Supplementary site for Hug CB, Grimaldi AG, Kruse K, Vaquerizas JM. (2017). Chromatin Architecture Emerges during Zygotic Genome Activation Independent of Transcription.
doi:10.1016/j.cell.2017.03.024
All genomic coordinates are based on Flybase r6.07.
TAD Boundary calls are provided as BED files including the boundary score in the 4th column, higher values represent stronger boundaries. Calls where performed using Hi-C matrices at three different binning resolutions.
Consensus boundary calls between developmental stages are provided as tab-separated text files. If boundaries at different stages were less than two bins away from each other they where considered to overlap and the median of the start and end coordinate were used as consensus boundary call. NA denotes boundaries not called or called with a score <0.5 at this stage.
Hi-C matrices binned at 5kb resolution are available from ArrayExpress E-MTAB-4918 in E-MTAB-4918.processed.1.zip and E-MTAB-4918.processed.2.zip. Reads from all replicates were merged to generate these matrices. They are provided in the Cooler format developed by the Mirny lab with matrix balancing information included in the file.
In order to extract the matrix in a flat text format, use:
cooler dump -t pixels --header -b --join -o 3-4h_repl_merged_5kb.tsv.gz 3-4h_repl_merged_5kb.coolThe flat file has the following records:
chrom1 start1 end1 chrom2 start2 end2 count balanced
X 50000 55000 X 50000 55000 7 0.0271974
X 50000 55000 X 120000 125000 12 0.0238841
X 50000 55000 X 125000 130000 33 0.0209088
X 50000 55000 X 130000 135000 19 0.010838
X 50000 55000 X 135000 140000 22 0.0103313
X 50000 55000 X 140000 145000 21 0.013437
X 50000 55000 X 145000 150000 27 0.0119021
X 50000 55000 X 150000 155000 27 0.0132561
X 50000 55000 X 155000 160000 22 0.012156