U2OS: Jang 2015 Track Settings
 
Ribosome profiling reveals an important role for translational control in circadian gene expression (Jang et al. 2015)   (All mRNA-seq Reads tracks)

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

Bmal1_kd_total_RNA_CT18 mRNA-seq unique mappers from Homo sapiens(Jang, et al. 2015)
Bmal1_kd_total_RNA_CT22 mRNA-seq unique mappers from Homo sapiens(Jang, et al. 2015)
Bmal1_kd_total_RNA_CT20 mRNA-seq unique mappers from Homo sapiens(Jang, et al. 2015)
WT_total_RNA_CT20 mRNA-seq unique mappers from Homo sapiens(Jang, et al. 2015)
WT_total_RNA_CT22 mRNA-seq unique mappers from Homo sapiens(Jang, et al. 2015)
WT_total_RNA_CT06 mRNA-seq unique mappers from Homo sapiens(Jang, et al. 2015)
WT_total_RNA_CT04 mRNA-seq unique mappers from Homo sapiens(Jang, et al. 2015)
WT_total_RNA_CT02 mRNA-seq unique mappers from Homo sapiens(Jang, et al. 2015)
WT_total_RNA_CT00 mRNA-seq unique mappers from Homo sapiens(Jang, et al. 2015)
Bmal1_kd_total_RNA_CT04 mRNA-seq unique mappers from Homo sapiens(Jang, et al. 2015)
Bmal1_kd_total_RNA_CT06 mRNA-seq unique mappers from Homo sapiens(Jang, et al. 2015)
Bmal1_kd_total_RNA_CT00 mRNA-seq unique mappers from Homo sapiens(Jang, et al. 2015)
Bmal1_kd_total_RNA_CT02 mRNA-seq unique mappers from Homo sapiens(Jang, et al. 2015)
WT_total_RNA_CT18 mRNA-seq unique mappers from Homo sapiens(Jang, et al. 2015)
Bmal1_kd_total_RNA_CT12 mRNA-seq unique mappers from Homo sapiens(Jang, et al. 2015)
Bmal1_kd_total_RNA_CT10 mRNA-seq unique mappers from Homo sapiens(Jang, et al. 2015)
Bmal1_kd_total_RNA_CT16 mRNA-seq unique mappers from Homo sapiens(Jang, et al. 2015)
Bmal1_kd_total_RNA_CT14 mRNA-seq unique mappers from Homo sapiens(Jang, et al. 2015)
WT_total_RNA_CT10 mRNA-seq unique mappers from Homo sapiens(Jang, et al. 2015)
WT_total_RNA_CT12 mRNA-seq unique mappers from Homo sapiens(Jang, et al. 2015)
WT_total_RNA_CT14 mRNA-seq unique mappers from Homo sapiens(Jang, et al. 2015)
WT_total_RNA_CT16 mRNA-seq unique mappers from Homo sapiens(Jang, et al. 2015)
WT_total_RNA_CT08 mRNA-seq unique mappers from Homo sapiens(Jang, et al. 2015)
Bmal1_kd_total_RNA_CT08 mRNA-seq unique mappers 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.