RNA-seq and LC-MS/MS of PDAC Spatial Subpopulations: Paired Proteotranscriptomic Profiles

Paired RNA-sequencing and liquid chromatography-tandem mass spectrometry (LC-MS/MS) data from spatially delineated intra-tumour subpopulations in three human pancreatic ductal adenocarcinoma (PDAC) tumours. The dataset, created by Yong Chiang Tan and last updated on 2026-05-18, was generated using intact-protein MALDI imaging mass spectrometry to isolate subpopulations for downstream paired proteotranscriptomic profiling. It aims to address limitations of conventional bulk proteomics and transcriptomics in capturing post-transcriptional regulation within distinct tumour microenvironments.

Use Cases

• Integrating spatial proteomic and transcriptomic signals to study post-transcriptional regulation in cancer based on the paired proteotranscriptomic profiling described.
• Analyzing distinct functional programmes within PDAC tumour subpopulations based on the isolated spatial regions profiled.
• Developing models of therapeutic resistance and recurrence in PDAC based on the characterization of intra-tumour heterogeneity.
• Benchmarking multi-omics data integration methods using a dataset with spatially matched RNA-seq and LC-MS/MS measurements.

Strengths

• Provides paired proteomic and transcriptomic data from the same spatial subpopulations, enabling direct correlation studies.
• Uses intact-protein MALDI imaging mass spectrometry for high-resolution spatial delineation of tumour regions.
• Profiles three distinct human PDAC tumours, offering a basis for inter-tumour comparison.
• Released under a permissive CC-BY-4.0 license, facilitating reuse and sharing.

Limitations

• Row count and dataset scale are unknown, which may limit suitability assessment for large-scale analyses.
• Column-level documentation is absent; field semantics must be inferred after download.
• The sample size of three tumours may limit the generalizability of findings.

Provenance

Source

figshare

Collection Method

Intact-protein MALDI imaging mass spectrometry was used to spatially delineate subpopulations, followed by RNA-sequencing and LC-MS/MS of each isolated subpopulation.

Freshness

Last updated 2026-05-18 23:18:46; freshness should be verified.