Journal ArticleDOI
High-throughput illumina strand-specific RNA sequencing library preparation.
Silin Zhong,Je-Gun Joung,Yi Zheng,Yun-Ru Chen,Bao Liu,Ying Shao,Jenny Xiang,Zhangjun Fei,James J. Giovannoni +8 more
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TLDR
This research presents a new probabilistic approach to assess the phytochemical properties of E.coli A, which has the potential to transform from a raw material for food to a feed for animals in a sustainable manner.Abstract:
Silin Zhong,1,2,5 Je-Gun Joung,1 Yi Zheng,1 Yun-ru Chen,1 Bao Liu,2 Ying Shao,3 Jenny Z. Xiang,3 Zhangjun Fei,1,4,5 and James J. Giovannoni1,4,5 Boyce Thompson Institute for Plant Research, Cornell University, Ithaca, NY 14853, USA Institute of Genetics and Cytology, Northeast Normal University, Changchun, 130024, China Weill Medical College, Cornell University, New York, NY 10021, USA U.S. Department of Agriculture/Agriculture Research Service, Plant, Soil, and Nutrition Laboratory, Ithaca, NY 14853, USAread more
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The tomato genome sequence provides insights into fleshy fruit evolution
Shusei Sato,Satoshi Tabata,Hideki Hirakawa,Erika Asamizu,Kenta Shirasawa,Sachiko Isobe,Takakazu Kaneko,Yasukazu Nakamura,Daisuke Shibata,Koh Aoki,Michael Egholm,James R. Knight,Robert Bogden,Changbao Li,Yang Shuang,Xun Xu,Shengkai Pan,Shifeng Cheng,Xin Liu,Yuanyuan Ren,Jun Wang,Alessandro Albiero,Francesca Dal Pero,Sara Todesco,Joyce Van Eck,Robert M. Buels,Aureliano Bombarely,Joseph Gosselin,Minyun Huang,Jonathan A. Leto,Naama Menda,Susan R. Strickler,Linyong Mao,Shan Gao,Isaak Y. Tecle,Thomas L. York,Yi Zheng,Julia Vrebalov,Je Min Lee,Silin Zhong,Lukas A. Mueller,Willem J. Stiekema,Paolo Ribeca,Tyler Alioto,Wencai Yang,Sanwen Huang,Yongchen Du,Zhonghua Zhang,Jianchang Gao,Yanmei Guo,Xiaoxuan Wang,Ying Li,Jun He,Chuanyou Li,Zhukuan Cheng,Jianru Zuo,Jianfeng Ren,Jiuhai Zhao,Liuhua Yan,Hongling Jiang,Bao Wang,Hongshuang Li,Zhenjun Li,Fuyou Fu,Bingtang Chen,Bin Han,Qi Feng,Danlin Fan,Ying Wang,Hong-Qing Ling,Yongbiao Xue,Doreen Ware,W. Richard McCombie,Zachary B. Lippman,Jer Ming Chia,Ke Jiang,Shiran Pasternak,Laura Gelley,Melissa Kramer,Lorinda K. Anderson,Song Bin Chang,Suzanne M. Royer,Lindsay A. Shearer,Stephen M. Stack,Jocelyn K. C. Rose,Yimin Xu,Nancy T. Eannetta,Antonio J. Matas,Ryan P. McQuinn,Steven D. Tanksley,Francisco Camara,Roderic Guigó,Stephane Rombauts,Jeffrey A. Fawcett,Yves Van de Peer,Dani Zamir,Chunbo Liang,Manuel Spannagl,Heidrun Gundlach,Rémy Bruggmann,Klaus F. X. Mayer,Zhiqi Jia,Junhong Zhang,Zhibiao Ye,Gerard J. Bishop,Sarah Butcher,Rosa Lopez-Cobollo,Daniel W. A. Buchan,Ioannis Filippis,James Abbott,Manju Singh,Alok Singh,Jitendra Kumar Pal,Awadhesh Pandit,Pradeep Kumar Singh,Ajay Kumar Mahato,Vivek Dogra,Kishor Gaikwad,Tilak Raj Sharma,Trilochan Mohapatra,Nagendra K. Singh,Mathilde Causse,Christophe Rothan,Céline Noirot,Arnaud Bellec,Christophe Klopp,Corinne Delalande,Hélène Bergès,Jérôme Mariette,Pierre Frasse,Sonia Vautrin,Toulouse Mohamed Zouine,Alain Latché,Christine Rousseau,Farid Regad,Jean-Claude Pech,Murielle Philippot,Mondher Bouzayen,Pierre Pericard,Sonia Osorio,Asuncion Fernandez Del Carmen,Antonio J. Monforte,Antonio Granell,Rafael Fernández-Muñoz,Mariana Conte,Gabriel Lichtenstein,Fernando Carrari,Gianluca De Bellis,Fabio Fuligni,Clelia Peano,Silvana Grandillo,Pasquale Termolino,Marco Pietrella,Elio Fantini,Giulia Falcone,Alessia Fiore,Giovanni Giuliano,Loredana Lopez,Paolo Facella,Gaetano Perrotta,Loretta Daddiego,Glenn J. Bryan,Biology Modesto Orozco,Xavier Pastor,David Torrents,Marco G.M. Van Schriek,Richard Feron,Jan van Oeveren,Peter De Heer,Lorena Da Ponte,Saskia Jacobs-Oomen,Mike Cariaso,Marcel Prins,Michael Josephus Theresia Van Eijk,Antoine Janssen,J. J. Van Haaren,Sung HwanJo,Jungeun Kim,Suk-Yoon Kwon,Sangmi Kim,Dal-Hoe Koo,Sanghyeob Lee,Christopher Clouser,Alain Rico,Asis Hallab,Christiane Gebhardt,Kathrin Klee,Anika Jöcker,Jens Warfsmann,Ulrike Göbel,Shingo Kawamura,Kentaro Yano,Jamie D. Sherman,Hiroyuki Fukuoka,Satomi Negoro,Sarita Bhutty,Parul Chowdhury,Debasis Chattopadhyay,Erwin Datema,Sandra Smit,Elio Schijlen,José van de Belt,Jan C. van Haarst,Sander Peters,Marjo J. van Staveren,Marleen H.C. Henkens,Paul Mooyman,Thamara Hesselink,Roeland C. H. J. van Ham,Guoyong Jiang,Marcus Droege,Doil Choi,Byung Cheol Kang,Byung-Dong Kim,Minkyu Park,Seungill Kim,Seon-In Yeom,Yong-Hwan Lee,Yang Do Choi,Guangcun Li,Jianwei Gao,Yongsheng Liu,Shengxiong Huang,Victoria Fernandez-Pedrosa,Carmen Collado,Sheila Zuñ Iga,Guoping Wang,Rebecca Cade,Robert A. Dietrich,Jane Rogers,Sandra Knapp,Zhangjun Fei,Zhangjun Fei,Ruth White,Ruth White,Theodore W. Thannhauser,Theodore W. Thannhauser,James J. Giovannoni,James J. Giovannoni,Miguel A. Botella,Louise Gilbert,Fabra Ramon Gonzalez,Jose Luis Goicoechea,Yeisoo Yu,David Kudrna,Kristi Collura,Marina Wissotski,Rod A. Wing,Blake C. Meyers,Aishwarya Bala Gurazada,Pamela J. Green,Saloni Mathur,Shailendra Vyas,Amolkumar U. Solanke,Rajesh Kumar,Vikrant Gupta,Arun Sharma,Paramjit Khurana,Jitendra P. Khurana,Akhilesh K. Tyagi,Tamas Dalmay,Irina Mohorianu,Brandon Walts,Srikar Chamala,W. Brad Barbazuk,Jingping Li,Hui Guo,Tae-Ho Lee,Yupeng Wang,Dong Zhang,Andrew H. Paterson,Xiyin Wang,Xiyin Wang,Haibao Tang,Haibao Tang,Amalia Barone,Maria Luisa Chiusano,Maria Raffaella Ercolano,Nunzio D’Agostino,Miriam Di Filippo,Alessandra Traini,Walter Sanseverino,Luigi Frusciante,Graham B. Seymour,Mounir Elharam,Ying Fu,Axin Hua,Steven Kenton,Jennifer Lewis,Shaoping Lin,Fares Z. Najar,Hongshing Lai,Baifang Qin,Ruihua Shi,Chunmei Qu,Douglas White,James R. White,Yanbo Xing,Keqin Yang,Jing Yi,Ziyun Yao,Liping Zhou,Bruce A. Roe,Alessandro Vezzi,Michela D'Angelo,Rosanna Zimbello,Riccardo Schiavon,Elisa Caniato,Chiara Rigobello,Davide Campagna,Nicola Vitulo,Giorgio Valle,David R. Nelson,Emanuele De Paoli,Dóra Szinay,Hans H. De Jong,Yuling Bai,Richard G. F. Visser,Reném Klein Lankhorst,Helen Beasley,Karen McLaren,Christine Nicholson,Claire Riddle,Giulio Gianese +323 more
TL;DR: A high-quality genome sequence of domesticated tomato is presented, a draft sequence of its closest wild relative, Solanum pimpinellifolium, is compared, and the two tomato genomes are compared to each other and to the potato genome.
Journal ArticleDOI
Pancreatic cancer exosomes initiate pre-metastatic niche formation in the liver
Bruno Costa-Silva,Nicole M. Aiello,Allyson J. Ocean,Swarnima Singh,Haiying Zhang,Basant Kumar Thakur,Basant Kumar Thakur,Annette Becker,Ayuko Hoshino,Milica Tesic Mark,Henrik Molina,Jenny Xiang,Tuo Zhang,Till Martin Theilen,Guillermo García-Santos,Caitlin Williams,Yonathan Ararso,Yujie Huang,Gonçalo Rodrigues,Tang-Long Shen,Knut Jørgen Labori,Inger Marie Bowitz Lothe,Elin H. Kure,Jonathan M. Hernandez,Alexandre Doussot,Saya H. Ebbesen,Paul M. Grandgenett,Michael A. Hollingsworth,Maneesh Jain,Kavita Mallya,Surinder K. Batra,William R. Jarnagin,Robert E. Schwartz,Irina Matei,Héctor Peinado,Ben Z. Stanger,Jacqueline Bromberg,David Lyden,David Lyden +38 more
TL;DR: It is shown that PDAC-derived exosomes induce liver pre-metastatic niche formation in naive mice and consequently increase liver metastatic burden and suggests that exosomal MIF primes the liver for metastasis and may be a prognostic marker for the development of PDAC liver metastasis.
Journal ArticleDOI
Global Epigenomic Reconfiguration During Mammalian Brain Development
Ryan Lister,Ryan Lister,Eran A. Mukamel,Joseph R. Nery,Mark A. Urich,Clare A. Puddifoot,Nicholas D. Johnson,Jacinta Lucero,Yun Huang,Andrew J. Dwork,Matthew D. Schultz,Matthew D. Schultz,Miao Yu,Julian Tonti-Filippini,Holger Heyn,Shijun Hu,Joseph C. Wu,Anjana Rao,Manel Esteller,Chuan He,Fatemeh Haghighi,Terrence J. Sejnowski,Terrence J. Sejnowski,M. Margarita Behrens,Joseph R. Ecker +24 more
TL;DR: The results extend the knowledge of the unique role of DNA methylation in brain development and function, and offer a new framework for testing the role of the epigenome in healthy function and in pathological disruptions of neural circuits.
Journal ArticleDOI
Genome-wide quantitative enhancer activity maps identified by STARR-seq.
Cosmas D. Arnold,Daniel Gerlach,Christoph Stelzer,Łukasz M. Boryń,Martina Rath,Alexander Stark +5 more
TL;DR: STARR-seq identifies thousands of cell type–specific enhancers across a broad continuum of strengths, links differential gene expression to differences in enhancer activity, and creates a genome-wide quantitative enhancer map, revealing the highly complex regulation of transcription.
Journal ArticleDOI
Genome sequence of the hot pepper provides insights into the evolution of pungency in Capsicum species
Seungill Kim,Minkyu Park,Seon-In Yeom,Yong-Min Kim,Je Min Lee,Hyun-Ah Lee,Eunyoung Seo,Jaeyoung Choi,Kyeongchae Cheong,Ki-Tae Kim,Kyongyong Jung,Gir-Won Lee,Sang-Keun Oh,Chungyun Bae,Saet-Byul Kim,Hyeyoung Lee,Shin Young Kim,Myung-Shin Kim,Byoung-Cheorl Kang,Yeong Deuk Jo,Hee Bum Yang,Hee-Jin Jeong,Won-Hee Kang,Jin Kyung Kwon,Chanseok Shin,Jae Yun Lim,June Hyun Park,Jin Hoe Huh,June Sik Kim,Byung-Dong Kim,Oded Cohen,Ilan Paran,Mi Chung Suh,Saet Buyl Lee,Yeon Ki Kim,Younhee Shin,Seung-Jae Noh,Junhyung Park,Young Sam Seo,Suk-Yoon Kwon,Hyun A Kim,Jeong Mee Park,Hyunjin Kim,Sang Bong Choi,Paul W. Bosland,Gregory Reeves,Sung Hwan Jo,Bong Woo Lee,Hyung-Taeg Cho,Hee-Seung Choi,Min-Soo Lee,Yeisoo Yu,Yang Do Choi,Beom Seok Park,Allen Van Deynze,Hamid Ashrafi,Theresa Hill,Woo Taek Kim,Hyun Sook Pai,Hee-Kyung Ahn,Inhwa Yeam,James J. Giovannoni,James J. Giovannoni,Jocelyn K. C. Rose,Iben Sørensen,Sang Jik Lee,Ryan W. Kim,Ik-Young Choi,Beom-Soon Choi,Jong-Sung Lim,Yong-Hwan Lee,Doil Choi +71 more
TL;DR: The genome size of the hot pepper was approximately fourfold larger than that of its close relative tomato, and the genome showed an accumulation of Gypsy and Caulimoviridae family elements.
References
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RNA-Seq: a revolutionary tool for transcriptomics
TL;DR: The RNA-Seq approach to transcriptome profiling that uses deep-sequencing technologies provides a far more precise measurement of levels of transcripts and their isoforms than other methods.
Journal ArticleDOI
Transcriptome analysis by strand-specific sequencing of complementary DNA
Dmitri Parkhomchuk,Tatiana Borodina,Vyacheslav Amstislavskiy,Maria Banaru,Linda Hallen,Sylvia Krobitsch,Hans Lehrach,Alexey Soldatov +7 more
TL;DR: It is demonstrated that knowing the transcript's orientation allows more accurate determination of the structure and expression of genes and helps to identify new genes and enables studying promoter-associated and antisense transcription.
Journal ArticleDOI
Identification of genetic variants using bar-coded multiplexed sequencing
David Craig,John V. Pearson,Szabolcs Szelinger,Aswin Sekar,Margot Redman,Jason J. Corneveaux,Traci Pawlowski,Trisha Laub,Gary Nunn,Dietrich A. Stephan,Nils Homer,Matthew J. Huentelman +11 more
TL;DR: This work developed a generalized framework for multiplexed resequencing of targeted human genome regions on the Illumina Genome Analyzer using degenerate indexed DNA bar codes ligated to fragmented DNA before sequencing and evaluated the use of Bayes factors for discovering and genotyping polymorphisms.
Journal ArticleDOI
Strand-specific deep sequencing of the transcriptome
TL;DR: DSSS is proposed as a simple and efficient strategy for strand-specific transcriptome sequencing and as a tool for genome annotation exploiting the increased read lengths that next-generation sequencing technology now is capable to deliver.