README.md

TBXT chromatin looping analysis in lung cancer

Authors: Reuben M. Yaa

README updated: Aug-31-2022

Introduction

While high levels of TBXT have been detected in metastatic lung cancer, we used circularised chromosome capture combined with sequencing (4C-seq) to characterise if physical genome wide cis -interactions differences around TBXT loci in (1) lung cancer cells (H460), a TBXT expressing cell line and (2) lung cancer cells (H358 and A549), non-TBXT expressers have association with TBXT regulation

4C template and library

A543, H358 and H460 4C templates and libraries were prepared in replicates using NlaIII and DpnII restriction enzymes and sequenced at 150bp PE

4C data analysis

Mapping

Reads were processed using 4C pipeline

Interaction landscape calling

Statistically interacting fragments were called using peakC embedded in interact_calling pipeline

Downstream analysis

Analysis of the statistically interacting fragments

The fragments now called loops were analysed in different ways as follows;

• Venn diagrams for comparing loops between TBXT expression conditions
• Merged loop for visualisation of the regulation landscape linear genome using spider_plots
• Clustering of loops as shared, gained or lost using Bedtools suit
• Density analysis of clustered loops done using 4C_changing density
• Motif analysis of gained loops using RSAT

Epigenome enrichment analysis

ChIP-seq analysis of H358, A549 and H460 publicly available datasets using ChIP_pipeline. Track collections are saved in UCSC lung_TBXT

---