Stem cell transcriptome profiling via massive-scale mRNA sequencing (original) (raw)

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Acknowledgements

A.R.R.F. and S.M.G. are funded by the Australian National Health and Medical Research Council. A.R.R.F. is a C.J. Martin fellow (428261), and S.M.G. is a senior research fellow. N.C. is a University of Queensland postdoctoral fellow. G.J.F. and M.K.B. are supported by Australian Postgraduate awards. We acknowledge the Australian Research Council Centre for Functional and Applied Genomics Array Facility for expression profiling, and R. Nutter, G. Weightman and L. Stubberfield for support of this initiative.

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Author notes

1. Alistair R R Forrest
   Present address: Present address: The Eskitis Institute for Cell and Molecular Therapies, Griffith University, Nathan, Queensland, 4111, Australia.,
2. Nicole Cloonan, Alistair R R Forrest and Gabriel Kolle: These authors contributed equally to this work.

Authors and Affiliations

1. Expression Genomics Laboratory, Institute for Molecular Bioscience, The University of Queensland, 306 Carmody Road, St. Lucia, 4072, Queensland, Australia
   Nicole Cloonan, Alistair R R Forrest, Gabriel Kolle, Brooke B A Gardiner, Geoffrey J Faulkner, Mellissa K Brown, Darrin F Taylor, Anita L Steptoe, Shivangi Wani, Graeme Bethel, Alan J Robertson, Andrew C Perkins, Stephen J Bruce & Sean M Grimmond
2. Applied Biosystems Inc., 500 Cummings Center, Beverly, 01915, Massachusetts, USA
   Clarence C Lee, Swati S Ranade, Heather E Peckham, Jonathan M Manning & Kevin J McKernan

Authors

1. Nicole Cloonan
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2. Alistair R R Forrest
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3. Gabriel Kolle
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4. Brooke B A Gardiner
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5. Geoffrey J Faulkner
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6. Mellissa K Brown
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7. Darrin F Taylor
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8. Anita L Steptoe
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9. Shivangi Wani
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10. Graeme Bethel
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11. Alan J Robertson
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12. Andrew C Perkins
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13. Stephen J Bruce
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14. Clarence C Lee
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15. Swati S Ranade
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16. Heather E Peckham
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17. Jonathan M Manning
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18. Kevin J McKernan
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19. Sean M Grimmond
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Contributions

N.C. created and integrated the sequence mapping and visualization pipeline, performed SOLiD sequencing bioinformatics, SNP analysis and splicing studies. A.R.R.F. conceived and pioneered the SQRL library strategy, performed preliminary genomic analysis, and developed the initial visualization methods. G.K. led the array-SQRL analyses, RT-PCR, pathway analysis and contributed to SNP analysis. B.B.A.G., M.K.B., G.K. and N.C. contributed to method design. A.L.S., G.K., S.J.B. and A.C.P. contributed to sample generation. G.K., A.R.R.F. and B.B.A.G. constructed libraries. C.C.L., S.S.R., B.B.A.G., G.B. and K.J.M. contributed to library sequencing. N.C., G.K., G.J.F., A.R.R.F., S.M.G., D.F.T., H.E.P. and J.M.M. contributed to data analysis. G.K., A.J.R., S.W., N.C. and A.L.S. contributed to experimental validation. S.M.G. supervised the work and prepared the manuscript with N.C., G.K. and A.R.R.F.

Corresponding author

Correspondence toSean M Grimmond.

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Competing interests

C.C.L., S.S.R., H.E.P., J.M.M. and K.J.M. are employed by Applied Biosystems, a manufacturer of DNA sequencing instrumentation and supplies.

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Cloonan, N., Forrest, A., Kolle, G. et al. Stem cell transcriptome profiling via massive-scale mRNA sequencing.Nat Methods 5, 613–619 (2008). https://doi.org/10.1038/nmeth.1223

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• Received: 25 February 2008
• Accepted: 19 May 2008
• Published: 30 May 2008
• Issue Date: July 2008
• DOI: https://doi.org/10.1038/nmeth.1223