Project description:We present the NEUTRA database, a catalogue of the Neurospora transcriptome, based on RNA-Seq, RNAPII ChIP-Seq and ribosome fractionation studies. The database also includes genome-wide binding sites of transcription factors involved in regulation of circadian gene expression. In a comprehensive analysis of the transcriptome we identified and characterized 1478 long intergenic non-coding RNAs (lincRNAs) and 1056 natural antisense transcripts. Both classes of long non-coding RNAs accumulate at lower levels than protein-coding mRNAs and they are considerably shorter. We also confirmed annotated splice sites and identified new splice junctions and alternative splice sites, which are rare in Neurospora. Our analysis revealed that the vast majority of lincRNAs and antisense transcripts do not contain introns. NEUTRA is the first database to provide a collection of genome-wide deep sequencing data for the model organism Neurospora crassa and thus provides a tool that facilitates future research.
Project description:In vivo pulldown of the long non-coding RNA lncREST combined with LC-MS/MS in HCT116 cells in non-treated and Hydroxyurea treated conditions
