GEO series

Multiomic assessments of LNCaP and derived cell strains reveal determinants of prostate cancer pathobiology (ATAC-Seq)

GSE288843 Homo sapiens Genome binding/occupancy profiling by high throughput sequencing 30 samples Submitted 2025/08/21 Platform GPL30173

Summary

Overall, the LNCaP line has served as a remarkably versatile PC model, though the molecular characteristics of several important substrains have not been established nor compared in a systematic manner. In this study, we used genome-scale approaches to characterize the genomic and transcriptomic features of the parental LNCaP_FGC line, and a spectrum of 12 derivative models that have been deployed for studies of PC. These studies provide insights into the biochemical features that endow PC with the potential to resist AR-directed therapy and identify features that may underlie the metastatic and treatment resistant phenotypes observed in patients. An important but under-appreciated feature of LNCaP concerns the remarkable heterogeneity of the original LNCaP isolate and the current LNCaP_FGC line which was never subjected to clonal selection. This feature, coupled with the inherent DNA mismatch repair deficiency and genomic instability, has produced a remarkable spectrum of sublines that have provided important insights into PC pathobiology, but also challenge reproducibility and the accurate interpretation of experimental findings.

Published in

Multiomic assessments of LNCaP and derived cell strains reveal determinants of prostate cancer pathobiology

Bose A, Bankhead A 3rd, Coleman I et al. · The Journal of clinical investigation 2025 · PMID 40956611 · doi:10.1172/JCI194727

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Direct links to NCBI, no account and no request form: the whole study as GSE288843_RAW.tar, processed values as the series matrix, the supplementary file directory, and per-sample supplementary files for any of the 30 samples. Raw sequencing reads are also available from ENA.

Whole study · RAW.tar ↓ Series matrix ↓ All supplementary files ↗ Raw reads on ENA ↗

Also filed as BioProject PRJNA1219600 and SRA study SRP561789. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40956611) ↗

Study design

12 conditions, mostly in duplicate

42F ×4 16D ×3 Abl ×3 42D ×2 95 ×2 APIPC ×2 AR_907 ×2 AR_909 ×2 +6 more

Supports a between-group comparison across 28 samples.

12 replicated groups read from 30 sample titles; they account for 28 of them. Check it against the sample list below before relying on it.

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