Supplementary Material

Apostolou E, Ferrari E, Walsh RM, Bar-Nur O, Stadtfeld M, Cheloufi S, Stuart HT, Polo JM, Ohsumi TK, Borowsky ML, Kharchenko PV, Park PJ, and Hochedlinger K. Cell Stem Cell (2013).

Data files:

1. List of m4C-seq samples (1.3Kb)
2. Annotations for HindIII fragments (11Mb)
3. Datamatrix of fragment level read counts (9.4Mb)
4. Datamatrix of gene level read counts (527Kb)

• HindIII resctriction fragments in mm9 genome assembly are defined as the genomic region between two consecutive HindIII restriction site. The start/end coordinates are the midlle position within the HindIII restriction sites.
• Read counts per fragments are reads mapped at either the 5'-end or 3'-end of the HindIII fragment. Reads at bait fragments and other potential outliers have been excluded, as described in the article.
• Read counts per gene are obtained by summing read counts at individual fragments overlapping the gene locus or a 20kb window upstream the annotated transcription start site.
• Fragments annotations are reported as RefSeq genes where the fragment is overlapping either the gene body or a 20kb window upstream or downstream the annotated gene coordinates.