RT Journal
A1 Wen, Jiayu
A1 Mohammed, Jaaved
A1 Bortolamiol-Becet, Diane
A1 Tsai, Harrison
A1 Robine, Nicolas
A1 Westholm, Jakub O.
A1 Ladewig, Erik
A1 Dai, Qi
A1 Okamura, Katsutomo
A1 Flynt, Alex S.
A1 Zhang, Dayu
A1 Andrews, Justen
A1 Cherbas, Lucy
A1 Kaufman, Thomas C.
A1 Cherbas, Peter
A1 Siepel, Adam
A1 Lai, Eric C.
T1 Diversity of miRNAs, siRNAs, and piRNAs across 25 Drosophila cell lines
JF Genome Research 
JO Genome Research 
YR 2014 
FD July 01 
VO 24 
IS 7 
SP 1236 
OP 1250 
DO 10.1101/gr.161554.113 
UL http://genome.cshlp.org/content/24/7/1236.abstract 
AB We expanded the knowledge base for Drosophila cell line transcriptomes by deeply sequencing their small RNAs. In total, we analyzed more than 1 billion raw reads from 53 libraries across 25 cell lines. We verify reproducibility of biological replicate data sets, determine common and distinct aspects of miRNA expression across cell lines, and infer the global impact of miRNAs on cell line transcriptomes. We next characterize their commonalities and differences in endo-siRNA populations. Interestingly, most cell lines exhibit enhanced TE-siRNA production relative to tissues, suggesting this as a common aspect of cell immortalization. We also broadly extend annotations of cis-NAT-siRNA loci, identifying ones with common expression across diverse cells and tissues, as well as cell-restricted loci. Finally, we characterize small RNAs in a set of ovary-derived cell lines, including somatic cells (OSS and OSC) and a mixed germline/somatic cell population (fGS/OSS) that exhibits ping-pong piRNA signatures. Collectively, the ovary data reveal new genic piRNA loci, including unusual configurations of piRNA-generating regions. Together with the companion analysis of mRNAs described in a previous study, these small RNA data provide comprehensive information on the transcriptional landscape of diverse Drosophila cell lines. These data should encourage broader usage of fly cell lines, beyond the few that are presently in common usage.