TitleSelective single cell isolation for genomics using microraft arrays
Data descriptionSingle-cell RNA-seq of human pancreatic cancer cells
Doi10.1093/nar/gkw700
Web-link of the paperhttps://academic.oup.com/nar/article/44/17/8292/2468056
Data typescRNA-seq
DatabaseGEO
Accession numberGSE85183
URL of the datahttps://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE85183
SpeciesHuman
TissuePancreas
Cell typePancreatic cancer cell
Number of cells120
Cell capture platformMicroraft array
Library preparation protocolNA
Unique molecular identifier (Y/N)Y
Spike-in (Y/N)Y
Full-length (Y/N)N
Brief summary of the scientific questionThey demonstrate that microraft arrays, which are arrays containing thousands of individual cell culture sites, can be used to select single cells based on a variety of phenotypes, such as cell surface markers, cell proliferation and drug response. They show that data generated using microrafts and our modified RNAseq protocol compared favorably with the Fluidigm C1. They then used microraft arrays to select pancreatic cancer cells that proliferate in spite of cytotoxic drug treatment. The single cell RNA-seq data identified several expected and novel gene expression changes associated with early drug resistance.
Brief summary of the bioinformatics processingComparison between RNA-seq from cells isolated with microrafts and Fluidigm C1, in the aspect of read coverage, gene detection and chromosome condensation;
Expression difference analysis;
CitationWelch, J. D., Williams, L. A., DiSalvo, M., Brandt, A. T., Marayati, R., Sims, C. E., . . . Jones, C. D. (2016). Selective single cell isolation for genomics using microraft arrays. Nucleic Acids Res, 44(17), 8292-8301. doi:10.1093/nar/gkw700
Web-link of the paperhttps://academic.oup.com/nar/article/44/17/8292/2468056