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Series GSE74253 Query DataSets for GSE74253
Status Public on Mar 14, 2018
Title mRNA-seq Analysis of Transcriptomes of the PC9R and PC9 cells
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Summary 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.
 
Overall design The genome-wdie transcriptome study of gefitinib-resistant NSCLC cells (PC9R) comparing with the sensitive cells (PC9) using mRNA-seq technology
 
Contributor(s) Zhang F, Li D, Chen S
Citation(s) 29552290
Submission date Oct 21, 2015
Last update date Mar 13, 2020
Contact name FAN ZHANG
E-mail(s) fzhang@tongji.edu.cn
Organization name Clinical Translational Research Center, Shanghai Pulmonary Hospital, Tongji University School of Medicine
Street address 507 Zhengmin Road
City Shanghai
State/province Shanghai
ZIP/Postal code 200433
Country China
 
Platforms (1)
GPL11154 Illumina HiSeq 2000 (Homo sapiens)
Samples (2)
GSM1915712 PC9R
GSM1915713 PC9
Relations
BioProject PRJNA299577
SRA SRP065204

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE74253_PC9RvsPC9_rep.diff.txt.gz 365.7 Kb (ftp)(http) TXT
GSE74253_RAW.tar 500.0 Kb (http)(custom) TAR (of TXT)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record
Processed data provided as supplementary file

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