GEO series
Targeted DNA sequencing of barcoded SUM159PT cells
Summary
Cancer is a heterogeneous disease, where multiple, phenotypically distinct subpopulations co-exist. Tumour evolution is a result of a complex interplay of genetic and epigenetic factors. To predict the molecular drivers of distinct cancer responses, we apply single-cell lineage tracing (scRNA-Seq of barcoded cells) on a triple-negative breast cancer model. We propose GALILEO, a framework providing lineage tracing, transcriptomic, and chromatin accessibility information simultaneously at single-cell resolution (Multiome ATAC + gene expression on barcoded cells). The combination of single-cell lineage tracing with phenotypic assays allows to link a cell state with its fate.
Published in
Nadalin F, Marzi MJ, Pirra Piscazzi M et al.
· Nature communications 2024
· PMID 39218912
· doi:10.1038/s41467-024-51424-4
This dataset
Download
Direct links to NCBI, no account and no request form: the whole study as GSE221495_RAW.tar, processed values as the series matrix, the supplementary file directory, and per-sample supplementary files for any of the 47 samples.
Also filed as BioProject PRJNA914689. Searching any of these in the dataset finder brings you back here.
Study design
40 conditions, each sampled once — no replicated groups
Read from the first 40 of 47 sample titles: 40 distinct titles with little repetition. Check it against the sample list below before relying on it.
Samples in this study
0 selected
- GSM6876541 d0, replicate 1, targeted DNA-Seq
- GSM6876542 d3, PTX, replicate 1, targeted DNA-Seq
- GSM6876543 d9, PTX, replicate 1, targeted DNA-Seq
- GSM6876544 d13, PTX, replicate 1, targeted DNA-Seq
- GSM6876545 d17, PTX, replicate 1, targeted DNA-Seq
- GSM6876546 d24, PTX, replicate 1, targeted DNA-Seq
- GSM6876547 d0, replicate 2.1, targeted DNA-Seq
- GSM6876548 d0, replicate 2.2, targeted DNA-Seq
- GSM6876549 d15, replicate 2.1, targeted DNA-Seq
- GSM6876550 d15, replicate 2.2, targeted DNA-Seq
- GSM6876551 d15, replicate 2.3, targeted DNA-Seq
- GSM6876552 d15, PTX, replicate 2.1, targeted DNA-Seq
- GSM6876553 d15, PTX, replicate 2.2, targeted DNA-Seq
- GSM6876554 d15, PTX, replicate 2.3, targeted DNA-Seq
- GSM6876555 d0, replicate 3, targeted DNA-Seq
- GSM6876556 d15, replicate 3.1, targeted DNA-Seq
- GSM6876557 d15, replicate 3.2, targeted DNA-Seq
- GSM6876558 d15, replicate 3.3, targeted DNA-Seq
- GSM6876559 d15, PTX, replicate 3.1, targeted DNA-Seq
- GSM6876560 d15, PTX, replicate 3.2, targeted DNA-Seq
- GSM6876561 d15, PTX, replicate 3.3, targeted DNA-Seq
- GSM6876562 d15, PTX, replicate 3.4, targeted DNA-Seq
- GSM6876563 d15, PTX, replicate 3.5, targeted DNA-Seq
- GSM6876564 pre-treated, d0, replicate 1, targeted DNA-Seq
- GSM6876565 pre-treated, d0, replicate 2, targeted DNA-Seq
- GSM6876566 pre-treated, d3, PTX, targeted DNA-Seq
- GSM6876567 pre-treated, d10, PTX, targeted DNA-Seq
- GSM6876568 pre-treated, d17, PTX, targeted DNA-Seq
- GSM6876569 pre-treated, d20, PTX, targeted DNA-Seq
- GSM6876570 d0, replicate 1.2, targeted DNA-Seq
- GSM6876571 d0, replicate 2, targeted DNA-Seq
- GSM6876572 in vivo, replicate 1, targeted DNA-Seq
- GSM6876573 in vivo, replicate 2, targeted DNA-Seq
- GSM6876574 d0, replicate 3.2, targeted DNA-Seq
- GSM6876575 in vivo, replicate 3, targeted DNA-Seq
- GSM6876576 in vivo, replicate 4, targeted DNA-Seq
- GSM6876577 in vivo, replicate 5, targeted DNA-Seq
- GSM6876578 in vivo, replicate 6, targeted DNA-Seq
- GSM6876579 in vivo, replicate 7, targeted DNA-Seq
- GSM6876580 in vivo, replicate 8, targeted DNA-Seq
+ 7 more — browse all 47 samples with per-sample file links →
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