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- Table of Contents
HDAC11 / Histone deacetylase 11 · Western blot design guide
Design a Western Blot for HDAC11
Real validated HDAC11 Western blot protocols, expected-band and isoform facts, troubleshooting for weak or shifted signal, and recommended anti-HDAC11 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
HDAC11 Western Blot Experimental Design Guide
Expected bands, validated protocols, controls and antibodies — the at-a-glance facts below, then the full design guide.
Must know before running
| Expected band | ~39.2 kDa | |
| Gel | 12–15% (standard starting point) | |
| Negative control | Suggested KO / knockdown lysate |
Important caveats
Reasons your observed band may differ from the expected size.
| PTM | — | |
| Caveat | — | |
| Gene-set association | MSigDB Hallmark membership | |
| Isoform | 2 isoform(s) |
Section 1
Real Curated HDAC11 Western Blot Protocols
The M06209 protocol combines labelled catalog values with standard starting conditions. Published comparisons retain their own sample, reagent and detection scope.
| Sample / lysate | (1) Jurkat cell lysate;(2) MCF7 cell lysate (catalog M06209) |
| Gel % | 12–15% (standard starting point) |
| Load | 20–30 µg total protein per lane; optimize for abundance (standard starting point) |
| Transfer | Standard semi-dry transfer; verify efficiency (standard starting point) |
| Membrane | 0.45 µm PVDF (standard starting point) |
| Blocking | 5% milk or 5% BSA in TBST (standard starting point) |
| Primary antibody | M06209; use the WB datasheet starting dilution (standard starting point) |
| Primary incubation | Overnight at 4 °C (standard starting point) |
| Secondary antibody | Species-matched HRP conjugate at validated dilution (standard starting point) |
| Secondary incubation | 1 h at room temperature (standard starting point) |
| Wash | 3 × 5 min in TBST (standard starting point) |
| Detection | ECL; bracket exposures to avoid saturation (standard starting point) |
Section 2
What Is the Expected HDAC11 Western Blot Band Size?
HDAC11 is predicted at 39.2 kDa; two annotated isoforms could affect migration, but no distinct bands or empirical band size are established.
| Band near 39.2 kDa | consistent with the predicted HDAC11 mass; confirm identity with a control |
| Several bands | isoforms 1 and 2 are annotated, but distinct migration is unverified |
| One band without an isoform doublet | the two annotated isoforms need not resolve separately |
| Band enriched in a nuclear fraction | consistent with HDAC11's annotated nuclear location |
💡Expected HDAC11 appearanceHDAC11 has a predicted mass of 39.2 kDa, but no empirical band size is supplied; confirm any candidate band with an HDAC11 identity control.
| Predicted molecular mass | 39.2 kDa is the sequence-based reference, not a measured migration |
| Isoform 1 | its individual mass and migration are not supplied |
| Isoform 2 | its individual mass and migration are not supplied |
| Alternative splicing | could yield different band positions, but a resolvable difference is unverified |
| Situation | Likely cause | Next action |
|---|---|---|
| No band in lysate | HDAC11 is annotated in the nucleus; extraction may be insufficient | check a nuclear fraction and an HDAC11 positive control |
| Band higher than expected | identity or migration of the band is unverified | compare with an HDAC11 knockdown control |
| Band lower than expected | an isoform is possible, but its mass is unknown | test band identity with HDAC11 knockdown |
| Multiple bands | two isoforms are annotated, but distinct bands are unverified | check which bands respond to HDAC11 knockdown |
| Weak or no signal | limited recovery of nuclear HDAC11 is possible | assess nuclear extraction and load a positive control |
Experiment evidence
Western blot images showing HDAC11 band
M06209 · HDAC11
PB9630 · HDAC11
← swipe / scroll for more images →
Real WB data behind the band-size expectations in this section.
Sample controls for HDAC11 Western blot
🧪For positive controls for HDAC11 in Western blot, you can use a validated HDAC11-positive cell lysate, although the supplied HPA evidence identifies no positive tissue or cell line.
Positive control: No high/medium HPA tissue identified
Negative control: Suggested KO / knockdown lysate
Loading controls: Run GAPDH, β-actin, and a total-protein stain alongside the samples.
⚠️Feasibility: HPA has no expression data for HDAC11, so tissue-based controls cannot be selected from this evidence.
HPA tissue expression evidence for HDAC11
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 |
|---|---|---|---|---|
| No high/medium HPA tissues identified in the supplied evidence. | ||||
Lower expression tissues · IHC evidence, not confirmed WB-negative controls
| Tissue | Cell type | Level | Evidence | Source |
|---|---|---|---|---|
| No lower-expression tissue rows available in the supplied evidence. | ||||
Section 3
Advanced HDAC11 Western Blot Tips
Deeper troubleshooting and optimisation questions for HDAC11, answered from its protein features.
Where should the canonical HDAC11 band appear?
Band shift · The predicted mass is 39.2 kDa. No observed band position is supplied, so use this as a starting point rather than an exact migration target.
Compare the bands with the 39.2 kDa predicted mass and consider isoform 2, which lacks canonical residues 1–28 and 85–107. Check the antibody epitope against those regions. The supplied features do not identify observed band positions or confirm the identity of any extra band.
Compare the bands with the 39.2 kDa predicted mass and consider isoform 2, which lacks canonical residues 1–28 and 85–107. Check the antibody epitope against those regions. The supplied features do not identify observed band positions or confirm the identity of any extra band.
Could HDAC11 isoforms produce different bands?
Isoforms · Yes. UniProt lists two isoforms. Isoform 2 lacks residues 1–28 and 85–107 relative to the canonical sequence, so it has a shorter sequence. These features alone do not establish where either isoform migrates on a blot.
Check the antibody epitope against the canonical sequence. An epitope within residues 1–28 or 85–107 would fall in a region missing from isoform 2; an epitope elsewhere may detect both forms.
Check the antibody epitope against the canonical sequence. An epitope within residues 1–28 or 85–107 would fall in a region missing from isoform 2; an epitope elsewhere may detect both forms.
Can annotated modifications explain a shifted HDAC11 band?
PTM · No modified residues or glycosylation sites are listed in the supplied features. They provide no basis for assigning a band shift to a particular modification. A shift also cannot be inferred solely from the listed isoform differences.
Does this guide establish induction of HDAC11?
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 HDAC11?
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 M06209 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 HDAC11 be quantified in nuclear samples?
Quantitation · HDAC11 is annotated in the nucleus. Compare the same band across consistently prepared nuclear samples, and account for the two isoforms if more than one band is measured.
Does HDAC6 interaction explain an unexpected HDAC11 band?
Interpretation · HDAC11 is reported to interact with HDAC6, but that interaction alone does not establish a distinct Western-blot band or its apparent mass. Check whether an unexpected band is recognized by an antibody targeting a different HDAC11 region.
Boster reagents
HDAC11 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-HDAC11/Histone Deacetylase 11 Rabbit Monoclonal Antibody
Cat # M06209
Real WB data
Anti-HDAC11 Antibody Picoband®
Cat # PB9630
Two the supplier anti-HDAC11 antibodies have WB images. Product captions show M06209 in Jurkat and MCF7 lysates, and PB9630 in HepG2, rat brain and heart, and mouse brain and heart lysates. No publication evidence was supplied.
Which to pick: Choose M06209 for the documented Jurkat or MCF7 context. PB9630 has reported human, mouse, and rat reactivity, with WB lanes for HepG2 and rat and mouse brain and heart. Its caption reports a band near 37 kDa versus 39 kDa expected.
Source: BosterBio HDAC11 gene-info card — filtered to Western-blot-capable antibodies; each card shows that product's actual WB validation figure.
References
- UniProt Consortium. UniProt entry Q96DB2.
- Human Protein Atlas. HDAC11 tissue expression.
- PMC8352640 — target-verified WB comparison
- PMC12083684 — target-verified WB comparison
- PMC12755028 — target-verified WB comparison