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PC9 cell line scRNAseq datasets

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posted on 2023-09-21, 05:05 authored by Raffaele CalogeroRaffaele Calogero

In GEO NCBI repository are available single cell data on PC9 untreated lung cancer cell line done in two different labs, using both 10XGenomics and Drop-seq platforms and produced from in vitro culture or xenograph experiments.

  • set1: GSM3972657 PC9 in vitro dropseq Chicago (2500 cells)
  • set2: SM4494347 PC9 in vitro dropseq Chicago (12000 cells)
  • set3: GSM3972651 PC9 in vitro 10XGenomics Chicago (12649 cells)
  • set4: GSM6106787 PC9 in vitro 10XGenomics Berkeley (413 cells)
  • set5: GSM4869650 PC9 xenograft dropseq Chicago (29983 cells)
  • set6: GSM3972674 PC9 and U937 in vitro dropseq Chicago (2634 cells)
  • set7 BE1 GSE243665 PC9 in vitro 10XGenomics Turin (4492 cells)

These datasets, because of their differences, i.e. platforms, growth, labs, represent an ideal instrument to benchmark batch removal methods as well as integration methods. The seven sets are available as datasets with the same gene annotation (ensemblID:Symbol). Each set has the cellID with the extension _s(1:5) and set6 has two extensions _s6PC9 and _s6U937, set7 has extension _PC9.

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