BMC Genomics
Volume 9

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Research article

Detailed characterization of the mouse embryonic stem cell transcriptome reveals novel genes and intergenic splicing associated with pluripotency

Galih Kunarso¹ , Kee-Yew Wong² , Lawrence W Stanton²^,3 and Leonard Lipovich¹^,4^,5

¹Computational & Mathematical Biology, Genome Institute of Singapore, 60 Biopolis Street #02-01, Singapore 138672, Singapore

²Stem Cell & Developmental Biology, Genome Institute of Singapore, 60 Biopolis Street #02-01, Singapore 138672, Singapore

³Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore 117543, Singapore

⁴School of Computer Engineering, Nanyang Technological University, Block N4, Nanyang Avenue, Singapore 639798, Singapore

⁵Center for Molecular Medicine and Genetics & Department of Neurology, School of Medicine, Wayne State University, 3228 Scott Hall, 540 E. Canfield Street, Detroit, MI 48201, USA

author email corresponding author email

BMC Genomics 2008, 9:155doi:10.1186/1471-2164-9-155


Published:	9 April 2008

Additional files

Additional file 1:

Detailed PET sequences used in this analysis and the genomic properties of the 16 novel and putative intergenically spliced TUs selected for experimental validation from the GIS PET-transcriptome dataset.

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Additional file 2:

Full-length sequences of all splice isoforms of all the 5 TUs studied and the intergenically spliced transcript found in [11].

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Additional file 3:

Oct4, Nanog, and Sox2 binding sites in the 100 kb vicinity of the TUs identified from chromatin immunoprecipitation paired-end diTags (ChIP-PET) [3] and ChIP-seq [H. H. Ng et al., unpublished].

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Additional file 4:

Expression levels of the pluripotency markers Oct4, Sox2, Nanog, and Klf4 upon RA-, DMSO-, and HMBA-induced differentiation.

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Additional file 5:

Primer sequences used to characterize the TUs identified in this study.

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Additional file 6:

Catalog numbers of mouse total RNA (BD Biosciences Clontech) used in the multi-tissue panel expression analysis.

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Additional file 7:

Catalog numbers of TaqMan probes (Applied Biosystems) used in the QRTPCR.

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Additional file 8:

Sequences of the custom siRNA (Dharmacon) designed for the TUs.

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