Computational protocol: DNA context represents transcription regulation of the gene in mouse embryonic stem cells

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Protocol publication

[…] The raw RNA-seq of mESC was obtained from a previous study. The RNA-seq analysis was performed using the Tuxedo software package with default settings. RNA-seq reads were mapped to the mouse genome (NCBI37/mm9) using Bowtie2. Tophat with default settings was used to detect splice sites. The Cufflinks software package was used to assemble transcripts based on the Refseq mRNA sequence database (mm9). A total of 48,228 transcripts were detected from two RNA-seq replicate experiments and their mean values were used for further analysis. Log2 values of the FPKM were used as target mRNA levels of the prediction models. Not significantly detected transcripts were defined as having expression levels between 0 and 1 FPKM. […]

Pipeline specifications

Software tools Tuxedo, Bowtie2, TopHat, Cufflinks
Application RNA-seq analysis
Organisms Mus musculus