Description Description fromGSE37744: Ribosome profiling in cultured mammalian cells under three different footprinting conditions
Methods Raw sequence data were obtainedfrom NCBI FTP directory(SRP012648).
Data from the following samples were processed:
| HEK293_medium | Ribosome profiles from elongating ribosomes Homo sapiens(Ingolia, et al. 2012) |
| HEK293_high | Ribosome profiles from elongating ribosomes Homo sapiens(Ingolia, et al. 2012) |
| HEK293_low | Ribosome profiles from elongating ribosomes Homo sapiens(Ingolia, et al. 2012) |
Adapter sequence CTGTAGGCACCATCAAT 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.
An offset of 12 nucleotides was then used to get the corresponding P-site of each read.These tracks contains the uniquely mapping reads.,ReferencesIngolia NT, Brar GA, Rouskin S, McGeachy AM, Weissman JS (2012) The ribosome profiling strategy for monitoring translation in vivo by deep sequencing of ribosome-protected mRNA fragments. .Nat Protoc. 2012 Jul 26;7(8):1534-50. doi: 10.1038/nprot.2012.086. Research Support, N.I.H., Extramural; Research Support, Non-U.S. Gov't
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