HeLa:Zur 2016 Track Settings
 
Complementary Post Transcriptional Regulatory Information is Detected by PUNCH-P and Ribosome Profiling. (Zur et al. 2016)   (All mRNA-seq Reads tracks)

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     G1 RNA Seq Exp1  mRNA Coverage of ribosomes from Homo sapiens (Zur et al. 2016)   Schema 
     G1 RNA Seq Exp2  mRNA Coverage of ribosomes from Homo sapiens (Zur et al. 2016)   Schema 
     M RNA Seq Exp1  mRNA Coverage of ribosomes from Homo sapiens (Zur et al. 2016)   Schema 
     M RNA Seq Exp2  mRNA Coverage of ribosomes from Homo sapiens (Zur et al. 2016)   Schema 

Description

Two Ribo-Seq experiments, which included parallel RNA-Seq, one with 3 replicates, and the other with one replicate, totalling 4 technical replicates for the G1 and M phases of the cell cycle, respectively (totalling 16 samples), were performed.

Methods

Raw sequence data were obtained from NCBI FTP directory(SRP064313). Data from the following samples were processed:

G1_RNA_Seq_Exp2 mRNA-seq unique mappers from Homo sapiens(Zur, et al. 2016)
M_RNA_Seq_Exp2 mRNA-seq unique mappers from Homo sapiens(Zur, et al. 2016)
M_RNA_Seq_Exp1 mRNA-seq unique mappers from Homo sapiens(Zur, et al. 2016)
G1_RNA_Seq_Exp1 mRNA-seq unique mappers from Homo sapiens(Zur, et al. 2016)

Adapter sequence CTGTAGGCACCATCAAT and ATCTCGTATGCCGTCTT 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 reads below 25nt were discarded. These tracks contains the uniquely mapping reads.

References

Zur H, Aviner R, Tuller T (2016) Complementary Post Transcriptional Regulatory Information is Detected by PUNCH-P and Ribosome Profiling. . Sci Rep. 2016 Feb 22;6:21635. doi: 10.1038/srep21635. Research Support, Non-U.S. Gov't