Files and code used for de Mendoza, A., Nguyen, T., Ford, E. et al. "Large-scale manipulation of promoter DNA methylation reveals context-specific transcriptional responses and stability ". Genome Biology, 2022.
Code
- RNAseq_processing.R
- RNAseq_analysis.R
- WGBS_processing_and_DMRs.R
- PromoterDMR_vs_Txn.R
- ChIP-seq_processing.R
- ATAC-seq_processing.R
Files
ZF_RNAseq_SpikeDesign.tsv: ERCC-spike in design for the RNA-seq samples.DMRs.tsv.gz: DMRs obtained from dmrseq comparing noDox vs Dox and filtered by FDR < 0.1.genes.gtf.gz: Version of UCSC hg19 annotation file used in the study.PMDs_noDox.bed.gz: Partially Methylated Domains for noDox obtained with MethylSeekR.UMRsLMRs_noDox.bed.gz: Unmethylated and Lowly Methylated Regions for noDox obtained with MethylSeekR.ZF_Counts_table.tsv.gz: mRNA-seq counts table.ZF598_D3awt_P2A_GFP_HA_ChIP.nofilt.idr_peaks.gz: ZF-D3A-wt ChIP-seq peaks merged with IDR.ZF598_D3amut_FEER_P2A_GFP_HA_ChIP.nofilt.idr_peaks.gz: ZF-D3A-mut ChIP-seq peaks merged with IDR.hg19_ZF598_scan.bed.gz: Motif scan for the ZF-D3A motif obtained using HOMER2.ATACall_peaks_merge.bed.gz: ATAC-seq peaks for all samples merged.