GSE39524
GSE39524: RNA-seq from ENCODE/UW
Summary:   This data was generated by ENCODE. If you have questions about the data, contact the submitting laboratory directly (Richard Sandstrom mailto:sull@u.washington.edu). If you have questions about the Genome Browser track associated with this data, contact ENCODE (mailto:genome@soe.ucsc.edu).  This track was produced as part of the mouse ENCODE Project. This track shows RNA-seq measured genome-wide in mouse tissues and cell lines (http://hgwdev.cse.ucsc.edu/cgi-bin/hgEncodeVocab?type=cellType). Poly-A selected mRNA was used as the source for transcriptome profiling of tissues and cell types that also had corresponding DNase I hypersensitive profiles.  For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf Overall Design: Cells were grown according to the approved ENCODE cell culture protocols. Fresh tissues were harvested from mice and stored until used for preparing total RNA samples. The total RNA was used as starting material to select poly-A RNA and used for constructing SOLiD libraries according to the protocols supplied by the manufacturer. All RNA samples were spiked in with NIST standards before libraries were constructed. The RNA-seq libraries were sequenced on ABI SOLiD sequencing platform as 50-base reads according to the manufacturer's recommendations.Reads were aligned to the mm9 reference genome using ABI BioScope software version 1.2.1. Colorspace FASTQ format files were created using Heng Li's solid2fastq.pl script version 0.1.4 (Li et al., 2009a), representing 0, 1, 2, 3 color codes with the letters A, C, G, T respectively. Signal files were created from the BAM (Li et al., 2009b) alignments using BEDTools (Quinlan et al., 2010).