@article{Ramilowski01072020,
author = {Ramilowski, Jordan A. and Yip, Chi Wai and Agrawal, Saumya and Chang, Jen-Chien and Ciani, Yari and Kulakovskiy, Ivan V. and Mendez, Mickaël and Ooi, Jasmine Li Ching and Ouyang, John F. and Parkinson, Nick and Petri, Andreas and Roos, Leonie and Severin, Jessica and Yasuzawa, Kayoko and Abugessaisa, Imad and Akalin, Altuna and Antonov, Ivan V. and Arner, Erik and Bonetti, Alessandro and Bono, Hidemasa and Borsari, Beatrice and Brombacher, Frank and Cameron, Christopher J.F. and Cannistraci, Carlo Vittorio and Cardenas, Ryan and Cardon, Melissa and Chang, Howard and Dostie, Josée and Ducoli, Luca and Favorov, Alexander and Fort, Alexandre and Garrido, Diego and Gil, Noa and Gimenez, Juliette and Guler, Reto and Handoko, Lusy and Harshbarger, Jayson and Hasegawa, Akira and Hasegawa, Yuki and Hashimoto, Kosuke and Hayatsu, Norihito and Heutink, Peter and Hirose, Tetsuro and Imada, Eddie L. and Itoh, Masayoshi and Kaczkowski, Bogumil and Kanhere, Aditi and Kawabata, Emily and Kawaji, Hideya and Kawashima, Tsugumi and Kelly, S. Thomas and Kojima, Miki and Kondo, Naoto and Koseki, Haruhiko and Kouno, Tsukasa and Kratz, Anton and Kurowska-Stolarska, Mariola and Kwon, Andrew Tae Jun and Leek, Jeffrey and Lennartsson, Andreas and Lizio, Marina and López-Redondo, Fernando and Luginbühl, Joachim and Maeda, Shiori and Makeev, Vsevolod J. and Marchionni, Luigi and Medvedeva, Yulia A. and Minoda, Aki and Müller, Ferenc and Muñoz-Aguirre, Manuel and Murata, Mitsuyoshi and Nishiyori, Hiromi and Nitta, Kazuhiro R. and Noguchi, Shuhei and Noro, Yukihiko and Nurtdinov, Ramil and Okazaki, Yasushi and Orlando, Valerio and Paquette, Denis and Parr, Callum J.C. and Rackham, Owen J.L. and Rizzu, Patrizia and Sánchez Martinez, Diego Fernando and Sandelin, Albin and Sanjana, Pillay and Semple, Colin A.M. and Shibayama, Youtaro and Sivaraman, Divya M. and Suzuki, Takahiro and Szumowski, Suzannah C. and Tagami, Michihira and Taylor, Martin S. and Terao, Chikashi and Thodberg, Malte and Thongjuea, Supat and Tripathi, Vidisha and Ulitsky, Igor and Verardo, Roberto and Vorontsov, Ilya E. and Yamamoto, Chinatsu and Young, Robert S. and Baillie, J. Kenneth and Forrest, Alistair R.R. and Guigó, Roderic and Hoffman, Michael M. and Hon, Chung Chau and Kasukawa, Takeya and Kauppinen, Sakari and Kere, Juha and Lenhard, Boris and Schneider, Claudio and Suzuki, Harukazu and Yagi, Ken and de Hoon, Michiel J.L. and Shin, Jay W. and Carninci, Piero}, 
title = {Functional annotation of human long noncoding RNAs via molecular phenotyping},
volume = {30}, 
number = {7}, 
pages = {1060-1072}, 
year = {2020}, 
doi = {10.1101/gr.254219.119}, 
abstract ={Long noncoding RNAs (lncRNAs) constitute the majority of transcripts in the mammalian genomes, and yet, their functions remain largely unknown. As part of the FANTOM6 project, we systematically knocked down the expression of 285 lncRNAs in human dermal fibroblasts and quantified cellular growth, morphological changes, and transcriptomic responses using Capped Analysis of Gene Expression (CAGE). Antisense oligonucleotides targeting the same lncRNAs exhibited global concordance, and the molecular phenotype, measured by CAGE, recapitulated the observed cellular phenotypes while providing additional insights on the affected genes and pathways. Here, we disseminate the largest-to-date lncRNA knockdown data set with molecular phenotyping (over 1000 CAGE deep-sequencing libraries) for further exploration and highlight functional roles for ZNF213-AS1 and lnc-KHDC3L-2.}, 
URL = {http://genome.cshlp.org/content/30/7/1060.abstract}, 
eprint = {http://genome.cshlp.org/content/30/7/1060.full.pdf+html}, 
journal = {Genome Research} 
}