sblab-bioinformatics/GWscreen_G4sensitivity

Computational methods genome-wide shRNA screen with G-quadruplex ligands sensitisation

This repository contains details about the data availability and the computational methods developed for our manuscript.

Data

All the sequencing data have been deposited in the ArrayExpress database at EMBL-EBI under accession number E-MTAB-6367.

Code

• Pilot screen Pool8 A375:

  • Preliminary exploration
  • Data processing 1
  • Analysis 1
  • Data processing 2
  • Analysis 2

• Genome-wide screen A375:

  • 1st sequencing round:
    • Pools 1, 2, 5 and 10: data processing and analysis
    • Pools 3, 4, 6 and 7: data processing and analysis
    • Pools 8, 9, 11 and 12: data processing and analysis
  • 2nd sequencing round:
    • Pools 1-6 and 10-12: data processing and analysis
  • 3rd sequencing round:
    • Pools 3, 11 and 12: data processing and analysis
  • Integration of all sequencing runs: creating the integrated dataset and additional plots

• Focussed screens A375 and HT1080:

  • Data processing
  • Analysis

• Functional analyses:

  • GO and KEGG
  • COSMIC: preliminary and advanced

• Literature and database searches:

  • UniprotKB and GO
  • MeSH and PolySearch2

• Submission to ArrayExpress:

  • Script

Sofware requirements

• FastQC v0.11.3
• FASTX-Toolkit v0.0.14
• Bowtie 2 v2.2.6
• Unix tools (cat, cut, awk, sort and uniq)
• Python programming language v2.7.10. Libraries used:
  • os
  • csv
  • Biopython
• R programming language v3.2.1. Libraries used:
  • edgeR
  • data.table
  • ggplot2
  • VennDiagram
  • reshape
  • Biostrings
• PolySearch2