Dovetail™ Micro-C Service Project

Catalogue #: 20019 (TADs), 20020 (loops)

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Specifications

Delivery Time

10 weeks

Library

Dovetail™ Hi-C

Sequencing Platform

Illumina

Analysis Platform

Dovetail™ QC pipeline

Project Types

1. TADs: 30X coverage, 10kb resolution

2. Loops: 90X coverage, 1kb resolution

Service Description

Let Dovetail™ scientists take on your entire Micro-C project from sample to sequence data and contact matrices ready for downstream analysis and interpretation. Dovetail Genomics commits to delivering a minimum of 30X coverage for TAD analysis or 90X coverage for chromatin loop analysis per sample enabling the generation of contact matrices down to 10 kb or 1 kb resolution, respectively, sufficient for detection and visualization of topological features such as A/B compartments, topologically associated domains (TADs), and/or chromatin loops.

  • Sequence independent chromatin fragmentation enables even genome-wide detection of chromatin contacts (up to 20% of the genome lacks coverage using restriction enzyme based Hi-C approaches)
  • Ultra-high nucleosome-level resolution of chromatin contacts
  • Highest signal-to-noise data with both enrichment of long-range informative reads and nucleosome protected fragments
  • QC Report
  • Sequence data (fastq file format)
  • Contact matrices (mcool and hic file formats)

Dovetail™ Micro-C Libraries Enrich For Desirable Hi-C Properties   MNase enzyme possesses both sequence-independent endonuclease and exonuclease activities, thereby generating nucleosome length (146 bp) fragments, while the proximity ligation portion of the protocol is optimized to maximize long-range interactions. The resulting highly uniform, short fragments enable nucleosome-level resolution of chromatin contacts, a theoretical resolution maximum.

Improved calling of topological features    The ability to detect higher-order features – such as chromatin loops – in proximity ligation data is dependent on enriching long-range, informative reads to capture chromatin interaction frequency. The increased number of chromosome conformation-informative reads, combined with ultra-high-resolution, improves loop calling as compared to RE-based methods.

Dovetail™ Micro-C uniquely captures nucleosome positioning   Chromatin digested with MNase reveals a genome-wide nucleosome map that is visible in the Dovetail™ Micro-C libraries. The map consists of sequence read peaks correlating to DNA that is protected by the nucleosome and troughs representing intervening DNA that is accessible to MNase digestion. This oscillation occurs at a frequency of ~146 bp (the length of DNA wrapped around a mono-nucleosome) and is a feature unique to Micro-C data, but absent from RE-based approaches. The combined genome-wide nucleosome positioning and ultra-resolution chromosome topology enabled by Dovetail™ Micro-C facilitates mapping from nucleosome-to-nucleosome chromatin contacts.

Materials & Deliverables

Mammalian cells, tissue, or blood

  • QC Report
  • Sequence data (fastq file format)
  • Contact matrices (mcool and hic file formats)

Documents

Software

  • Dovetail™ QC Pipeline

Scientific Literature

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