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MRNA-seq Analysis of Transcriptomes of the PC9R and PC9 cells

ABSTRACT: The goals of this study is to compare the whole genome transcriptome of gefitinib-resistant NSCLC cell line (PC9R) with its gefitinib-sensitive counterpart (PC9) using RNA-seq tecnology Methods: Genome-wide mRNA profiles of the PC9R and PC9 cells were generated by deep sequencing, using Illumina Hiseq2000. The sequence reads that passed quality filters were analyzed in the following steps: 1) RNA-seq reads were aligned to the hg19 genome assembly using TopHat (http://bioinformatics.oxfordjournals.org/content/25/9/1105.short) with the default parameters; 2) Expression index was generated using GFOLD V1.0.9 job count (http://bioinformatics.oxfordjournals.org/content/early/2012/08/23/bioinformatics.bts515); 3) Differential expression were calculated using GFOLD V1.0.9 job diff. Gene expression was quantified in rpkm (reads per kilobase of exon per million mapped sequence reads); 4) GFOLD, a generalized fold change, was used to rank the differentially expressed genes from the RNA-seq data. The GFOLD value can be considered as a reliable log2-fold change when only a single biological replicate is available Results: We found that hundreds of genes were either down- or up-regulated in the PC9R cells compared with the PC9 cells. Specifically, 6% of the total detected genes (1487 genes) were up-regulated in the PC9R cells, with a GFOLD value over 1, and 5% of the total detected genes (1112 genes) were down-regulated, with a GFOLD value less than -1. Conclusions: Our study reveals the differentially expressed genes in gefitinib-resistant NSCLC cells comparing with the sensitive cells in a genome-wide scale. This results help to provide the novel insight into the gefitinib-resistant mechanism.

ORGANISM(S): Homo sapiens

PROVIDER: GSE74253 | GEO | 2018/03/14

REPOSITORIES: GEO

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