Description Please see individual series. In short, For AUF1 PAR-CLIP, the four isoforms of AUF1 (p37, p40, p42, and p45) tagged with a Flag epitope were expressed in HEK293 cells. For total RNA-Seq HEK293 cells were transfected with Control siRNA, AUF1 siRNA, Empty Vector, Flag-AUF1 p37, p40, p42, or p45 as well as WI-38 cells were collected at PDL 15 and 55 and also transfected with Control siRNA, AUF1 siRNA, HuR siRNA. For Ribo-Seq HeLa cells were transfected with Control siRNA, AUF1 siRNA, or HuR siRNA. MethodsRaw sequence data were obtained from NCBI FTP directory(SRP033503). Data from the following samples were processed:
| Ribosome_Profiling_with_Control_siRNA | Ribosome profiling data from Homo sapiens(Yoon, et al. 2014) |
| Ribosome_Profiling_with_AUF1_siRNA | Ribosome profiling data from Homo sapiens(Yoon, et al. 2014) |
| Ribosome_Profiling_with_HuR_siRNA | Ribosome profiling data from Homo sapiens(Yoon, et al. 2014) |
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. 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
Yoon JH, De S, Srikantan S, Abdelmohsen K, Grammatikakis I, Kim J, Kim KM, Noh JH, White EJ, Martindale JL, Yang X, Kang MJ, Wood WH 3rd, Noren Hooten N, Evans MK, Becker KG, Tripathi V, Prasanth KV, Wilson GM, Tuschl T, Ingolia NT, Hafner M, Gorospe M (2014) PAR-CLIP analysis uncovers AUF1 impact on target RNA fate and genome integrity. . Nat Commun. 2014 Nov 4;5:5248. doi: 10.1038/ncomms6248. Research Support, N.I.H., Extramural; Research Support, Non-U.S. Gov't
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