Highly rearranged chromosomes reveal uncoupling between genome topology and gene expression.

All coordinates are relative to the dm6 assembly

Normalized Hi-C contact maps in 5 kb resolution, in HiCExplorer h5 format:

• All Reads
• Wild-type
• Balancer

RNA-seq read counts:

• Paternal
• Maternal
• Female
• CyO
• TM3
• CyO:TM3

Differential analysis:

• Differential expression analysis results
• Differential expression analysis explanation

VCF:

• SNVs used for allele separation

Raw data are available at ArrayExpress:

• Accession E-MTAB-7510 — Whole-genome sequencing and mate pair sequencing of Drosophila melanogaster carrying second (CyO) and third (TM3) balancer chromosomes
• Accession E-MTAB-7511 — RNA-seq of Drosophila melanogaster carrying second (CyO) and third (TM3) balancer chromosomes
• Accession E-MTAB-7512 — HiC of Drosophila melanogaster carrying second (CyO) and third (TM3) balancer chromosomes
• Accession E-MTAB-7513 — Capture-C of Drosophila melanogaster carrying second (CyO) and third (TM3) balancer chromosomes