Project description:HeLa is the most widely used model cell line for studying human cellular and molecular biology. To date, no genomic reference for this cell line has been released, and experiments have relied on the human reference genome. Effective design and interpretation of molecular genetic studies performed using HeLa cells require accurate genomic information. Here we present a detailed genomic and transcriptomic characterization of a HeLa cell line. We performed DNA and RNA sequencing of a HeLa Kyoto cell line and analyzed its mutational portfolio and gene expression profile. Segmentation of the genome according to copy number revealed a remarkably high level of aneuploidy and numerous large structural variants at unprecedented resolution. Some of the extensive genomic rearrangements are indicative of catastrophic chromosome shattering, known as chromothripsis. Our analysis of the HeLa gene expression profile revealed that several pathways, including cell cycle and DNA repair, exhibit significantly different expression patterns from those in normal human tissues. Our results provide the first detailed account of genomic variants in the HeLa genome, yielding insight into their impact on gene expression and cellular function as well as their origins. This study underscores the importance of accounting for the strikingly aberrant characteristics of HeLa cells when designing and interpreting experiments, and has implications for the use of HeLa as a model of human biology.
Project description:Purpose: The goals of this study are to compare NGS-derived total transcriptome profiling (RNA-seq) of CNOT1-depleted cells (using siRNA) with control HeLa cells before and after DNA damage to examine quantitative gene expression.
Project description:This SuperSeries is composed of the following subset Series: GSE16581: Genomic landscape of meningiomas: gene expression GSE16583: Genomic landscape of meningiomas: genotyping Refer to individual Series
Project description:The aim of the experiment was to identify nucleolus-associated chromosomal domains. HeLa exp samples represent DNA from isolated nucleoli, whereas HeLa ref samples total genomic DNA of HeLa cells. "exp" samples were Cy5 labeled and hybridized together with Cy3-labeled "ref" samples on a Nimblegen 385K WG CGH platform. The DNA samples were not amplified.