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BRD9 / Bromodomain-containing protein 9 · Western blot design guide
Design a Western Blot for BRD9
Source-linked BRD9 Western blot protocol options, expected-band and isoform facts, troubleshooting for weak or shifted signal, and recommended anti-BRD9 WB antibodies. Everything you need to plan the experiment before you commit precious samples.
Evidence assembled September 2026 · For research use; verify linked source records and product datasheet before use
BRD9 Western Blot Experimental Design Guide
Expected bands, source-linked protocol options, controls and antibodies — the at-a-glance facts below, then the full design guide.
Must know before running
| Expected band | ~67 kDa | |
| Observed band | ~80 kDa | |
| Gel | 5–20% (catalog A08420-1) | |
| Positive control | Adipose tissue (IHC candidate; verify WB) +4 more | |
| Negative control | Liver (IHC candidate; verify WB) |
Important caveats
Reasons your observed band may differ from the expected size.
| PTM | Phosphorylated + Acetylated | |
| Caveat | Modification-state controls | |
| Gene-set association | MSigDB C7 membership | |
| Isoform | 6 isoform(s) |
Section 1
Source-Linked BRD9 Western Blot Protocol Options
The A08420-1 protocol combines labelled catalog values with standard starting conditions. Published comparisons retain their own sample, reagent and detection scope.
| Sample / lysate | human SiHa, human MOLT-4, human Hela, rat brain, mouse brain, mouse lung (catalog A08420-1) |
| Gel % | 5–20% (catalog A08420-1) |
| Load | 30 ug; reducing conditions (catalog A08420-1) |
| Transfer | a nitrocellulose membrane at 150 mA for 50-90 minutes (catalog A08420-1) |
| Membrane | nitrocellulose membrane (catalog A08420-1) |
| Blocking | 5% non-fat milk/TBS for 1.5 hour at RT (catalog A08420-1) |
| Primary antibody | A08420-1 · 0.5 μg/mL (catalog A08420-1) |
| Primary incubation | overnight at 4°C (catalog A08420-1) |
| Secondary antibody | goat anti-rabbit IgG-HRP, 1:5000 (catalog A08420-1) |
| Secondary incubation | 1.5 hour at RT (catalog A08420-1) |
| Wash | TBS-0.1%Tween 3 times with 5 minutes each (catalog A08420-1) |
| Detection | ECL (catalog A08420-1) |
Section 2
What Is the Expected BRD9 Western Blot Band Size?
BRD9 is predicted at 67 kDa but observed near 80 kDa; the cause of this difference is not established.
| Band near 80 kDa | Empirical BRD9 band; confirm identity with appropriate controls |
| Band near 67 kDa | Near the predicted BRD9 mass; identity requires confirmation |
| Several bands at different positions | Could reflect isoforms 1 through 6 if their migration differs |
| Little signal in a cytoplasmic fraction | BRD9 is localized to the nucleus |
💡Expected BRD9 appearanceBRD9 has a predicted mass of 67 kDa and an empirical band near 80 kDa; the cause of the difference is unestablished, so confirm band identity with suitable controls.
| Predicted BRD9 mass | 67 kDa by sequence prediction; the empirical band is near 80 kDa |
| Isoform 1 | Its individual apparent size is not supplied |
| Isoforms 2 and 3 | Splicing could alter size, but individual masses and migration are not supplied |
| Isoforms 4, 5 and 6 | Splicing could alter size, but individual masses and migration are not supplied |
| Situation | Likely cause | Next action |
|---|---|---|
| No band in lysate | Nuclear BRD9 may be poorly recovered | Check nuclear extraction and a positive control |
| Band higher than expected | The observed 80 kDa band exceeds the 67 kDa prediction for an unestablished reason | Check molecular weight markers and validate identity with BRD9 depletion |
| Band lower than expected | An isoform is possible, but its mass is unknown | Compare with a validated BRD9 control and test band loss after depletion |
| Multiple bands | Six isoforms are listed, but distinct migration is unverified | Use BRD9 depletion to identify specific bands |
| Weak or no signal | Low recovery of nuclear BRD9 is possible | Check nuclear enrichment, loading, and a positive control |
Experiment evidence
Western blot images showing BRD9 band
A08420-1 · BRD9
← swipe / scroll for more images →
Real WB data behind the band-size expectations in this section.
Sample controls for BRD9 Western blot
🧪HPA-IHC candidate guidance (verify in WB): For positive controls for BRD9 in Western blot, you can use adipose tissue, which HPA scores High.
Positive control: Adipose tissue (IHC candidate; verify WB)
Negative control: Liver (IHC candidate; verify WB)
Loading controls: Run GAPDH, β-actin, and a total-protein stain alongside the samples.
⚠️Feasibility: BRD9 is nuclear, so its signal may be diluted in whole-tissue lysate.
HPA tissue expression evidence for BRD9
Comprehensive Human Protein Atlas IHC scoring per tissue. Rows are taken directly from the HPA tissue chart — click any row's HPA link to view the source.
Higher expression tissues · candidate positive controls from IHC
| Tissue | Cell type | Level | Evidence | Source |
|---|---|---|---|---|
| Adipose tissue | adipocytes | High | Protein (IHC) | HPA → |
| Bone marrow | hematopoietic cells | High | Protein (IHC) | HPA → |
| Bronchus | respiratory epithelial cells | High | Protein (IHC) | HPA → |
| Cerebral cortex | neuronal cells | High | Protein (IHC) | HPA → |
| Colon | peripheral nerve/ganglion | High | Protein (IHC) | HPA → |
Lower expression tissues · IHC evidence, not confirmed WB-negative controls
| Tissue | Cell type | Level | Evidence | Source |
|---|---|---|---|---|
| Liver | cholangiocytes | Not detected | Protein (IHC) | HPA → |
| Parathyroid gland | glandular cells | Not detected | Protein (IHC) | HPA → |
| Adrenal gland | glandular cells | Medium | Protein (IHC) | HPA → |
| Appendix | glandular cells | Medium | Protein (IHC) | HPA → |
| Breast | adipocytes | Medium | Protein (IHC) | HPA → |
Section 3
Advanced BRD9 Western Blot Tips
Deeper troubleshooting and optimisation questions for BRD9, answered from its protein features.
How should BRD9 band migration be interpreted?
Band shift · Use the separately labelled calculated mass and catalog-observed evidence above. A sequence annotation does not establish an observed migration shift. Verify target identity with orthogonal controls.
Which BRD9 isoforms could produce different bands?
Isoforms · UniProt lists six isoforms. Isoform 2 lacks canonical residues 1–391; isoforms 3–6 lack residues 1–116, and isoform 4 also lacks 350–597. Other sequence replacements occur. These differences may affect apparent size, but the supplied features do not establish which isoforms are present in your sample.
Check the epitope against the canonical sequence changes. Canonical residues 1–116 are missing from isoforms 2–6, and residues 350–597 are missing from isoform 4. An antibody to a missing region would not recognize that region in the affected isoform.
Check the epitope against the canonical sequence changes. Canonical residues 1–116 are missing from isoforms 2–6, and residues 350–597 are missing from isoform 4. An antibody to a missing region would not recognize that region in the affected isoform.
Which BRD9 modifications should I consider when interpreting bands?
PTM · UniProt lists phosphoserine at canonical positions 56, 566, and 588, plus alternate N6-acetyllysine at canonical position 373. These are UniProt coordinates; antibody or paper numbering may differ. Their presence does not by itself predict a visible band shift.
Does this guide establish induction of BRD9?
Induction · No general induction response is established by this guide. A pathway or gene-set association is not evidence of induction in a particular specimen. Verify the relevant treatment and control in a target-specific experiment.
How should transfer be checked for BRD9?
Transfer · Standard workflow guidance: verify transfer efficiency for the intended target size before interpreting a weak signal. Use total-protein assessment and optimize transfer for the membrane, gel and apparatus; the labelled catalog values take precedence.
How should blocking be optimized?
Blocking · Standard workflow guidance: follow the A08420-1 datasheet where specified. Otherwise compare 5% milk or 5% BSA in TBST; for a phospho-specific assay start with BSA. Optimize background and specific signal with matched controls.
How should BRD9 be quantified?
Quantitation · Standard workflow guidance: quantify only a validated target band within the linear exposure range. Use consistent sample preparation and loading, retain biological replicates, and avoid interpreting saturation or loading differences as regulation.
Why might BRD9 appear near 80 kDa instead of 67 kDa?
Interpretation · The supplied apparent band is about 80 kDa, versus a predicted mass of 67 kDa. UniProt lists alternative isoforms and modified residues, but those features alone do not establish the cause of the difference or demonstrate a visible shift. Confirm band identity with a BRD9-specific control.
BRD9 is listed as nuclear and as a component of a SWI/SNF chromatin-remodeling subcomplex. Use comparable nuclear sample preparation and quantify the same identified band across samples. If multiple bands appear, establish their identities before combining their signals.
Compare it with the documented isoform sequence changes, particularly the large missing regions in isoforms 2 and 4. Size alone cannot identify an isoform. Check whether the antibody epitope is retained in the proposed isoform and verify the band's identity with a BRD9-specific control.
BRD9 is listed as nuclear and as a component of a SWI/SNF chromatin-remodeling subcomplex. Use comparable nuclear sample preparation and quantify the same identified band across samples. If multiple bands appear, establish their identities before combining their signals.
Compare it with the documented isoform sequence changes, particularly the large missing regions in isoforms 2 and 4. Size alone cannot identify an isoform. Check whether the antibody epitope is retained in the proposed isoform and verify the band's identity with a BRD9-specific control.
Boster reagents
BRD9 Western Blot Antibodies
Catalog antibodies with Western blot application and product-specific WB images. Evaluate suitability with the reported sample, controls and experimental conditions.
Real WB data
Anti-BRD9 Antibody Picoband®
Cat # A08420-1
The catalog reports one anti-BRD9 antibody for WB: A08420-1, with stated human, mouse, and rat reactivity. Its WB caption reports a band near 80 kDa, versus an expected 67 kDa. No orthogonal validation is supplied.
Which to pick: A08420-1 is the only listed option and has a WB image using human SiHa, MOLT-4, and HeLa cell lysates, rat brain, and mouse brain and lung lysates. Consider the reported 80 kDa band when planning controls.
Source: BosterBio BRD9 gene-info card — filtered to Western-blot-capable antibodies; each card shows that product's actual WB validation figure.
References
- UniProt Consortium. UniProt entry Q9H8M2.
- Human Protein Atlas. BRD9 tissue expression.
- PMC13446069 — target-verified WB comparison
- PMC11576511 — target-verified WB comparison
- PMC8797396 — target-verified WB comparison