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Dynamic Regulation of a Ribosome Rescue Pathway in Erythroid Cells and Platelets. (Mills et al. 2016)   (All Elongating Ribosomes (A-site) tracks)

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     flowcell276 pair1 ACGACT  Ribosome profiles from elongating ribosomes (Mills et al. 2016)   Schema 
     flowcell276 pair1 ATCAGT  Ribosome profiles from elongating ribosomes (Mills et al. 2016)   Schema 
     flowcell276 pair1 CAGCAT  Ribosome profiles from elongating ribosomes (Mills et al. 2016)   Schema 
     flowcell276 pair1 CGACGT  Ribosome profiles from elongating ribosomes (Mills et al. 2016)   Schema 
     flowcell276 pair1 GCAGCT  Ribosome profiles from elongating ribosomes (Mills et al. 2016)   Schema 
     flowcell276 pair1 TACGAT  Ribosome profiles from elongating ribosomes (Mills et al. 2016)   Schema 
     K562 GFP 0d  Ribosome profiles from elongating ribosomes (Mills et al. 2016)   Schema 
     K562 GFP 2d  Ribosome profiles from elongating ribosomes (Mills et al. 2016)   Schema 
     K562 GFP 4d  Ribosome profiles from elongating ribosomes (Mills et al. 2016)   Schema 
     K562 GFP 6d  Ribosome profiles from elongating ribosomes (Mills et al. 2016)   Schema 
     K562 GFP shABCE1  Ribosome profiles from elongating ribosomes (Mills et al. 2016)   Schema 
     K562 GFP shCtrl  Ribosome profiles from elongating ribosomes (Mills et al. 2016)   Schema 
     K562 PH 0d  Ribosome profiles from elongating ribosomes (Mills et al. 2016)   Schema 
     K562 PH 2d  Ribosome profiles from elongating ribosomes (Mills et al. 2016)   Schema 
     K562 PH 4d  Ribosome profiles from elongating ribosomes (Mills et al. 2016)   Schema 
     K562 PH 6d  Ribosome profiles from elongating ribosomes (Mills et al. 2016)   Schema 
     K562 PH shABCE1  Ribosome profiles from elongating ribosomes (Mills et al. 2016)   Schema 
     K562 PH shCtrl  Ribosome profiles from elongating ribosomes (Mills et al. 2016)   Schema 
     Meg01 GFP  Ribosome profiles from elongating ribosomes (Mills et al. 2016)   Schema 
     Meg01 PH  Ribosome profiles from elongating ribosomes (Mills et al. 2016)   Schema 
     Meg01 Ribo  Ribosome profiles from elongating ribosomes (Mills et al. 2016)   Schema 
     PLP GFP  Ribosome profiles from elongating ribosomes (Mills et al. 2016)   Schema 
     PLP highsalt Ribo  Ribosome profiles from elongating ribosomes (Mills et al. 2016)   Schema 
     PLP PH  Ribosome profiles from elongating ribosomes (Mills et al. 2016)   Schema 
     PLP Ribo  Ribosome profiles from elongating ribosomes (Mills et al. 2016)   Schema 
     Primary PLT Ribo Thr1  Ribosome profiles from elongating ribosomes (Mills et al. 2016)   Schema 
     Primary PLT Ribo Thr2  Ribosome profiles from elongating ribosomes (Mills et al. 2016)   Schema 
     Retic Ribo Globin  Ribosome profiles from elongating ribosomes (Mills et al. 2016)   Schema 
     Retic Ribo Gold  Ribosome profiles from elongating ribosomes (Mills et al. 2016)   Schema 
    

Description

Description fromGSE85864: Analysis of ribosome profiling and RNA sequencing data from primary human platelets, primary human reticulocytes, in vitro derived platelet-like particles, and hemin-induced differentiation of K562 cells; manipulation by knockdown and overexpression of Pelota (PELO) and HBS1L in K562 cells and Meg01/platelet-like particles.

Methods

Raw sequence data were obtainedfrom NCBI FTP directory(SRP082436). Data from the following samples were processed:

Primary_PLT_Ribo_Rest Ribosome profiles from elongating ribosomes Homo sapiens(Mills, et al. 2016)
flowcell276_pair1_GCAGCT Ribosome profiles from elongating ribosomes Homo sapiens(Mills, et al. 2016)
flowcell276_pair1_ACGACT Ribosome profiles from elongating ribosomes Homo sapiens(Mills, et al. 2016)
K562_GFP_shABCE1 Ribosome profiles from elongating ribosomes Homo sapiens(Mills, et al. 2016)
K562_GFP_shCtrl Ribosome profiles from elongating ribosomes Homo sapiens(Mills, et al. 2016)
Retic_Ribo_Globin Ribosome profiles from elongating ribosomes Homo sapiens(Mills, et al. 2016)
PLP_Ribo Ribosome profiles from elongating ribosomes Homo sapiens(Mills, et al. 2016)
PLP_PH Ribosome profiles from elongating ribosomes Homo sapiens(Mills, et al. 2016)
K562_PH_4d Ribosome profiles from elongating ribosomes Homo sapiens(Mills, et al. 2016)
K562_PH_0d Ribosome profiles from elongating ribosomes Homo sapiens(Mills, et al. 2016)
Retic_Ribo_Gold Ribosome profiles from elongating ribosomes Homo sapiens(Mills, et al. 2016)
K562_GFP_0d Ribosome profiles from elongating ribosomes Homo sapiens(Mills, et al. 2016)
K562_GFP_2d Ribosome profiles from elongating ribosomes Homo sapiens(Mills, et al. 2016)
flowcell276_pair1_ATCAGT Ribosome profiles from elongating ribosomes Homo sapiens(Mills, et al. 2016)
K562_PH_shCtrl Ribosome profiles from elongating ribosomes Homo sapiens(Mills, et al. 2016)
PLP_GFP Ribosome profiles from elongating ribosomes Homo sapiens(Mills, et al. 2016)
K562_GFP_4d Ribosome profiles from elongating ribosomes Homo sapiens(Mills, et al. 2016)
Meg01_Ribo Ribosome profiles from elongating ribosomes Homo sapiens(Mills, et al. 2016)
K562_PH_shABCE1 Ribosome profiles from elongating ribosomes Homo sapiens(Mills, et al. 2016)
Primary_PLT_Ribo_Thr1 Ribosome profiles from elongating ribosomes Homo sapiens(Mills, et al. 2016)
flowcell276_pair1_TACGAT Ribosome profiles from elongating ribosomes Homo sapiens(Mills, et al. 2016)
K562_GFP_6d Ribosome profiles from elongating ribosomes Homo sapiens(Mills, et al. 2016)
Meg01_GFP Ribosome profiles from elongating ribosomes Homo sapiens(Mills, et al. 2016)
PLP_highsalt_Ribo Ribosome profiles from elongating ribosomes Homo sapiens(Mills, et al. 2016)
flowcell276_pair1_CAGCAT Ribosome profiles from elongating ribosomes Homo sapiens(Mills, et al. 2016)
K562_PH_2d Ribosome profiles from elongating ribosomes Homo sapiens(Mills, et al. 2016)
Primary_PLT_Ribo_Thr2 Ribosome profiles from elongating ribosomes Homo sapiens(Mills, et al. 2016)
flowcell276_pair1_CGACGT Ribosome profiles from elongating ribosomes Homo sapiens(Mills, et al. 2016)
Meg01_PH Ribosome profiles from elongating ribosomes Homo sapiens(Mills, et al. 2016)
K562_PH_6d Ribosome profiles from elongating ribosomes Homo sapiens(Mills, et al. 2016)

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. An offset of 15 nucleotides was then used to get the corresponding A-site of each read.These tracks contains the uniquely mapping reads.

References

Mills EW, Wangen J, Green R, Ingolia NT. (2016) Dynamic Regulation of a Ribosome Rescue Pathway in Erythroid Cells and Platelets.. DOI: 10.1016/j.celrep.2016.08.088