Application of massively parallel sequencing to microRNA profiling and discovery in human embryonic stem cells

@article{citeulike:2400243, abstract = {MicroRNAs (miRNAs) are emerging as important, albeit poorly characterized, regulators of biological processes. Key to further elucidation of their roles is the generation of more complete lists of their numbers and expression changes in different cell states. Here, we report a new method for surveying the expression of small RNAs, including microRNAs, using Illumina sequencing technology. We also present a set of methods for annotating sequences deriving from known miRNAs, identifying variability in mature miRNA sequences, and identifying sequences belonging to previously unidentified miRNA genes. Application of this approach to RNA from human embryonic stem cells obtained before and after their differentiation into embryoid bodies revealed the sequences and expression levels of 334 known plus 104 novel miRNA genes. One hundred seventy-one known and 23 novel microRNA sequences exhibited significant expression differences between these two developmental states. Owing to the increased number of sequence reads, these libraries represent the deepest miRNA sampling to date, spanning nearly six orders of magnitude of expression. The predicted targets of those miRNAs enriched in either sample shared common features. Included among the high-ranked predicted gene targets are those implicated in differentiation, cell cycle control, programmed cell death, and transcriptional regulation. 10.1101/gr.7179508}, author = {Morin, Ryan D. and O'Connor, Michael D. and Griffith, Malachi and Kuchenbauer, Florian and Delaney, Allen and Prabhu, Anna-Liisa and Zhao, Yongjun and Mcdonald, Helen and Zeng, Thomas and Hirst, Martin and Eaves, Connie J. and Marra, Marco A. }, citeulike-article-id = {2400243}, doi = {10.1101/gr.7179508}, journal = {Genome Res.}, keywords = {deep\_sequencing, mirna, stem\_cell}, month = {February}, pages = {gr.7179508+}, posted-at = {2008-05-16 10:35:12}, priority = {2}, title = {Application of massively parallel sequencing to microRNA profiling and discovery in human embryonic stem cells}, url = {http://dx.doi.org/10.1101/gr.7179508}, year = {2008} }

TY - JOUR ID - citeulike:2400243 L3 - citeulike-article-id:2400243 TI - Application of massively parallel sequencing to microRNA profiling and discovery in human embryonic stem cells JF - Genome Res. SP - gr.7179508 N2 - MicroRNAs (miRNAs) are emerging as important, albeit poorly characterized, regulators of biological processes. Key to further elucidation of their roles is the generation of more complete lists of their numbers and expression changes in different cell states. Here, we report a new method for surveying the expression of small RNAs, including microRNAs, using Illumina sequencing technology. We also present a set of methods for annotating sequences deriving from known miRNAs, identifying variability in mature miRNA sequences, and identifying sequences belonging to previously unidentified miRNA genes. Application of this approach to RNA from human embryonic stem cells obtained before and after their differentiation into embryoid bodies revealed the sequences and expression levels of 334 known plus 104 novel miRNA genes. One hundred seventy-one known and 23 novel microRNA sequences exhibited significant expression differences between these two developmental states. Owing to the increased number of sequence reads, these libraries represent the deepest miRNA sampling to date, spanning nearly six orders of magnitude of expression. The predicted targets of those miRNAs enriched in either sample shared common features. Included among the high-ranked predicted gene targets are those implicated in differentiation, cell cycle control, programmed cell death, and transcriptional regulation. 10.1101/gr.7179508 KW - deep_sequencing KW - mirna KW - stem_cell AU - Morin, Ryan AU - O'Connor, Michael AU - Griffith, Malachi AU - Kuchenbauer, Florian AU - Delaney, Allen AU - Prabhu, Anna-Liisa AU - Zhao, Yongjun AU - Mcdonald, Helen AU - Zeng, Thomas AU - Hirst, Martin AU - Eaves, Connie AU - Marra, Marco PY - 2008/02/19/ UR - http://dx.doi.org/10.1101/gr.7179508 ER -