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Multi-modal single-cell and whole-genome sequencing of small, frozen clinical specimens

ABSTRACT: Multi-modal single-cell and whole-genome sequencing of small, frozen clinical specimens

PROVIDER: PRJNA892707 | ENA |

REPOSITORIES: ENA

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Project description:We provide 5' and/or 3' single cell and single nuclei RNA sequencing data for matched comparisons of profiling from fresh (single cells) and frozen (single nuclei) samples of a non small cell lung cancer sample, a cutaneous melanoma sample , and a primary uveal melanoma sample. We also provide matched samples processed with published dissociation protocols (*TST and *CST) for two samples as comparison. Next, we profiled three sequential biopsies (one pre-treatment and two on-treatment) from the KEYNOTE-001 trial by 5' single-nuclei RNA sequencing from frozen specimens. For these three datapoints we provide matched SlideSeq V2 spatial transcriptomic data. Finally, we provide 5' single nuclei RNA-sequencing data for 7 liver-metastatic uveal melanoma samples profiled at pre, on, and post treatment timepoints with MEK-inhibitor selumetinib. For all samples profiled with 5' capture we also provide TCR receptor information. This study provides a framework for the application of single nuclei RNA-sequencing on clinical grade specimens, and demonstrates the feasibility of this approach to dissect the biology of archival specimens or rare diseases.

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