hESC: Werner 2015 Track Settings
 
Cell fate determination by ubiquitin-dependent regulation of translation (Werner et al. 2015)   (All mRNA-seq Reads tracks)

Display mode:       Reset to defaults

Overlay method:
Type of graph:
Track height: pixels (range: 11 to 128)
Data view scaling: Always include zero: 
Vertical viewing range: min:  max:   (range: 0 to 127)
Transform function:Transform data points by: 
Windowing function: Smoothing window:  pixels
Negate values:
Draw y indicator lines:at y = 0.0:    at y =
Graph configuration help
All subtracks:
List subtracks: only selected/visible    all    ()  
     rna hES shControl  mRNA Coverage of elongating ribosomes from Homo sapiens (Werner et al. 2015)   Schema 
     rna hES shKBTBD8  mRNA Coverage of elongating ribosomes from Homo sapiens (Werner et al. 2015)   Schema 
     rna hES shTCOF1  mRNA Coverage of elongating ribosomes from Homo sapiens (Werner et al. 2015)   Schema 
     rna ND1 shControl  mRNA Coverage of elongating ribosomes from Homo sapiens (Werner et al. 2015)   Schema 
     rna ND1 shKBTBD8  mRNA Coverage of elongating ribosomes from Homo sapiens (Werner et al. 2015)   Schema 
     rna ND3 shControl  mRNA Coverage of elongating ribosomes from Homo sapiens (Werner et al. 2015)   Schema 
     rna ND3 shKBTBD8  mRNA Coverage of elongating ribosomes from Homo sapiens (Werner et al. 2015)   Schema 
     rna ND3 shTCOF1  mRNA Coverage of elongating ribosomes from Homo sapiens (Werner et al. 2015)   Schema 
     rna ND6 shControl  mRNA Coverage of elongating ribosomes from Homo sapiens (Werner et al. 2015)   Schema 
     rna ND6 shKBTBD8  mRNA Coverage 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:

rna_hES_shTCOF1 mRNA-seq unique mappers from Homo sapiens(Werner, et al. 2015)
rna_ND6_shKBTBD8 mRNA-seq unique mappers from Homo sapiens(Werner, et al. 2015)
rna_ND6_shControl mRNA-seq unique mappers from Homo sapiens(Werner, et al. 2015)
rna_hES_shKBTBD8 mRNA-seq unique mappers from Homo sapiens(Werner, et al. 2015)
rna_ND3_shKBTBD8 mRNA-seq unique mappers from Homo sapiens(Werner, et al. 2015)
rna_ND3_shControl mRNA-seq unique mappers from Homo sapiens(Werner, et al. 2015)
rna_hES_shControl mRNA-seq unique mappers from Homo sapiens(Werner, et al. 2015)
rna_ND3_shTCOF1 mRNA-seq unique mappers from Homo sapiens(Werner, et al. 2015)
rna_ND1_shKBTBD8 mRNA-seq unique mappers from Homo sapiens(Werner, et al. 2015)
rna_ND1_shControl mRNA-seq unique mappers 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.

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.