P-GSE45982-4 - P-GSE45982-4

normalization data transformation protocol
genome build: hg18 Illumina Casava1.8 software used for basecalling. RNA-seq data was aligned to transcripts using TopHat with default parameters. ChIP-seq data was aligned to the appropriate genome using ELAND. FPKM were obtained using CuffLinks with upper-quartile and GC normalization H3K4me3 ChIP-seq reads were called into peaks using the ChIPseeqer framework (p<10-15 and fold-change over input threshold 2) (Giannopoulou and Elemento, 2011) and H3K27me3 and EZH2 ChIP-seq reads were quantified in 1kb bins genome-wide, identifying regions of enrichment as consecutive bins with read counts greater than one standard deviation of the genome-wide mean. Supplementary_files_format_and_content: tab-delimited FPKM values for each Refseq transcript; WIG files were generatedand peak files were called using ChIPseeqer framework (
Experiment E-GEOD-45982