Data from: Fusion transcript discovery in formalin-fixed paraffin-embedded human breast cancer tissues reveals a link to tumor progression

Ma Y, Ambannavar R, Stephans J, Jeong J, dei Rossi A, Liu M, Levy S, Baker J, Qu K

Date Published: April 14, 2014

DOI: http://dx.doi.org/10.5061/dryad.98m0m

 

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Title SAM files containing RNA-seq reads supporting fusion transcripts in Providence and Rush cohorts
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Description These SAM files consist 2 directories, one for Providence cohort, and another for Rush cohort. Each sample has one individual SAM file under each cohort directory. The data were generated by gFuse, a RNA-seq fusion detection bioinformatics method, from archived FFPE human breast cancer patients. As a part of gFuse pipeline, the SAM files were generated by GSNAP via mapping supporting RNA-seq reads against the fasta sequences of 5 template sets of 100 unique fusion junctions in the length of 100bp, which are available here in the file “100fusiontemplates.fa”. The sequences and sample IDs are also described in Supplementary Table 1 of the manuscript titled “Fusion transcript discovery in formalin-fixed paraffin-embedded human breast cancer tissues reveals a link to tumor progression”.
Download fusion_read_alignment.sam.tar.gz (343.0 Kb)
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When using this data, please cite the original publication:

Ma Y, Ambannavar R, Stephans J, Jeong J, dei Rossi A, Liu M, Levy S, Baker J, Qu K, Friedman AJ, Londry JJ, Abramson R, Beasley EM (2014) Fusion transcript discovery in formalin-fixed paraffin-embedded human breast cancer tissues reveals a link to tumor progression. PLoS ONE 9(4): e94202. http://dx.doi.org/10.1371/journal.pone.0094202

Additionally, please cite the Dryad data package:

Ma Y, Ambannavar R, Stephans J, Jeong J, dei Rossi A, Liu M, Levy S, Baker J, Qu K (2014) Data from: Fusion transcript discovery in formalin-fixed paraffin-embedded human breast cancer tissues reveals a link to tumor progression. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.98m0m
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