hESC: Werner 2015 Track Settings
 
Cell fate determination by ubiquitin-dependent regulation of translation (Werner et al. 2015)   (All Elongating Ribosomes (A-site) tracks)

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     ribo hES shControl  Ribosome Profiles of elongating ribosomes from Homo sapiens (Werner et al. 2015)   Schema 
     ribo hES shKBTBD8  Ribosome Profiles of elongating ribosomes from Homo sapiens (Werner et al. 2015)   Schema 
     ribo hES shTCOF1  Ribosome Profiles of elongating ribosomes from Homo sapiens (Werner et al. 2015)   Schema 
     ribo ND1 shControl  Ribosome Profiles of elongating ribosomes from Homo sapiens (Werner et al. 2015)   Schema 
     ribo ND1 shKBTBD8  Ribosome Profiles of elongating ribosomes from Homo sapiens (Werner et al. 2015)   Schema 
     ribo ND3 shControl  Ribosome Profiles of elongating ribosomes from Homo sapiens (Werner et al. 2015)   Schema 
     ribo ND3 shKBTBD8  Ribosome Profiles of elongating ribosomes from Homo sapiens (Werner et al. 2015)   Schema 
     ribo ND3 shTCOF1  Ribosome Profiles of elongating ribosomes from Homo sapiens (Werner et al. 2015)   Schema 
     ribo ND6 shControl  Ribosome Profiles of elongating ribosomes from Homo sapiens (Werner et al. 2015)   Schema 
     ribo ND6 shKBTBD8  Ribosome Profiles of elongating ribosomes from Homo sapiens (Werner et al. 2015)   Schema 
    

Description

Ribosome profiling and mRNA-Seq.

Methods

Raw sequence data were obtained from NCBI FTP directory(SRP048825). Data from the following samples were processed:

ribo_hES_shControl Ribosome profiling data from Homo sapiens(Werner, et al. 2015)
ribo_ND3_shControl Ribosome profiling data from Homo sapiens(Werner, et al. 2015)
ribo_ND6_shControl Ribosome profiling data from Homo sapiens(Werner, et al. 2015)
ribo_ND6_shKBTBD8 Ribosome profiling data from Homo sapiens(Werner, et al. 2015)
ribo_ND3_shKBTBD8 Ribosome profiling data from Homo sapiens(Werner, et al. 2015)
ribo_hES_shKBTBD8 Ribosome profiling data from Homo sapiens(Werner, et al. 2015)
ribo_ND1_shKBTBD8 Ribosome profiling data from Homo sapiens(Werner, et al. 2015)
ribo_ND1_shControl Ribosome profiling data from Homo sapiens(Werner, et al. 2015)
ribo_ND3_shTCOF1 Ribosome profiling data from Homo sapiens(Werner, et al. 2015)
ribo_hES_shTCOF1 Ribosome profiling data from Homo sapiens(Werner, et al. 2015)

Adapter sequence CTGTAGGCACCATCAAT, AGATCGGAAGAGC 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 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

Werner A, Iwasaki S, McGourty CA, Medina-Ruiz S, Teerikorpi N, Fedrigo I, Ingolia NT, Rape M (2015) Cell fate determination by ubiquitin-dependent regulation of translation . Nature. 2015 Sep 24;525(7570):523-7. doi: 10.1038/nature14978. Research Support, N.I.H., Extramural; Research Support, Non-U.S. Gov't; Research Support, U.S. Gov't, Non-P.H.S.