MEF & Liver: Gao 2014 Track Settings
 
mRNA coverage plots from MEF and liver tissue (Gao et al. 2014)   (All mRNA-seq Reads tracks)

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     Liver:control  mRNA-seq unique mappers from control liver cells (Gao et al. 2014)   Schema 
     Liver:fasting  mRNA-seq unique mappers from liver cells from mice fasting overnight (Gao et al. 2014).   Schema 
     MEF:control  mRNA-seq unique mappers from control MEFs (Gao et al. 2014)   Schema 
     MEF:starvation  mRNA-seq unique mappers from MEFs undergoing amino acid starvation (Gao et al. 2014).   Schema 

Description

mRNA coverage plots from MEF and liver tissue which underwent starvation and the corresponding controls (Gao et al. 2014)

Methods

Raw sequence data were obtained from NCBI SRA database (SRA160745). Data from the following samples was used for processing:

SRR1630836RNA-Seq of MEF Cell (Control)
SRR1630837RNA-Seq of MEF Cell (Amino Acid Starvation)
SRR1630834RNA-Seq of Liver Cell for Control Mouse
SRR1630835RNA-Seq of Liver Cell for Fasting Mouse

Adaptor sequences had already been removed from reads. An alignment to ribosomal RNA was performed using Bowtie, and aligning reads were discarded. An alignment to the mm10 genome assembly was then performed using Bowtie and these tracks contain the coverage data for uniquely mapping reads from the alignments.

References

Gao, X., Wan, J., Liu, B., Ming, M., Shen, B., Qian, S.B. (2014). Quantitative profiling of initiating ribosomes in vivo. Nat Methods. doi: 10.1038/nmeth.3208