Project description:X1 neoblasts (G2/S/M cells) were isolated by FACS from injury site-proximal tissue in a timeseries during head (anterior) and tail (posterior) regeneration in Schmidtea mediterranea
Project description:We introduce an approach to transcript discovery coupled with a statistical model for RNA-Seq experiments that produces estimates of transcript abundances. Our algorithms are implemented in an open source software program called Cufflinks. To test Cufflinks, we sequenced and analyzed more than 430 million paired 75bp RNA-Seq reads from a mouse myoblast cell line representing a differentiation timeseries. We detected 13,689 known transcripts and 3,724 previously unannotated ones, 62% of which are supported by independent expression data or by homologous genes in other species. Analysis of transcript expression over the timeseries revealed complete switches in the dominant transcription start site (TSS) or splice-isoform in 330 genes, along with more subtle shifts in a further 1,304 genes. These dynamics suggest substantial regulatory flexibility and complexity in this well-studied model of muscle development.
Project description:We introduce an approach to transcript discovery coupled with a statistical model for RNA-Seq experiments that produces estimates of transcript abundances. Our algorithms are implemented in an open source software program called Cufflinks. To test Cufflinks, we sequenced and analyzed more than 430 million paired 75bp RNA-Seq reads from a mouse myoblast cell line representing a differentiation timeseries. We detected 13,689 known transcripts and 3,724 previously unannotated ones, 62% of which are supported by independent expression data or by homologous genes in other species. Analysis of transcript expression over the timeseries revealed complete switches in the dominant transcription start site (TSS) or splice-isoform in 330 genes, along with more subtle shifts in a further 1,304 genes. These dynamics suggest substantial regulatory flexibility and complexity in this well-studied model of muscle development. Timeseries of C2C12 myoblast RNA-Seq
Project description:Temporal mapping of C/EBPα and –β binding during liver regeneration reveals dynamic occupancy and specific regulatory codes for homeostatic and cell cycle gene batteries. Timeseries ChIP-seq of transcription factors C/EBPα and –β, and Pol II in time points 0, 3, 8, 16, 24, 36, 48, 168 hours after partial hepatectomy. Additionally, an IgG mock to 0h was sequenced, as well as the transcription factor Egr1.