Project description:SUM159PT cells were grown either in vitro (in culture) or in vivo (mouse), after which RPL10a tagged with GFP was used to perform extraction by immoprecipitation and subsequent ribosome profiling
Project description:SUM149PT, SUM185PE, SUM229PE, SUM159PT and SUM1315MO2 are triple negative breast cancer cell lines. They were sequenced to test the contrastive learning-based algorithm we developed to predict Afatinib sensitivity in TNBC.
Project description:MDA231, BT549, and SUM159PT basal-like breast cancer cell lines were transfected with non-targeting siRNA (siCONTROL), siRNA targeting DUSP4 (siDUSP4), or siCONTROL + 4 or 24 hr of 1uM selumetinib. Cells were harvested at 96 hr post-siRNA transfection. Data were Log2 RMA normalized.
Project description: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. SUM159PT cells infected with a lentiviral barcode library (Perturb-seq Library) were sorted according to the presence of BFP signal, treated or not with paclitaxel (PTX), multiplexed with MULTI-Seq protocol, and then processed by scRNA-Seq.
Project description:SUM159PT cells were grown either in vitro (in culture) or in vivo (mouse), after which RPL10a tagged with GFP was used to perform extraction by immoprecipitation and subsequent ribosome profiling Two batches of in vitro grown cells, each having 2 replicates. Two batches of in vivo grown cells from tumors grown in two individual mice, each having tumors on left (first batch) and right side (second batch). Extraction and ribosome profiling was done independently for the two batches of samples.
Project description: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. SUM159PT cells infected with a lentiviral barcode library (Perturb-seq Library) were sorted according to the presence of BFP signal, treated or not with paclitaxel (PTX), and then processed by scRNA-Seq or Multiome.
Project description:MDA231, BT549, and SUM159PT basal-like breast cancer cell lines were transfected with non-targeting siRNA (siCONTROL), siRNA targeting DUSP4 (siDUSP4), or siCONTROL + 4 or 24 hr of 1uM selumetinib. Cells were harvested at 96 hr post-siRNA transfection. Data were Log2 RMA normalized. We sought to identify changes in gene expression after MEK inhibition, or after loss of DUSP4 function in breast cancer cell lines.