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Volumn 4, Issue JUNE 2015, 2015, Pages 1-29

A panel of induced pluripotent stem cells from chimpanzees: A resource for comparative functional genomics

(20)  Romero, Irene Gallego a   Pavlovic, Bryan J a   Hernando Herraez, Irene b   Zhou, Xiang c   Ward, Michelle C a   Banovich, Nicholas E a   Kagan, Courtney L a   Burnett, Jonathan E a   Huang, Constance H a   Mitrano, Amy a   Chavarria, Claudia I a   Ben Nun, Inbar Friedrich d,h   Li, Yingchun e,f   Sabatini, Karen d,e,f   Leonardo, Trevor R d,e,f   Parast, Mana e,f   Marques Bonet, Tomas b,g   Laurent, Louise C e,f   Loring, Jeanne F d   Gilad, Yoav a  


Author keywords

[No Author keywords available]

Indexed keywords

EPSTEIN BARR VIRUS ANTIGEN 1; ORGANIC CATION TRANSPORTER 3; PROTEIN; REX1 PROTEIN; TRANSCRIPTION FACTOR NANOG; TRANSCRIPTION FACTOR SOX2; UNCLASSIFIED DRUG;

EID: 85042249404     PISSN: None     EISSN: 2050084X     Source Type: Journal    
DOI: 10.7554/eLife.07103.001     Document Type: Article
Times cited : (95)

References (91)
  • 1
    • 33745626459 scopus 로고    scopus 로고
    • Improved scoring of functional groups from gene expression data by decorrelating GO graph structure
    • Alexa A, Rahnenführer J, Lengauer T. 2006. Improved scoring of functional groups from gene expression data by decorrelating GO graph structure. Bioinformatics 22:1600-1607. doi: 10.1093/bioinformatics/btl140.
    • (2006) Bioinformatics , vol.22 , pp. 1600-1607
    • Alexa, A.1    Rahnenführer, J.2    Lengauer, T.3
  • 4
    • 0001677717 scopus 로고
    • Controlling the false discovery rate: A practical and powerful approach to Multiple Testing
    • Benjamini Y, Hochberg Y. 1995. Controlling the false discovery rate: a practical and powerful approach to Multiple Testing. Journal of the Royal Statistical Society B 57:289-300.
    • (1995) Journal of the Royal Statistical Society B , vol.57 , pp. 289-300
    • Benjamini, Y.1    Hochberg, Y.2
  • 6
    • 85042579925 scopus 로고    scopus 로고
    • A database of orthologous exons in primates for comparative analysis of RNA-seq data
    • Blekhman R. 2012. A database of orthologous exons in primates for comparative analysis of RNA-seq data. Nature Precedings.
    • (2012) Nature Precedings
    • Blekhman, R.1
  • 7
    • 75649102520 scopus 로고    scopus 로고
    • Sex-specific and lineage-specific alternative splicing in primates
    • Blekhman R, Marioni JC, Zumbo P, Stephens M, Gilad Y. 2010. Sex-specific and lineage-specific alternative splicing in primates. Genome Research 20:180-189. doi: 10.1101/gr.099226.109.
    • (2010) Genome Research , vol.20 , pp. 180-189
    • Blekhman, R.1    Marioni, J.C.2    Zumbo, P.3    Stephens, M.4    Gilad, Y.5
  • 8
    • 57149084867 scopus 로고    scopus 로고
    • Gene regulation in primates evolves under tissuespecific selection pressures
    • Blekhman R, Oshlack A, Chabot AE, Smyth GK, Gilad Y. 2008. Gene regulation in primates evolves under tissuespecific selection pressures. PLOS Genetics 4:e1000271. doi: 10.1371/journal.pgen.1000271.
    • (2008) PLOS Genetics , vol.4
    • Blekhman, R.1    Oshlack, A.2    Chabot, A.E.3    Smyth, G.K.4    Gilad, Y.5
  • 11
    • 0015070886 scopus 로고
    • Repetitive and non-repetitive DNA sequences and a specualation on the origins of evolutionary novelty
    • Britten RJ, Davidson EH. 1971. Repetitive and non-repetitive DNA sequences and a specualation on the origins of evolutionary novelty. The Quarterly Review of Biology 46:111-138. doi: 10.1086/406830.
    • (1971) The Quarterly Review of Biology , vol.46 , pp. 111-138
    • Britten, R.J.1    Davidson, E.H.2
  • 14
    • 79955403252 scopus 로고    scopus 로고
    • Gene expression differences among primates are associated with changes in a histone epigenetic modification
    • Cain CE, Blekhman R, Marioni JC, Gilad Y. 2011. Gene expression differences among primates are associated with changes in a histone epigenetic modification. Genetics 187:1225-1234. doi: 10.1534/genetics.110.126177.
    • (2011) Genetics , vol.187 , pp. 1225-1234
    • Cain, C.E.1    Blekhman, R.2    Marioni, J.C.3    Gilad, Y.4
  • 15
    • 22744439568 scopus 로고    scopus 로고
    • Evolution at two levels: On genes and form
    • Carroll SB. 2005. Evolution at two levels: on genes and form. PLOS Biology 3:e245. doi: 10.1371/journal.pbio.0030245.
    • (2005) PLOS Biology , vol.3
    • Carroll, S.B.1
  • 16
    • 46149104377 scopus 로고    scopus 로고
    • Evo-devo and an expanding evolutionary synthesis: A genetic theory of morphological evolution
    • Carroll SB. 2008. Evo-devo and an expanding evolutionary synthesis: a genetic theory of morphological evolution. Cell 134:25-36. doi: 10.1016/j.cell.2008.06.030.
    • (2008) Cell , vol.134 , pp. 25-36
    • Carroll, S.B.1
  • 17
    • 77957916358 scopus 로고    scopus 로고
    • Reprogramming huntington monkey skin cells into pluripotent stem cells
    • Chan AWS, Cheng PH, Neumann A, Yang JJ. 2010. Reprogramming huntington monkey skin cells into pluripotent stem cells. Cellular Reprogramming 12:509-517. doi: 10.1089/cell.2010.0019.
    • (2010) Cellular Reprogramming , vol.12 , pp. 509-517
    • Chan, A.1    Cheng, P.H.2    Neumann, A.3    Yang, J.J.4
  • 21
    • 79952900560 scopus 로고    scopus 로고
    • Turning straw into gold: Directing cell fate for regenerative medicine. Nature Reviews
    • Cohen DE, Melton D. 2011. Turning straw into gold: directing cell fate for regenerative medicine. Nature Reviews. Genetics 12:243-252. doi: 10.1038/nrg2938.
    • (2011) Genetics , vol.12 , pp. 243-252
    • Cohen, D.E.1    Melton, D.2
  • 23
    • 79960083404 scopus 로고    scopus 로고
    • Development of histocompatible primate-induced pluripotent stem cells for neural transplantation
    • Deleidi M, Hargus G, Hallett P, Osborn T, Isacson O. 2011. Development of histocompatible primate-induced pluripotent stem cells for neural transplantation. Stem cells 29:1052-1063. doi: 10.1002/stem.662.
    • (2011) Stem Cells , vol.29 , pp. 1052-1063
    • Deleidi, M.1    Hargus, G.2    Hallett, P.3    Osborn, T.4    Isacson, O.5
  • 24
    • 46249088370 scopus 로고    scopus 로고
    • Lumi: A pipeline for processing Illumina microarray
    • Du P, Kibbe WA, Lin SM. 2008. Lumi: a pipeline for processing Illumina microarray. Bioinformatics 24:1547-1548. doi: 10.1093/bioinformatics/btn224.
    • (2008) Bioinformatics , vol.24 , pp. 1547-1548
    • Du, P.1    Kibbe, W.A.2    Lin, S.M.3
  • 25
    • 3042666256 scopus 로고    scopus 로고
    • MUSCLE: Multiple sequence alignment with high accuracy and high throughput
    • Edgar RC. 2004. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Research 32:1792-1797. doi: 10.1093/nar/gkh340.
    • (2004) Nucleic Acids Research , vol.32 , pp. 1792-1797
    • Edgar, R.C.1
  • 28
    • 84863885448 scopus 로고    scopus 로고
    • Comparative studies of gene expression and the evolution of gene regulation
    • Gallego Romero I, Ruvinsky I, Gilad Y. 2012. Comparative studies of gene expression and the evolution of gene regulation. Nature Reviews Genetics 13:505-516. doi: 10.1038/nrg3229.
    • (2012) Nature Reviews Genetics , vol.13 , pp. 505-516
    • Gallego Romero, I.1    Ruvinsky, I.2    Gilad, Y.3
  • 30
    • 19844365733 scopus 로고    scopus 로고
    • Multi-species microarrays reveal the effect of sequence divergence on gene expression profiles
    • Gilad Y, Rifkin Sa, Bertone P, Gerstein M, White KP. 2005. Multi-species microarrays reveal the effect of sequence divergence on gene expression profiles. Genome Research 15:674-680. doi: 10.1101/gr.3335705.
    • (2005) Genome Research , vol.15 , pp. 674-680
    • Gilad, Y.1    Sa, R.2    Bertone, P.3    Gerstein, M.4    White, K.P.5
  • 33
    • 33750598248 scopus 로고    scopus 로고
    • Chromatin-binding regions of EBNA1 protein facilitate the enhanced transfection of Epstein-Barr virus-based vectors
    • Howden SE, Wardan H, Voullaire L, McLenachan S, Williamson R, Ioannou P, Vadolas J. 2006. Chromatin-binding regions of EBNA1 protein facilitate the enhanced transfection of Epstein-Barr virus-based vectors. Human Gene Therapy 17:833-844. doi: 10.1089/hum.2006.17.833.
    • (2006) Human Gene Therapy , vol.17 , pp. 833-844
    • Howden, S.E.1    Wardan, H.2    Voullaire, L.3    McLenachan, S.4    Williamson, R.5    Ioannou, P.6    Vadolas, J.7
  • 35
    • 0017771466 scopus 로고
    • Evolution and tinkering
    • Jacob F. 1977. Evolution and tinkering. Science 196:1161-1166. doi: 10.1126/science.860134.
    • (1977) Science , vol.196 , pp. 1161-1166
    • Jacob, F.1
  • 36
    • 39149130361 scopus 로고    scopus 로고
    • Stem cells, the molecular circuitry of pluripotency and nuclear reprogramming
    • Jaenisch R, Young R. 2008. Stem cells, the molecular circuitry of pluripotency and nuclear reprogramming. Cell 132:567-582. doi: 10.1016/j.cell.2008.01.015.
    • (2008) Cell , vol.132 , pp. 567-582
    • Jaenisch, R.1    Young, R.2
  • 37
    • 0016669094 scopus 로고
    • Evolution at two levels in humans and chimpanzees
    • King MC, Wilson A. 1975. Evolution at two levels in humans and chimpanzees. Science 188:107-116. doi: 10.1126/science.1090005.
    • (1975) Science , vol.188 , pp. 107-116
    • King, M.C.1    Wilson, A.2
  • 39
    • 84896735766 scopus 로고    scopus 로고
    • Voom: Precision weights unlock linear model analysis tools for RNA-seq read counts
    • Law CW, Chen Y, Shi W, Smyth GK. 2014. Voom: precision weights unlock linear model analysis tools for RNA-seq read counts. Genome Biology 15:R29. doi: 10.1186/gb-2014-15-2-r29.
    • (2014) Genome Biology , vol.15
    • Law, C.W.1    Chen, Y.2    Shi, W.3    Smyth, G.K.4
  • 40
    • 67649884743 scopus 로고    scopus 로고
    • Fast and accurate short read alignment with Burrows-Wheeler transform
    • Li H, Durbin R. 2009. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25: 1754-1760. doi: 10.1093/bioinformatics/btp324.
    • (2009) Bioinformatics , vol.25 , pp. 1754-1760
    • Li, H.1    Durbin, R.2
  • 42
    • 84872016692 scopus 로고    scopus 로고
    • Directed cardiomyocyte differentiation from human pluripotent stem cells by modulating Wnt/β-catenin signaling under fully defined conditions
    • Lian X, Zhang J, Azarin SM, Zhu K, Hazeltine LB, Bao X, Hsiao C, Kamp TJ, Palecek SP. 2013. Directed cardiomyocyte differentiation from human pluripotent stem cells by modulating Wnt/β-catenin signaling under fully defined conditions. Nature Protocols 8:162-175. doi: 10.1038/nprot.2012.150.
    • (2013) Nature Protocols , vol.8 , pp. 162-175
    • Lian, X.1    Zhang, J.2    Azarin, S.M.3    Zhu, K.4    Hazeltine, L.B.5    Bao, X.6    Hsiao, C.7    Kamp, T.J.8    Palecek, S.P.9
  • 43
    • 84897397058 scopus 로고    scopus 로고
    • FeatureCounts: An efficient general purpose program for assigning sequence reads to genomic features
    • Liao Y, Smyth GK, Shi W. 2013. featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. Bioinformatics 30:923-930. doi: 10.1093/bioinformatics/btt656.
    • (2013) Bioinformatics , vol.30 , pp. 923-930
    • Liao, Y.1    Smyth, G.K.2    Shi, W.3
  • 46
    • 84882245890 scopus 로고    scopus 로고
    • Genetic and epigenetic stability of human pluripotent stem cells. Nature Reviews
    • Lund RJ, Närvä E, Lahesmaa R. 2012. Genetic and epigenetic stability of human pluripotent stem cells. Nature Reviews. Genetics 13:732-744. doi: 10.1038/nrg3271.
    • (2012) Genetics , vol.13 , pp. 732-744
    • Lund, R.J.1    Närvä, E.2    Lahesmaa, R.3
  • 48
    • 84901460449 scopus 로고    scopus 로고
    • Proposing a model for studying primate development using induced pluripotent stem cells
    • Gage FH, Christen Y, editors, Berlin, Heidelberg: Springer Berlin Heidelberg
    • Marchetto MC, Muotri AR, Gage FH. 2013a. Proposing a model for studying primate development using induced pluripotent stem cells. In: Gage FH, Christen Y, editors. Programmed cells from basic neuroscience to therapy. Berlin, Heidelberg: Springer Berlin Heidelberg. p. 31-39.
    • (2013) Programmed Cells from Basic Neuroscience to Therapy , pp. 31-39
    • Marchetto, M.C.1    Muotri, A.R.2    Gage, F.H.3
  • 52
    • 45849151146 scopus 로고    scopus 로고
    • Protocols for cytogenetic studies of human embryonic stem cells
    • Meisner LF, Johnson JA. 2008. Protocols for cytogenetic studies of human embryonic stem cells. Methods 45: 133-141. doi: 10.1016/j.ymeth.2008.03.005.
    • (2008) Methods , vol.45 , pp. 133-141
    • Meisner, L.F.1    Johnson, J.A.2
  • 53
    • 84878852415 scopus 로고    scopus 로고
    • Modeling human disease with pluripotent stem cells: From genome association to function
    • Merkle FT, Eggan K. 2013. Modeling human disease with pluripotent stem cells: from genome association to function. Cell Stem Cell 12:656-668. doi: 10.1016/j.stem.2013.05.016.
    • (2013) Cell Stem Cell , vol.12 , pp. 656-668
    • Merkle, F.T.1    Eggan, K.2
  • 57
    • 79955615662 scopus 로고    scopus 로고
    • The transcriptional and signalling networks of pluripotency
    • Ng HH, Surani MA. 2011. The transcriptional and signalling networks of pluripotency. Nature Cell Biology 13: 490-496. doi: 10.1038/ncb0511-490.
    • (2011) Nature Cell Biology , vol.13 , pp. 490-496
    • Ng, H.H.1    Surani, M.A.2
  • 58
    • 84855387733 scopus 로고    scopus 로고
    • Induction of retinal pigment epithelial cells from monkey iPS cells
    • Okamoto S, Takahashi M. 2011. Induction of retinal pigment epithelial cells from monkey iPS cells. Investigative Ophthalmology & Visual Science 52:8785-8790. doi: 10.1167/iovs.11-8129.
    • (2011) Investigative Ophthalmology & Visual Science , vol.52 , pp. 8785-8790
    • Okamoto, S.1    Takahashi, M.2
  • 60
    • 79958252915 scopus 로고    scopus 로고
    • Chromatin connections to pluripotency and cellular reprogramming
    • Orkin SH, Hochedlinger K. 2011. Chromatin connections to pluripotency and cellular reprogramming. Cell 145: 835-850. doi: 10.1016/j.cell.2011.05.019.
    • (2011) Cell , vol.145 , pp. 835-850
    • Orkin, S.H.1    Hochedlinger, K.2
  • 62
    • 1042304216 scopus 로고    scopus 로고
    • APE: Analyses of phylogenetics and evolution in R language
    • Paradis E, Claude J, Strimmer K. 2004. APE: analyses of phylogenetics and evolution in R language. Bioinformatics 20:289-290. doi: 10.1093/bioinformatics/btg412.
    • (2004) Bioinformatics , vol.20 , pp. 289-290
    • Paradis, E.1    Claude, J.2    Strimmer, K.3
  • 66
    • 84868484735 scopus 로고    scopus 로고
    • Epigenomic annotation of enhancers predicts transcriptional regulators of human neural crest
    • Rada-Iglesias A, Bajpai R, Prescott S, Brugmann Sa, Swigut T, Wysocka J. 2012. Epigenomic annotation of enhancers predicts transcriptional regulators of human neural crest. Cell Stem Cell 11:633-648. doi: 10.1016/j.stem.2012.07.006.
    • (2012) Cell Stem Cell , vol.11 , pp. 633-648
    • Rada-Iglesias, A.1    Bajpai, R.2    Prescott, S.3    Sa, B.4    Swigut, T.5    Wysocka, J.6
  • 67
    • 84867772337 scopus 로고    scopus 로고
    • Characterization of human-induced pluripotent stem cell-derived cardiomyocytes: Bioenergetics and utilization in safety screening
    • Rana P, Anson B, Engle S, Will Y. 2012. Characterization of human-induced pluripotent stem cell-derived cardiomyocytes: bioenergetics and utilization in safety screening. Toxicological Sciences 130:117-131. doi: 10.1093/toxsci/kfs233.
    • (2012) Toxicological Sciences , vol.130 , pp. 117-131
    • Rana, P.1    Anson, B.2    Engle, S.3    Will, Y.4
  • 71
    • 67649834440 scopus 로고    scopus 로고
    • ChIP-seq: Using high-throughput sequencing to discover protein-DNA interactions
    • Schmidt D, Wilson MD, Spyrou C, Brown GD, Hadfield J, Odom DT. 2009. ChIP-seq: using high-throughput sequencing to discover protein-DNA interactions. Methods 48:240-248. doi: 10.1016/j.ymeth.2009.03.001.
    • (2009) Methods , vol.48 , pp. 240-248
    • Schmidt, D.1    Wilson, M.D.2    Spyrou, C.3    Brown, G.D.4    Hadfield, J.5    Odom, D.T.6
  • 72
    • 67650841125 scopus 로고    scopus 로고
    • Analysis of Rex1 (Zfp42) function in embryonic stem cell differentiation
    • Scotland KB, Chen S, Sylvester R, Gudas LJ. 2009. Analysis of Rex1 (zfp42) function in embryonic stem cell differentiation. Developmental Dynamics 238:1863-1877. doi: 10.1002/dvdy.22037.
    • (2009) Developmental Dynamics , vol.238 , pp. 1863-1877
    • Scotland, K.B.1    Chen, S.2    Sylvester, R.3    Gudas, L.J.4
  • 73
    • 4544341015 scopus 로고    scopus 로고
    • Linear models and empirical bayes methods for assessing differential expression in microarray experiments
    • Smyth GK. 2004. Linear models and empirical bayes methods for assessing differential expression in microarray experiments. Statistical Applications in Genetics and Molecular Biology 3:Article3. doi: 10.2202/1544-6115.1027.
    • (2004) Statistical Applications in Genetics and Molecular Biology , vol.3
    • Smyth, G.K.1
  • 75
    • 84887987260 scopus 로고    scopus 로고
    • Unveiling the critical role of REX1 in the regulation of human stem cell pluripotency
    • Son MY, Choi H, Han YM, Cho YS. 2013. Unveiling the critical role of REX1 in the regulation of human stem cell pluripotency. Stem Cells 31:2374-2387. doi: 10.1002/stem.1509.
    • (2013) Stem Cells , vol.31 , pp. 2374-2387
    • Son, M.Y.1    Choi, H.2    Han, Y.M.3    Cho, Y.S.4
  • 76
    • 79952598545 scopus 로고    scopus 로고
    • Identifying dispersed epigenomic domains from ChIP-Seq data
    • Song Q, Smith AD. 2011. Identifying dispersed epigenomic domains from ChIP-Seq data. Bioinformatics 27: 870-871. doi: 10.1093/bioinformatics/btr030.
    • (2011) Bioinformatics , vol.27 , pp. 870-871
    • Song, Q.1    Smith, A.D.2
  • 77
    • 36248966518 scopus 로고    scopus 로고
    • Induction of pluripotent stem cells from adult human fibroblasts by defined factors
    • Takahashi K, Tanabe K, Ohnuki M, Narita M, Ichisaka T, Tomoda K, Yamanaka S. 2007. Induction of pluripotent stem cells from adult human fibroblasts by defined factors. Cell 131:861-872. doi: 10.1016/j.cell.2007.11.019.
    • (2007) Cell , vol.131 , pp. 861-872
    • Takahashi, K.1    Tanabe, K.2    Ohnuki, M.3    Narita, M.4    Ichisaka, T.5    Tomoda, K.6    Yamanaka, S.7
  • 78
    • 33747195353 scopus 로고    scopus 로고
    • Induction of pluripotent stem cells from mouse embryonic and adult fibroblast cultures by defined factors
    • Takahashi K, Yamanaka S. 2006. Induction of pluripotent stem cells from mouse embryonic and adult fibroblast cultures by defined factors. Cell 126:663-676. doi: 10.1016/j.cell.2006.07.024.
    • (2006) Cell , vol.126 , pp. 663-676
    • Takahashi, K.1    Yamanaka, S.2
  • 79
    • 84872564830 scopus 로고    scopus 로고
    • A beta-mixture quantile normalization method for correcting probe design bias in Illumina Infinium 450 k DNA methylation data
    • Teschendorff AE, Marabita F, Lechner M, Bartlett T, Tegner J, Gomez-Cabrero D, Beck S. 2013. A beta-mixture quantile normalization method for correcting probe design bias in Illumina Infinium 450 k DNA methylation data. Bioinformatics 29:189-196. doi: 10.1093/bioinformatics/bts680.
    • (2013) Bioinformatics , vol.29 , pp. 189-196
    • Teschendorff, A.E.1    Marabita, F.2    Lechner, M.3    Bartlett, T.4    Tegner, J.5    Gomez-Cabrero, D.6    Beck, S.7
  • 82
    • 65449136284 scopus 로고    scopus 로고
    • TopHat: Discovering splice junctions with RNA-Seq
    • Trapnell C, Pachter L, Salzberg SL. 2009. TopHat: discovering splice junctions with RNA-Seq. Bioinformatics 25: 1105-1111. doi: 10.1093/bioinformatics/btp120.
    • (2009) Bioinformatics , vol.25 , pp. 1105-1111
    • Trapnell, C.1    Pachter, L.2    Salzberg, S.L.3
  • 86
    • 77952290826 scopus 로고    scopus 로고
    • Generation of induced pluripotent stem cells from newborn marmoset skin fibroblasts
    • Wu Y, Zhang Y, Mishra A, Tardif SD, Hornsby PJ. 2010. Generation of induced pluripotent stem cells from newborn marmoset skin fibroblasts. Stem Cell Research 4:180-188. doi: 10.1016/j.scr.2010.02.003.
    • (2010) Stem Cell Research , vol.4 , pp. 180-188
    • Wu, Y.1    Zhang, Y.2    Mishra, A.3    Tardif, S.D.4    Hornsby, P.J.5


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