Aboobaker Lab Schmidtea mediterranea transcriptome dataset

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:

-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

-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

-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

-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

-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

The following files are included in this fileset:

OX_smed_1.0.fa - transcriptome sequences in fasta format.

OX_smed_1.0.blast - cleaned blast results for transcriptome. Hits to hypotheticals or unknowns are filtered out.

OX_smed_1.0.go - Gene ontology results for transcriptome.

OX_smed_1.0.pfam - PFAM HMM-A scan results for transcriptome.

OX_smed_1.0.tf - Potential transcription factors found in the transcriptome using DBD transcription factor database.

OX_smed_1.0.source - The source transcripts/EST that made up each consolidated transcript.

OX_Gtig_0.1.fa - G. tigrina transcriptome assembled from Roche 454 reads.

Supp01-08 - Supplemental files for publication in submission.