Proteomic Changes From SMARCA4 Knockdown In Medulloblastoma

Quantitative mass spectrometry data profiles proteomic changes following SMARCA4 knockdown in HD-MB03 cells, a model for Group 3 medulloblastoma. The dataset was generated by Medha Gayathri J. Pai and published on figshare in March 2026. It captures dysregulated proteins and pathways, including SWI/SNF complex subunits and lipid metabolism enzymes.

Use Cases

• Identify protein expression changes like SMARCA2, CRABP2, or FABP5 following SMARCA4 knockdown for candidate validation.
• Analyze enrichment of pathways such as steroid biosynthesis or fatty acid biosynthesis from proteomic profiles.
• Correlate suppressed processes like DNA replication or amino acid catabolism with SMARCA4 loss using GSEA results.
• Validate top candidate proteins (e.g., CYP27A1, SCP2) identified in the discovery set against the separate validatory set.

Strengths

• Data generated using DIA-MS with an in-house library, noted for superior proteome depth over DDA.
• Findings validated in a separate validatory set for key protein candidates.
• Dataset captures specific functional impacts on chromatin architecture and lipid metabolism.

Limitations

• Dataset size is 1.3 MB, indicating a small-scale proteomic study.
• Data is derived from a single cell line model (HD-MB03), limiting generalizability.
• Row count and precise number of quantified protein features are unknown.

Provenance

Source

figshare, authored by Medha Gayathri J. Pai.

Collection Method

Quantitative mass spectrometry (DIA-MS) on HD-MB03 cells with doxycycline-inducible SMARCA4 shRNA knockdown.

Freshness

Last updated March 2026.