Resources

  • Resource |

    A library of mutant mouse lung endothelial cells expressing a comprehensive repertoire of heparin sulfate structure modifications enables studies of the structure–function relationships of this complex polysaccharide.

    • Hong Qiu
    • , Songshan Shi
    • , Jingwen Yue
    • , Meng Xin
    • , Alison V. Nairn
    • , Lei Lin
    • , Xinyue Liu
    • , Guoyun Li
    • , Stephanie A. Archer-Hartmann
    • , Mitche Dela Rosa
    • , Melina Galizzi
    • , Shunchun Wang
    • , Fuming Zhang
    • , Parastoo Azadi
    • , Toin H. van Kuppevelt
    • , Wellington V. Cardoso
    • , Koji Kimata
    • , Xingbin Ai
    • , Kelley W. Moremen
    • , Jeffrey D. Esko
    • , Robert J. Linhardt
    •  & Lianchun Wang
  • Resource |

    A CHO cell library displaying a near-complete repertoire of glycosaminoglycan (GAG) modifications provides a resource for cell-based binding assays, recombinant proteoglycan expression, and assembly of GAG glycan microarrays.

    • Yen-Hsi Chen
    • , Yoshiki Narimatsu
    • , Thomas M. Clausen
    • , Catarina Gomes
    • , Richard Karlsson
    • , Catharina Steentoft
    • , Charlotte B. Spliid
    • , Tobias Gustavsson
    • , Ali Salanti
    • , Andrea Persson
    • , Anders Malmström
    • , Daniel Willén
    • , Ulf Ellervik
    • , Eric P. Bennett
    • , Yang Mao
    • , Henrik Clausen
    •  & Zhang Yang
  • Resource |

    Metagenomic mining generates a rich resource of regulatory sequences with species-selective and universal activity, making it possible to engineer synthetic circuits with tunable gene expression across diverse bacterial hosts.

    • Nathan I Johns
    • , Antonio L C Gomes
    • , Sung Sun Yim
    • , Anthony Yang
    • , Tomasz Blazejewski
    • , Christopher S Smillie
    • , Mark B Smith
    • , Eric J Alm
    • , Sriram Kosuri
    •  & Harris H Wang
  • Resource |

    A collection of 1,406 high-quality, immunoprecipitation- and immunoblotting-grade monoclonal antibodies to 737 human transcription factors is made available as a community resource, along with all validation data.

    • Anand Venkataraman
    • , Kun Yang
    • , Jose Irizarry
    • , Mark Mackiewicz
    • , Paolo Mita
    • , Zheng Kuang
    • , Lin Xue
    • , Devlina Ghosh
    • , Shuang Liu
    • , Pedro Ramos
    • , Shaohui Hu
    • , Diane Bayron Kain
    • , Sarah Keegan
    • , Richard Saul
    • , Simona Colantonio
    • , Hongyan Zhang
    • , Florencia Pauli Behn
    • , Guang Song
    • , Edisa Albino
    • , Lillyann Asencio
    • , Leonardo Ramos
    • , Luvir Lugo
    • , Gloriner Morell
    • , Javier Rivera
    • , Kimberly Ruiz
    • , Ruth Almodovar
    • , Luis Nazario
    • , Keven Murphy
    • , Ivan Vargas
    • , Zully Ann Rivera-Pacheco
    • , Christian Rosa
    • , Moises Vargas
    • , Jessica McDade
    • , Brian S Clark
    • , Sooyeon Yoo
    • , Seva G Khambadkone
    • , Jimmy de Melo
    • , Milanka Stevanovic
    • , Lizhi Jiang
    • , Yana Li
    • , Wendy Y Yap
    • , Brittany Jones
    • , Atul Tandon
    • , Elliot Campbell
    • , Gaetano T Montelione
    • , Stephen Anderson
    • , Richard M Myers
    • , Jef D Boeke
    • , David Fenyö
    • , Gordon Whiteley
    • , Joel S Bader
    • , Ignacio Pino
    • , Daniel J Eichinger
    • , Heng Zhu
    •  & Seth Blackshaw
  • Resource |

    Based on machine learning-predicted interaction interfaces, this resource enables interpretation of genomic variants and disease mutations in light of the protein-protein interactome.

    • Michael J Meyer
    • , Juan Felipe Beltrán
    • , Siqi Liang
    • , Robert Fragoza
    • , Aaron Rumack
    • , Jin Liang
    • , Xiaomu Wei
    •  & Haiyuan Yu
  • Resource |

    This resource paper describes the steps involved in carrying out quantitative multicolour imaging in tissue. It is applied to cleared mouse bone and plots the spatial distribution of specific cell populations within the marrow.

    • Daniel L Coutu
    • , Konstantinos D Kokkaliaris
    • , Leo Kunz
    •  & Timm Schroeder
  • Resource | | open

    This Resource describes the Image Data Resource (IDR), a prototype online system for biological image data that links experimental and analytic data across multiple data sets and promotes image data sharing and reanalysis.

    • Eleanor Williams
    • , Josh Moore
    • , Simon W Li
    • , Gabriella Rustici
    • , Aleksandra Tarkowska
    • , Anatole Chessel
    • , Simone Leo
    • , Bálint Antal
    • , Richard K Ferguson
    • , Ugis Sarkans
    • , Alvis Brazma
    • , Rafael E Carazo Salas
    •  & Jason R Swedlow
  • Resource |

    A large-scale resource, iMPAQT, provides multiple reaction monitoring (MRM)–mass spectrometry assays for targeted quantitative analysis of mTRAQ-labeled human proteins.

    • Masaki Matsumoto
    • , Fumiko Matsuzaki
    • , Kiyotaka Oshikawa
    • , Naoki Goshima
    • , Masatoshi Mori
    • , Yoshifumi Kawamura
    • , Koji Ogawa
    • , Eriko Fukuda
    • , Hirokazu Nakatsumi
    • , Tohru Natsume
    • , Kazuhiko Fukui
    • , Katsuhisa Horimoto
    • , Takeshi Nagashima
    • , Ryo Funayama
    • , Keiko Nakayama
    •  & Keiichi I Nakayama
  • Resource |

    A newly developed algorithm enabled clustering of all 256 million (66 million identified and 190 million unidentified) peptide MS/MS spectra available in the PRIDE Archive database, allowing the detection of millions of consistently unidentified spectra across different data sets, of which roughly 20% could be identified using multiple complementary analysis tools.

    • Johannes Griss
    • , Yasset Perez-Riverol
    • , Steve Lewis
    • , David L Tabb
    • , José A Dianes
    • , Noemi del-Toro
    • , Marc Rurik
    • , Mathias Walzer
    • , Oliver Kohlbacher
    • , Henning Hermjakob
    • , Rui Wang
    •  & Juan Antonio Vizcaíno
  • Resource |

    Z-Brain is an atlas of the larval zebrafish brain. It can be combined with pERK-based neural-activity measurements from freely behaving zebrafish to identify brain regions involved in generating behavior.

    • Owen Randlett
    • , Caroline L Wee
    • , Eva A Naumann
    • , Onyeka Nnaemeka
    • , David Schoppik
    • , James E Fitzgerald
    • , Ruben Portugues
    • , Alix M B Lacoste
    • , Clemens Riegler
    • , Florian Engert
    •  & Alexander F Schier
  • Resource |

    A collection of single-gene-mutant human cells is described. This growing resource is based on gene-trap mutagenesis of a near-haploid human cell line and covers almost 3,500 human genes.

    • Tilmann Bürckstümmer
    • , Carina Banning
    • , Philipp Hainzl
    • , Richard Schobesberger
    • , Claudia Kerzendorfer
    • , Florian M Pauler
    • , Doris Chen
    • , Nicole Them
    • , Fiorella Schischlik
    • , Manuele Rebsamen
    • , Michal Smida
    • , Ferran Fece de la Cruz
    • , Ana Lapao
    • , Melissa Liszt
    • , Benjamin Eizinger
    • , Philipp M Guenzl
    • , Vincent A Blomen
    • , Tomasz Konopka
    • , Bianca Gapp
    • , Katja Parapatics
    • , Barbara Maier
    • , Johannes Stöckl
    • , Wolfgang Fischl
    • , Sejla Salic
    • , M Rita Taba Casari
    • , Sylvia Knapp
    • , Keiryn L Bennett
    • , Christoph Bock
    • , Jacques Colinge
    • , Robert Kralovics
    • , Gustav Ammerer
    • , Georg Casari
    • , Thijn R Brummelkamp
    • , Giulio Superti-Furga
    •  & Sebastian M B Nijman
  • Resource |

    The Contaminant Repository for Affinity Purification (CRAPome) is a database of annotated negative control-data that can be used for filtering out nonspecific interactions in affinity purification-mass spectrometry experiments.

    • Dattatreya Mellacheruvu
    • , Zachary Wright
    • , Amber L Couzens
    • , Jean-Philippe Lambert
    • , Nicole A St-Denis
    • , Tuo Li
    • , Yana V Miteva
    • , Simon Hauri
    • , Mihaela E Sardiu
    • , Teck Yew Low
    • , Vincentius A Halim
    • , Richard D Bagshaw
    • , Nina C Hubner
    • , Abdallah al-Hakim
    • , Annie Bouchard
    • , Denis Faubert
    • , Damian Fermin
    • , Wade H Dunham
    • , Marilyn Goudreault
    • , Zhen-Yuan Lin
    • , Beatriz Gonzalez Badillo
    • , Tony Pawson
    • , Daniel Durocher
    • , Benoit Coulombe
    • , Ruedi Aebersold
    • , Giulio Superti-Furga
    • , Jacques Colinge
    • , Albert J R Heck
    • , Hyungwon Choi
    • , Matthias Gstaiger
    • , Shabaz Mohammed
    • , Ileana M Cristea
    • , Keiryn L Bennett
    • , Mike P Washburn
    • , Brian Raught
    • , Rob M Ewing
    • , Anne-Claude Gingras
    •  & Alexey I Nesvizhskii
  • Resource |

    An improved Brainbow toolbox for expression in the mouse is presented in this Resource. The collection includes transgenic lines, plasmids and viral vectors with improved performance and added capabilities relative to the original Brainbow constructs.

    • Dawen Cai
    • , Kimberly B Cohen
    • , Tuanlian Luo
    • , Jeff W Lichtman
    •  & Joshua R Sanes
  • Resource |

    Interactome3D is an interactive resource allowing biologists to use available structural information to model protein-protein interactions and structurally annotate protein interaction networks.

    • Roberto Mosca
    • , Arnaud Céol
    •  & Patrick Aloy
  • Resource |

    A collection of opsins for two-photon modulation of neuronal activity in vitro and in vivo is presented in this resource. The opsins have kinetic, expression and spectral properties ideally suited to typical raster-scanning two-photon microscopy. Also online, Packer et al. use the red-shifted opsin C1V1T and simple raster-scanning illumination to stimulate individual spines and dendrites and map synaptic circuits.

    • Rohit Prakash
    • , Ofer Yizhar
    • , Benjamin Grewe
    • , Charu Ramakrishnan
    • , Nancy Wang
    • , Inbal Goshen
    • , Adam M Packer
    • , Darcy S Peterka
    • , Rafael Yuste
    • , Mark J Schnitzer
    •  & Karl Deisseroth
  • Resource |

    A comparison of the proteomes and phosphoproteomes of four human embryonic stem cell lines and four induced pluripotent stem cell lines is reported, revealing subtle differences in these cell types at the protein level. Also introduced is the Stem Cell-Omics Repository (SCOR), a database of quantitative information for transcripts, proteins and post-translational modifications.

    • Douglas H Phanstiel
    • , Justin Brumbaugh
    • , Craig D Wenger
    • , Shulan Tian
    • , Mitchell D Probasco
    • , Derek J Bailey
    • , Danielle L Swaney
    • , Mark A Tervo
    • , Jennifer M Bolin
    • , Victor Ruotti
    • , Ron Stewart
    • , James A Thomson
    •  & Joshua J Coon
  • Resource |

    A collection of functionally characterized BAC transgenic mouse lines in which the channelrhodopsin-2 H134R variant is specifically and stably expressed in GABAergic, cholinergic, serotonergic or parvalbumin-positive neurons is reported.

    • Shengli Zhao
    • , Jonathan T Ting
    • , Hisham E Atallah
    • , Li Qiu
    • , Jie Tan
    • , Bernd Gloss
    • , George J Augustine
    • , Karl Deisseroth
    • , Minmin Luo
    • , Ann M Graybiel
    •  & Guoping Feng
  • Resource |

    Described is a randomly inserting transposon that can be swapped for gene traps, coding insertions or protein tag genes, thus expanding the toolkit for Drosophila melanogaster genome engineering.

    • Koen J T Venken
    • , Karen L Schulze
    • , Nele A Haelterman
    • , Hongling Pan
    • , Yuchun He
    • , Martha Evans-Holm
    • , Joseph W Carlson
    • , Robert W Levis
    • , Allan C Spradling
    • , Roger A Hoskins
    •  & Hugo J Bellen
  • Resource |

    A genetic platform allows refinement of tissue-specific expression using the upstream activating sequence–GAL4 system in Drosophila melanogaster, facilitating the segmentation of complex expression patterns and allowing GAL4 expression patterns to be repurposed.

    • Daryl M Gohl
    • , Marion A Silies
    • , Xiaojing J Gao
    • , Sheetal Bhalerao
    • , Francisco J Luongo
    • , Chun-Chieh Lin
    • , Christopher J Potter
    •  & Thomas R Clandinin
  • Resource |

    This resource describes a human MAP kinase interactome. Yeast two hybrid-derived protein interaction maps of MAP kinase pathway members are refined using multiple criteria, tested against reference sets, and functionally validated using knockdown with siRNA.

    • Sourav Bandyopadhyay
    • , Chih-yuan Chiang
    • , Jyoti Srivastava
    • , Merril Gersten
    • , Suhaila White
    • , Russell Bell
    • , Cornelia Kurschner
    • , Christopher H Martin
    • , Mike Smoot
    • , Sudhir Sahasrabudhe
    • , Diane L Barber
    • , Sumit K Chanda
    •  & Trey Ideker
  • Resource |

    This resource provides a comprehensive evaluation of rodent locomotor profiles after different types of lesions to the central nervous system. The data set can guide the selection of suitable lesion paradigms, locomotor tasks and readouts in future animal studies.

    • Björn Zörner
    • , Linard Filli
    • , Michelle L Starkey
    • , Roman Gonzenbach
    • , Hansjörg Kasper
    • , Martina Röthlisberger
    • , Marc Bolliger
    •  & Martin E Schwab
  • Resource |

    Paired-end sequencing of human genomic DNA reveals at least 2.8 Mb of new sequence at 720 distinct loci. Complete sequencing of 1.67 Mb at 192 loci reveals extensive copy-number variation and provides a resource for genotyping these 'missing' sequences.

    • Jeffrey M Kidd
    • , Nick Sampas
    • , Francesca Antonacci
    • , Tina Graves
    • , Robert Fulton
    • , Hillary S Hayden
    • , Can Alkan
    • , Maika Malig
    • , Mario Ventura
    • , Giuliana Giannuzzi
    • , Joelle Kallicki
    • , Paige Anderson
    • , Anya Tsalenko
    • , N Alice Yamada
    • , Peter Tsang
    • , Rajinder Kaul
    • , Richard K Wilson
    • , Laurakay Bruhn
    •  & Evan E Eichler
  • Resource |

    High-throughput yeast two-hybrid screening is used to generate the largest C. elegans interactome resource available thus far. Using an empirical quality control framework presented in Venkatesan et al., also online, the data set is evaluated for quality and is used to estimate the total size of the worm interactome.

    • Nicolas Simonis
    • , Jean-François Rual
    • , Anne-Ruxandra Carvunis
    • , Murat Tasan
    • , Irma Lemmens
    • , Tomoko Hirozane-Kishikawa
    • , Tong Hao
    • , Julie M Sahalie
    • , Kavitha Venkatesan
    • , Fana Gebreab
    • , Sebiha Cevik
    • , Niels Klitgord
    • , Changyu Fan
    • , Pascal Braun
    • , Ning Li
    • , Nono Ayivi-Guedehoussou
    • , Elizabeth Dann
    • , Nicolas Bertin
    • , David Szeto
    • , Amélie Dricot
    • , Muhammed A Yildirim
    • , Chenwei Lin
    • , Anne-Sophie de Smet
    • , Huey-Ling Kao
    • , Christophe Simon
    • , Alex Smolyar
    • , Jin Sook Ahn
    • , Muneesh Tewari
    • , Mike Boxem
    • , Stuart Milstein
    • , Haiyuan Yu
    • , Matija Dreze
    • , Jean Vandenhaute
    • , Kristin C Gunsalus
    • , Michael E Cusick
    • , David E Hill
    • , Jan Tavernier
    • , Frederick P Roth
    •  & Marc Vidal
  • Resource |

    A collection of 33,275 human Gateway entry clones and complementary in vitro protein expression methodologies are described that allow proteome-scale production of human proteins. This 'human protein factory' was validated by expression of 13,364 human proteins and assessment of activity in a variety of assays.

    • Naoki Goshima
    • , Yoshifumi Kawamura
    • , Akiko Fukumoto
    • , Aya Miura
    • , Reiko Honma
    • , Ryohei Satoh
    • , Ai Wakamatsu
    • , Jun-ichi Yamamoto
    • , Kouichi Kimura
    • , Tetsuo Nishikawa
    • , Taichi Andoh
    • , Yuki Iida
    • , Kumiko Ishikawa
    • , Emi Ito
    • , Naoko Kagawa
    • , Chie Kaminaga
    • , Kei-ichi Kanehori
    • , Bunsei Kawakami
    • , Kiyokazu Kenmochi
    • , Rie Kimura
    • , Miki Kobayashi
    • , Toshihiro Kuroita
    • , Hisashi Kuwayama
    • , Yukio Maruyama
    • , Kiyoshi Matsuo
    • , Kazuyoshi Minami
    • , Mariko Mitsubori
    • , Masatoshi Mori
    • , Riyo Morishita
    • , Atsushi Murase
    • , Akira Nishikawa
    • , Shigemichi Nishikawa
    • , Toshihiko Okamoto
    • , Noriko Sakagami
    • , Yutaka Sakamoto
    • , Yukari Sasaki
    • , Tomoe Seki
    • , Saki Sono
    • , Akio Sugiyama
    • , Tsuyoshi Sumiya
    • , Tomoko Takayama
    • , Yukiko Takayama
    • , Hiroyuki Takeda
    • , Takushi Togashi
    • , Kazuhide Yahata
    • , Hiroko Yamada
    • , Yuka Yanagisawa
    • , Yaeta Endo
    • , Fumio Imamoto
    • , Yasutomo Kisu
    • , Shigeo Tanaka
    • , Takao Isogai
    • , Jun-ichi Imai
    • , Shinya Watanabe
    •  & Nobuo Nomura