DLBCL_projects

Ribosome Termination Pausing as an Adaptive Translational Checkpoint and Druggable Vulnerability in Human Diffuse Large B-cell Lymphoma

Li Wang^1†, Haoran Duan^2,3†, Huihong Li^2,3, Hai Fang¹, Chaohui Bao¹, Shuaiyao Wang^2,3, Tong Yin¹,Ruihong Zhang¹,Dieter A. Wolf^2,3*,Weili Zhao^1*,and Fajin Li^2,3*†

¹ Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China. ² Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China. ³ School of Medicine, Westlake University, Hangzhou, Zhejiang, China. ^† These authors contributed equally to this work ^* Corresponding author. Email: lfj17[at]tsinghua[dot]org[dot]cn

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Introduction

This file is a description of how the results presented in the manuscript were generated, including codes of pre-processing and codes for generating the figures. All scripts used for processing BAM files should be excuted in Linux platform and other scripts can be both used in Linux and windows platform.

Dependencies

The softwares and their versions are listed in the requirements.txt file.

Codes

• 00.preprocessing and 00.preprocessing.Rmd: The codes for preprocessing of RNA-seq and Ribo-seq data.
• 01.transcriptomeAssembly and 01.transcriptomeAssembly.Rmd: The codes for transcriptome assembly using STAR and Stringtie.
• 02.re-processing with assembled references and 02.re-processing with assembled references.Rmd: The codes for reprocessing of RNA-seq and Ribo-seq data using the assembled reference genome.
• 03.formal-analysis and 03.formal-analysis.Rmd: The codes for formal analysis, which were used for generating all figures in the manuscript.