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Method: SLIC-CAGE: high-resolution transcription start site mapping using nanogram-levels of total RNA
- Nevena Cvetesic,
- Harry G. Leitch,
- Malgorzata Borkowska,
- Ferenc Müller,
- Piero Carninci,
- Petra Hajkova,
- and Boris Lenhard
Genome Res. December 2018 28: 1943-1956; Published in Advance November 7, 2018, doi:10.1101/gr.235937.118
...in SLIC-CAGE libraries prepared from 5 or 10 ng of S. cerevisiae total RNA and in the reference nAnT-iCAGE library. (D) Dinucleotide composition of all CTSSs (left panel) or dominant CTSSs (right panel) identified in SLIC-CAGE libraries prepared from 5 or 10 ng of S. cerevisiae total RNA and in the n...
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Method: Dissection of complex adult traits in a mouse synthetic population
- David T. Burke,
- Kenneth M. Kozloff,
- Shu Chen,
- Joshua L. West,
- Jodi M. Wilkowski,
- Steven A. Goldstein,
- Richard A. Miller,
- and Andrzej T. Galecki
Genome Res. August 2012 22: 1549-1557; Published in Advance May 15, 2012, doi:10.1101/gr.135582.111
...Dissection of complex adult traits in a mouse synthetic population David T. Burke 1 , 6 , Kenneth M. Kozloff 2 , Shu Chen 3 , Joshua L. West 1 , Jodi M. Wilkowski 1 , Steven A. Goldstein 2 , Richard A. Miller 3 , 4 , 5...
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Resource: Natural variation in genome architecture among 205 Drosophila melanogaster Genetic Reference Panel lines
- Wen Huang,
- Andreas Massouras,
- Yutaka Inoue,
- Jason Peiffer,
- Miquel Ràmia,
- Aaron M. Tarone,
- Lavanya Turlapati,
- Thomas Zichner,
- Dianhui Zhu,
- Richard F. Lyman,
- Michael M. Magwire,
- Kerstin Blankenburg,
- Mary Anna Carbone,
- Kyle Chang,
- Lisa L. Ellis,
- Sonia Fernandez,
- Yi Han,
- Gareth Highnam,
- Carl E. Hjelmen,
- John R. Jack,
- Mehwish Javaid,
- Joy Jayaseelan,
- Divya Kalra,
- Sandy Lee,
- Lora Lewis,
- Mala Munidasa,
- Fiona Ongeri,
- Shohba Patel,
- Lora Perales,
- Agapito Perez,
- LingLing Pu,
- Stephanie M. Rollmann,
- Robert Ruth,
- Nehad Saada,
- Crystal Warner,
- Aneisa Williams,
- Yuan-Qing Wu,
- Akihiko Yamamoto,
- Yiqing Zhang,
- Yiming Zhu,
- Robert R.H. Anholt,
- Jan O. Korbel,
- David Mittelman,
- Donna M. Muzny,
- Richard A. Gibbs,
- Antonio Barbadilla,
- J. Spencer Johnston,
- Eric A. Stone,
- Stephen Richards,
- Bart Deplancke,
- and Trudy F.C. Mackay
Genome Res. July 2014 24: 1193-1208; Published in Advance April 8, 2014, doi:10.1101/gr.171546.113
...traits (Flint and Mackay 2009; Mackay et al. 2009). Efforts to utilize naturally occurring genetic variation in D. melanogaster to add to our understanding of functional DNA elements have been greatly expedited by the Drosophila Genetic Reference Panel (DGRP), a publicly available population of 205...
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Review: Contrasting genetic architectures in different mouse reference populations used for studying complex traits
- David A. Buchner and
- Joseph H. Nadeau
Genome Res. June 2015 25: 775-791; Published in Advance May 7, 2015, doi:10.1101/gr.187450.114
..., including Bardet-Biedl andHirschsprung’s, are largely determined bymutations in a small number of genes, most traits in humans, mice, and other species do not share this genetic simplicity. Large-scale international efforts are underway to dissect the genetics of these common conditions (Cornelis et al...
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Resource: Genetic dissection of a model complex trait using the Drosophila Synthetic Population Resource
- Elizabeth G. King,
- Chris M. Merkes,
- Casey L. McNeil,
- Steven R. Hoofer,
- Saunak Sen,
- Karl W. Broman,
- Anthony D. Long,
- and Stuart J. Macdonald
Genome Res. August 2012 22: 1558-1566; Published in Advance April 10, 2012, doi:10.1101/gr.134031.111
...detail the properties of the mapping panel of >1600 genotyped RILs, and provide an empirical demonstration of the utility of the approach by genetically dissecting alcohol dehydrogenase (ADH) enzyme activity. We confirm that a large fraction of the variation in this classic quantitative trait is due...
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Perspective: Genetic architecture of quantitative traits in mice, flies, and humans
- Jonathan Flint and
- Trudy F.C. Mackay
Genome Res. May 2009 19: 723-733; doi:10.1101/gr.086660.108
...expression. As yet there are very few instances where homologous quantitative trait loci, or quantitative trait genes, have been identified in multiple species, but the availability of high-resolution mapping data will soon make it possible to test the degree of overlap between species. Footnotes...
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Research: Genetic analysis of complex traits in the emerging Collaborative Cross
- David L. Aylor,
- William Valdar,
- Wendy Foulds-Mathes,
- Ryan J. Buus,
- Ricardo A. Verdugo,
- Ralph S. Baric,
- Martin T. Ferris,
- Jeff A. Frelinger,
- Mark Heise,
- Matt B. Frieman,
- Lisa E. Gralinski,
- Timothy A. Bell,
- John D. Didion,
- Kunjie Hua,
- Derrick L. Nehrenberg,
- Christine L. Powell,
- Jill Steigerwalt,
- Yuying Xie,
- Samir N.P. Kelada,
- Francis S. Collins,
- Ivana V. Yang,
- David A. Schwartz,
- Lisa A. Branstetter,
- Elissa J. Chesler,
- Darla R. Miller,
- Jason Spence,
- Eric Yi Liu,
- Leonard McMillan,
- Abhishek Sarkar,
- Jeremy Wang,
- Wei Wang,
- Qi Zhang,
- Karl W. Broman,
- Ron Korstanje,
- Caroline Durrant,
- Richard Mott,
- Fuad A. Iraqi,
- Daniel Pomp,
- David Threadgill,
- Fernando Pardo-Manuel de Villena,
- and Gary A. Churchill
Genome Res. August 2011 21: 1213-1222; Published in Advance March 15, 2011, doi:10.1101/gr.111310.110
...CC strains.We observed variation in a broad range of phenotypes, examined the genetic properties of the panel, and developed and tested data analysis strategies that will also apply to the finished CC strains. The pre-CC study used partially inbred mice from 220 CC lines that were initiated...
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Research: Collaborative Cross mice and their power to map host susceptibility to Aspergillus fumigatus infection
- Caroline Durrant,
- Hanna Tayem,
- Binnaz Yalcin,
- James Cleak,
- Leo Goodstadt,
- Fernando Pardo-Manuel de Villena,
- Richard Mott,
- and Fuad A. Iraqi
Genome Res. August 2011 21: 1239-1248; Published in Advance April 14, 2011, doi:10.1101/gr.118786.110
.... Genealogies of mouse inbred strains. Nat Genet 24: 23–25. Bennett BJ, Farber CR, Orozco L, Min Kang H, Ghazalpour A, Siemers N, Neubauer M, Neuhaus I, Yordanova R, Guan B, et al. 2010. A highresolution association mapping panel for the dissection of complex traits in mice. Genome Res 20: 281–290. Bowman JC...
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LETTER: Pleiotropy, Homeostasis, and Functional Networks Based on Assays of Cardiovascular Traits in Genetically Randomized Populations
- Joseph H. Nadeau,
- Lindsay C. Burrage,
- Joe Restivo,
- Yoh-Han Pao,
- Gary Churchill,
- and Brian D. Hoit
Genome Res. September 2003 13: 2082-2091; doi:10.1101/gr.1186603
...excessive pressure on the chest. A warming pad (Deltaphase Isothermal Pad, Braintree Scientific) was used to maintain normothermia. Mice were imaged in the shallow left lateral decubitus using a depth setting of 2 cm in high-resolution mode. The transmit zone was adjusted to maximize the frame rates (166 Hz...
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Methods: Integrative Genomics: In Silico Coupling of Rat Physiology and Complex Traits With Mouse and Human Data
- Simon N. Twigger,
- Jeff Nie,
- Victor Ruotti,
- Jiaming Yu,
- Dan Chen,
- Dawei Li,
- Jed Mathis,
- Vijay Narayanasamy,
- Gopal R. Gopinath,
- Dean Pasko,
- Mary Shimoyama,
- Norberto de la Cruz,
- Susan Bromberg,
- Anne E. Kwitek,
- Howard J. Jacob,
- and Peter J. Tonellato
Genome Res. April 2004 14: 651-660; doi:10.1101/gr.1974504
.... Received September 13, 2003. Cold Spring Harbor Laboratory Press References ↵ al-Majali, K.M., Glazier, A.M., Norsworthy, P.J., Wahid, F.N., Cooper, L.D., Wallace, C.A., Scott, J., Lausen, B., and Aitman, T.J. 1999 . A high-resolution radiation hybrid map of the proximal region of rat chromosome 4. Mamm...

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