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@article{Ramilowski:2020:10.1101/gr.254219.119,
author = {Ramilowski, JA and Yip, CW and Agrawal, S and Chang, J-C and Ciani, Y and Kulakovskiy, IV and Mendez, M and Ooi, JLC and Ouyang, JF and Parkinson, N and Petri, A and Roos, L and Severin, J and Yasuzawa, K and Abugessaisa, I and Akalin, A and Antonov, IV and Arner, E and Bonetti, A and Bono, H and Borsari, B and Brombacher, F and Cameron, CJF and Cannistraci, CV and Cardenas, R and Cardon, M and Chang, H and Dostie, J and Ducoli, L and Favorov, A and Fort, A and Garrido, D and Gil, N and Gimenez, J and Guler, R and Handoko, L and Harshbarger, J and Hasegawa, A and Hasegawa, Y and Hashimoto, K and Hayatsu, N and Heutink, P and Hirose, T and Imada, EL and Itoh, M and Kaczkowski, B and Kanhere, A and Kawabata, E and Kawaji, H and Kawashima, T and Kelly, ST and Kojima, M and Kondo, N and Koseki, H and Kouno, T and Kratz, A and Kurowska-Stolarska, M and Kwon, ATJ and Leek, J and Lennartsson, A and Lizio, M and Lopez-Redondo, F and Luginbuhl, J and Maeda, S and Makeev, VJ and Marchionni, L an},
doi = {10.1101/gr.254219.119},
journal = {Genome Research},
pages = {1060--1072},
title = {Functional annotation of human long noncoding RNAs via molecular phenotyping},
url = {http://dx.doi.org/10.1101/gr.254219.119},
volume = {30},
year = {2020}
}

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TY  - JOUR
AB  - 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.
AU  - Ramilowski,JA
AU  - Yip,CW
AU  - Agrawal,S
AU  - Chang,J-C
AU  - Ciani,Y
AU  - Kulakovskiy,IV
AU  - Mendez,M
AU  - Ooi,JLC
AU  - Ouyang,JF
AU  - Parkinson,N
AU  - Petri,A
AU  - Roos,L
AU  - Severin,J
AU  - Yasuzawa,K
AU  - Abugessaisa,I
AU  - Akalin,A
AU  - Antonov,IV
AU  - Arner,E
AU  - Bonetti,A
AU  - Bono,H
AU  - Borsari,B
AU  - Brombacher,F
AU  - Cameron,CJF
AU  - Cannistraci,CV
AU  - Cardenas,R
AU  - Cardon,M
AU  - Chang,H
AU  - Dostie,J
AU  - Ducoli,L
AU  - Favorov,A
AU  - Fort,A
AU  - Garrido,D
AU  - Gil,N
AU  - Gimenez,J
AU  - Guler,R
AU  - Handoko,L
AU  - Harshbarger,J
AU  - Hasegawa,A
AU  - Hasegawa,Y
AU  - Hashimoto,K
AU  - Hayatsu,N
AU  - Heutink,P
AU  - Hirose,T
AU  - Imada,EL
AU  - Itoh,M
AU  - Kaczkowski,B
AU  - Kanhere,A
AU  - Kawabata,E
AU  - Kawaji,H
AU  - Kawashima,T
AU  - Kelly,ST
AU  - Kojima,M
AU  - Kondo,N
AU  - Koseki,H
AU  - Kouno,T
AU  - Kratz,A
AU  - Kurowska-Stolarska,M
AU  - Kwon,ATJ
AU  - Leek,J
AU  - Lennartsson,A
AU  - Lizio,M
AU  - Lopez-Redondo,F
AU  - Luginbuhl,J
AU  - Maeda,S
AU  - Makeev,VJ
AU  - Marchionni,L
AU  - Medvedeva,YA
AU  - Minoda,A
AU  - Mueller,F
AU  - Munoz-Aguirre,M
AU  - Murata,M
AU  - Nishiyori,H
AU  - Nitta,KR
AU  - Noguchi,S
AU  - Noro,Y
AU  - Nurtdinov,R
AU  - Okazaki,Y
AU  - Orlando,V
AU  - Paquette,D
AU  - Parr,CJC
AU  - Rackham,OJL
AU  - Rizzu,P
AU  - Martinez,DFS
AU  - Sandelin,A
AU  - Sanjana,P
AU  - Semple,CAM
AU  - Shibayama,Y
AU  - Sivaraman,DM
AU  - Suzuki,T
AU  - Szumowski,SC
AU  - Tagami,M
AU  - Taylor,MS
AU  - Terao,C
AU  - Thodberg,M
AU  - Thongjuea,S
AU  - Tripathi,V
AU  - Ulitsky,I
AU  - Verardo,R
AU  - Vorontsov,IE
AU  - Yamamoto,C
AU  - Young,RS
AU  - Baillie,JK
AU  - Forrest,ARR
AU  - Guigo,R
AU  - Hoffman,MM
AU  - Hon,CC
AU  - Kasukawa,T
AU  - Kauppinen,S
AU  - Kere,J
AU  - Lenhard,B
AU  - Schneider,C
AU  - Suzuki,H
AU  - Yagi,K
AU  - de,Hoon MJL
AU  - Shin,JW
AU  - Carninci,P
DO  - 10.1101/gr.254219.119
EP  - 1072
PY  - 2020///
SN  - 1054-9803
SP  - 1060
TI  - Functional annotation of human long noncoding RNAs via molecular phenotyping
T2  - Genome Research
UR  - http://dx.doi.org/10.1101/gr.254219.119
UR  - http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=WOS:000554900100011&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=1ba7043ffcc86c417c072aa74d649202
UR  - https://genome.cshlp.org/content/30/7/1060.short
UR  - http://hdl.handle.net/10044/1/87378
VL  - 30
ER  -

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