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Diversity of miRNAs, siRNAs, and piRNAs across 25 Drosophila cell lines

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...

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Detalles Bibliográficos
Autores principales: Wen, Jiayu, Mohammed, Jaaved, Bortolamiol-Becet, Diane, Tsai, Harrison, Robine, Nicolas, Westholm, Jakub O., Ladewig, Erik, Dai, Qi, Okamura, Katsutomo, Flynt, Alex S., Zhang, Dayu, Andrews, Justen, Cherbas, Lucy, Kaufman, Thomas C., Cherbas, Peter, Siepel, Adam, Lai, Eric C.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Cold Spring Harbor Laboratory Press 2014
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4079977/
https://www.ncbi.nlm.nih.gov/pubmed/24985917
http://dx.doi.org/10.1101/gr.161554.113
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author Wen, Jiayu
Mohammed, Jaaved
Bortolamiol-Becet, Diane
Tsai, Harrison
Robine, Nicolas
Westholm, Jakub O.
Ladewig, Erik
Dai, Qi
Okamura, Katsutomo
Flynt, Alex S.
Zhang, Dayu
Andrews, Justen
Cherbas, Lucy
Kaufman, Thomas C.
Cherbas, Peter
Siepel, Adam
Lai, Eric C.
author_facet Wen, Jiayu
Mohammed, Jaaved
Bortolamiol-Becet, Diane
Tsai, Harrison
Robine, Nicolas
Westholm, Jakub O.
Ladewig, Erik
Dai, Qi
Okamura, Katsutomo
Flynt, Alex S.
Zhang, Dayu
Andrews, Justen
Cherbas, Lucy
Kaufman, Thomas C.
Cherbas, Peter
Siepel, Adam
Lai, Eric C.
author_sort Wen, Jiayu
collection PubMed
description 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.
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spelling pubmed-40799772014-07-17 Diversity of miRNAs, siRNAs, and piRNAs across 25 Drosophila cell lines Wen, Jiayu Mohammed, Jaaved Bortolamiol-Becet, Diane Tsai, Harrison Robine, Nicolas Westholm, Jakub O. Ladewig, Erik Dai, Qi Okamura, Katsutomo Flynt, Alex S. Zhang, Dayu Andrews, Justen Cherbas, Lucy Kaufman, Thomas C. Cherbas, Peter Siepel, Adam Lai, Eric C. Genome Res Resource 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. Cold Spring Harbor Laboratory Press 2014-07 /pmc/articles/PMC4079977/ /pubmed/24985917 http://dx.doi.org/10.1101/gr.161554.113 Text en © 2014 Wen et al.; Published by Cold Spring Harbor Laboratory Press http://creativecommons.org/licenses/by-nc/4.0/ This article, published in Genome Research, is available under a Creative Commons License (Attribution-NonCommercial 4.0 International), as described at http://creativecommons.org/licenses/by-nc/4.0/.
spellingShingle Resource
Wen, Jiayu
Mohammed, Jaaved
Bortolamiol-Becet, Diane
Tsai, Harrison
Robine, Nicolas
Westholm, Jakub O.
Ladewig, Erik
Dai, Qi
Okamura, Katsutomo
Flynt, Alex S.
Zhang, Dayu
Andrews, Justen
Cherbas, Lucy
Kaufman, Thomas C.
Cherbas, Peter
Siepel, Adam
Lai, Eric C.
Diversity of miRNAs, siRNAs, and piRNAs across 25 Drosophila cell lines
title Diversity of miRNAs, siRNAs, and piRNAs across 25 Drosophila cell lines
title_full Diversity of miRNAs, siRNAs, and piRNAs across 25 Drosophila cell lines
title_fullStr Diversity of miRNAs, siRNAs, and piRNAs across 25 Drosophila cell lines
title_full_unstemmed Diversity of miRNAs, siRNAs, and piRNAs across 25 Drosophila cell lines
title_short Diversity of miRNAs, siRNAs, and piRNAs across 25 Drosophila cell lines
title_sort diversity of mirnas, sirnas, and pirnas across 25 drosophila cell lines
topic Resource
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4079977/
https://www.ncbi.nlm.nih.gov/pubmed/24985917
http://dx.doi.org/10.1101/gr.161554.113
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