Aboobaker Lab Schmidtea mediterranea transcriptome dataset

<p>This fileset contains data associated with the consolidated Schmidtea mediterranea transcriptome. The publication associated with this fileset is currently under review. This transcriptome was consolidated using 5 independently assembled transcriptomes:</p> <p>-Blythe MJ, Kao D, Malla S, Rowsell J, Wilson R, et al. (2010) A Dual Platform Approach to Transcript Discovery for the Planarian Schmidtea Mediterranea to Establish RNAseq for Stem Cell and Regeneration Biology. PLoS ONE 5(12): e15617. doi:10.1371/journal.pone.0015617</p> <p>-Catherine Adamidi, Yongbo Wang, Dominic Gruen, et al. (2011) De novo assembly and validation of planaria transcriptome by massive parallel sequencing and shotgun proteomics. Genome Research 2011. doi:10.1101/gr.113779.110</p> <p>-Thomas Sandmann, Matthias C Vogg, Suthira Owlarn, et al. (2011) The head-regeneration transcriptome of the planarian Schmidtea mediterranea. Genome Biology 2011, 12:R76 doi:10.1186/gb-2011-12-8-r76</p> <p>-Resch AM, Palakodeti D, Lu Y-C, Horowitz M, Graveley BR (2012) Transcriptome Analysis Reveals Strain-Specific and Conserved Stemness Genes in Schmidtea mediterranea. PLoS ONE 7(4): e34447. doi:10.1371/journal.pone.0034447</p> <p>-Labbé, R. M., Irimia, M., Currie, K. W., Lin, A., Zhu, S. J., Brown, D. D.R., Ross, E. J., Voisin, V., Bader, G. D., Blencowe, B. J. and Pearson, B. J. (2012), A Comparative Transcriptomic Analysis Reveals Conserved Features of Stem Cell Pluripotency in Planarians and Mammals. STEM CELLS, 30: 1734–1745. doi: 10.1002/stem.1144</p> <p> </p> <p>The following files are included in this fileset:</p> <p>OX_smed_1.0.fa - transcriptome sequences in fasta format.</p> <p>OX_smed_1.0.blast - cleaned blast results for transcriptome. Hits to hypotheticals or unknowns are filtered out.</p> <p>OX_smed_1.0.go - Gene ontology results for transcriptome.</p> <p>OX_smed_1.0.pfam - PFAM HMM-A scan results for transcriptome.</p> <p>OX_smed_1.0.tf - Potential transcription factors found in the transcriptome using DBD transcription factor database.</p> <p>OX_smed_1.0.source - The source transcripts/EST that made up each consolidated transcript.</p> <p>OX_Gtig_0.1.fa - G. tigrina transcriptome assembled from Roche 454 reads.</p> <p>Supp01-08 - Supplemental files for publication in submission.</p