Description Taken from GEO Datasets page (GSE51584) : Most circRNAs are expressed in only a few cell types and at low abundance, but they are no more cell-type specific than are mRNAs with similar overall expression levels. Although most circRNAs overlap protein-coding sequences, ribosome profiling provides no evidence for their translation. MethodsRaw sequence data were obtained from NCBI FTP directory(SRP031849). Data from the following samples were processed:
| miR_transfected_ribosome_profiling | Ribosome profiling data from Homo sapiens(Guo, et al. 2014) |
| mock_transfected_ribosome_profiling | Ribosome profiling data from Homo sapiens(Guo, et al. 2014) |
| miR_155_transfected_ribosome_profiling | Ribosome profiling data from Homo sapiens(Guo, et al. 2014) |
Adapter sequence TCGTATGCCGTCTTCTG 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.An offset of 15 nucleotides was then used to get the corresponding A-site of each read.
References
Guo JU, Agarwal V, Guo H, Bartel DP (2014) Expanded identification and characterization of mammalian circular RNAs. . Genome Biol. 2014 Jul 29;15(7):409. doi: 10.1186/s13059-014-0409-z. Research Support, N.I.H., Extramural; Research Support, Non-U.S. Gov't; Research Support, U.S. Gov't, Non-P.H.S.
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