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Resource: Generation and analysis of a mouse multitissue genome annotation atlas
- Matthew Adams and
- Christopher Vollmers
Genome Res. November 2024 34: 2108-2117; Published in Advance October 23, 2024, doi:10.1101/gr.279217.124
.... 2001; The ENCODE Project Consortium 2004; McGarvey et al. 2015; Frankish et al. 2019). These reference annotations are absolutely essential for virtually all transcriptomics research and beyond, but they lack information on what tissues and cell types express what isoforms and at what level.A resource...
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Research: De novo genome assemblies of two cryptodiran turtles with ZZ/ZW and XX/XY sex chromosomes provide insights into patterns of genome reshuffling and uncover novel 3D genome folding in amniotes
- Basanta Bista,
- Laura González-Rodelas,
- Lucía Álvarez-González,
- Zhi-qiang Wu,
- Eugenia E. Montiel,
- Ling Sze Lee,
- Daleen B. Badenhorst,
- Srihari Radhakrishnan,
- Robert Literman,
- Beatriz Navarro-Dominguez,
- John B. Iverson,
- Simon Orozco-Arias,
- Josefa González,
- Aurora Ruiz-Herrera,
- and Nicole Valenzuela
Genome Res. October 2024 34: 1553-1569; Published in Advance October 16, 2024, doi:10.1101/gr.279443.124
...a fragment of the short- and long-arm of a chromosome, respectively, whereas “b” denotes a fragment of an acrocentric chromosome or of the same chromosome arm. (B) Ideograms depicting BAC positions and chromosomal homology across species (Badenhorst et al. 2015). (C) Major chromosomal fusions and fissions...
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RESOURCE: Integrated and Sequence-Ordered BAC- and YAC-Based Physical Maps for the Rat Genome
- Martin Krzywinski,
- John Wallis,
- Claudia Gösele,
- Ian Bosdet,
- Readman Chiu,
- Tina Graves,
- Oliver Hummel,
- Dan Layman,
- Carrie Mathewson,
- Natasja Wye,
- Baoli Zhu,
- Derek Albracht,
- Jennifer Asano,
- Sarah Barber,
- Mabel Brown-John,
- Susanna Chan,
- Steve Chand,
- Alison Cloutier,
- Jonathon Davito,
- Chris Fjell,
- Tony Gaige,
- Detlev Ganten,
- Noreen Girn,
- Kurtis Guggenheimer,
- Heinz Himmelbauer,
- Thomas Kreitler,
- Stephen Leach,
- Darlene Lee,
- Hans Lehrach,
- Michael Mayo,
- Kelly Mead,
- Teika Olson,
- Pawan Pandoh,
- Anna-Liisa Prabhu,
- Heesun Shin,
- Simone Tänzer,
- Jason Thompson,
- Miranda Tsai,
- Jason Walker,
- George Yang,
- Mandeep Sekhon,
- LaDeana Hillier,
- Heike Zimdahl,
- Andre Marziali,
- Kazutoyo Osoegawa,
- Shaying Zhao,
- Asim Siddiqui,
- Pieter J. de Jong,
- Wes Warren,
- Elaine Mardis,
- John D. McPherson,
- Richard Wilson,
- Norbert Hübner,
- Steven Jones,
- Marco Marra,
- and Jacqueline Schein
Genome Res. April 2004 14: 766-779; doi:10.1101/gr.2336604
...sequence and functional genomic approaches that rely on the availability of sequence-anchored clones. We undertook the construction of the Rattus norvegicus BAC map as part of the international effort to sequence the entire ( Rat Genome Sequencing Project Consortium 2004 ). The BAC map was constructed...
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RESOURCE: A BAC-based physical map of the Drosophila buzzatii genome
- Josefa González,
- Michael Nefedov,
- Ian Bosdet,
- Ferran Casals,
- Oriol Calvete,
- Alejandra Delprat,
- Heesun Shin,
- Readman Chiu,
- Carrie Mathewson,
- Natasja Wye,
- Roger A. Hoskins,
- Jacqueline E. Schein,
- Pieter de Jong,
- and Alfredo Ruiz
Genome Res. June 2005 15: 885-892; doi:10.1101/gr.3263105
...., Shu, C.L., Ren, T., Cao, Q., Vessere, G.M., Lutz, M.M., Jensen-Seaman, M.I., Zhao, S., and de Jong, P.J. 2004 . BAC resources for the rat project. Genome Res. 14 : 780 -785. Podemski, L., Ferrer, C., and Locke, J. 2001 . Whole arm inversions of chromosome 4 in Drosophila species. Chromosoma 110 : 305...
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Research: The genome sequence of the spontaneously hypertensive rat: Analysis and functional significance
- Santosh S. Atanur,
- İnanç Birol,
- Victor Guryev,
- Martin Hirst,
- Oliver Hummel,
- Catherine Morrissey,
- Jacques Behmoaras,
- Xose M. Fernandez-Suarez,
- Michelle D. Johnson,
- William M. McLaren,
- Giannino Patone,
- Enrico Petretto,
- Charles Plessy,
- Kathleen S. Rockland,
- Charles Rockland,
- Kathrin Saar,
- Yongjun Zhao,
- Piero Carninci,
- Paul Flicek,
- Ted Kurtz,
- Edwin Cuppen,
- Michal Pravenec,
- Norbert Hubner,
- Steven J.M. Jones,
- Ewan Birney,
- and Timothy J. Aitman
Genome Res. June 2010 20: 791-803; Published in Advance April 29, 2010, doi:10.1101/gr.103499.109
...Sequence Read Archive ( http://www.ebi.ac.uk/ ) under accession no. ERA000170. SNPs have been submitted to dbSNP ( http://www.ncbi.nlm.nih.gov/projects/SNP/ ) under batch id 2010-1_SHR. The complete set of SNPs is also available on Ensembl ( ftp://ftp.ebi.ac.uk/pub/databases/ensembl/snp/rat/shr/ ). All...
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Perspective: Enabling functional genomics with genome engineering
- Isaac B. Hilton and
- Charles A. Gersbach
Genome Res. October 2015 25: 1442-1455; doi:10.1101/gr.190124.115
...the potential to dramatically improve medicine, agriculture, biotechnology, and our fundamental understanding of living systems. Recent advances have generated extensive annotation of genomic and epigenomic regulatory modules within chromatin (Bernstein et al. 2010; The ENCODE Project Consortium 2012; Roadmap...
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Resource: Upgrading short-read animal genome assemblies to chromosome level using comparative genomics and a universal probe set
- Joana Damas,
- Rebecca O'Connor,
- Marta Farré,
- Vasileios Panagiotis E. Lenis,
- Henry J. Martell,
- Anjali Mandawala,
- Katie Fowler,
- Sunitha Joseph,
- Martin T. Swain,
- Darren K. Griffin,
- and Denis M. Larkin
Genome Res. May 2017 27: 875-884; Published in Advance November 30, 2016, doi:10.1101/gr.213660.116
...-sized scaffolds. Moreover, several hundred are currently being assembled to scaffold level by individual projects or consortia such as Genome10K (Koepfli et al. 2015). Building a mammalian universal BAC set would be a greater challenge than in birds as mammalian s have more repetitive sequences and are about...
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METHODS: Mouse BAC Ends Quality Assessment and Sequence Analyses
- Shaying Zhao,
- Sofiya Shatsman,
- Bola Ayodeji,
- Keita Geer,
- Getahun Tsegaye,
- Margaret Krol,
- Elizabeth Gebregeorgis,
- Alla Shvartsbeyn,
- Daniel Russell,
- Larry Overton,
- Lingxia Jiang,
- George Dimitrov,
- Kevin Tran,
- Jyoti Shetty,
- Joel A. Malek,
- Tamara Feldblyum,
- William C. Nierman,
- and Claire M. Fraser
Genome Res. October 1, 2001 11: 1736-1745; Published in Advance September 20, 2001, doi:10.1101/gr.179201
...will be a valuable resource to the community. Because of the high stability ( Shizuya et al. 1992 ; Kim et al. 1996a , b ), libraries constructed in bacterial artificial chromosome (BAC) vectors have become the standard clone sets in high-throughput genomic sequencing projects of organisms with large s. End...
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Methods: Mapping segmental and sequence variations among laboratory mice using BAC array CGH
- Antoine M. Snijders,
- Norma J. Nowak,
- Bing Huey,
- Jane Fridlyand,
- Sindy Law,
- Jeffrey Conroy,
- Taku Tokuyasu,
- Kubilay Demir,
- Readman Chiu,
- Jian-Hua Mao,
- Ajay N. Jain,
- Steven J.M. Jones,
- Allan Balmain,
- Daniel Pinkel,
- and Donna G. Albertson
Genome Res. February 2005 15: 302-311; doi:10.1101/gr.2902505
...from the mouse sequencing program as the sequencing and radiation hybrid mapping projects progressed. Given the available resources at the time we assembled the array, this procedure resulted in redundant clones and a nonrandom distribution of BACs among the different chromosomes. In the assembly...
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Resource: Efficient de novo assembly of highly heterozygous genomes from whole-genome shotgun short reads
- Rei Kajitani,
- Kouta Toshimoto,
- Hideki Noguchi,
- Atsushi Toyoda,
- Yoshitoshi Ogura,
- Miki Okuno,
- Mitsuru Yabana,
- Masayuki Harada,
- Eiji Nagayasu,
- Haruhiko Maruyama,
- Yuji Kohara,
- Asao Fujiyama,
- Tetsuya Hayashi,
- and Takehiko Itoh
Genome Res. August 2014 24: 1384-1395; Published in Advance April 22, 2014, doi:10.1101/gr.170720.113
...by the other assemblers. Real data from the highly heterozygous and repetitive oyster We input whole- shotgun data sequenced in the Oyster Genome Project into the assemblers. The heterozygosity of the oyster was estimated to be 0.923% by mapping pairedends to eight BACs a total of 1,081,613 bp in length...
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