U2OS: Jang 2015 Track Settings
 
Ribosome profiling reveals an important role for translational control in circadian gene expression (Jang et al. 2015)   (All Elongating Ribosomes (Footprints) tracks)

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     Bmal1 kd ribo profile CT00  Ribosome Coverage of elongating ribosomes from Homo sapiens (Jang et al. 2015)   Schema 
     Bmal1 kd ribo profile CT02  Ribosome Coverage of elongating ribosomes from Homo sapiens (Jang et al. 2015)   Schema 
     Bmal1 kd ribo profile CT04  Ribosome Coverage of elongating ribosomes from Homo sapiens (Jang et al. 2015)   Schema 
     Bmal1 kd ribo profile CT06  Ribosome Coverage of elongating ribosomes from Homo sapiens (Jang et al. 2015)   Schema 
     Bmal1 kd ribo profile CT08  Ribosome Coverage of elongating ribosomes from Homo sapiens (Jang et al. 2015)   Schema 
     Bmal1 kd ribo profile CT10  Ribosome Coverage of elongating ribosomes from Homo sapiens (Jang et al. 2015)   Schema 
     Bmal1 kd ribo profile CT12  Ribosome Coverage of elongating ribosomes from Homo sapiens (Jang et al. 2015)   Schema 
     Bmal1 kd ribo profile CT14  Ribosome Coverage of elongating ribosomes from Homo sapiens (Jang et al. 2015)   Schema 
     Bmal1 kd ribo profile CT16  Ribosome Coverage of elongating ribosomes from Homo sapiens (Jang et al. 2015)   Schema 
     Bmal1 kd ribo profile CT18  Ribosome Coverage of elongating ribosomes from Homo sapiens (Jang et al. 2015)   Schema 
     Bmal1 kd ribo profile CT20  Ribosome Coverage of elongating ribosomes from Homo sapiens (Jang et al. 2015)   Schema 
     Bmal1 kd ribo profile CT22  Ribosome Coverage of elongating ribosomes from Homo sapiens (Jang et al. 2015)   Schema 
     WT ribo profile CT00  Ribosome Coverage of elongating ribosomes from Homo sapiens (Jang et al. 2015)   Schema 
     WT ribo profile CT02  Ribosome Coverage of elongating ribosomes from Homo sapiens (Jang et al. 2015)   Schema 
     WT ribo profile CT04  Ribosome Coverage of elongating ribosomes from Homo sapiens (Jang et al. 2015)   Schema 
     WT ribo profile CT06  Ribosome Coverage of elongating ribosomes from Homo sapiens (Jang et al. 2015)   Schema 
     WT ribo profile CT08  Ribosome Coverage of elongating ribosomes from Homo sapiens (Jang et al. 2015)   Schema 
     WT ribo profile CT10  Ribosome Coverage of elongating ribosomes from Homo sapiens (Jang et al. 2015)   Schema 
     WT ribo profile CT12  Ribosome Coverage of elongating ribosomes from Homo sapiens (Jang et al. 2015)   Schema 
     WT ribo profile CT14  Ribosome Coverage of elongating ribosomes from Homo sapiens (Jang et al. 2015)   Schema 
     WT ribo profile CT16  Ribosome Coverage of elongating ribosomes from Homo sapiens (Jang et al. 2015)   Schema 
     WT ribo profile CT18  Ribosome Coverage of elongating ribosomes from Homo sapiens (Jang et al. 2015)   Schema 
     WT ribo profile CT20  Ribosome Coverage of elongating ribosomes from Homo sapiens (Jang et al. 2015)   Schema 
     WT ribo profile CT22  Ribosome Coverage of elongating ribosomes from Homo sapiens (Jang et al. 2015)   Schema 
    

Description

U2-OS cell time course over one day of 12 wildtype total RNA-seq samples, 12 wildtype ribosome profiling samples, 12 Bmal1 knockdown total RNA-seq samples and 12 Bmal1 knockdown ribosome profiling samples. All samples have duplicates..

Methods

Raw sequence data were obtained from NCBI FTP directory(SRP041298). Data from the following samples were processed:

WT_ribo_profile_CT02 Ribosome coverage data from Homo sapiens(Jang, et al. 2015)
WT_ribo_profile_CT00 Ribosome coverage data from Homo sapiens(Jang, et al. 2015)
WT_ribo_profile_CT20 Ribosome coverage data from Homo sapiens(Jang, et al. 2015)
WT_ribo_profile_CT22 Ribosome coverage data from Homo sapiens(Jang, et al. 2015)
WT_ribo_profile_CT08 Ribosome coverage data from Homo sapiens(Jang, et al. 2015)
WT_ribo_profile_CT06 Ribosome coverage data from Homo sapiens(Jang, et al. 2015)
WT_ribo_profile_CT04 Ribosome coverage data from Homo sapiens(Jang, et al. 2015)
Bmal1_kd_ribo_profile_CT18 Ribosome coverage data from Homo sapiens(Jang, et al. 2015)
Bmal1_kd_ribo_profile_CT16 Ribosome coverage data from Homo sapiens(Jang, et al. 2015)
Bmal1_kd_ribo_profile_CT14 Ribosome coverage data from Homo sapiens(Jang, et al. 2015)
Bmal1_kd_ribo_profile_CT12 Ribosome coverage data from Homo sapiens(Jang, et al. 2015)
Bmal1_kd_ribo_profile_CT10 Ribosome coverage data from Homo sapiens(Jang, et al. 2015)
WT_ribo_profile_CT10 Ribosome coverage data from Homo sapiens(Jang, et al. 2015)
WT_ribo_profile_CT12 Ribosome coverage data from Homo sapiens(Jang, et al. 2015)
WT_ribo_profile_CT14 Ribosome coverage data from Homo sapiens(Jang, et al. 2015)
WT_ribo_profile_CT16 Ribosome coverage data from Homo sapiens(Jang, et al. 2015)
WT_ribo_profile_CT18 Ribosome coverage data from Homo sapiens(Jang, et al. 2015)
Bmal1_kd_ribo_profile_CT22 Ribosome coverage data from Homo sapiens(Jang, et al. 2015)
Bmal1_kd_ribo_profile_CT20 Ribosome coverage data from Homo sapiens(Jang, et al. 2015)
Bmal1_kd_ribo_profile_CT08 Ribosome coverage data from Homo sapiens(Jang, et al. 2015)
Bmal1_kd_ribo_profile_CT04 Ribosome coverage data from Homo sapiens(Jang, et al. 2015)
Bmal1_kd_ribo_profile_CT06 Ribosome coverage data from Homo sapiens(Jang, et al. 2015)
Bmal1_kd_ribo_profile_CT00 Ribosome coverage data from Homo sapiens(Jang, et al. 2015)
Bmal1_kd_ribo_profile_CT02 Ribosome coverage data from Homo sapiens(Jang, et al. 2015)

Adapter sequence CTGTAGGCACCATCAAT 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

Jang C, Lahens NF, Hogenesch JB, Sehgal A (2015) Ribosome profiling reveals an important role for translational control in circadian gene expression . Genome Res. 2015 Dec;25(12):1836-47. doi: 10.1101/gr.191296.115. Epub 2015 Sep 3.