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Acetylation of Cytidine in mRNA Promotes Translation Efficiency. (Arango et al. 2018)   (All Elongating Ribosomes (Footprints) tracks)

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     NAT10 KO Riboseq Bio 1 protected RNA  Ribosome coverage data from elongating ribosomes (SRR5886321, SRR5886320) (Arango et al. 2018)   Schema 
     NAT10 KO Riboseq Bio 2 protected RNA  Ribosome coverage data from elongating ribosomes (SRR5886323, SRR5886322) (Arango et al. 2018)   Schema 
     WT Riboseq Bio 1 protected RNA  Ribosome coverage data from elongating ribosomes (SRR5886316, SRR5886317) (Arango et al. 2018)   Schema 
     WT Riboseq Bio 2 protected RNA  Ribosome coverage data from elongating ribosomes (SRR5886318, SRR5886319) (Arango et al. 2018)   Schema 

Description

Description fromGSE102113: Detection of acetylated cytide in RNA with immunoprecipitation (RIP), along with RNA-Seq, Ribo-Seq, and BRIC-Seq to analyze effects on RNA processing and stability.

Methods

Raw sequence data were obtainedfrom NCBI FTP directory(SRP114504). Data from the following samples were processed:

WT_Riboseq_Bio_2_protected_RNA Ribosome coverage data from elongating ribosomes Homo sapiens(Arango, et al. 2018)
NAT10_KO_Riboseq_Bio_2_total_RNA Ribosome coverage data from elongating ribosomes Homo sapiens(Arango, et al. 2018)
NAT10_KO_Riboseq_Bio_2_protected_RNA Ribosome coverage data from elongating ribosomes Homo sapiens(Arango, et al. 2018)
WT_Riboseq_Bio_1_total_RNA Ribosome coverage data from elongating ribosomes Homo sapiens(Arango, et al. 2018)
NAT10_KO_Riboseq_Bio_1_protected_RNA Ribosome coverage data from elongating ribosomes Homo sapiens(Arango, et al. 2018)
WT_Riboseq_Bio_1_protected_RNA Ribosome coverage data from elongating ribosomes Homo sapiens(Arango, et al. 2018)
NAT10_KO_Riboseq_Bio_1_total_RNA Ribosome coverage data from elongating ribosomes Homo sapiens(Arango, et al. 2018)
WT_Riboseq_Bio_2_total_RNA Ribosome coverage data from elongating ribosomes Homo sapiens(Arango, et al. 2018)

Adapter sequence CTGTAGGCACCATCAAT and AGATCGGAAGAGCACAC 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 25 nt were discarded. These tracks contain the uniquely mapping reads.,

References

Arango D, Sturgill D, Alhusaini N, Dillman AA, Sweet TJ, Hanson G, Hosogane M, Sinclair WR, Nanan KK, Mandler MD, Fox SD, Zengeya TT, Andresson T, Meier JL, Coller J, Oberdoerffer S (2018) Acetylation of Cytidine in mRNA Promotes Translation Efficiency. .Cell. 2018 Nov 12. pii: S0092-8674(18)31383-7. doi: 10.1016/j.cell.2018.10.030. [Epub ahead of print]