Figure 1

sLADs/LADs in MEFs and myoblasts (MB). (A) Chromosome 1 is presented in UCSC genome browser (see Additional file 2: Figure S1 for the entire map; [30]). Tracks “Dam.w2k” and “LmnB1.w2k” plot read densities (RPKM) in non-overlapping, contiguous 2 kb windows along the chromosome. Similarly, the track “log2FC.w2k” plots log2 RPKM ratios of LmnB1 over Dam at a 2 kb resolution. The track “mouse LaminB1 MEF” is taken from the published data [15] which plots the log2 fluorescent signal ratio of LmnB1 over Dam for each microarray probe. Tracks “sLADs” and “LADs” depict the LADs/sLADs (black regions), non-LADs/non-sLADs (grey regions) and undetermined regions (blank regions). (B) Estimate of sequencing depths. Random samples of various sizes are generated from 43.3 million of MEF LmnB1 reads, each with three replicates. The plotted genome coverage by sLADs at a sequencing depth is averaged from the three replicates. The red data point represents the result based on the full dataset of 43.3 million reads. (C) Estimate of concordance of sLADs identified at different sequencing depths. The sampled sequencing depths are the same set as (B). Concordant 2 kb sLAD windows are 2 kb windows that are identified as sLADs at both the given lower sequencing depth and the highest sequencing depth (the full dataset), and the corresponding percentage is to divide the number of concordant 2 kb sLAD windows by the total number of 2 kb sLAD windows identified at the given sequencing depth. Similarly, missed 2 kb sLAD windows are those identified as non-sLADs at the given lower sequencing depth but as sLADs at the highest sequencing depth, and the percentage is to divide the number of missed 2 kb sLAD windows by the total number of 2 kb non-sLAD windows at the given sequencing depth.