This is the 1st published paper I have contributed to using RNA-seq and has my affiliation as Penn State Hershey as well!
Darsh, my talented ex-student, and I have helped Sofia for RNA-seq processing of the spatio-temporal mouse somatosensory neocortex. Her critical perspective on the developmental neurobiology has brought out lots of interesting findings and discussions. Mingfeng has been great (as always!) dissecting the high dimensional NGS data. Vedrana and Daniel are such meticulous neuroanatomists! And of course, Nenad and Mike have been great brilliant mentors! Thank you ALL!!!
3-4 more Yale projects have been brewing and hope all of them will come out this year!!!
Laminar and Temporal Expression Dynamics of Coding and Noncoding RNAs in the Mouse Neocortex.
The hallmark of the cerebral neocortex is its organization into six layers, each containing a characteristic set of cell types and synaptic connections. The transcriptional events involved in laminar development and function still remain elusive. Here, we employed deep sequencing of mRNA and small RNA species to gain insights into transcriptional differences among layers and their temporal dynamics during postnatal development of the mouse primary somatosensory neocortex. We identify a number of coding and noncoding transcripts with specific spatiotemporal expression and splicing patterns. We also identify signature trajectories and gene coexpression networks associated with distinct biological processes and transcriptional overlap between these processes. Finally, we provide data that allow the study of potential miRNA and mRNA interactions. Overall, this study provides an integrated view of the laminar and temporal expression dynamics of coding and noncoding transcripts in the mouse neocortex and a resource for studies of neurodevelopment and transcriptome.