Project description:To investigate the effect on chromatin accessibility with reduced ERBB2 signalling in oesophageal adenocarcinoma, we performed ATAC-seq in OE19 cells treated with either siNT or siERBB2.
Project description:To investigate the effects of gene expression of reduced ERBB2 signalling in oesophageal adenocarcinoma, we performed RNA-seq of OE19 cells treated with either siNT or siERBB2.
Project description:To investigate changes to gene expression associated with resistance to lapatinib, we performed ATAC-seq on OE19 cells treated with 500 nM lapatinib for 1, 7 and 35 days and vehicle control (DMSO) for 1 day.
Project description:Kethoxal-assisted ssDNA sequencing (KAS-seq) is gaining popularity as a robust and effective approach to study the dynamics of transcriptionally engaged RNA polymerases through profiling of genome-wide single-stranded DNA (ssDNA). Its latest variant, spKAS-seq, a strand-specific version of KAS-seq, has been developed to map genome-wide R-loop structures by detecting imbalances of ssDNA on two strands. However, user-friendly, open-source, and specific bioinformatic analyzer for KAS-seq data are still lacking. Here we present KAS-Analyzer as a flexible and integrated toolkit to facilitate the analysis and interpretation of KAS-seq data. KAS-Analyzer can perform standard analyses such as quality control, read alignment, and differential RNA polymerase activity analysis. In addition, KAS-Analyzer introduces many novel features, including, but not limited to: calculation of transcriptional indexes, identification of single-stranded transcribing enhancers, and high-resolution mapping of R-loops. We use benchmark datasets to demonstrate that KAS-Analyzer provides a powerful framework to study transient transcriptional regulatory programs. KAS-Analyzer is available at https://github.com/Ruitulyu/KAS-Analyzer.
Project description:The genome-wide binding sites of transcription factors provide insight into their regulatory function. We used chromatin immunoprecipitaition with high-throughput sequencing (ChIP-seq) to identify the genomic binding sites of HNF4A and GATA6 in OE19 cells.
Project description:To investigate changes to chromatin accessibility associated with resistance to lapatinib, we performed ATAC-seq on OE19 cells treated with 500 nM lapatinib for 1, 7 and 35 days and vehicle control (DMSO) for 1 day.
Project description:To determine genes regulated by the transcriptional co-activator PPARGC1A in OAC cells and whether PPARGC1A activity is altered by lapatinib we performed RNA-seq on OE19 cells treated with non-targeting siRNA or siRNA targeting PPARGC1A. 24 hours post-transfection, cells were also treated with either DMSO or 500 nM lapatinib for 24 hours.
Project description:This dataset consists of in situ HiC-seq data from a human oesophageal adenocarcinoma cell line (OE19). In total, the dataset includes 2 biological replicated samples. The Hi-C sample and library preparations were generated using Arima-HiC Kit (A510008, ARIMA Genomics) and Arima Library Prep module (A303011, ARIMA Genomics), respectively.