Sample: UNI1803


Analysis summary

Feature Count
A Compartments 132 (50.77%)
B Compartments 137 (48.77%)
TADs at 10 kbp resolution 1,306
TADs at 25 kbp resolution 1,864
TADs at 50 kbp resolution 1,385
Isochores 0
CTCF Binding Sites 20,145

TAD statistics at different resolutions

Resolution (kbp) Number of TADs Mean TAD Size (bp) Basepairs in TADs (kbp) Percent genome contained in TADs
10 1,306 300,658 3,807 16.58%
25 1,864 625,295 10,582 46.08%
50 1,385 1,271,588 13,666 59.51%

Notes about data processing

  • Contact Maps

    We generated Hi-C contact matrices in two formats, namely cool and hic. Both contact matrices were generated from the same BAM file by using read pairs where both ends were aligned with a mapping quality of 60.

  • TADs

    TADs were identified using the Arrowhead program implemented in the Juicertools package. We call TADs at 3 different resolutions: 10 kbp, 25 kbp, and 50 kbp. The parameters used were -k KR -m 2000 -r 10000 , -k KR -m 2000 -r 25000, and -k KR -m 2000 -r 50000

  • A/B Compartments

    A/B compartments were identified at 1 Mbp using the eigenvector program implemented in the Juicertools package. The parameters used were KR BP 1000000.

  • Isochores

    Isochores were predicted using the isofinder program. The parameters used were 0.90 p2 3000. The output was post-processed to convert it to a bedpe format.

  • CTCF sites

    CTCF sites were predicted using the cread program. The position weight matrix was downloaded from CTCFBSDB 2.0 website. The output was then post-processed to convert it to a bed file.

  • Multires files

    Multires files were generated using the clodius package. These files can be loaded in HiGlass: an open source visualization tool.


Glossary

  • Topologically Associated Domains (TADs)

    One of the fundamental units of chromatin topology. TADs are regions of chromatin wherein all of the chromatin is in closer physical proximity. It is thought that regulatory signals can be conveyed more easily within a TAD than between TADs. TAD boundaries often occur at CTCF binding sites and are thought to be established and maintained by Cohesin/CTCF complex.

  • A/B compartments

    The whole genome could be divided into two spatial compartments, namely A and B. A compartments are associated with active/euchromatin and B compartments are associated with inactive/heterochromatin.

  • Isochores

    Extended genomic regions (typically 300kb to multimegabase) of uniform, characteristic GC content.

  • CTCF sites

    CCCTC-binding factor (CTCF) is a DNA binding protein, established as the main player in physical establishment of TAD boundaries.