Combined RNA-seq and RAT-seq mapping of long noncoding RNAs in pluripotent reprogramming

Pluripotent stem cells hold great investigative potential for developmental biology and regenerative medicine. Recent studies suggest that long noncoding RNAs (lncRNAs) may function as key regulators of the maintenance and the lineage differentiation of stem cells. However, the underlying mechanisms by which lncRNAs affect the reprogramming process of somatic cells into pluripotent cells remain largely unknown. Using fibroblasts and induced pluripotent stem cells (iPSCs) at different stages of reprogramming, we performed RNA transcriptome sequencing (RNA-Seq) to identify lncRNAs that are differentially-expressed in association with pluripotency. An RNA reverse transcription-associated trap sequencing (RAT-seq) approach was then utilized to generate a database to map the regulatory element network for lncRNA candidates. Integration of these datasets can facilitate the identification of functional lncRNAs that are associated with reprogramming. Identification of lncRNAs that regulate pluripotency may lead to new strategies for enhancing iPSC induction in regenerative medicine. Design Type(s) transcription profiling design • cellular data analysis objective Measurement Type(s) lnc_RNA Technology Type(s) RNA sequencing Factor Type(s) sequence_variant Sample Characteristic(s) Mus musculus • induced pluripotent stem cell Machine-accessible metadata file describing the reported data (ISA-Tab format)