Supplementary Material

Erica Larschan, Eric P. Bishop, Peter V. Kharchenko, Leighton J. Core, John T. Lis, Peter J. Park, and Mitzi I. Kuroda. Nature (2011).

Data files:

1. Table of EDIs, PIs, EDI Ratios and PI Ratios for Expressed Genes (658Kb)
2. GROSeq, Untreated Sample, Positive Strand Read Density (Not Yet Normalized By Copy Number) (66Mb)
3. GROSeq, Untreated Sample, Negative Strand Read Density (Not Yet Normalized By Copy Number) (66Mb)
4. GROSeq, Control RNAi Sample, Positive Strand Read Density (Not Yet Normalized By Copy Number) (75Mb)
5. GROSeq, Control RNAi Sample, Negative Strand Read Density (Not Yet Normalized By Copy Number) (75Mb)
6. GROSeq, MSL2 RNAi Sample, Positive Strand Read Density (Not Yet Normalized By Copy Number) (77Mb)
7. GROSeq, MSL2 RNAi Sample, Negatvive Strand Read Density (Not Yet Normalized By Copy Number) (77Mb)
8. Genomic Read Density (For Copy Number Normalization) (99Mb)

Read density files represent smoothed read density (gaussian smoothing, bandwidth=200bp), normalized for dataset size, but not yet by copy number. An additional file containing smoothed read density of genomic sequencing data is provided for copy number normalization. All coordinates are for dm3 assembly.

Note that PI/EDIs are not derived from smoothed read density, provided above, but from ratios of unsmoothed read density, as described in the methods section.