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. 2021 Jul 13;49(18):e105. doi: 10.1093/nar/gkab604

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© The Author(s) 2021. Published by Oxford University Press on behalf of Nucleic Acids Research.

This is an Open Access article distributed under the terms of the Creative Commons Attribution-NonCommercial License (https://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com

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Figure 4. — capCLIP of rapamycin-treated and control HeLa cells. (A) PCA of the control and rapamycin sequencing datasets. (B) Log₂ fold change in eIF4E affinity for 3365 individual mRNAs versus mRNA abundance (log₂ of peak area). Eighty-six mRNAs show a statistically significant log₂ fold change in eIF4E binding (P > 0.01; FDR > 0.05). Average log₂ fold change in eIF4E binding of the total mRNA population is −0.02. (C) Distribution of capCLIP tags as a function of the normalized distance along the transcript for the single control (DMSO) replicate and two rapamycin (rapa) replicates. (D) IGV gene-level views, reformatted to aid visualization (all genes displayed 5′ to 3′, left to right). Displayed above each gene are histogram plots of control (in blue) and rapamycin (in red) capCLIP tag alignments, along with HeLa CAGE data (in grey). Numbers to the left of each tag histogram indicate raw tag counts at the highest point of each 5′-UTR tag peak.