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Functional annotation of human long noncoding RNAs via molecular phenotyping. / Ramilowski, Jordan A.; Yip, Chi Wai; Agrawal, Saumya; Chang, Jen-Chien; Ciani, Yari; Kulakovskiy, Ivan V.; Mendez, Mickaël; Ooi, Jasmine Li Ching; Ouyang, John F.; Parkinson, Nick; Petri, Andreas; Roos, Leonie; Severin, Jessica; Yasuzawa, Kayoko; Abugessaisa, Imad; Akalin, Altuna; Antonov, Ivan V.; Arner, Erik; Bonetti, Alessandro; Bono, Hidemasa; Borsari, Beatrice; Brombacher, Frank; Cameron, Chris J. F.; Cannistraci, Carlo Vittorio; Cardenas, Ryan; Cardon, Melissa; Chang, Howard; Dostie, Josee; Ducoli, Luca; Favorov, Alexander; Fort, Alexandre; Garrido, Diego; Gil, Noa; Gimenez, Juliette; Guler, Reto; Handoko, Lusy; Harshbarger, Jayson; Hasegawa, Akira; Hasegawa, Yuki; Hashimoto, Kosuke; Hayatsu, Norihito; Heutink, Peter; Hirose, Tetsuro; Imada, Eddie L.; Itoh, Masayoshi; Kaczkowski, Bogumil; Kanhere, Aditi; Kawabata, Emily; Kawaji, Hideya; Kawashima, Tsugumi; Kelly, S. Thomas; Kojima, Miki; Kondo, Naoto; Koseki, Haruhiko; Kouno, Tsukasa; Kratz, Anton; Kurowska-Stolarska, Mariola; Kwon, Andrew Tae Jun; Leek, Jeffrey; Lennartsson, Andreas; Lizio, Marina; Lopez-Redondo, Fernando; Luginbühl, Joachim; Maeda, Shiori; Makeev, Vsevolod J.; Marchionni, Luigi; Medvedeva, Yulia A.; Minoda, Aki; Müller, Ferenc; Muñoz-Aguirre, Manuel; Murata, Mitsuyoshi; Nishiyori, Hiromi; Nitta, Kazuhiro R.; Noguchi, Shuhei; Noro, Yukihiko; Nurtdinov, Ramil; Okazaki, Yasushi; Orlando, Valerio; Paquette, Denis; Parr, Callum J. C.; Rackham, Owen J. L.; Rizzu, Patrizia; Martinez, Diego Fernando Sánchez; Sandelin, Albin; Sanjana, Pillay; Semple, Colin A. M.; Shibayama, Youtaro; Sivaraman, Divya M.; Suzuki, Takahiro; Szumowski, Suzannah C.; Tagami, Michihira; Taylor, Martin S.; Terao, Chikashi; Thodberg, Malte; Thongjuea, Supat; Tripathi, Vidisha; Ulitsky, Igor; Verardo, Roberto; Vorontsov, Ilya E.; Yamamoto, Chinatsu; Young, Robert S.; Baillie, J. Kenneth; Forrest, Alistair R. R.; Guigó, Roderic; Hoffman, Michael M.; Hon, Chung Chau; Kasukawa, Takeya; Kauppinen, Sakari; Kere, Juha; Lenhard, Boris; Schneider, Claudio; Suzuki, Harukazu; Yagi, Ken; de Hoon, Michiel J. L.; Shin, Jay W.; Carninci, Piero.
I:
Genome Research, Bind 30, Nr. 7, 2020, s. 1060-1072.
Publikation: Bidrag til tidsskrift › Tidsskriftartikel › Forskning › fagfællebedømt
Harvard
Ramilowski, JA, Yip, CW, Agrawal, S, Chang, J-C, Ciani, Y, Kulakovskiy, IV, Mendez, M, Ooi, JLC, Ouyang, JF, Parkinson, N, Petri, A, Roos, L, Severin, J, Yasuzawa, K, Abugessaisa, I, Akalin, A, Antonov, IV, Arner, E, Bonetti, A, Bono, H, Borsari, B, Brombacher, F, Cameron, CJF, Cannistraci, CV, Cardenas, R, Cardon, M, Chang, H, Dostie, J, Ducoli, L, Favorov, A, Fort, A, Garrido, D, Gil, N, Gimenez, J, Guler, R, Handoko, L, Harshbarger, J, Hasegawa, A, Hasegawa, Y, Hashimoto, K, Hayatsu, N, Heutink, P, Hirose, T, Imada, EL, Itoh, M, Kaczkowski, B, Kanhere, A, Kawabata, E, Kawaji, H, Kawashima, T, Kelly, ST, Kojima, M, Kondo, N, Koseki, H, Kouno, T, Kratz, A, Kurowska-Stolarska, M, Kwon, ATJ, Leek, J, Lennartsson, A, Lizio, M, Lopez-Redondo, F, Luginbühl, J, Maeda, S, Makeev, VJ, Marchionni, L, Medvedeva, YA, Minoda, A, Müller, F, Muñoz-Aguirre, M, Murata, M, Nishiyori, H, Nitta, KR, Noguchi, S, Noro, Y, Nurtdinov, R, Okazaki, Y, Orlando, V, Paquette, D, Parr, CJC, Rackham, OJL, Rizzu, P, Martinez, DFS
, Sandelin, A, Sanjana, P, Semple, CAM, Shibayama, Y, Sivaraman, DM, Suzuki, T, Szumowski, SC, Tagami, M, Taylor, MS, Terao, C
, Thodberg, M, Thongjuea, S, Tripathi, V, Ulitsky, I, Verardo, R, Vorontsov, IE, Yamamoto, C, Young, RS, Baillie, JK, Forrest, ARR, Guigó, R, Hoffman, MM, Hon, CC, Kasukawa, T, Kauppinen, S, Kere, J, Lenhard, B, Schneider, C, Suzuki, H, Yagi, K, de Hoon, MJL, Shin, JW & Carninci, P 2020, '
Functional annotation of human long noncoding RNAs via molecular phenotyping',
Genome Research, bind 30, nr. 7, s. 1060-1072.
https://doi.org/10.1101/gr.254219.119APA
Ramilowski, J. A., Yip, C. W., Agrawal, S., Chang, J-C., Ciani, Y., Kulakovskiy, I. V., Mendez, M., Ooi, J. L. C., Ouyang, J. F., Parkinson, N., Petri, A., Roos, L., Severin, J., Yasuzawa, K., Abugessaisa, I., Akalin, A., Antonov, I. V., Arner, E., Bonetti, A., ... Carninci, P. (2020).
Functional annotation of human long noncoding RNAs via molecular phenotyping.
Genome Research,
30(7), 1060-1072.
https://doi.org/10.1101/gr.254219.119Vancouver
Ramilowski JA, Yip CW, Agrawal S, Chang J-C, Ciani Y, Kulakovskiy IV o.a.
Functional annotation of human long noncoding RNAs via molecular phenotyping.
Genome Research. 2020;30(7):1060-1072.
https://doi.org/10.1101/gr.254219.119Author
Ramilowski, Jordan A. ; Yip, Chi Wai ; Agrawal, Saumya ; Chang, Jen-Chien ; Ciani, Yari ; Kulakovskiy, Ivan V. ; Mendez, Mickaël ; Ooi, Jasmine Li Ching ; Ouyang, John F. ; Parkinson, Nick ; Petri, Andreas ; Roos, Leonie ; Severin, Jessica ; Yasuzawa, Kayoko ; Abugessaisa, Imad ; Akalin, Altuna ; Antonov, Ivan V. ; Arner, Erik ; Bonetti, Alessandro ; Bono, Hidemasa ; Borsari, Beatrice ; Brombacher, Frank ; Cameron, Chris J. F. ; Cannistraci, Carlo Vittorio ; Cardenas, Ryan ; Cardon, Melissa ; Chang, Howard ; Dostie, Josee ; Ducoli, Luca ; Favorov, Alexander ; Fort, Alexandre ; Garrido, Diego ; Gil, Noa ; Gimenez, Juliette ; Guler, Reto ; Handoko, Lusy ; Harshbarger, Jayson ; Hasegawa, Akira ; Hasegawa, Yuki ; Hashimoto, Kosuke ; Hayatsu, Norihito ; Heutink, Peter ; Hirose, Tetsuro ; Imada, Eddie L. ; Itoh, Masayoshi ; Kaczkowski, Bogumil ; Kanhere, Aditi ; Kawabata, Emily ; Kawaji, Hideya ; Kawashima, Tsugumi ; Kelly, S. Thomas ; Kojima, Miki ; Kondo, Naoto ; Koseki, Haruhiko ; Kouno, Tsukasa ; Kratz, Anton ; Kurowska-Stolarska, Mariola ; Kwon, Andrew Tae Jun ; Leek, Jeffrey ; Lennartsson, Andreas ; Lizio, Marina ; Lopez-Redondo, Fernando ; Luginbühl, Joachim ; Maeda, Shiori ; Makeev, Vsevolod J. ; Marchionni, Luigi ; Medvedeva, Yulia A. ; Minoda, Aki ; Müller, Ferenc ; Muñoz-Aguirre, Manuel ; Murata, Mitsuyoshi ; Nishiyori, Hiromi ; Nitta, Kazuhiro R. ; Noguchi, Shuhei ; Noro, Yukihiko ; Nurtdinov, Ramil ; Okazaki, Yasushi ; Orlando, Valerio ; Paquette, Denis ; Parr, Callum J. C. ; Rackham, Owen J. L. ; Rizzu, Patrizia ; Martinez, Diego Fernando Sánchez ; Sandelin, Albin ; Sanjana, Pillay ; Semple, Colin A. M. ; Shibayama, Youtaro ; Sivaraman, Divya M. ; Suzuki, Takahiro ; Szumowski, Suzannah C. ; Tagami, Michihira ; Taylor, Martin S. ; Terao, Chikashi ; Thodberg, Malte ; Thongjuea, Supat ; Tripathi, Vidisha ; Ulitsky, Igor ; Verardo, Roberto ; Vorontsov, Ilya E. ; Yamamoto, Chinatsu ; Young, Robert S. ; Baillie, J. Kenneth ; Forrest, Alistair R. R. ; Guigó, Roderic ; Hoffman, Michael M. ; Hon, Chung Chau ; Kasukawa, Takeya ; Kauppinen, Sakari ; Kere, Juha ; Lenhard, Boris ; Schneider, Claudio ; Suzuki, Harukazu ; Yagi, Ken ; de Hoon, Michiel J. L. ; Shin, Jay W. ; Carninci, Piero. / Functional annotation of human long noncoding RNAs via molecular phenotyping. I: Genome Research. 2020 ; Bind 30, Nr. 7. s. 1060-1072.
Bibtex
@article{ee40a7d2612948a9800aa8a1cba1a32a,
title = "Functional annotation of human long noncoding RNAs via molecular phenotyping",
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-todate 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.",
keywords = "ADULT HUMAN FIBROBLASTS, GENE-EXPRESSION, UNIQUE FEATURES, CELLS, TRANSCRIPTION, REVEALS, DIFFERENTIATION, TRANSLATION, PRINCIPLES, REGULATORS",
author = "Ramilowski, {Jordan A.} and Yip, {Chi Wai} and Saumya Agrawal and Jen-Chien Chang and Yari Ciani and Kulakovskiy, {Ivan V.} and Micka{\"e}l Mendez and Ooi, {Jasmine Li Ching} and Ouyang, {John F.} and Nick Parkinson and Andreas Petri and Leonie Roos and Jessica Severin and Kayoko Yasuzawa and Imad Abugessaisa and Altuna Akalin and Antonov, {Ivan V.} and Erik Arner and Alessandro Bonetti and Hidemasa Bono and Beatrice Borsari and Frank Brombacher and Cameron, {Chris J. F.} and Cannistraci, {Carlo Vittorio} and Ryan Cardenas and Melissa Cardon and Howard Chang and Josee Dostie and Luca Ducoli and Alexander Favorov and Alexandre Fort and Diego Garrido and Noa Gil and Juliette Gimenez and Reto Guler and Lusy Handoko and Jayson Harshbarger and Akira Hasegawa and Yuki Hasegawa and Kosuke Hashimoto and Norihito Hayatsu and Peter Heutink and Tetsuro Hirose and Imada, {Eddie L.} and Masayoshi Itoh and Bogumil Kaczkowski and Aditi Kanhere and Emily Kawabata and Hideya Kawaji and Tsugumi Kawashima and Kelly, {S. Thomas} and Miki Kojima and Naoto Kondo and Haruhiko Koseki and Tsukasa Kouno and Anton Kratz and Mariola Kurowska-Stolarska and Kwon, {Andrew Tae Jun} and Jeffrey Leek and Andreas Lennartsson and Marina Lizio and Fernando Lopez-Redondo and Joachim Luginb{\"u}hl and Shiori Maeda and Makeev, {Vsevolod J.} and Luigi Marchionni and Medvedeva, {Yulia A.} and Aki Minoda and Ferenc M{\"u}ller and Manuel Mu{\~n}oz-Aguirre and Mitsuyoshi Murata and Hiromi Nishiyori and Nitta, {Kazuhiro R.} and Shuhei Noguchi and Yukihiko Noro and Ramil Nurtdinov and Yasushi Okazaki and Valerio Orlando and Denis Paquette and Parr, {Callum J. C.} and Rackham, {Owen J. L.} and Patrizia Rizzu and Martinez, {Diego Fernando S{\'a}nchez} and Albin Sandelin and Pillay Sanjana and Semple, {Colin A. M.} and Youtaro Shibayama and Sivaraman, {Divya M.} and Takahiro Suzuki and Szumowski, {Suzannah C.} and Michihira Tagami and Taylor, {Martin S.} and Chikashi Terao and Malte Thodberg and Supat Thongjuea and Vidisha Tripathi and Igor Ulitsky and Roberto Verardo and Vorontsov, {Ilya E.} and Chinatsu Yamamoto and Young, {Robert S.} and Baillie, {J. Kenneth} and Forrest, {Alistair R. R.} and Roderic Guig{\'o} and Hoffman, {Michael M.} and Hon, {Chung Chau} and Takeya Kasukawa and Sakari Kauppinen and Juha Kere and Boris Lenhard and Claudio Schneider and Harukazu Suzuki and Ken Yagi and {de Hoon}, {Michiel J. L.} and Shin, {Jay W.} and Piero Carninci",
year = "2020",
doi = "10.1101/gr.254219.119",
language = "English",
volume = "30",
pages = "1060--1072",
journal = "Genome Research",
issn = "1088-9051",
publisher = "Cold Spring Harbor Laboratory Press",
number = "7",
}
RIS
TY - JOUR
T1 - Functional annotation of human long noncoding RNAs via molecular phenotyping
AU - Ramilowski, Jordan A.
AU - Yip, Chi Wai
AU - Agrawal, Saumya
AU - Chang, Jen-Chien
AU - Ciani, Yari
AU - Kulakovskiy, Ivan V.
AU - Mendez, Mickaël
AU - Ooi, Jasmine Li Ching
AU - Ouyang, John F.
AU - Parkinson, Nick
AU - Petri, Andreas
AU - Roos, Leonie
AU - Severin, Jessica
AU - Yasuzawa, Kayoko
AU - Abugessaisa, Imad
AU - Akalin, Altuna
AU - Antonov, Ivan V.
AU - Arner, Erik
AU - Bonetti, Alessandro
AU - Bono, Hidemasa
AU - Borsari, Beatrice
AU - Brombacher, Frank
AU - Cameron, Chris J. F.
AU - Cannistraci, Carlo Vittorio
AU - Cardenas, Ryan
AU - Cardon, Melissa
AU - Chang, Howard
AU - Dostie, Josee
AU - Ducoli, Luca
AU - Favorov, Alexander
AU - Fort, Alexandre
AU - Garrido, Diego
AU - Gil, Noa
AU - Gimenez, Juliette
AU - Guler, Reto
AU - Handoko, Lusy
AU - Harshbarger, Jayson
AU - Hasegawa, Akira
AU - Hasegawa, Yuki
AU - Hashimoto, Kosuke
AU - Hayatsu, Norihito
AU - Heutink, Peter
AU - Hirose, Tetsuro
AU - Imada, Eddie L.
AU - Itoh, Masayoshi
AU - Kaczkowski, Bogumil
AU - Kanhere, Aditi
AU - Kawabata, Emily
AU - Kawaji, Hideya
AU - Kawashima, Tsugumi
AU - Kelly, S. Thomas
AU - Kojima, Miki
AU - Kondo, Naoto
AU - Koseki, Haruhiko
AU - Kouno, Tsukasa
AU - Kratz, Anton
AU - Kurowska-Stolarska, Mariola
AU - Kwon, Andrew Tae Jun
AU - Leek, Jeffrey
AU - Lennartsson, Andreas
AU - Lizio, Marina
AU - Lopez-Redondo, Fernando
AU - Luginbühl, Joachim
AU - Maeda, Shiori
AU - Makeev, Vsevolod J.
AU - Marchionni, Luigi
AU - Medvedeva, Yulia A.
AU - Minoda, Aki
AU - Müller, Ferenc
AU - Muñoz-Aguirre, Manuel
AU - Murata, Mitsuyoshi
AU - Nishiyori, Hiromi
AU - Nitta, Kazuhiro R.
AU - Noguchi, Shuhei
AU - Noro, Yukihiko
AU - Nurtdinov, Ramil
AU - Okazaki, Yasushi
AU - Orlando, Valerio
AU - Paquette, Denis
AU - Parr, Callum J. C.
AU - Rackham, Owen J. L.
AU - Rizzu, Patrizia
AU - Martinez, Diego Fernando Sánchez
AU - Sandelin, Albin
AU - Sanjana, Pillay
AU - Semple, Colin A. M.
AU - Shibayama, Youtaro
AU - Sivaraman, Divya M.
AU - Suzuki, Takahiro
AU - Szumowski, Suzannah C.
AU - Tagami, Michihira
AU - Taylor, Martin S.
AU - Terao, Chikashi
AU - Thodberg, Malte
AU - Thongjuea, Supat
AU - Tripathi, Vidisha
AU - Ulitsky, Igor
AU - Verardo, Roberto
AU - Vorontsov, Ilya E.
AU - Yamamoto, Chinatsu
AU - Young, Robert S.
AU - Baillie, J. Kenneth
AU - Forrest, Alistair R. R.
AU - Guigó, Roderic
AU - Hoffman, Michael M.
AU - Hon, Chung Chau
AU - Kasukawa, Takeya
AU - Kauppinen, Sakari
AU - Kere, Juha
AU - Lenhard, Boris
AU - Schneider, Claudio
AU - Suzuki, Harukazu
AU - Yagi, Ken
AU - de Hoon, Michiel J. L.
AU - Shin, Jay W.
AU - Carninci, Piero
PY - 2020
Y1 - 2020
N2 - 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-todate 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.
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-todate 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.
KW - ADULT HUMAN FIBROBLASTS
KW - GENE-EXPRESSION
KW - UNIQUE FEATURES
KW - CELLS
KW - TRANSCRIPTION
KW - REVEALS
KW - DIFFERENTIATION
KW - TRANSLATION
KW - PRINCIPLES
KW - REGULATORS
U2 - 10.1101/gr.254219.119
DO - 10.1101/gr.254219.119
M3 - Journal article
C2 - 32718982
VL - 30
SP - 1060
EP - 1072
JO - Genome Research
JF - Genome Research
SN - 1088-9051
IS - 7
ER -
