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Methods: Application of massively parallel sequencing to microRNA profiling and discovery in human embryonic stem cells
- Ryan D. Morin,
- Michael D. O’Connor,
- Malachi Griffith,
- Florian Kuchenbauer,
- Allen Delaney,
- Anna-Liisa Prabhu,
- Yongjun Zhao,
- Helen McDonald,
- Thomas Zeng,
- Martin Hirst,
- Connie J. Eaves,
- and Marco A. Marra
Genome Res. April 2008 18: 610-621; Published in Advance February 19, 2008, doi:10.1101/gr.7179508
...al. 2007 ; Kasschau et al. 2007 ; Yao et al. 2007 ) using the massively parallel signature sequencing (MPSS) methodology ( Nakano et al. 2006 ) and more recently the Roche/454 platform ( Margulies et al. 2005 ). The recently released Illumina sequencing platform provides approximately two orders...
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Research: Transcriptome dynamics through alternative polyadenylation in developmental and environmental responses in plants revealed by deep sequencing
- Yingjia Shen,
- R.C. Venu,
- Kan Nobuta,
- Xiaohui Wu,
- Varun Notibala,
- Caghan Demirci,
- Blake C. Meyers,
- Guo-Liang Wang,
- Guoli Ji,
- and Qingshun Q. Li
Genome Res. September 2011 21: 1478-1486; Published in Advance August 3, 2011, doi:10.1101/gr.114744.110
...-scale DNA sequencing technologies have made the study of the polyadenylated transcriptome easier. The digital gene expression (DGE) protocol sequenced by massively parallel signature sequencing (MPSS) or Illumina’s GAII-based sequencing-by-synthesis (SBS) (Meyers et al. 2004c; Simon et al. 2009), called...
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Research: Deep-transcriptome and ribonome sequencing redefines the molecular networks of pluripotency and the extracellular space in human embryonic stem cells
- Gabriel Kolle,
- Jill L. Shepherd,
- Brooke Gardiner,
- Karin S. Kassahn,
- Nicole Cloonan,
- David L.A. Wood,
- Ehsan Nourbakhsh,
- Darrin F. Taylor,
- Shivangi Wani,
- Hun S. Chy,
- Qi Zhou,
- Kevin McKernan,
- Scott Kuersten,
- Andrew L. Laslett,
- and Sean M. Grimmond
Genome Res. December 2011 21: 2014-2025; Published in Advance October 31, 2011, doi:10.1101/gr.119321.110
...expression of genes (n = 2990 genes) previously described as being inactive in hESCs based on microarray and massively parallel signature sequencing (MPSS) data (Boyer et al. 2005; Guenther et al. 2007). Despite the stringent criteria by which the inactive gene set was originally defined, we found that ;20...
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Resource: Open chromatin defined by DNaseI and FAIRE identifies regulatory elements that shape cell-type identity
- Lingyun Song,
- Zhancheng Zhang,
- Linda L. Grasfeder,
- Alan P. Boyle,
- Paul G. Giresi,
- Bum-Kyu Lee,
- Nathan C. Sheffield,
- Stefan Gräf,
- Mikael Huss,
- Damian Keefe,
- Zheng Liu,
- Darin London,
- Ryan M. McDaniell,
- Yoichiro Shibata,
- Kimberly A. Showers,
- Jeremy M. Simon,
- Teresa Vales,
- Tianyuan Wang,
- Deborah Winter,
- Zhuzhu Zhang,
- Neil D. Clarke,
- Ewan Birney,
- Vishwanath R. Iyer,
- Gregory E. Crawford,
- Jason D. Lieb,
- and Terrence S. Furey
Genome Res. October 2011 21: 1757-1767; Published in Advance July 12, 2011, doi:10.1101/gr.121541.111
...data support the hypothesis that COREs control gene activity required for the maintenance of cell-type identity. This publicly available atlas of regulatory elements may prove valuable in identifying noncoding DNA sequence variants that are causally linked to human disease. Footnotes ↵ 10...
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Resource: Genome-wide dynamics of alternative polyadenylation in rice
- Haihui Fu,
- Dewei Yang,
- Wenyue Su,
- Liuyin Ma,
- Yingjia Shen,
- Guoli Ji,
- Xinfu Ye,
- Xiaohui Wu,
- and Qingshun Q. Li
Genome Res. December 2016 26: 1753-1760; Published in Advance October 12, 2016, doi:10.1101/gr.210757.116
.... This is termed alternative polyadenylation, or APA. For example, studies showed that ∼50% and 82% of genes in rice had more than one poly(A) site using the expressed sequence tags (EST) database, restriction enzyme digestion–mediated massively parallel signature sequencing (MPSS), or Illumina sequencing...
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Resource: Dynamics of microRNA expression during mouse prenatal development
- Sorena Rahmanian,
- Rabi Murad,
- Alessandra Breschi,
- Weihua Zeng,
- Mark Mackiewicz,
- Brian Williams,
- Carrie A. Davis,
- Brian Roberts,
- Sarah Meadows,
- Dianna Moore,
- Diane Trout,
- Chris Zaleski,
- Alex Dobin,
- Lei-Hoon Sei,
- Jorg Drenkow,
- Alex Scavelli,
- Thomas R. Gingeras,
- Barbara J. Wold,
- Richard M. Myers,
- Roderic Guigó,
- and Ali Mortazavi
Genome Res. November 2019 29: 1900-1909; Published in Advance October 23, 2019, doi:10.1101/gr.248997.119
...in diverse metazoans and plants (Lagos-Quintana et al. 2002; Wienholds et al. 2005; Ehrenreich and Purugganan 2008). Mineno et al. (2006) used massively parallel signature sequencing (MPSS) technology to profile miRNAs in mouse whole embryos during three embryonic stages (E9.5, E10.5, and E11.5) and were...
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Resource: Benchmark and integration of resources for the estimation of human transcription factor activities
- Luz Garcia-Alonso,
- Christian H. Holland,
- Mahmoud M. Ibrahim,
- Denes Turei,
- and Julio Saez-Rodriguez
Genome Res. August 2019 29: 1363-1375; Published in Advance July 24, 2019, doi:10.1101/gr.240663.118
...preferences to specific DNA sequences, referred to as “binding motifs” (Stormo 2000; Khan et al. 2018; Kulakovskiy et al. 2018). TF binding motifs, generally modeled as position weight matrices (PWMs), are then used to scan the regulatory sequences in a to identify candidate target genes (Sinha 2006...
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LETTER: Genome-wide identification and analysis of small RNAs originated from natural antisense transcripts in Oryza sativa
- Xuefeng Zhou,
- Ramanjulu Sunkar,
- Hailing Jin,
- Jian-Kang Zhu,
- and Weixiong Zhang
Genome Res. January 2009 19: 70-78; Published in Advance October 29, 2008, doi:10.1101/gr.084806.108
...-NAT pairs in Arabidopsis , and further analysis of full-length cDNAs and massively parallel signature sequencing (MPSS) data confirmed sense and antisense transcripts of 957 cis -NAT pairs ( Wang et al. 2005 ). Based on some qualitative criteria, these studies concluded that the majority of cis -NATs...
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LETTER: A diverse set of microRNAs and microRNA-like small RNAs in developing rice grains
- Qian-Hao Zhu,
- Andrew Spriggs,
- Louisa Matthew,
- Longjiang Fan,
- Gavin Kennedy,
- Frank Gubler,
- and Chris Helliwell
Genome Res. September 2008 18: 1456-1465; Published in Advance August 7, 2008, doi:10.1101/gr.075572.107
...al. 2005 ) or massively parallel signature sequencing (MPSS) (for review, see Meyers et al. 2006 ) have been used in rice for miRNA discovery ( Johnson et al. 2007 ; Lu et al. 2008 ; Morin et al. 2008 ; Sunkar et al. 2008 ) and comparison of small RNA populations in various tissues, including...
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Method: Comprehensive prediction in 78 human cell lines reveals rigidity and compactness of transcription factor dimers
- Aleksander Jankowski,
- Ewa Szczurek,
- Ralf Jauch,
- Jerzy Tiuryn,
- and Shyam Prabhakar
Genome Res. August 2013 23: 1307-1318; Published in Advance April 3, 2013, doi:10.1101/gr.154922.113
...:// bioputer.mimuw.edu.pl/papers/tfdimers/), matches the NFAT– FOS–JUN trimer that is known to synergistically regulate several immune-response genes (Chen et al. 1998b). This trimer was predicted by our algorithm because the sequence recognized by the FOS–JUN (AP-1) dimer was present as a single motif...
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