Fibroblast:Xu 2016 Track Settings
 
Improved transcription and translation with L-leucine stimulation of mTORC1 in Roberts syndrome. (Xu et al. 2016)   (All Elongating Ribosomes (A-site) tracks)

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     10 mut l leucine RPF  Ribosome Profiles of elongating ribosomes from Homo sapiens (Xu et al. 2016)   Schema 
     11 mut d leucine RPF  Ribosome Profiles of elongating ribosomes from Homo sapiens (Xu et al. 2016)   Schema 
     12 mut l leucine RPF  Ribosome Profiles of elongating ribosomes from Homo sapiens (Xu et al. 2016)   Schema 
     corr d leucine RPF  Ribosome Profiles of elongating ribosomes from Homo sapiens (Xu et al. 2016)   Schema 
     corr l leucine RPF  Ribosome Profiles of elongating ribosomes from Homo sapiens (Xu et al. 2016)   Schema 
     mut d leucine RPF  Ribosome Profiles of elongating ribosomes from Homo sapiens (Xu et al. 2016)   Schema 
     wt d leucine RPF  Ribosome Profiles of elongating ribosomes from Homo sapiens (Xu et al. 2016)   Schema 
     wt l leucine RPF  Ribosome Profiles of elongating ribosomes from Homo sapiens (Xu et al. 2016)   Schema 
    

Description

42 samples of human fibroblast cell lines with various genotypes (wt, corrected, and esco2 mutants) are treated with l-leucine or d-leucine (control) for 3 or 24 hours. Biological replicates are present.

Methods

Raw sequence data were obtained from NCBI FTP directory(SRP052229). Data from the following samples were processed:

corr_d_leucine_RPF Ribosome profiling data from Homo sapiens(Xu, et al. 2016)
12_mut_l_leucine_RPF Ribosome profiling data from Homo sapiens(Xu, et al. 2016)
wt_l_leucine_RPF Ribosome profiling data from Homo sapiens(Xu, et al. 2016)
corr_l_leucine_RPF Ribosome profiling data from Homo sapiens(Xu, et al. 2016)
11_mut_d_leucine_RPF Ribosome profiling data from Homo sapiens(Xu, et al. 2016)
wt_d_leucine_RPF Ribosome profiling data from Homo sapiens(Xu, et al. 2016)
mut_d_leucine_RPF Ribosome profiling data from Homo sapiens(Xu, et al. 2016)
10_mut_l_leucine_RPF Ribosome profiling data from Homo sapiens(Xu, et al. 2016)

Adapter sequence AGATCGGAAGAGCACAC was removed from reads using Cutadapt An alignment to ribosomal RNA was performed using Bowtie, and aligning reads were discarded. An alignment to the hg38 genome assembly was performed using Bowtie, and reads below 25nt were discarded. These tracks contains the uniquely mapping reads.An offset of 15 nucleotides was then used to get the corresponding A-site of each read.

References

Xu B, Gogol M, Gaudenz K, Gerton JL (2016) Improved transcription and translation with L-leucine stimulation of mTORC1 in Roberts syndrome. . BMC Genomics. 2016 Jan 5;17:25. doi: 10.1186/s12864-015-2354-y. Research Support, Non-U.S. Gov't