RIP-seq to identify transcripts interacting with pluripotency factors in mouse embryonic stem cells

Sox2 is a master transcriptional regulator of embryonic development. Having found that Sox2 interacts with RNA-binding proteins, we designed an experiment to discover RNAs associated with Sox2 and other pluripotency factors. Briefly, we used RNA immunoprecipitation followed by high-throughput sequencing (RIP-seq) to sequence transcriptomes enriched for RNAs associated with Klf4, Nanog, Oct4, Sox2 and Suz12. For completeness, this submission includes all RIP-seq data from this study, although some of the data was only used for exploratory analyses. Such analysis indicated that it was important to include input samples for each of the the cell lines that were to be compared, to account for differences in gene expression (e.g. between J1-birA with and without bioSox2), and that overnight IP was more informative than 3 h IP. Therefore, the analysis described in the associated manuscript used samples from experiment batch 3 and 4 only (samples 11-18).