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| 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
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| 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.
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| Overall design |
The genome-wdie transcriptome study of gefitinib-resistant NSCLC cells (PC9R) comparing with the sensitive cells (PC9) using mRNA-seq technology
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| Contributor(s) |
Zhang F, Li D, Chen S |
| Citation(s) |
29552290 |
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| Submission date |
Oct 21, 2015 |
| Last update date |
Mar 13, 2020 |
| Contact name |
FAN ZHANG |
| E-mail(s) |
fzhang@tongji.edu.cn
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| Organization name |
Clinical Translational Research Center, Shanghai Pulmonary Hospital, Tongji University School of Medicine
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| Street address |
507 Zhengmin Road
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| City |
Shanghai |
| State/province |
Shanghai |
| ZIP/Postal code |
200433 |
| Country |
China |
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| Platforms (1) |
| GPL11154 |
Illumina HiSeq 2000 (Homo sapiens) |
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| Samples (2) |
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| Relations |
| BioProject |
PRJNA299577 |
| SRA |
SRP065204 |
| 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 Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
| Processed data provided as supplementary file |
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