Next-Generation Sequencing for Whole Transcriptome Analysis in Scrambled Control and EGFR Knockdown Cells Cultured under Normoxia and Hypoxia

ABSTRACT: Purpose: The goal of this study is to identify the mRNA clusters that are regulated by EGFR under normoxia or hypoxia. Method: Total RNAs were extracted from HeLa cells expressing scrambled control or EGFR shRNA-E1 that cultured under normoxia or hypoxia (1% O2) for 24h. Customized Next-Generation RNA Deep Sequencing, including both small RNA application and whole transcriptome analysis, was performed according to the standard procedure instructed by Applied Biosystems. For whole transcriptome analysis, SOLiD fragment colorspace transcriptome reads (50nt) were mapped to the human genome (hg19) and assigned to ensemble transcripts using Bioscope 1.3.1 (Life Technologies). The values of reads per kilobase per million reads (RPKM) were determined by Bioscope 1.3.1 CountTags tool using default

ORGANISM(S): Homo sapiens

SUBMITTER: Mien-Chie Hung 

PROVIDER: E-GEOD-44801 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress