Effects of Chemotherapy on Human Pancreatic Adenocarcinoma and its Tumor Microenvironment
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ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE205013 | GEO | 2023/01/09
REPOSITORIES: GEO
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Project description:This study contains single cell RNA-seq of the non-small cell lung cancer line HCC827 in three conditions. Firstly we have sequenced the RNA of single cells of a culture of HCC827 cells grown in normal conditions (POT). In our study we then evolved two arms of the cell line, one in the presence of the drug gefitinib (40nM, G1) and the other in the presence of trametinib (100nM, T4) in HYPERflasks to avoid replating. These data were analysed using cellRanger using GRCh38. Output from cellRanger was filtered for a minimum number of detected genes and UMIs. Mitochondrial reads were excluded from analysis (Acar_2020_single_cell_raw_data.txt). The data was then imported and scaled using the package Seurat. Scaled data was then filtered for low expression of housekeeping genes. Additionally genes expressed in fewer than 20 cells were excluded from analysis. Data was then renormalised using linear normalisation and scaling on the filtered raw data (Acar_2020_single_cell_processed_data.txt). Principal component analysis was run on variable genes identified using Seurat and the top 44 component were used as input for t-SNE analysis. Clusters were then identified using FindClusters in Seurat (Acar_2020_single_cell_metadata.txt). For a full description see the associated publication.
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