Compare the same sections using a second validated epitope, if available, and assess nuclear staining against matched controls (standard IHC practice). Keep retrieval and detection conditions matched when comparing antibodies (standard IHC practice).
How can IF help resolve an ambiguous CHD2 IHC localisation pattern?
Use IF as a complementary localisation check, while interpreting this page’s catalog evidence as paraffin-section IHC evidence (caption A04079). Multiplex CHD2 with a marker for the expected cell type, such as a neuronal marker when examining cerebral cortex neurons, and include a nuclear counterstain (HPA tissue IHC: High in cerebral cortex neuronal cells; standard IF practice). Choose fluorophores after checking the specimen’s autofluorescence and acquire single-label controls to assess channel bleed-through (standard IF practice). Because CHD2 is annotated as nuclear and lacks a transmembrane segment, use a permeabilisation condition that permits antibody access to nuclear epitopes (UniProt O14647: nucleus, no transmembrane segment; standard IF practice). Compare nuclear and extranuclear signals cell by cell (standard IF practice).
What should I check when DAB obscures CHD2-positive nuclei?
First compare the stained section with a no-primary control and inspect whether color follows nuclei or accumulates at folds, edges, and damaged regions (standard IHC practice). The selected caption used 10% goat serum blocking, a biotinylated goat anti-rabbit secondary, streptavidin-biotin detection, and DAB (caption A04079). Check peroxidase blocking and assess endogenous biotin or detection-reagent background with suitable controls when using that chemistry (standard IHC practice). If background persists, titrate the primary below the caption’s 1 μg/ml condition and adjust wash stringency while retaining a positive tissue control (caption A04079; standard IHC practice). Judge improvement by clearer nuclear signal relative to background, rather than by overall darkness (standard IHC practice).
How should I score variable CHD2 staining across tissue compartments? ⚠ ANSWER MARKED FOR VERIFICATION
Define the cell population and score nuclear CHD2 only after confirming compartment assignment with morphology and a counterstain (UniProt O14647: nucleus; standard IHC practice). Report an H-score or the percentage of positive nuclei, with intensity thresholds set from control sections before reviewing study groups (standard IHC practice). For spatial analyses, report positive nuclei per mm² and normalise to the total evaluable nuclei or viable tissue area in the same compartment (standard IHC practice). Keep acquisition, DAB development, and scoring rules consistent across sections, and exclude folds, edges, and necrotic regions using predefined criteria (standard IHC practice). Stratify cell types because HPA reports variable nuclear expression across tissues (HPA tissue IHC).
When is an apparent CHD2-positive region likely to be artefactual?
A credible positive pattern includes interpretable nuclear staining in the expected cells, such as cerebral cortex neurons or cerebellar granular-layer cells (UniProt O14647: nucleus; HPA tissue IHC: High in those cells). Treat staining confined to section edges, folds, or necrotic tissue as suspect and compare it with adjacent well-preserved tissue (standard IHC practice). Diffuse DAB without nuclei, or color reproduced in a no-primary control, calls for evaluation of detection background and endogenous enzyme activity (standard IHC practice). HPA also reports additional Golgi and vesicular localisation in subcellular imaging, so isolated extranuclear staining should be documented but not scored as nuclear IHC positivity (HPA subcellular; standard IHC practice). Compare the pattern with a positive control from the same staining run (standard IHC practice).
Boster reagents
Best CHD2 / ATP-dependent chromatin remodeler CHD2 IHC Antibodies
The IHC-validated antibody A04079 has paraffin-section images from rat, mouse, and human brain (A04079 image captions). No IF/ICC image is supplied (A04079 catalog).
Real IHC data
Anti-CHD2 Antibody ®
Cat # A04079
A04079 is the only SKU that will render; its IHC captions document rat, mouse, and human brain paraffin sections (A04079 image captions). The catalog lists IHC and WB applications and Human, Monkey, Mouse, and Rat reactivity (A04079 catalog).
Which to pick: For tissue IHC, choose A04079, a rabbit antibody with paraffin-section IHC images from rat, mouse, and human brain; the fixative is unreported (A04079 catalog and image captions). No listed SKU has IF/ICC data: A04079 has no IF image or dilution, and its clonality is unreported (A04079 catalog). For cross-species work, A04079 lists Human, Monkey, Mouse, and Rat reactivity, although its IHC captions document only rat, mouse, and human paraffin sections (A04079 catalog and image captions).
Each figure is that product's own IHC / IF validation image from its datasheet.
References
- UniProt Consortium. UniProt entry O14647 (CHD2_HUMAN, ATP-dependent chromatin remodeler CHD2).
- Human Protein Atlas. CHD2 tissue IHC expression (reliability: Enhanced).
- Human Protein Atlas. CHD2 subcellular location (ICC-IF): Mainly localized to the nucleoplasm. In addition localized to the nucleoli, the Golgi apparatus and vesicles..
- Human Protein Atlas. CHD2 antibody validation summary (2 antibodies).
- Chromodomain helicase DNA-binding domain 2 maintains spermatogonial self-renewal by promoting chromatin accessibility and mRNA stability. iScience 2022 — PMC9700024.
- TDP-43 Promotes Neurodegeneration by Impairing Chromatin Remodeling. Current biology : CB 2017 — PMC5720388.
- CHD2 Regulates Neuron-Glioma Interactions in Pediatric Glioma. Cancer discovery 2024 — PMC11456263.
- PubMed PMID:9326634 — UniProt-cited evidence.
- PubMed PMID:16572171 — UniProt-cited evidence.
- PubMed PMID:15489334 — UniProt-cited evidence.
Immunohistochemistry protocol sheet for CHD2 (ATP-dependent chromatin remodeler CHD2). Expected localisation Variable nuclear staining in most tissues (HPA tissue IHC). Antigen retrieval: Citrate pH 6 HIER, heat-mediated (datasheet A04079). Validated IHC antibody: A04079 at 0.5-1μg/ml (the product's own IHC validation image is shown). Controls (HPA): positive Cerebellum (Cells in granular layer); negative Adipose tissue. IHC-P workflow on paraffin sections; fixative unspecified. Protocol steps: 1. Sample: Paraffin-embedded rat brain tissue; fixative not specified (datasheet A04079); 2. Fixation: Image fixative and duration unreported (datasheet A04079); 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: Citrate pH 6 , 20 min (datasheet A04079); 6. Peroxidase block: 3% H2O2, 10 min , room temperature (standard); 7. Blocking: 10% goat serum (datasheet A04079); 8. Primary antibody: Rabbit anti-CHD2, 0.5-1μg/ml (datasheet A04079); 9. Primary incubation: Overnight at 4 °C (datasheet A04079). Watch for: Fixation: Keep fixation consistent across sections. (standard IHC practice; not target-specific); Caveat: Skeletal myocytes may be unstained (HPA tissue IHC); Isoform / epitope: 3 isoforms; epitope coverage is unspecified (UniProt); Regulation: Variable levels by tissue (HPA tissue IHC). Evidence: UniProt O14647, HPA tissue IHC · Enhanced, HPA ICC-IF · Mainly localized to the nucleoplasm. In addition localized to the…, Datasheet A04079, PMC9700024. QR code links to https://www.bosterbio.com/bosterbio-gene-info-cards/CHD2/immunohistochemistry-ihc-guide.