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- Table of Contents
KDM1A / Lysine-specific histone demethylase 1A · Western blot design guide
Design a Western Blot for KDM1A
Real validated KDM1A Western blot protocols, expected-band and isoform facts, troubleshooting for weak or shifted signal, and recommended anti-KDM1A 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
KDM1A 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 | ~92.9 kDa | |
| Observed band | ~100 kDa | |
| Gel | 10% (catalog M00532-1) | |
| Positive control | Adrenal gland (IHC candidate; verify WB) +4 more | |
| Negative control | Prostate (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 | 4 isoform(s) |
Section 1
Real Curated KDM1A Western Blot Protocols
The M00532-1 protocol combines labelled catalog values with standard starting conditions. Published comparisons retain their own sample, reagent and detection scope.
| Sample / lysate | human SIHA, human SH-SY5Y, human HepG2 (catalog M00532-1) |
| Gel % | 10% (catalog M00532-1) |
| Load | 30 ug; reducing conditions (catalog M00532-1) |
| Transfer | a nitrocellulose membrane at 150 mA for 50-90 minutes (catalog M00532-1) |
| Membrane | nitrocellulose membrane (catalog M00532-1) |
| Blocking | 5% non-fat milk/TBS for 1.5 hour at RT (catalog M00532-1) |
| Primary antibody | M00532-1 · 1: 1000 (catalog M00532-1) |
| Primary incubation | overnight at 4°C (catalog M00532-1) |
| Secondary antibody | goat anti-rabbit IgG-HRP, 1:5000 (catalog M00532-1) |
| Secondary incubation | 1.5 hour at RT (catalog M00532-1) |
| Wash | TBS-0.1%Tween 3 times with 5 minutes each (catalog M00532-1) |
| Detection | ECL (catalog M00532-1) |
Section 2
What Is the Expected KDM1A Western Blot Band Size?
KDM1A is predicted at 92.9 kDa and observed near 100 kDa; the cause of this difference is not established.
| Band near 100 kDa | Empirical KDM1A band in whole-cell lysates; confirm identity with controls. |
| Band near 93 kDa | Near the 92.9 kDa predicted mass; identity requires confirmation. |
| Multiple discrete bands | Could reflect isoforms 1, 2, 3, or 4; their migration is unknown. |
| Weak or absent band in soluble lysate | Chromatin-associated nuclear KDM1A may be poorly recovered. |
💡Expected KDM1A appearanceKDM1A has a predicted mass of 92.9 kDa, while antibody QC shows a band near 100 kDa; the cause of the difference is unestablished, so confirm identity with appropriate controls.
| Predicted KDM1A mass | 92.9 kDa from sequence; the empirical band is near 100 kDa. |
| Splice isoform 1 | Apparent size relative to other isoforms is not supplied. |
| Splice isoform 2 | Could migrate differently if its sequence length differs; size is not supplied. |
| Splice isoform 3 | Could migrate differently if its sequence length differs; size is not supplied. |
| Splice isoform 4 | Could migrate differently if its sequence length differs; size is not supplied. |
| Situation | Likely cause | Next action |
|---|---|---|
| No band in lysate | Chromatin-associated nuclear KDM1A may be missed by soluble extraction. | Check nuclear or chromatin-enriched extracts and an expression-positive control. |
| Band higher than expected | The observed 100 kDa band exceeds the 92.9 kDa prediction; the cause is unestablished. | Confirm identity with KDM1A depletion or an independent antibody. |
| Band lower than expected | An isoform is possible, but isoform masses are not supplied. | Check KDM1A depletion and compare isoform expression. |
| Multiple bands | Isoforms 1 through 4 are annotated, but distinct band positions are unproven. | Use KDM1A depletion to identify specific bands. |
| Weak or no signal | Nuclear and chromatin association may limit recovery. | Assess extraction and include a positive lysate control. |
Experiment evidence
Western blot images showing KDM1A band
M00532-1 · KDM1A
← swipe / scroll for more images →
Real WB data behind the band-size expectations in this section.
Sample controls for KDM1A Western blot
🧪HPA-IHC candidate guidance (verify in WB): For positive controls for KDM1A in Western blot, you can use adrenal gland tissue, which HPA rates as highly positive.
Positive control: Adrenal gland (IHC candidate; verify WB)
Negative control: Prostate (IHC candidate; verify WB)
Loading controls: Run GAPDH, β-actin, and a total-protein stain such as Ponceau alongside the samples.
⚠️Feasibility: KDM1A is nuclear and chromatin associated, so nuclear lysate may improve detection.
HPA tissue expression evidence for KDM1A
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 |
|---|---|---|---|---|
| Adrenal gland | glandular cells | High | Protein (IHC) | HPA → |
| Bone marrow | hematopoietic cells | High | Protein (IHC) | HPA → |
| Cerebellum | cells in granular layer | High | Protein (IHC) | HPA → |
| Endometrium | cells in endometrial stroma | High | Protein (IHC) | HPA → |
| Gallbladder | glandular cells | High | Protein (IHC) | HPA → |
Lower expression tissues · IHC evidence, not confirmed WB-negative controls
| Tissue | Cell type | Level | Evidence | Source |
|---|---|---|---|---|
| Prostate | glandular cells | Not detected | Protein (IHC) | HPA → |
| Adipose tissue | adipocytes | Low | Protein (IHC) | HPA → |
| Appendix | lymphoid tissue | Low | Protein (IHC) | HPA → |
| Oral mucosa | squamous epithelial cells | Low | Protein (IHC) | HPA → |
| Small intestine | glandular cells | Low | Protein (IHC) | HPA → |
Section 3
Advanced KDM1A Western Blot Tips
Deeper troubleshooting and optimisation questions for KDM1A, answered from its protein features.
How should KDM1A 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.
Could KDM1A isoforms produce different bands?
Isoforms · UniProt lists four isoforms. Isoforms 2 and 3 have a sequence insertion at canonical position 173; isoforms 2 and 4 have one at position 369. Check which isoforms your sample and antibody can detect when interpreting nearby bands. These annotations alone do not predict their apparent positions.
Which phosphorylation sites matter when interpreting KDM1A bands?
PTM · In UniProt canonical numbering, phosphorylation is annotated at Thr59, Thr104, Ser126, Ser131, Tyr135, Ser137, Ser166, Ser611, and position 849, which is listed as phosphoserine and phosphothreonine. Check the numbering convention of a site-specific antibody before comparing labels. These sites do not establish a visible band shift.
UniProt lists N6-acetyllysine at canonical positions 432, 433, and 436. Check whether an antibody recognizes a region containing these residues when comparing signals. Their presence does not establish a visible shift or explain the approximately 100 kDa band.
UniProt lists N6-acetyllysine at canonical positions 432, 433, and 436. Check whether an antibody recognizes a region containing these residues when comparing signals. Their presence does not establish a visible shift or explain the approximately 100 kDa band.
Does this guide establish induction of KDM1A?
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 KDM1A?
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 M00532-1 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 KDM1A 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 does KDM1A appear near 100 kDa instead of 92.9 kDa?
Interpretation · The supplied blot observation is approximately 100 kDa, while the predicted mass is 92.9 kDa. Apparent migration can differ from calculated mass. The listed isoforms and modifications do not, by themselves, establish the cause of this difference.
KDM1A is annotated in the nucleus and on chromosomes, with chromatin association. A nuclear or chromatin-containing preparation is relevant when assessing a weak signal; keep the fraction consistent across samples.
Because KDM1A associates with chromatin and forms complexes with RCOR1 and with RCOR/GFI/HDAC components, compare like fractions prepared the same way. Normalize for loading within that fraction, and distinguish a change in fraction recovery from a change in KDM1A abundance.
Compare them with the approximately 100 kDa observed band and consider the four annotated isoforms and listed modifications as possibilities to investigate. No signal peptide, propeptide, or glycosylation site is listed. The supplied features alone cannot identify an unexpected band or assign its cause.
KDM1A is annotated in the nucleus and on chromosomes, with chromatin association. A nuclear or chromatin-containing preparation is relevant when assessing a weak signal; keep the fraction consistent across samples.
Because KDM1A associates with chromatin and forms complexes with RCOR1 and with RCOR/GFI/HDAC components, compare like fractions prepared the same way. Normalize for loading within that fraction, and distinguish a change in fraction recovery from a change in KDM1A abundance.
Compare them with the approximately 100 kDa observed band and consider the four annotated isoforms and listed modifications as possibilities to investigate. No signal peptide, propeptide, or glycosylation site is listed. The supplied features alone cannot identify an unexpected band or assign its cause.
Boster reagents
KDM1A 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-KDM1/LSD1 KDM1A Rabbit Monoclonal Antibody
Cat # M00532-1
The catalog reports one anti-KDM1A antibody, M00532-1, with stated human, mouse, and rat reactivity. Its WB image uses three human cell lysates and shows a band near 100 kDa; the expected size is 93 kDa. Mouse and rat WB samples are not shown.
Which to pick: M00532-1 is the only listed option. Its WB image supports use in the tested human SIHA, SH-SY5Y, and HepG2 lysates at 1:1000; assess mouse or rat samples separately, since the supplied WB image covers human lysates only.
Source: BosterBio KDM1A gene-info card — filtered to Western-blot-capable antibodies; each card shows that product's actual WB validation figure.
References
- UniProt Consortium. UniProt entry O60341.
- Human Protein Atlas. KDM1A tissue expression.
- PMC8328692 — target-verified WB comparison
- PMC8114778 — target-verified WB comparison
- PMC11671590 — target-verified WB comparison