Increasing quality, throughput and speed of sample preparation for strand-specific messenger RNA sequencing

Autor: Simon Haile, Richard D. Corbett, Tina MacLeod, Steve Bilobram, Duane Smailus, Philip Tsao, Heather Kirk, Helen McDonald, Pawan Pandoh, Miruna Bala, Martin Hirst, Diane Miller, Richard A. Moore, Andrew J. Mungall, Jacquie Schein, Robin J. Coope, Yussanne Ma, Yongjun Zhao, Rob A. Holt, Steven J. Jones, Marco A. Marra

Publikováno v: BMC Genomics, Vol 18, Iss 1, Pp 1-14 (2017)

Abstract Background RNA-Sequencing (RNA-seq) is now commonly used to reveal quantitative spatiotemporal snapshots of the transcriptome, the structures of transcripts (splice variants and fusions) and landscapes of expressed mutations. However, standa

Externí odkaz: https://doaj.org/article/0567feec5d9240578c381c3fcd372ebe

miR-509-3p is clinically significant and strongly attenuates cellular migration and multi-cellular spheroids in ovarian cancer

Autor: Upal Basu-Roy, Andy Chu, Andrew J. Mungall, Yunfei Wen, Jacquie Schein, Denise Brooks, Alka Mansukhani, Jinsong Liu, Cristian Coarfa, Sagar L. Patil, Amy C. Rowat, Nina Thiessen, Xinna Zhang, Anil K. Sood, Preethi H. Gunaratne, Marco A. Marra, Anadulce Hernandez-Herrera, Reanne Bowlby, Emilia L. Lim, Lykke Pedersen, Chad V. Pecot, Yinghong Pan, Steven J.M. Jones, Clara K. Chan, Yussanne Ma, Payal Sipahimalani, Gordon Robertson, Richard A. Moore

Publikováno v: Oncotarget
Pan, Y, Robertson, G, Pedersen, L, Lim, E, Hernandez-Herrera, A, Rowat, A C, Patil, S L, Chan, C K, Wen, Y, Zhang, X, Basu-Roy, U, Mansukhani, A, Chu, A, Sipahimalani, P, Bowlby, R, Brooks, D, Thiessen, N, Coarfa, C, Ma, Y, Moore, R A, Schein, J E, Mungall, A J, Liu, J, Pecot, C V, Sood, A K, Jones, S J M, Marra, M A & Gunaratne, P H 2016, ' miR-509-3p is clinically significant and strongly attenuates cellular migration and multi-cellular spheroids in ovarian cancer ', OncoTarget, vol. 7, no. 18, pp. 25930-25948 . https://doi.org/10.18632/oncotarget.8412
Oncotarget, vol 7, iss 18

Ovarian cancer presents as an aggressive, advanced stage cancer with widespread metastases that depend primarily on multicellular spheroids in the peritoneal fluid. To identify new druggable pathways related to metastatic progression and spheroid for

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::44d4dceb597daff05602e4f9bdd22d87
http://europepmc.org/articles/PMC5041955

Somatic mutations altering EZH2 (Tyr641) in follicular and diffuse large B-cell lymphomas of germinal-center origin

Autor: Hong Qian, Ryan D. Morin, Inanc Birol, Tesa M. Severson, Richard Varhol, Bruce Woolcock, Yongjun Zhao, Richard Corbett, Florian Kuchenbauer, Charlot Jf, Rodrigo Goya, Tcherpakov M, Joseph M. Connors, Marco A. Marra, Douglas E. Horsman, Randy D. Gascoyne, Nathalie A. Johnson, Robert A. Holt, Richard A. Moore, Andrew J. Mungall, Allen Delaney, Samuel Aparicio, Angela K Y Tam, Hao Zhu, Michelle Moksa, Jacquie Schein, Shashkin P, Martin Hirst, Damian Yap, Jianghong An, Steven J.M. Jones, Kimbara M, Humphries Rk, Paul Je, Merrill Boyle, Obi L. Griffith, Sohrab P. Shah, Duane E Smailus

Publikováno v: Nature genetics

Follicular lymphoma (FL) and the GCB subtype of diffuse large B-cell lymphoma (DLBCL) derive from germinal center B cells. Targeted resequencing studies have revealed mutations in various genes encoding proteins in the NF-kappaB pathway that contribu

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::49477fcb0e9279c3f093d5763660e568
https://doi.org/10.1038/ng.518

The Genome of the Kinetoplastid Parasite,Leishmania major

Autor: Kathy Seeger, G. Bothe, Rob Squares, Lee Murphy, Valentina Tosato, Michael A. Quail, Angela Lord, Alasdair Ivens, Christopher S. Peacock, Simon Rutter, Joel Rinta, Audrey Fraser, Dhileep Sivam, Carlo V. Bruschi, Nigel Fosker, Arlette Goble, Jenefer M. Blackwell, Silke Müller-Auer, K. Borzym, Robert L. Davies, Heather Munden, Holger Wedler, André Goffeau, Ellen Adlem, Christy Vogt, Susan O'Neil, David C. Schwartz, Siri Nelson, Bénédicte Purnelle, Angela K. Cruz, Martin Pentony, Deborah F. Smith, Michael A. Rieger, Laura Ciarloni, Kenneth Stuart, Marco A. Marra, Sven Klages, David L. Saunders, Alfred Beck, Marie-Adèle Rajandream, David Masuy, Andrew J Knights, Atashi Anupama, Karen Oliver, Helmut Hilbert, Rolf Wambutt, David Harris, Gabriella Bianchettin, Sarah Sharp, Nathalie Bason, Alberto C.C. Frasch, Matt Collins, Heesun Shin, Jeronimo C. Ruiz, Jeremy C. Mottram, David Horn, Richard M.R. Coulson, Elizabeth A. Worthey, Amber Seyler, Christopher Bauser, Natasha Larke, Bart Barrell, Ester Rabbinowitsch, John Woodward, Zina Apostolou, Christine Clayton, Christiane Hertz-Fowler, Ellen Sisk, Steve Squares, Gholam Fazelina, Laura Robertson, Johan Robben, T. Warren, Halina Norbertczak, Javier G. De Gaudenzi, Monika Fuchs, Shulamit Michaeli, Matthew Berriman, Claudia Gabel, Melanie Schäfer, Peter J. Myler, Thomas M. Pohl, Tin Louie, Rita Aert, Claire Price, Stephen M. Beverley, Guido Volckaert, Deborah E. Dobson, Richard Reinhardt, Lyudmila Litvin, Andreas Duesterhoeft, Ann Cronin, Jacquie Schein, Shiguo Zhou, Wolfgang Zimmermann, Gautam Aggarwal, Eithon Cadag, Yiting Huang, Michael Kube, Philip Attipoe, Keith R. Matthews

Publikováno v: Ivens, A C, Peacock, C S, Worthey, E A, Murphy, L, Aggarwal, G, Berriman, M, Sisk, E, Rajandream, M-A, Adlem, E, Aert, R, Anupama, A, Apostolou, Z, Attipoe, P, Bason, N, Bauser, C, Beck, A, Beverley, S M, Bianchettin, G, Borzym, K, Bothe, G, Bruschi, C V, Collins, M, Cadag, E, Ciarloni, L, Clayton, C, Coulson, R M R, Cronin, A, Cruz, A K, Davies, R M, De Gaudenzi, J, Dobson, D E, Duesterhoeft, A, Fazelina, G, Fosker, N, Frasch, A C, Fraser, A, Fuchs, M, Gabel, C, Goble, A, Goffeau, A, Harris, D, Hertz-Fowler, C, Hilbert, H, Horn, D, Huang, Y, Klages, S, Knights, A, Kube, M, Larke, N, Litvin, L, Lord, A, Louie, T, Marra, M, Masuy, D, Matthews, K, Michaeli, S, Mottram, J C, Müller-Auer, S, Munden, H, Nelson, S, Norbertczak, H, Oliver, K, O'neil, S, Pentony, M, Pohl, T M, Price, C, Purnelle, B, Quail, M A, Rabbinowitsch, E, Reinhardt, R, Rieger, M, Rinta, J, Robben, J, Robertson, L, Ruiz, J C, Rutter, S, Saunders, D, Schäfer, M, Schein, J, Schwartz, D C, Seeger, K, Seyler, A, Sharp, S, Shin, H, Sivam, D, Squares, R, Squares, S, Tosato, V, Vogt, C, Volckaert, G, Wambutt, R, Warren, T, Wedler, H, Woodward, J, Zhou, S, Zimmermann, W, Smith, D F, Blackwell, J M, Stuart, K D, Barrell, B & Myler, P J 2005, ' The genome of the kinetoplastid parasite, Leishmania major ', Science, vol. 309, no. 5733, pp. 436-42 . https://doi.org/10.1126/science.1112680

Leishmaniaspecies cause a spectrum of human diseases in tropical and subtropical regions of the world. We have sequenced the 36 chromosomes of the 32.8-megabase haploid genome ofLeishmania major(Friedlin strain) and predict 911 RNA genes, 39 pseudoge

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::605efc1a4f8db0eb1ecd8e2397fa9e1a
https://doi.org/10.1126/science.1112680

The ENCODE (ENCyclopedia Of DNA Elements) Project

Autor: Jonathan H. Dennis, Michael Brudno, Anindya Dutta, Richard M. Myers, Ian Dunham, Eduardo Eyras, S. S. Marticke, Alexandre Reymond, Anason S. Halees, Greg Schuler, M. G. Rosenfeld, Mikhail Nefedov, Robert E. Kingston, Elizabeth Anton, Tyra G. Wolfsberg, Alice C. Young, Kris A. Wetterstrand, C. K. Glass, Nancy F. Hansen, Gayle K. Clelland, Diane I. Schroeder, Jean L. Chang, H. Shin, Zhou Zhu, Nigel P. Carter, William Stafford Noble, Jenny McDowell, Ugrappa Nagalakshmi, Heike Fiegler, Philipp Kapranov, Peggy J. Farnham, Joanna C. Fowler, S. C. Harvey, Michael O. Dorschner, D. R. Inman, George V. Popescu, Jan-Jaap Wesselink, P. Groth, Baoli Zhu, H. Hirsch, James C. Wallace, Elise A. Feingold, S. Jin, Gabriel Robins, Thomas R. Gingeras, F. Denoeud, W. Tongprasit, Robert Castelo, Ross C. Hardison, John A. Stamatoyannopoulos, Joel Rozowsky, Eric A. Stone, Zheng Lian, J. E. Norton, Y. S. Kwon, Viktor Stolc, Michael C. Pirrung, Min-Feng Yu, A. Yang, W. J. Kent, Peter J. Sabo, Stephen Hartman, Stylianos E. Antonarakis, Tae Hoon Kim, H. Kim, Baishali Maskeri, Thomas Royce, R. Luna, Sherman M. Weissman, Tim Hubbard, Oliver M. Dovey, Ewan Birney, Kate R. Rosenbloom, Robert M. Andrews, Damian Keefe, Arend Sidow, D. Zhou, Jane Grimwood, Ulas Karaoz, Zhiping Weng, H. Burden, Michael C. Zody, Hiram Clawson, Gerry Bouffard, S. van Calcar, Mark Dickson, Kevin Struhl, Ingeborg Holt, Emmanouil T. Dermitzakis, T. J. Vasicek, Peter J. Good, Charles R. Cantor, Hari Tammana, Josée Dostie, Prachi Shah, Elliott H. Margulies, Peter D. Ellis, Mark S. Guyer, Christopher M. Taylor, Patrick A. Navas, Dione Kampa, Colin N. Dewey, Lior Pachter, Christof Koch, George Asimenos, James R R Whittle, Gregory E. Crawford, Jane B. Lian, Pamela J. Thomas, Kazutoyo Osoegawa, Webb Miller, Chunxu Qu, Nele Gheldof, Keith D. James, Sandeep Patel, Todd Richmond, Jacquelyn R. Idol, Michael A. Singer, Tomoko M. Tabuchi, Adam Siepel, Yutao Fu, David Vetrie, Long H. Nguyen, Michael Snyder, William H. Majoros, Michael R. Brent, Nathan D. Trinklein, Leah O. Barrera, Mark Gerstein, Srinka Ghosh, Sara J. Hartman, Jade P. Vinson, C. L. Middle, Sambath Chung, George Stamatoyannopoulos, Y. Nakayama, George M. Church, Job Dekker, Olof Emanuelsson, Julien Lagarde, Roderic Guigó, Marco A. Marra, Jeremy Schmutz, Daryl J. Thomas, Yong Yu, M. R. McCormick, Xiang-Dong Fu, Richard Humbert, Jennifer L. Ashurst, Alexander E. Urban, Sarah Wilcox, Ghia Euskirchen, Michael Kamal, Cordelia Langford, Jacquie Schein, Gregory M. Cooper, Paul Bertone, Eric S. Lander, C. Ding, Antonio Piccolboni, Steven L. Salzberg, Rhonda Harrison, Matthew J. Oberley, E. A. Sekinger, Mihaela Pertea, Bing Ren, H. K. Kim, Roland Green, Shelley Force Aldred, Laura Elnitski, Michael Hawrylycz, Andrew J. Mungall, Kerstin Lindblad-Toh, David B. Jaffe, Andreas D. Baxevanis, L. Liefer, Michele Clamp, David Haussler, Jill Cheng, John L. Rinn, S. Kamholz, Vicki L. Wraight, H. Sethi, Francis S. Collins, Steven J.M. Jones, Serafim Batzoglou, P. J. De Jong, Matthew E. Portnoy, Stefan Bekiranov, M. McArthur, Shu-Jin Luo, Eric D. Green, Robert W. Blakesley, Tarjei S. Mikkelsen, Z. Ye, Pawandeep Dhami, Neerja Karnani

Publikováno v: Science. 306:636-640

The ENCyclopedia Of DNA Elements (ENCODE) Project aims to identify all functional elements in the human genome sequence. The pilot phase of the Project is focused on a specified 30 megabases (∼1%) of the human genome sequence and is organized as an

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::cf8541955a585a60527e3acae6baff99
https://doi.org/10.1126/science.1105136