HAP1: Jakobsson17 Track Settings
 
Methylation of human eukaryotic elongation factor alpha (eEF1A) by a member of a novel protein lysine methyltransferase family modulates mRNA trans... (Jakobsson et al. 2017)   (All Elongating Ribosomes (Footprints) 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
List subtracks: only selected/visible    all  
     KO1 RPF  Ribosome coverage data from elongating ribosomes (SRR5382420) (Jakobsson et al. 2017)   Schema 
     KO2 RPF  Ribosome coverage data from elongating ribosomes (SRR5382421) (Jakobsson et al. 2017)   Schema 
     KO3 RPF  Ribosome coverage data from elongating ribosomes (SRR5382422) (Jakobsson et al. 2017)   Schema 
     WT1 RPF  Ribosome coverage data from elongating ribosomes (SRR5382423) (Jakobsson et al. 2017)   Schema 
     WT2 RPF  Ribosome coverage data from elongating ribosomes (SRR5382424) (Jakobsson et al. 2017)   Schema 

Description

Description fromGSE97140: Ribosome profiling and RNAseq data for wt and EEF1AKMT4 knockout cells.This study includes the re-use of samples GSM2445294 and GSM2445295 from GSE93133. These two samples have been re-accessioned here so that the complete study is available from the SRP ID.

Methods

Raw sequence data were obtainedfrom NCBI FTP directory(SRP102616). Data from the following samples were processed:

KO3_RPF Ribosome coverage data from elongating ribosomes Homo sapiens(Jakobsson, et al. 2017)
WT1_RPF Ribosome coverage data from elongating ribosomes Homo sapiens(Jakobsson, et al. 2017)
KO1_RPF Ribosome coverage data from elongating ribosomes Homo sapiens(Jakobsson, et al. 2017)
WT2_RPF Ribosome coverage data from elongating ribosomes Homo sapiens(Jakobsson, et al. 2017)
KO2_RPF Ribosome coverage data from elongating ribosomes Homo sapiens(Jakobsson, et al. 2017)

Adapter 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 hg38 genome assembly was performed using Bowtie, and reads below 25nt were discarded. These tracks contain the uniquely mapping reads.,

References

Jakobsson ME, Malecki J, Nilges BS, Moen A, Leidel SA, Falnes P.O (2017) Methylation of human eukaryotic elongation factor alpha (eEF1A) by a member of a novel protein lysine methyltransferase family modulates mRNA trans... .Nucleic Acids Res. 2017 May 18. doi: 10.1093/nar/gkx432. [Epub ahead of print]