ChIP-seq data from IMR90 cells [28] was retrieved from the NCBI SRA (Table 1) and aligned to hg18 using Bowtie v0.12.7 allowing only uniquely mapped reads (-k 1). A modified version of HTSeq v0.5.3p (described above) was used to count reads mapping to lincRNAs and RefSeq NM genes. The ratio of IP reads to matched input control reads was used as the measure of ChIP signal. RNA-seq data from IMR90 cells [29] was also analyzed to obtain FPKM values for lincRNAs and RefSeq NM genes using the same procedure used for lincRNA discovery. The whiskers of the box and whisker plot extend to +/−1.5 times the interquartile range or the most extreme data point.
