Journal ArticleDOI
The Immunological Genome Project: networks of gene expression in immune cells
Tracy Heng,Michio W. Painter,Kutlu G. Elpek,Veronika Lukacs-Kornek,Nora Mauermann,Shannon J. Turley,Daphne Koller,Francis S. Kim,Amy J. Wagers,Natasha Asinovski,Scott Davis,Marlys S. Fassett,Markus Feuerer,Daniel H.D. Gray,Sokol Haxhinasto,Jonathan A. Hill,Gordon Hyatt,Catherine Laplace,Kristen Leatherbee,Diane Mathis,Christophe Benoist,Radu Jianu,David H. Laidlaw,J Adam Best,Jamie Knell,Ananda W. Goldrath,Jessica Jarjoura,Joseph C. Sun,Yanan Zhu,Lewis L. Lanier,Ayla Ergun,Zheng Li,James J. Collins,Susan A. Shinton,Richard R. Hardy,Randall Friedline,Katelyn Sylvia,Joonsoo Kang +37 more
TLDR
The Immunological Genome Project combines immunology and computational biology laboratories in an effort to establish a complete 'road map' of gene-expression and regulatory networks in all immune cells.Abstract:
nology is an ideal field for the application of systems approaches, with its detailed descriptions of cell types (over 200 immune cell types are defined in the scope of the Immunological Genome Project (ImmGen)), wealth of reagents and easy access to cells. Thanks to the broad and robust approaches allowed by gene-expression microarrays and related techniques, the transcriptome is probably the only ‘-ome’ that can be reliably tackled in its entirety. Generating a complete perspective of gene expression in the immune systemread more
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“Bioinformatics” 특집을 내면서
TL;DR: Assessment of medical technology in the context of commercialization with Bioentrepreneur course, which addresses many issues unique to biomedical products.
Journal ArticleDOI
Reference-based analysis of lung single-cell sequencing reveals a transitional profibrotic macrophage
Dvir Aran,Agnieszka P. Looney,Leqian Liu,Esther Wu,Valerie Fong,Austin Hsu,Suzanna Chak,Ram P. Naikawadi,Paul J. Wolters,Adam R. Abate,Adam R. Abate,Atul J. Butte,Mallar Bhattacharya +12 more
TL;DR: Using scRNA-seq analysis, Bhattacharya and colleagues identify a subset of profibrotic lung macrophages that have a gene expression signature intermediate between those of monocytes and alveolar macrophage.
Journal ArticleDOI
Gene-expression profiles and transcriptional regulatory pathways that underlie the identity and diversity of mouse tissue macrophages
Emmanuel L. Gautier,Tal Shay,Tal Shay,Jennifer Miller,Melanie Greter,Claudia Jakubzick,Stoyan Ivanov,Julie Helft,Andrew Chow,Kutlu G. Elpek,Simon Gordonov,Amin R. Mazloom,Avi Ma'ayan,Wei-Jen Chua,Ted H. Hansen,Shannon J. Turley,Miriam Merad,Gwendalyn J. Randolph +17 more
TL;DR: It is identified how well-characterized surface markers, including MerTK and FcγR1 (CD64), along with a cluster of previously unidentified transcripts, were distinctly and universally associated with mature tissue macrophages and how these transcripts and the proteins they encode facilitated distinguishing macrophage from dendritic cells.
Journal ArticleDOI
Transcriptome-Based Network Analysis Reveals a Spectrum Model of Human Macrophage Activation
Jia Xue,Susanne Schmidt,Jil Sander,Astrid M. Draffehn,Wolfgang Krebs,Inga Quester,Dominic De Nardo,Trupti D. Gohel,Martina Emde,Lisa Schmidleithner,Hariharasudan Ganesan,Andrea Niño-Castro,Michael R. Mallmann,Larisa I. Labzin,Heidi Theis,Michael Kraut,Marc Beyer,Eicke Latz,Eicke Latz,Tom C. Freeman,Thomas Ulas,Joachim L. Schultze +21 more
TL;DR: By integrating murine data from the ImmGen project, this work proposes a refined, activation-independent core signature for human and murine macrophages that serves as a framework for future research into regulation of macrophage activation in health and disease.
Journal ArticleDOI
A rapid and robust method for single cell chromatin accessibility profiling
Xi Chen,Ricardo J. Miragaia,Ricardo J. Miragaia,Kedar Nath Natarajan,Sarah A. Teichmann,Sarah A. Teichmann +5 more
TL;DR: A simple and robust plate-based single-cell ATAC-seq method that works in fresh and cryopreserved cells and identifies distinct immune cell types and reveal cell type-specific regulatory regions and related transcription factors is developed.
References
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“Bioinformatics” 특집을 내면서
TL;DR: Assessment of medical technology in the context of commercialization with Bioentrepreneur course, which addresses many issues unique to biomedical products.
Journal ArticleDOI
A gene atlas of the mouse and human protein-encoding transcriptomes
Andrew I. Su,Tim Wiltshire,Serge Batalov,Hilmar Lapp,Keith A. Ching,David Block,Jie Zhang,Richard Soden,Mimi Hayakawa,Gabriel Kreiman,Gabriel Kreiman,Michael P. Cooke,John R. Walker,John B. Hogenesch,John B. Hogenesch +14 more
TL;DR: In this paper, high-density oligonucleotide arrays offer the opportunity to examine patterns of gene expression on a genome scale, and the authors have designed custom arrays that interrogate the expression of the vast majority of proteinencoding human and mouse genes and have used them to profile a panel of 79 human and 61 mouse tissues.
Journal ArticleDOI
Regulatory T Cell Lineage Specification by the Forkhead Transcription Factor Foxp3
Jason D. Fontenot,Jeffrey P. Rasmussen,Luke M. Williams,James Dooley,Andrew G. Farr,Alexander Y. Rudensky +5 more
TL;DR: Analysis of Foxp3 expression during thymic development suggests that this mechanism is not hard-wired but is dependent on TCR/MHC ligand interactions, and it is shown that expression ofFoxp3 is highly restricted to the subset alphabeta of T cells and, irrespective of CD25 expression, correlates with suppressor activity.
Journal ArticleDOI
The MicroArray Quality Control (MAQC) project shows inter- and intraplatform reproducibility of gene expression measurements
Leming Shi,Laura H. Reid,Wendell D. Jones,Richard Shippy,Janet A. Warrington,Shawn C. Baker,Patrick J. Collins,Francoise de Longueville,Ernest S. Kawasaki,Kathleen Y. Lee,Yuling Luo,Yongming Andrew Sun,James C. Willey,Robert Setterquist,Gavin M. Fischer,Weida Tong,Yvonne P. Dragan,David J. Dix,Felix W. Frueh,Federico Goodsaid,Damir Herman,Roderick V. Jensen,Charles D. Johnson,Edward K. Lobenhofer,Raj K. Puri,Uwe Scherf,Jean Thierry-Mieg,Charles Wang,Michael A Wilson,Paul K. Wolber,Lu Zhang,William Slikker,Shashi Amur,Wenjun Bao,Catalin Barbacioru,Anne Bergstrom Lucas,Vincent Bertholet,Cecilie Boysen,Bud Bromley,Donna Brown,Alan Brunner,Roger D. Canales,Xiaoxi Megan Cao,Thomas A. Cebula,James J. Chen,Jing Cheng,Tzu Ming Chu,Eugene Chudin,John F. Corson,J. Christopher Corton,Lisa J. Croner,Christopher Davies,Timothy Davison,Glenda C. Delenstarr,Xutao Deng,David Dorris,Aron Charles Eklund,Xiaohui Fan,Hong Fang,Stephanie Fulmer-Smentek,James C. Fuscoe,Kathryn Gallagher,Weigong Ge,Lei Guo,Xu Guo,Janet Hager,Paul K. Haje,Jing Han,Tao Han,Heather Harbottle,Stephen C. Harris,Eli Hatchwell,Craig A. Hauser,Susan D. Hester,Huixiao Hong,Patrick Hurban,Scott A. Jackson,Hanlee P. Ji,Charles R. Knight,Winston Patrick Kuo,J. Eugene LeClerc,Shawn Levy,Quan Zhen Li,Chunmei Liu,Ying Liu,Michael Lombardi,Yunqing Ma,Scott R. Magnuson,Botoul Maqsodi,Timothy K. McDaniel,Nan Mei,Ola Myklebost,Baitang Ning,Natalia Novoradovskaya,Michael S. Orr,Terry Osborn,Adam Papallo,Tucker A. Patterson,Roger Perkins,Elizabeth Herness Peters,Ron L. Peterson,Kenneth L. Philips,P. Scott Pine,Lajos Pusztai,Feng Qian,Hongzu Ren,Mitch Rosen,Barry A. Rosenzweig,Raymond R. Samaha,Mark Schena,Gary P. Schroth,Svetlana Shchegrova,Dave D. Smith,Frank Staedtler,Zhenqiang Su,Hongmei Sun,Zoltan Szallasi,Zivana Tezak,Danielle Thierry-Mieg,Karol L. Thompson,Irina Tikhonova,Yaron Turpaz,Beena Vallanat,Christophe Van,Stephen J. Walker,Sue Jane Wang,Yonghong Wang,Russell D. Wolfinger,Alexander Wong,Jie Wu,Chunlin Xiao,Qian Xie,Jun Xu,Wen Yang,Liang Zhang,Sheng Zhong,Yaping Zong +136 more
TL;DR: This study describes the experimental design and probe mapping efforts behind the MicroArray Quality Control project and shows intraplatform consistency across test sites as well as a high level of interplatform concordance in terms of genes identified as differentially expressed.
Journal ArticleDOI
Interferon and Granulopoiesis Signatures in Systemic Lupus Erythematosus Blood
Lynda Bennett,A. Karolina Palucka,Edsel Arce,Edsel Arce,Victoria Cantrell,Victoria Cantrell,Josef Borvak,Jacques Banchereau,Virginia Pascual,Virginia Pascual +9 more
TL;DR: Microarray analysis of blood cells reveals that immature granulocytes may be involved in SLE pathogenesis, and the IFN signature confirms the central role of this cytokine in Sle, using oligonucleotide microarrays.