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29 results on '"Ng, Bee Ling"'

1. A chromosome-level genome assembly of the Hispid cotton rat (Sigmodon hispidus), a model for human pathogenic virus infections

Author

Lilue, Jingtao, primary, Corvelo, André, additional, Gómez-Garrido, Jèssica, additional, Yang, Fengtang, additional, Akagi, Keiko, additional, Green, Gia, additional, Ng, Bee Ling, additional, Fu, Beiyuan, additional, Chorostecki, Uciel Pablo, additional, Warner, Sarah, additional, Marcet-Houben, Marina, additional, Keane, Thomas, additional, Mullikin, James C., additional, Alioto, Tyler, additional, Gabaldón, Toni, additional, Hubert, Benjamin, additional, Symer, David E., additional, and Niewiesk, Stefan, additional

Published
2024
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10. Hi‐C scaffolded short‐ and long‐read genome assemblies of the California sea lion are broadly consistent for syntenic inference across 45 million years of evolution

Author

Peart, Claire R., primary, Williams, Christina, additional, Pophaly, Saurabh D., additional, Neely, Benjamin A., additional, Gulland, Frances M. D., additional, Adams, David J., additional, Ng, Bee Ling, additional, Cheng, William, additional, Goebel, Michael E., additional, Fedrigo, Olivier, additional, Haase, Bettina, additional, Mountcastle, Jacquelyn, additional, Fungtammasan, Arkarachai, additional, Formenti, Giulio, additional, Collins, Joanna, additional, Wood, Jonathan, additional, Sims, Ying, additional, Torrance, James, additional, Tracey, Alan, additional, Howe, Kerstin, additional, Rhie, Arang, additional, Hoffman, Joseph I., additional, Johnson, Jeremy, additional, Jarvis, Erich D., additional, Breen, Matthew, additional, and Wolf, Jochen B. W., additional

Published
2021
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11. Hi‐C scaffolded short‐ and long‐read genome assemblies of the California sea lion are broadly consistent for syntenic inference across 45 million years of evolution

Author

Peart, Claire R., Williams, Christina, Pophaly, Saurabh D., Neely, Benjamin A., Gulland, Frances M.D., Adams, David J., Ng, Bee Ling, Cheng, William, Goebel, Michael E., Fedrigo, Olivier, Haase, Bettina, Mountcastle, Jacquelyn, Fungtammasan, Arkarachai, Formenti, Giulio, Collins, Joanna, Wood, Jonathan, Sims, Ying, Torrance, James, Tracey, Alan, Howe, Kerstin, Rhie, Arang, Hoffman, Joseph I., Johnson, Jeremy, Jarvis, Erich D., Breen, Matthew, Wolf, Jochen B.W., Peart, Claire R., Williams, Christina, Pophaly, Saurabh D., Neely, Benjamin A., Gulland, Frances M.D., Adams, David J., Ng, Bee Ling, Cheng, William, Goebel, Michael E., Fedrigo, Olivier, Haase, Bettina, Mountcastle, Jacquelyn, Fungtammasan, Arkarachai, Formenti, Giulio, Collins, Joanna, Wood, Jonathan, Sims, Ying, Torrance, James, Tracey, Alan, Howe, Kerstin, Rhie, Arang, Hoffman, Joseph I., Johnson, Jeremy, Jarvis, Erich D., Breen, Matthew, and Wolf, Jochen B.W.

Abstract

With the advent of chromatin-interaction maps, chromosome-level genome assemblies have become a reality for a wide range of organisms. Scaffolding quality is, however, difficult to judge. To explore this gap, we generated multiple chromosome-scale genome assemblies of an emerging wild animal model for carcinogenesis, the California sea lion (Zalophus californianus). Short-read assemblies were scaffolded with two independent chromatin interaction mapping data (Hi-C and Chicago), and long-read assemblies with three data types (Hi-C, optical maps, and 10X linked reads) following the ‘Vertebrate Genomes Project (VGP)’ pipeline. In both approaches, 18 major scaffolds recovered the karyotype (2n=36), with scaffold N50s of 138 Mb and 147 Mb, respectively. Synteny relationships at the chromosome-level with other pinniped genomes (2n=32-36), ferret (2n=34), red panda (2n=36) and domestic dog (2n=78) were consistent across approaches and recovered known fissions and fusions. Comparative chromosome painting and multicolor chromosome tiling with a panel of 264 genome-integrated single-locus canine bacterial artificial chromosome (BAC) probes provided independent evaluation of genome organization. Broad-scale discrepancies between the approaches were observed within chromosomes, most commonly in translocations centered around centromeres and telomeres, which were better resolved in the VGP assembly. Genomic and cytological approaches agreed on near-perfect synteny of the X chromosome, and in combination allowed detailed investigation of autosomal rearrangements between dog and sea lion. This study presents high-quality genomes of an emerging cancer model and highlights that even highly fragmented short-read assemblies scaffolded with Hi-C can yield reliable chromosome level scaffolds suitable for comparative genomic analyses.

Published
2021

14. Characterizing Mutational Signatures in Human Cancer Cell Lines Reveals Episodic APOBEC Mutagenesis

Author

Universidade de Santiago de Compostela. Centro de Investigación en Medicina Molecular e Enfermidades Crónicas, Universidade de Santiago de Compostela. Departamento de Zooloxía, Xenética e Antropoloxía Física, Petljak, Mia, Alexandrov, Ludmil B., Brammeld, Jonathan S., Price, Stacey, Wedge, David C., Grossmann, Sebastian, Dawson, Kevin J., Ju, Young Seok, Ioro, Francesco, Castro Tubío, José Manuel, Koh, Ching Chiek, Georgakopoulos Soares, Ilias, Rodríguez Martín, Bernardo, Otlu, Burçak, O'Meara, Sarah, Butler, Adam P., Menzies, Andrew, Bhosle, Shriram G., Raine, Keiran, Jones, David R., Teague, Jon W., Beal, Kathryn, Latimer, Calli, O'Neill, Laura, Zamora Berna, Jorge Aurelio, Anderson, Elizabeth, Patel, Nikita, Maddison, Mark, Ng, Bee Ling, Graham, Jennifer, Garnett, Mathew J., McDermott, Ultan, Nik Zainal, Serena, Campbell, Peter J., Stratton, Michael R., Universidade de Santiago de Compostela. Centro de Investigación en Medicina Molecular e Enfermidades Crónicas, Universidade de Santiago de Compostela. Departamento de Zooloxía, Xenética e Antropoloxía Física, Petljak, Mia, Alexandrov, Ludmil B., Brammeld, Jonathan S., Price, Stacey, Wedge, David C., Grossmann, Sebastian, Dawson, Kevin J., Ju, Young Seok, Ioro, Francesco, Castro Tubío, José Manuel, Koh, Ching Chiek, Georgakopoulos Soares, Ilias, Rodríguez Martín, Bernardo, Otlu, Burçak, O'Meara, Sarah, Butler, Adam P., Menzies, Andrew, Bhosle, Shriram G., Raine, Keiran, Jones, David R., Teague, Jon W., Beal, Kathryn, Latimer, Calli, O'Neill, Laura, Zamora Berna, Jorge Aurelio, Anderson, Elizabeth, Patel, Nikita, Maddison, Mark, Ng, Bee Ling, Graham, Jennifer, Garnett, Mathew J., McDermott, Ultan, Nik Zainal, Serena, Campbell, Peter J., and Stratton, Michael R.

Abstract

Multiple signatures of somatic mutations have beenidentified in cancer genomes. Exome sequences of1,001 human cancer cell lines and 577 xenograftsrevealed most common mutational signatures,indicating past activity of the underlying processes,usually in appropriate cancer types. To investigateongoing patterns of mutational-signature genera-tion, cell lines were cultured for extended periodsand subsequently DNA sequenced. Signatures ofdiscontinued exposures, including tobacco smokeand ultraviolet light, were not generatedin vitro. Sig-natures of normal and defective DNA repair and repli-cation continued to be generated at roughly stablemutation rates. Signatures of APOBEC cytidinedeaminase DNA-editing exhibited substantial fluctu-ations in mutation rate over time with episodic burstsof mutations. The initiating factors for the burstsare unclear, although retrotransposon mobilizationmay contribute. The examined cell lines constitutea resource of live experimental models of mutationalprocesses, which potentially retain patterns ofactivity and regulation operative in primary humancancers

Published
2019

15. Single-cell atlas of the first intra-mammalian developmental stage of the human parasite Schistosoma mansoni

Author

Diaz Soria, Carmen Lidia, primary, Lee, Jayhun, additional, Chong, Tracy, additional, Coghlan, Avril, additional, Tracey, Alan, additional, Young, Matthew D, additional, Andrews, Tallulah, additional, Hall, Christopher, additional, Ng, Bee Ling, additional, Rawlinson, Kate, additional, Doyle, Stephen R., additional, Leonard, Steven, additional, Lu, Zhigang, additional, Bennett, Hayley M, additional, Rinaldi, Gabriel, additional, Newmark, Phillip A., additional, and Berriman, Matthew, additional

Published
2019
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17. Characterizing Mutational Signatures in Human Cancer Cell Lines Reveals Episodic APOBEC Mutagenesis

Author

Petljak, Mia, primary, Alexandrov, Ludmil B., additional, Brammeld, Jonathan S., additional, Price, Stacey, additional, Wedge, David C., additional, Grossmann, Sebastian, additional, Dawson, Kevin J., additional, Ju, Young Seok, additional, Iorio, Francesco, additional, Tubio, Jose M.C., additional, Koh, Ching Chiek, additional, Georgakopoulos-Soares, Ilias, additional, Rodríguez–Martín, Bernardo, additional, Otlu, Burçak, additional, O’Meara, Sarah, additional, Butler, Adam P., additional, Menzies, Andrew, additional, Bhosle, Shriram G., additional, Raine, Keiran, additional, Jones, David R., additional, Teague, Jon W., additional, Beal, Kathryn, additional, Latimer, Calli, additional, O’Neill, Laura, additional, Zamora, Jorge, additional, Anderson, Elizabeth, additional, Patel, Nikita, additional, Maddison, Mark, additional, Ng, Bee Ling, additional, Graham, Jennifer, additional, Garnett, Mathew J., additional, McDermott, Ultan, additional, Nik-Zainal, Serena, additional, Campbell, Peter J., additional, and Stratton, Michael R., additional

Published
2019
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22. The pig X and Y Chromosomes: structure, sequence, and evolution.

Author

Skinner, Benjamin M, Sargent, Carole A, Churcher, Carol, Hunt, Toby, Herrero, Javier, Loveland, Jane E, Dunn, Matt, Louzada, Sandra, Fu, Beiyuan, Chow, William, Gilbert, James, Austin-Guest, Siobhan, Beal, Kathryn, Carvalho-Silva, Denise, Cheng, William, Gordon, Daria, Grafham, Darren, Hardy, Matt, Harley, Jo, Hauser, Heidi, Howden, Philip, Howe, Kerstin, Lachani, Kim, Ellis, Peter J.I., Kelly, Daniel, Kerry, Giselle, Kerwin, James, Ng, Bee Ling, Threadgold, Glen, Wileman, Thomas, Wood, Jonathan M D, Yang, Fengtang, Harrow, Jen, Affara, Nabeel A, Tyler-Smith, Chris, Skinner, Benjamin M, Sargent, Carole A, Churcher, Carol, Hunt, Toby, Herrero, Javier, Loveland, Jane E, Dunn, Matt, Louzada, Sandra, Fu, Beiyuan, Chow, William, Gilbert, James, Austin-Guest, Siobhan, Beal, Kathryn, Carvalho-Silva, Denise, Cheng, William, Gordon, Daria, Grafham, Darren, Hardy, Matt, Harley, Jo, Hauser, Heidi, Howden, Philip, Howe, Kerstin, Lachani, Kim, Ellis, Peter J.I., Kelly, Daniel, Kerry, Giselle, Kerwin, James, Ng, Bee Ling, Threadgold, Glen, Wileman, Thomas, Wood, Jonathan M D, Yang, Fengtang, Harrow, Jen, Affara, Nabeel A, and Tyler-Smith, Chris

Abstract

We have generated an improved assembly and gene annotation of the pig X Chromosome, and a first draft assembly of the pig Y Chromosome, by sequencing BAC and fosmid clones from Duroc animals and incorporating information from optical mapping and fiber-FISH. The X Chromosome carries 1033 annotated genes, 690 of which are protein coding. Gene order closely matches that found in primates (including humans) and carnivores (including cats and dogs), which is inferred to be ancestral. Nevertheless, several protein-coding genes present on the human X Chromosome were absent from the pig, and 38 pig-specific X-chromosomal genes were annotated, 22 of which were olfactory receptors. The pig Y-specific Chromosome sequence generated here comprises 30 megabases (Mb). A 15-Mb subset of this sequence was assembled, revealing two clusters of male-specific low copy number genes, separated by an ampliconic region including the HSFY gene family, which together make up most of the short arm. Both clusters contain palindromes with high sequence identity, presumably maintained by gene conversion. Many of the ancestral X-related genes previously reported in at least one mammalian Y Chromosome are represented either as active genes or partial sequences. This sequencing project has allowed us to identify genes--both single copy and amplified--on the pig Y Chromosome, to compare the pig X and Y Chromosomes for homologous sequences, and thereby to reveal mechanisms underlying pig X and Y Chromosome evolution.

Published
2015

23. The pig X and Y Chromosomes: structure, sequence, and evolution

Author

Skinner, Benjamin M., primary, Sargent, Carole A., additional, Churcher, Carol, additional, Hunt, Toby, additional, Herrero, Javier, additional, Loveland, Jane E., additional, Dunn, Matt, additional, Louzada, Sandra, additional, Fu, Beiyuan, additional, Chow, William, additional, Gilbert, James, additional, Austin-Guest, Siobhan, additional, Beal, Kathryn, additional, Carvalho-Silva, Denise, additional, Cheng, William, additional, Gordon, Daria, additional, Grafham, Darren, additional, Hardy, Matt, additional, Harley, Jo, additional, Hauser, Heidi, additional, Howden, Philip, additional, Howe, Kerstin, additional, Lachani, Kim, additional, Ellis, Peter J.I., additional, Kelly, Daniel, additional, Kerry, Giselle, additional, Kerwin, James, additional, Ng, Bee Ling, additional, Threadgold, Glen, additional, Wileman, Thomas, additional, Wood, Jonathan M.D., additional, Yang, Fengtang, additional, Harrow, Jen, additional, Affara, Nabeel A., additional, and Tyler-Smith, Chris, additional

Published
2015
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24. Identification of disrupted AUTS2 and EPHA6 genes by array painting in a patient carrying a de novo balanced translocation t(3;7) with intellectual disability and neurodevelopment disorder

Author

Schneider, Anouck, primary, Puechberty, Jacques, additional, Ng, Bee Ling, additional, Coubes, Christine, additional, Gatinois, Vincent, additional, Tournaire, Magali, additional, Girard, Manon, additional, Dumont, Bruno, additional, Bouret, Pauline, additional, Magnetto, Julia, additional, Baghdadli, Amaria, additional, Pellestor, Franck, additional, and Geneviève, David, additional

Published
2015
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26. The pig X and Y chromosomes: structure, sequence and evolution

Author

Skinner, Benjamin M, primary, Sargent, Carole A, additional, Churcher, Carol, additional, Hunt, Toby, additional, Herrero, Javier, additional, Loveland, Jane, additional, Dunn, Matt, additional, Louzada, Sandra, additional, Fu, Beiyuan, additional, Chow, William, additional, Gilbert, James, additional, Austin-Guest, Siobhan, additional, Beal, Kathryn, additional, Carvalho-Silva, Denise, additional, Cheng, William, additional, Gordon, Daria, additional, Grafham, Darren, additional, Hardy, Matt, additional, Harley, Jo, additional, Hauser, Heidi, additional, Howden, Philip, additional, Howe, Kerstin, additional, Lachani, Kim, additional, Ellis, Peter JI, additional, Kelly, Daniel, additional, Kerry, Giselle, additional, Kerwin, James, additional, Ng, Bee Ling, additional, Threadgold, Glen, additional, Wileman, Thomas, additional, Wood, Jonathan MD, additional, Yang, Fengtang, additional, Harrow, Jen, additional, Affara, Nabeel A, additional, and Tyler-Smith, Chris, additional

Published
2014
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27. The pig X and Y Chromosomes: structure, sequence, and evolution

Author

Skinner, Benjamin M., Sargent, Carole A., Churcher, Carol, Hunt, Toby, Herrero, Javier, Loveland, Jane E., Dunn, Matt, Louzada, Sandra, Fu, Beiyuan, Chow, William, Gilbert, James, Austin-Guest, Siobhan, Beal, Kathryn, Carvalho-Silva, Denise, Cheng, William, Gordon, Daria, Grafham, Darren, Hardy, Matt, Harley, Jo, Hauser, Heidi, Howden, Philip, Howe, Kerstin, Lachani, Kim, Ellis, Peter J.I., Kelly, Daniel, Kerry, Giselle, Kerwin, James, Ng, Bee Ling, Threadgold, Glen, Wileman, Thomas, Wood, Jonathan M.D., Yang, Fengtang, Harrow, Jen, Affara, Nabeel A., and Tyler-Smith, Chris

Abstract

We have generated an improved assembly and gene annotation of the pig X Chromosome, and a first draft assembly of the pig Y Chromosome, by sequencing BAC and fosmid clones from Duroc animals and incorporating information from optical mapping and fiber-FISH. The X Chromosome carries 1033 annotated genes, 690 of which are protein coding. Gene order closely matches that found in primates (including humans) and carnivores (including cats and dogs), which is inferred to be ancestral. Nevertheless, several protein-coding genes present on the human X Chromosome were absent from the pig, and 38 pig-specific X-chromosomal genes were annotated, 22 of which were olfactory receptors. The pig Y-specific Chromosome sequence generated here comprises 30 megabases (Mb). A 15-Mb subset of this sequence was assembled, revealing two clusters of male-specific low copy number genes, separated by an ampliconic region including the HSFYgene family, which together make up most of the short arm. Both clusters contain palindromes with high sequence identity, presumably maintained by gene conversion. Many of the ancestral X-related genes previously reported in at least one mammalian Y Chromosome are represented either as active genes or partial sequences. This sequencing project has allowed us to identify genes—both single copy and amplified—on the pig Y Chromosome, to compare the pig X and Y Chromosomes for homologous sequences, and thereby to reveal mechanisms underlying pig X and Y Chromosome evolution.

Published
2016
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28. A high-throughput in vivomicronucleus assay for genome instability screening in mice

Author

Balmus, Gabriel, Karp, Natasha A, Ng, Bee Ling, Jackson, Stephen P, Adams, David J, and McIntyre, Rebecca E

Abstract

This protocol describes a sensitive, robust, high-throughput method for quantifying the formation of micronuclei in mouse erythrocytes. It detects low levels of genome instability and can be used to identify novel genome maintenance genes and models.

Published
2015
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29. Derivation and maintenance of mouse haploid embryonic stem cells

Author

David J. Adams, Josep V. Forment, Stephen P. Jackson, Bee Ling Ng, Jose R. Vicente, Beiyuan Fu, Josef M. Penninger, Fengtang Yang, Ulrich Elling, Michael Woods, Gabriel Balmus, Brendan Doe, Elling, Ulrich [0000-0002-4514-2809], Yang, Fengtang [0000-0002-3573-2354], Ng, Bee Ling [0000-0002-8338-4390], Balmus, Gabriel [0000-0003-2872-4468], and Apollo - University of Cambridge Repository

Subjects
Cellular differentiation, Cell Culture Techniques, Mutagenesis (molecular biology technique), Mice, Inbred Strains, Cell Separation, Biology, Haploidy, Genome, General Biochemistry, Genetics and Molecular Biology, Article, Cell Line, Workflow, 03 medical and health sciences, Mice, 0302 clinical medicine, Animals, Gene, 030304 developmental biology, 0303 health sciences, fungi, Chromosome, Mouse Embryonic Stem Cells, Embryonic stem cell, Cell biology, Mice, Inbred C57BL, Blastocyst, Female, Ploidy, 030217 neurology & neurosurgery, Genetic screen
Abstract

Ploidy represents the number of chromosome sets in a cell. Although gametes have a haploid genome (n), most mammalian cells have diploid genomes (2n). The diploid status of most cells correlates with the number of probable alleles for each autosomal gene and makes it difficult to target these genes via mutagenesis techniques. Here, we describe a 7-week protocol for the derivation of mouse haploid embryonic stem cells (hESCs) from female gametes that also outlines how to maintain the cells once derived. We detail additional procedures that can be used with cell lines obtained from the mouse Haplobank, a biobank of >100,000 individual mouse hESC lines with targeted mutations in 16,970 genes. hESCs can spontaneously diploidize and can be maintained in both haploid and diploid states. Mouse hESCs are genomically and karyotypically stable, are innately immortal and isogenic, and can be derived in an array of differentiated cell types; they are thus highly amenable to genetic screens and to defining molecular connectivity pathways.

Published
2019

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