Description

Ribosome profiles of initiating ribosomes using puromycin from THP-1 cells (Fritsch et al. 2012)

Methods

Raw sequence data were obtained from NCBI SRA database (Series SRP014542). Data from the following samples were concatenated before processing:

GSM971691: THP-1_puro_rep#1; Homo sapiens; RNA-Seq
GSM971692: THP-1_puro_rep#2; Homo sapiens; RNA-Seq
GSM971693: THP-1_puro_rep#3; Homo sapiens; RNA-Seq

Cutadapt was used to trim poly(A) adaptor sequences from reads, after which reads below 25 nucleotides in length were discarded. An alignment to ribosomal RNA was then performed using Bowtie, and aligning reads were discarded. Finally, an alignment to the hg19 genome assembly was performed using RUM, and this track contains coverage data for uniquely mapping reads that align to the P-site (using an offset of 12nt).

References

Claudia Fritsch, Alexander Herrmann, Michael Nothnagel, et al. (2012). Genome-wide search for novel human uORFs and N-terminal protein extensions using ribosomal footprinting. Genome Research. 2012 22: 2208-2218. doi:10.1101/gr.139568.112